title: Genome-wide mapping of 5-hydroxymethylcytosine (5hmC) during differentiation of P19.6 and 3T3-L1 cells

city: Rennes

first: Aurelien

last: Serandour

address: Bâtiment 13, Campus de Beaulieu

department: UMR CNRS 6290

institute: Université de Rennes 1

summary: Enhancers are developmentally-controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. Here, we show by genome-wide mapping that the newly discovered DNA modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells as well as during adipocyte differentiation of mouse 3T3-L1 cells. Functional annotation reveals that regions gaining 5hmC are associated with genes expressed either in neural tissues when P19 cells undergo neural differentiation or in adipose tissue when 3T3-L1 cells undergo adipocyte differentiation. Furthermore, distal regions gaining 5hmC together with H3K4me2 and H3K27ac in P19 cells behave as differentiation-dependent transcriptional enhancers. Identified regions are enriched in motifs for transcription factors regulating specific cell fates like Meis1 in P19 cells and PPARgamma in 3T3-L1 cells. Accordingly, a fraction of hydroxymethylated Meis1 sites were associated with a dynamic engagement of the 5mC hydroxylase Tet1. In addition, kinetic studies of cytosine hydroxymethylation of selected enhancers indicated that DNA hydroxymethylation is an early event of enhancer activation. Hence, acquisition of 5hmC in cell-specific distal regulatory regions may represent a major event of enhancer progression toward an active state and participate in selective activation of tissue-specific genes

overall_design:
Genome-wide 5hmC distribution was determined using hMeDIP-seq. Cells used in this study are P19.6 mouse embryonal carnicoma cells and P19.6 cells treated for 48 hours with 1µM all-trans retinoic acid (RA), as well as 3T3-L1 cells and 3T3-L1 derived adipocytes differentiated with dexamethasone, insulin and IBMX (differentiation cocktail - DC).
Individual hMeDIP samples from P19.6 ord 3T3-L1 cells were pooled for library preparation. Libraries were prepared and sequenced at the IBL sequencing facility (Lille, France) with an Illumina Genome Analyser II.

first: Stéphane

last: Avner

first: Gilles

last: Salbert


title: ORC2 Cl8 ChIP-Seq experiment

status: Public on Jun 07 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
modENCODE_submission_4351
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male;  EXPERIMENTAL FACTORS: Strain ; Antibody dORC2 (target is Drosophila ORC2p); read length (read_length)

first: David

last: MacAlpine

first: Heather

first: Joseph

last: Prinz


title: Comparative Profiling of Pseudomonas aeruginosa Strains Reveals Differential Expression of Novel Unique and Conserved Small RNAs

status: Public on Jun 04 2012

city: Milano

middle: Stephen

last: Horner

state: MI

address: Via Celoria 26

department: Molecular Biosciences and Biotechnology

country: Italy

institute: Università degli Studi di Milano

type: Non-coding RNA profiling by high throughput sequencing

summary: Pseudomonas aeruginosa is a highly adaptable bacterium which thrives in a broad range of ecological niches and can infect multiple hosts as diverse as plants, nematodes and mammals. In humans, it is an important opportunistic pathogen. This wide adaptability correlates with its broad genetic diversity. In this study, we used a deep-sequencing approach to explore the complement of small RNAs (sRNAs) in P. aeruginosa as the number of such regulatory molecules previously identified in this organism is relatively low, considering its genome size, phenotypic diversity and adaptability. We have performed a comparative analysis of PAO1 and PA14 strains which share the same host range but differ in pathogenicity, PA14 being considerably more virulent in several model organisms. Altogether, we have identified more than 150 novel candidate sRNAs and validated a third of them by Northern blotting. Interestingly, a number of these novel sRNAs are strain-specific or showed strain-specific expression, strongly suggesting that they could be involved in determining specific phenotypic traits.

overall_design: 2 cDNA samples (enriched for different size ranges ) from each of two strains of Pseudomonas aeruginoasa (PAO1 and PA14) were sequenced with the Roche 454 technology

middle: S

first: Silvia

last: Ferrara

first: Gianni

last: Dehò

first: Federica

last: Briani

first: Margherita

last: Brugnoli

first: Angela

last: De Bonis

first: Francesco

last: Delvillani

last: Righetti

first: Giovanni

last: Bertoni


title: Comparing two transcriptome technologies - sequencing match microarrays [RNA-Seq]

status: Public on Jun 10 2012

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

institute: Sacco Srl

type: Expression profiling by high throughput sequencing

summary: Next-generation sequencing has emerged as a promising platform for whole genome transcriptome profiling. The microarray technology has in contrast a long track record, but may suffer from issues related to background fluorescence and non-specific hybridization. The two technologies have been compared for eukaryotic transcriptomes in various studies. However, for prokaryotes information on comparative performance of the two technologies is sparse. We thus compared the two technologies for Streptococcus thermophilus. With just single experiments there was a strong correlation between the technologies.

overall_design: Two samples were analyzed

first: Thomas

middle: B

last: Rasmussen

first: Shruti

middle: H

last: Dantoft


title: Threonine-4 of Mammalian RNA Polymerase II CTD is Targeted by  Polo-like Kinase-3 and Required for Transcriptional Elongation

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

institute: EMBL

summary: Eukaryotic RNA polymerase II (Pol II) has evolved an array of heptad repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the carboxy-terminal domain (CTD) of the large subunit (Rpb1). Differential phosphorylation of Ser2, Ser5, and Ser7 in the 5’ and 3’ regions of genes coordinates the binding of transcription and RNA processing factors to the initiating and elongating polymerase complexes. Here, we report phosphorylation of Thr4 by Polo-like-kinase-3 in mammalian cells. ChIPseq analyses indicate an increase of Thr4-P levels in the 3’ region of genes occurring subsequently to an increase of Ser2-P levels. A Thr4/Ala mutant of Pol II displays a lethal phenotype. This mutant reveals a global defect in RNA elongation, while initiation is largely unaffected. Since Thr4 replacement mutants are viable in yeast we conclude that this amino acid has evolved an essential function(s) in the CTD of Pol II for gene transcription in mammalian  cells.

overall_design:
In this study, we investigated the function and ChIPseq genome-wide profiling of Thr4P residue (using the 6D7 antibody) of the Pol II CTD in Raji human B cells in comparison with either total Pol II profiling (N20 antibody, santa-cruz sc-899x), Ser5P CTD (3E8) or Ser2P (3E10) profiling in WT Raji cells. In another set of experiments, we also analysed total Pol II profiling (using an HA tag at the N-terminus of RPB1 and HA antibody Abcam ab9110) when endogenous enzyme is shut down by alpha-amanitin and replaced by either a recominant Pol II with 48 consensus repeats of the CTD (con48) or a mutated version where Thr4 residues were replaced by Ala (Thr4-Ala).In total 6 experimental sets (Pol IIt, Ser5P, Ser2P, Thr4P, con48, Thr4-Ala) were generated for our analysis and for each a biological replicate was performed. Biological replicates were merged when the data showed comparable signal noise ratio. Otherwise a unique replicate, showing the best noise ratio, was chosen for further analysis although the second replicate (for Ser2P and Thr4-Ala experiments). An input control (genomic DNA extracted after reverse crosslinking of the nuclear chip extracts) was performred and used for substraction to the ChIP experiments. One specific input material was used for wt cells, one for con48 and one for Thr4-Ala. Our data were processed to generate final wig files using our in house analysis pipeline essentially as described in Koch et al, (2011) NSMB 18 (8) p956.In brief, after alignment, sequence tags are: (i) artefact removed, (ii) elongated to an in silico optimized actual size of the initial fragments , (iii) input substracted, (iv) merged if applicable, (v) scaled for all experiments to correct for variation of tag number in between experiments.
Several of the raw data files were no longer available.

first: Corinna

last: Hintermair

last: Heidemann

first: Frederic

last: Koch

first: Nicolas

last: Descostes

first: Marta

last: Gut

first: Ivo

first: Romain

last: Fenouil

first: Pierre

last: Ferrier

first: Andrew

last: Flatley

first: Elisabeth

last: Kremmer

first: Rob

middle: D

last: Chapman

first: Jean-Christophe

last: Andrau

first: Dirk

last: Eick


title: Identification of Transcription Factor ZAG-1::GFP Binding Regions in L4

first: DCC

last: modENCODE

summary:
modENCODE_submission_3585
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP83(official name : OP83 genotype : unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by : R Waterston ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene zag-1; Strain OP83(official name : OP83 genotype : unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

status: Public on Jun 05 2012

city: Columbus

first: rui

last: wang

state: OHIO

address: 212 Biomedical Research Tower,460 West 12th Ave

country: USA

institute: Ohio State University

summary: The TCF7L2 transcription factor is linked to a variety of human diseases, including type 2 diabetes and cancer. One mechanism by which TCF7L2 could influence expression of genes involved in diverse diseases is by binding  to distinct regulatory regions in different tissues. To test this hypothesis, we performed ChIP-seq for TCF7L2 in 6 human cell lines. We identified 116,000 non-redundant TCF7L2 binding sites, with only 1,864  sites common to the 6 cell lines. Using ChIP-seq, we showed that many genomic regions that are marked by both H3K4me1 and H3K27Ac are also bound by TCF7L2, suggesting that TCF7L2 plays a critical role in enhancer  activity. Bioinformatic analysis of the cell type-specific TCF7L2 binding sites revealed enrichment for multiple transcription factors, including HNF4alpha and FOXA2 motifs in HepG2 cells and the GATA3 motif in MCF7 cells. ChIP-seq analysis revealed that TCF7L2 co-localizes with HNF4alpha and FOXA2 in HepG2 cells and with GATA3 in MCF7 cells. Interestingly, in MCF7 cells the TCF7L2 motif is enriched in most TCF7L2 sites but is not enriched in the sites bound by both GATA3 and TCF7L2. This analysis suggested that GATA3 might tether TCF7L2 to the genome at these sites. To test this hypothesis, we depleted GATA3 in MCF7 cells and showed that TCF7L2 binding was lost at a subset of sites. RNA-seq analysis suggested that TCF7L2 represses transcription when tethered to the genome via GATA3. Our studies demonstrate a novel relationship between GATA3 and TCF7L2,  and reveal important insights into TCF7L2-mediated gene regulation.

overall_design:
RNAseq analysis of MCF7 cells transfected with siCONTROL, siTCF7L2 or siGATA3.
ChIP-seq analysis of H3K27ac, H3K4me1, H3K27me3, H3K9me3 in MCF7 cells; H3K4me1 and H3K27ac in HCT116 cells.

first: Seth

last: Frietze

first: Peggy

last: Farnham


title: Acinetobacter oleivorans DR1 : Control vs. norfloxacin treated

city: Seoul

first: Jisun

address: Anam-Dong, Sungbuk-Gu

department: Environmental Science and Ecological Engineering

country: South Korea

institute: Korea university

summary: Transcriptional profiling of A. oleivorans DR1 cells comparing control untreated wild type cells with norfloxacin treated wild type cells.

overall_design: To identify genes important for norfloxacin stress response in A. oleivorans DR1, the cells were grown to exponential phase (OD600 ~0.5) and treated with norfloxacin (4μg/ml) over a period of 15 min.


title: RNA-Seq of eye tissues from A/J, BALB/c, and C57BL/6 background mice

status: Public on Jun 08 2012

city: Cleveland

first: Debarshi

last: Mustafi

state: OH

address: 2109 Aldelbert Rd

department: Pharmacology

institute: Case Western Reserve University

summary: We report RNA-Seq experiments of whole eye tissues from A/J, BALB/c, and C57BL/6 background mice.

overall_design: Examine ocular tissue from 3 different background mice that display varying rates of retinal degeneration.

first: Tadao

last: Maeda

first: Krzysztof

last: Palczewski


title: Cohesins Repress KSHV Immediate Early Gene Transcription During Latency

status: Public on Jun 02 2012

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Chromatin-organizing factors, like CTCF and cohesins, have been implicated in the control of complex viral regulatory programs.  We investigated the role of CTCF and cohesin in the control of the latent to lytic switch for Kaposi's Sarcoma-Associated Herpesvirus (KSHV).   We found that cohesin subunits, but not CTCF, were required for the repression of KSHV immediate early gene transcription.  Depletion of cohesin subunits Rad21, SMC1, or SMC3 resulted in lytic cycle gene transcription and viral DNA replication.  In contrast, depletion of CTCF failed to induce lytic transcription or DNA replication. ChiP-Seq analysis revealed that cohesins and CTCF bound to several sites within the immediate early control regions for ORF50 and more distal 5' sites that also regulate the divergently transcribed ORF45-46-47 gene cluster.  Rad21 depletion led to a robust increase in ORF45 and ORF47 transcripts, with similar kinetics to that observed with chemical induction by sodium butyrate.  During latency, the chromatin between the ORF45 and ORF50 transcription start sites was enriched in histone H3K4me3 with elevated H3K9ac at the ORF45 promoter and elevated H3K27me3 at the ORF50 promoter.  A paused form of RNA pol II was loosely associated with the ORF45 promoter region during latency, but was converted to an active elongating form upon reactivation induced by Rad21 depletion.  Butyrate-induced transcription of ORF45 and ORF47 was resistant to cyclohexamide, suggesting that these genes have immediate early features similar to ORF50.  Butyrate-treatment caused the rapid dissociation of cohesins and loss of CTCF binding at the immediate early gene locus, suggesting that cohesins may be a direct target of butyrate-mediated lytic induction.   Our findings implicate cohesins as a major repressor of KSHV lytic gene activation, and function coordinately with CTCF to regulate the switch between latent and lytic gene activity.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design: Study of chromatin-organizing factors, like CTCF and cohesins.

first: Horng

last: Chen

last: Wikramasinghe

first: Louise

last: Showe

first: Paul

middle: M

last: Lieberman


title: Deeply conserved gene-regulatory functions of carboxy-terminal domains in dictyostelid C-module-binding factors

status: Public on Jun 03 2012

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: We describe the gene expression pattern of a Dictyostelium discoideum mutant depleted in the C-module-binding factor (CbfA) and autonomous gene-regulatory activities of CbfA carboxy-terminal domains (CbfA-CTDs)

overall_design: Comparison of gene expression in growing cells of a CbfA mutant compared to wild-type

first: Thomas

last: Winckler


title: Transcriptome of 3 developmental stages of Colletotrichum graminicola during infection of Zea mays leaf sheaths

city: Lexington

first: Lisa

last: Vaillancourt

state: Kentucky

address: 201F Plant Science Building

department: Plant Pathology

institute: University of Kentucky

overall_design: 3 biological replicates per stage. The three stages are: pre-penetration appressoria (PA), early biotrophic phase (BP), and the switch from biotrophy to necrotrophy (NP). Each biological replicate of the first stage, the pre-penetration appressoria, was sequenced to a 2-fold greater depth due to its lower representation in the samples.

first: Stefan

last: Amyotte

first: Ester

last: Buiate

first: Maria

last: Torres


title: Whole-genome mapping of MEIS1, TET1, H3K4me2 and H3K27ac in P19.6 mouse embryonal carcinoma cells and P19.6 cells treated for 48 hours with all-trans retinoic acid

first: Aurelien

last: Serandour

country: France

overall_design: MEIS1 and H3K27ac genome-wide distributions were determined using ChIP-seq. Cells used in this study are P19.6 mouse embryonal carnicoma cells and P19.6 cells treated for 48 hours with 1µM all-trans retinoic acid (RA). ChIP samples were done by Sérandour A.A. Libraries were prepared and sequenced by the IGBMC sequencing facility (Strasbourg, France) by an Illumina Genome Analyzer II.

first: Aurélien

middle: A

last: Sérandour


title: The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [RNA-seq]

status: Public on Jun 01 2012

city: Berlin

first: Markus

last: Landthaler

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrück-Center for Molecular Medicine

summary: Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing. Application to a human embryonic kidney cell line identified close to 800 proteins. Close to one third of these proteins, were neither previously annotated nor could be functionally predicted to bind RNA. Protein occupancy profiling provides a transcriptome-wide catalog of potential cis-regulatory regions on mammalian mRNAs and showed that large stretches in 3' UTRs can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms. Our observations indicate the presence of a large number of unexpected mRNA-binders with novel molecular functions participating in combinatorial post-transcriptional gene-expression networks.

overall_design: To obtain a more detailed picture of the RNA present in the pooled precipitates of four consecutive oligo(dT)-purifications, we constructed a cDNA library by random priming of 4-thiouridine (4SU)- and 6-thioguanosine (6SG)-labeled RNA derived from UV-irradiated (365 nm)and non-irradiated cells. Digital gene expression analysis of the cDNA library of non-irradiated cells, labeled with 4SU and 6SG, was performed.  To monitor the incorporation of photoreactive nucleotides into mRNA, we isolated 4SU- and 6SG-labeled RNA from the oligo(dT) precipitate of non-crosslinked cells by biotinylation and streptavidin purification (Dolken et al., 2008).


title: Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

city: Lebanon

first: xiaoyang

last: zhang

address: 1 Medical Center Driver

institute: Dartmouth Medical School

summary: Genome-wide association studies (GWAS) are identifying genetic predisposition to various diseases. The rs1859962 single nucleotide polymorphism (SNP) part of the 17q24.3 locus is a risk factor for prostate cancer (PCa). It defines a 130kb linkage disequilibrium (LD) block that lies in a ~2Mb gene desert area. Despite a role for the proximal SOX9 gene in PCa development, the functional biology driving the risk of this 17q24.3 risk locus is unknown. In the present study, we integrate genome-wide chromatin landscape datasets, namely epigenomes and chromatin openness from diverse cell-types to identify one PCa specific enhancer within the rs1859962 risk LD block. We reveal that this enhancer is part of a 1Mb chromatin loop with the SOX9 gene in PCa cells. The rs8072254 and rs1859961 SNPs part of this LD block map to this enhancer and impose allele-specific gene expression. The variant allele of rs1859961 directly decreases FoxA1 binding while increasing AP-1 binding compared to the reference allele. This latter is key in driving allele-specific gene expression. Together, our results demonstrate the risk associated with the PCa rs1859962 risk LD block is accounted for by multiple genetic variants mapping to a unique enhancer looping to the SOX9 oncogene. Allele-specific recruitment of the transcription factor AP-1 accounts in part for the increased enhancer activity ascribed to this PCa risk LD block. This further demonstrates that an integrative genomics approach can identify the functional biology disrupted by genetic risk-variants.

overall_design: Examination of histone modification H3K36me3 in the prostate cancer LNCaP cell line under DHT treatment.

first: Xiaoyang

last: Zhang


title: Genome-Wide DNA Methylation Profiles in Hematopoietic Stem and Progenitor Cells Reveal Over-Representation of ETS Transcription Factor Binding Sites

city: Bethesda

first: Jens

last: Lichtenberg

state: MD

address: 49 Convent Dr 3A19

department: National Human Genome Research Institute

institute: National Institutes of Health

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an essential epigenetic mark that is required for normal development. Knockout of the DNA methyltransferase enzymes in the mouse hematopoietic compartment reveals that methylation is critical for hematopoietic differentiation. To better understand the role of DNA methylation in hematopoiesis, we characterized genome-wide DNA methylation in primary mouse hematopoietic stem cells (HSC), common myeloid progenitors (CMP), and erythroblasts (ERY). Methyl Binding Domain protein 2 (MBD) enrichment of DNA followed by massively-parallel sequencing (MBD-Seq) was used to map genome-wide DNA methylation. Globally, DNA methylation was most abundant in HSC, with a 40% reduction in CMP, and 67% reduction in ERY. Only 3% of peaks arise during differentiation demonstrating a genome-wide decline in DNA methylation during erythroid development. Analysis of genomic features revealed that 98% of promoter CpG islands are hypomethylated, while 20-25% of non-promoter CpG islands are methylated. Proximal promoter sequences of expressed genes are hypomethylated in all cell types, while gene body methylation positively correlates with gene expression in HSC and CMP. Elevated genome-wide DNA methylation in HSC and the positive association between methylation and gene expression demonstrates that DNA methylation is a mark of cellular plasticity in HSC.  Utilizing de novo motif discovery we identified overrepresented transcription factor consensus binding motifs in methylated sequences. Motifs for several ETS transcription factors, including GABPalpha and ELF1 are overrepresented in methylated regions. Our genome-wide survey demonstrates that DNA methylation is markedly altered during myeloid differentiation and identifies critical regions of the genome and transcription factor programs that contribute to hematopoiesis.

overall_design: Examination of changes in methylation profiles during hematopoietic stem cell differentiation

first: Amber

last: Hogart

first: Subramanian

last: Ajay

first: Stacie

last: Anderson

first: Elliot

last: Margulies

first: David

last: Bodine


title: The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [PAR-CLIP]

overall_design: PARCLIP was performed as in Hafner et al. 2010 Cell 141, 129–141, with HEK293 cell lines stably expressing HIS/FLAG/HA-tagged ALKBH5, C17orf85, C22orf28, CAPRIN1, and ZC3H7B. We used 4-thiouridine (4SU) to enhance the crosslink and generated two PAR-CLIP cDNA libraries per protein.


title: The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [protein occupancy profiling]

overall_design: We generated protein occupancy cDNA libraries for two biological replicates. Briefly, we crosslinked 4SU-labeled cells and purified protein-mRNA complexes using oligo(dT)-beads. The precipitate was treated with RNAse I to reduce the protein-crosslinked RNA fragments to a length of about 30-60 nt. To remove non-crosslinked RNA, protein-RNA complexes were precipitated with ammonium sulfate and blotted onto nitrocellulose. The RNA was recovered by Proteinase K treatment, ligated to cloning adapters, and reverse transcribed. The resulting cDNA libraries were PCR-amplified and next-generation sequenced


title: Genome-wide characterization of menin-dependent H3K4me3 reveals a specific role for menin in the regulation of genes implicated in MEN1-like tumors (ChIP-Seq)

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

summary: Inactivating mutations in the MEN1 gene predisposing to the multiple endocrine neoplasia type 1 (MEN1) syndrome can also cause sporadic pancreatic endocrine tumors. MEN1 encodes menin, a subunit of MLL1/MLL2-containing histone methyltransferase complexes that trimethylate histone H3 at lysine 4 (H3K4me3). The importance of menin-dependent H3K4me3 in normal and transformed pancreatic endocrine cells is unclear. To study the role of menin-dependent H3K4me3, we performed in vitro differentiation of wild-type as well as menin-null mouse embryonic stem cells (mESCs) into pancreatic islet-like endocrine cells (PILECs). Gene expression analysis and genome-wide H3K4me3 ChIP-Seq profiling in wild-type and menin-null mESCs and PILECs revealed menin-dependent H3K4me3 at the imprinted Dlk1-Meg3 locus in mESCs, and all four Hox loci in differentiated PILECs. Specific and significant loss of H3K4me3 and gene expression was observed for genes within the imprinted Dlk1-Meg3 locus in menin-null mESCs and the Hox loci in menin-null PILECs. Given that the reduced expression of genes within the DLK1-MEG3 locus and the HOX loci is associated with MEN1-like sporadic tumors, our data suggests a possible role for menin-dependent H3K4me3 at these genes in the initiation and progression of sporadic pancreatic endocrine tumors. Furthermore, our investigation also demonstrates that menin-null mESCs can be differentiated in vitro into islet-like endocrine cells, underscoring the utility of menin-null mESC-derived specialized cell types for genome-wide high-throughput studies.

overall_design: Genome-wide mapping of H3K4me3 and microarray gene expression profiling in TC-1 wild-type (WT) mESCs, menin-null (Men1-ko) mESCs (3.2N), pancreatic islet-like endocrine cells (PILECs) derived from WT mESCs, and PILECs derived from Men1-ko mESCs.

first: Sunita

last: Agarwal


title: The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia

city: New York

first: Altuna

last: Akalin

address: 1305 york

institute: Weill Cornell Medical College

summary: Here we used Illumina NGS for high-throughput profiling of the DNA methylome in two human colon cancer derived cell lines, two human normal bone marrow CD34+ controls and in five human Acutre Myeloid Leukeima patient samples.  These data can be used to determine the CpG cytosine methylation pattern at base pair resolution in each sample and to determine differentially methylated cytosines and regions between samples

overall_design: Reduced Representation Bisulfite Sequencing (RRBS) and Extended Reduced Representation Bisulfite Sequencing (ERRBS) on genomic DNA. We used colon cancer cell lines (two) to establish reproducbility and range of assay sensitivity.  We used Acute Myeloid Leukemia patient samples and CD34+ bone marrow cells as controls to determine the methylome pattern in the patient samples

first: Francine

middle: E

last: Garrett-Bakelman

first: Matthias

last: Kormaksson

first: Jennifer

last: Busuttil

first: Lu

first: Irina

last: Khrebtukova

first: Thomas

last: Milne

first: Yongsheng

last: Huang

first: Debabrata

last: Biswas

first: Jay

middle: L

last: Hess

first: C

last: Allis

first: Robert

middle: G

last: Roeder

first: Peter

last: Valk

first: Bob

last: Löwenberg

first: Ruud

last: Delwel

first: Hugo

middle: F

last: Fernandez

first: Elisabeth

last: Paietta

first: Martin

last: Tallman

first: Gary

middle: P

last: Schroth

first: Christopher

last: Mason

first: Ari

last: Melnick

last: Figueroa


title: ChIP-seq of the HOXA9 and MEIS1 transcription factors in SEM cells.

status: Public on May 31 2012

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: SEM cells were established from the peripheral blood of a 5-year-old girl in relapse with acute lymphoblastic leukaemia (ALL). SEM cells exhibit the t(4;11) chromosomal rearrangement, which leads to production of the MLL-AF4 fusion protein. Hematopoietic transcription factors including HOXA9 and MEIS1 are highly expressed in ALL.

overall_design: ChIP-seq was performed against HoxA9 and MEIS1 in SEM cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing.

first: Matthew

last: Guenther

first: Lee

middle: N

last: Lawton


title: Genome-wide characterization of menin-dependent H3K4me3 reveals a specific role for menin in the regulation of genes implicated in MEN1-like tumors

first: Raja

last: Jothi


title: Expression, ChIP-chip, and ChIP-Seq data from REH and SEM leukemia cell lines [ChIP-Seq]

summary: MLL-fusion proteins are potent inducers of cancer in hematopoietic cells, where they are known to cause changes in global gene expression. How MLL-fusion proteins interact with the genome has not been established, so we have limited understanding of the pathway by which these proteins generate aberrant gene expression programs. Here we describe how the MLL-AF4 protein occupies the genome in human leukemia cells and its striking effects on chromatin states. We find that the MLL-AF4 fusion protein selectively occupies regions of the genome that contain developmental regulatory genes important for hematopoietic stem cell identity and self-renewal. These MLL-AF4 bound regions have grossly altered chromatin structure, with histone modifications catalyzed by Trithorax Group (TrxG) proteins and Dot1 extending across unusually large domains. This indicates that a key feature of MLL-associated leukemogenesis is aberrant targeting of chromatin modifiers to regions of the genome controlling hematopoietic development. Our results define the direct targets of the MLL-fusion protein, reveal the global role of epigenetic misregulation in leukemia, and identify new targets for therapeutic intervention in human cancer.

overall_design:
This dataset includes expression data for two replicates each of SEM and REH leukemia cell lines, ChIP-chip data targeting RNAP2, H3K4me3, H3K79me2, ENL, AF4-C, and MLL-N in SEM and REH leukemia cell lines, and ChIP-Seq data of H3K79me2, H3K4me3, ans WCE in SEM and REH cell lines.
This Series contains the ChIP-Seq data only.  The expression and ChIP-chip data are provided in GEO Series GSE13313.


title: Dynamic hydroxymethylation of DNA marks differentiation-driven enhancers

city: Rennes

first: Aurelien

last: Serandour

address: Bâtiment 13, Campus de Beaulieu


title: De novo assembly of siRNA immunity in wild plants

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

country: China

institute: BGI-SHENZHEN

summary: We describe an application of deep sequencing and de novo assembly of short RNA reads to investigate small interfering (si)RNAs mediated immunity in leaf samples from eight tree taxa naturally occurring in Wytham Woods, Oxfordshire, UK.  BLAST search for homologues of contigs in the GenBank identified siRNA populations against a number of RNA viruses and a Ty1-copia retrotransposons in these tree species.

sample_organism:
Betula pendula
Acer pseudoplatanus
Corylus avellana
Fagus sylvatica
Fraxinus excelsior
Quercus robur
Aesculus hippocastanum
Tilia platyphyllos
Ulmus glabra

overall_design: Small RNA sequencing and de novo assembly

first: Hui

last: Wang

first: Hongzhi


title: Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

city: Wuhan

first: Xiyan

last: Yang

state: Hubei

address: Shizishan 1, Hongshan

institute: Huazhong Agricultural University

summary: We used a next-generation sequencing approach, Illumina Digital Gene Expression (DGE) technology, to Genome-wide profiling of gene expression during cotton SE. As a result, 5,076 differentially expressed genes were identified during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process. Transcription factor-encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein / indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE. We report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis.

overall_design: differential gene expression analysis at 9 time-points/stages during somatic embryogenesis in cotton by deep sequencing, using Illumina GAIIx.

first: Xianlong

last: Zhang


title: The let-7-Imp axis regulates aging of the Drosophila testis stem cell niche.

city: Cold Spring Harbor

first: Benjamin

last: Czech

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: Adult stem cells support tissue homeostasis and repair throughout the life of an individual. However, numerous intrinsic and extrinsic changes occur with age that result in altered stem cell behavior and reduced tissue maintenance and regeneration. In the Drosophila testis, stem cells surround and contact the apical hub, a cluster of somatic cells that express the self-renewal factor Unpaired (Upd), which activates the JAK-STAT pathway in adjacent stem cells. However, aging results in a dramatic decrease in upd expression, with a concomitant loss of germline stem cells (GSCs). Here we present genetic and biochemical data to demonstrate that IGF-II mRNA binding protein (Imp) counteracts endogenous small interfering RNAs to stabilize upd RNA and contribute to maintenance of the niche. However, Imp expression decreases in hub cells of older males, similar to upd, which is due to targeting of Imp by the heterochronic microRNA let-7. Therefore, in the absence of Imp, upd mRNA becomes unprotected and susceptible to degradation. Understanding the mechanistic basis for aging-related changes in stem cell behavior will lead to the development of strategies to treat age-onset diseases and facilitate stem cell based therapies in older individuals.

overall_design: Examination of small RNA levels in testes from young (1day old) and aged (30days old) males of Drosophila melanogaster by deep sequencing (using Illumina GAII).

first: Hila

last: Toledano

first: Cecilia

last: D'Alterio

first: Erel

last: Levine

first: D

last: Jones


title: Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing

city: Bronx

first: Saurabh

last: Gombar

address: 1301 Morris Park Avenue

department: Systems and Computational Biology

institute: Albert Einstein College of Medicine

summary: In this study, we employed massively parallel sequencing technology to identify miRNAs expressed in B-cells from Ashkenazi Jewish centenarians, i.e., those living to a hundred and a human model of exceptional longevity, and younger controls without a family history of longevity. With data from 26.7 million reads comprising 9.4x108 bp from 3 centenarian and 3 control individuals, we discovered a total of 276 known miRNAs and 8 unknown miRNAs ranging several orders of magnitude in expression levels. A total of 22 miRNAs were found to be significantly upregulated, with only 2 miRNAs downregulated, in centenarians as compared to controls.

overall_design: Examination of miRNA profile of two different ages

first: Yousin

last: Suh


title: Genome wide binding sites of Smad3 and JMJD3 in neural stem cells

status: Public on May 30 2012

city: Barcelona

first: Conchi

last: EI

address: Baldiri Reixac 15

country: Spain

institute: IBMB

summary: Neural development requires crosstalk between signaling pathways and chromatin. In this study, we demonstrate that neurogenesis is promoted by an interplay between the TGFβ pathway and the H3K27me3 histone demethylase (HDM) JMJD3. Genome-wide analysis showed that JMJD3 is targeted to gene promoters by Smad3 in neural stem cells (NSCs) and is essential to activate TGFβ-responsive genes. In vivo experiments in chick spinal cord revealed that the generation of neurons promoted by Smad3 is dependent on JMJD3 HDM activity. Overall, these findings indicate that JMJD3 function is required for the TGFβ developmental program to proceed.

overall_design: We immunoprecipitate endogenous Smad3 or JMJD3 proteins from neural stem cells treated with TGFb for 30 minutes.

last: Ibanez


title: 0-2 Hour RNA PolII ChIP-Seq experiment

status: Public on May 29 2012

city: Toronto

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3625
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Developmental Stage: Embryo 0-2h;  EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-2h; Antibody Anti-RNA polymerase II clone CTD4H8 (target is RNA polymerase II); read length (read_length)

first: David

last: MacAlpine

first: Heather

first: Matthew

last: Eaton

first: Joseph

last: Prinz


title: 0-2 Hour ORC ChIP-Seq experiment

summary:
modENCODE_submission_3628
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Developmental Stage: Embryo 0-2h;  EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-2h; Antibody dORC2 (target is Drosophila ORC2p); read length (read_length)


title: The H3K27 demethylase Utx facilitates somatic and germ cell epigenetic reprogramming to pluripotency [ChIP-Seq]

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Pluripotency can be induced in somatic cells by ectopic expression of defined transcription factors, however the identity of epigenetic regulators driving the progression of cellular reprogramming requires further investigation. Here we uncover a non-redundant role for the JmjC-domain-containing protein histone H3 methylated Lys 27 (H3K27) demethylase Utx, as a critical regulator for the induction, but not for the maintenance, of primed and naïve pluripotency in mice and in humans. Utx depletion results in aberrant H3K27me3 repressive chromatin demethylation dynamics, which subsequently hampers the reactivation of pluripotency promoting genes during reprogramming. Remarkably, Utx deficient primordial germ cells (PGCs) display a cell autonomous aberrant epigenetic reprogramming in vivo during their embryonic maturation, resulting in the lack of functional contribution to the germ-line lineage.

overall_design: H3K27me3 and H3K4me3 were measured genome-wide in the following cell types:  Utx+/Y (WT) and Utx-/Y (KO) mouse ES cells and mouse embryonic fibroblast (MEF) before and after DOX induction (initiating reprogramming by OSKM factors).

first: Ohad

last: Gafni


title: Small RNA profiling Tomato, wild tomato relative and series of introgression lines

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

summary: High throughput sequencing was used to investigate the production of small RNAs from cultivated tomato cultivar M82 and  its wild relative Solanum pennellii.  In order to understand the pattern of inheritance of the samll RNAs, interspecific hybrids (F1 and F2) along with series of introgressed lines comprising precise short genomic regions from S. pennellii in M82 background were used.

sample_organism: Solanum lycopersicum x Solanum pennellii

overall_design: Examination of small RNA production in several tomato lines.

first: Ruth

last: Dunn

first: Padubidri

last: Shivaprasad


title: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis (flowers RNA-seq)

status: Public on May 26 2012

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Illumina mRNA libraries for 7 RNA-directed DNA methylation mutants.

overall_design: Examining mRNA levels in floral tissue of RNA-directed DNA methylation mutants.

middle: C

first: Steve

last: Jacobsen


title: Profiling of differential allelic expression in horse, donkey, mule, and hinny placental tissues.

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

summary: In eutherian mammals, dosage compensation of X-linked genes is achieved by X chromosome inactivation. X inactivation is random in embryonic and adult tissues, but imprinted X inactivation (paternal X silencing) has been identified in the extraembryonic membranes of the mouse, rat, and cow.  Few other species have been studied for this trait, and the data from studies of the human placenta have been discordant or inconclusive.  Here, we quantify X inactivation using RNA sequencing of placental tissue from reciprocal hybrids of horse and donkey (mule and hinny).  In placental tissue from the equid hybrids and the horse parent the allelic expression pattern was consistent with random X inactivation, and imprinted X inactivation can clearly be excluded. We characterized horse and donkey XIST gene, and demonstrated that XIST allelic expression in female hybrid placental and fetal tissues is negatively correlated with the other X-linked genes chromosome-wide, which is consistent with the XIST-mediated mechanism of X inactivation discovered previously in mice.  As the most structurally and morphologically diverse organ in mammals, the placenta also appears to show diverse mechanisms for dosage compensation that may result in differences in conceptus development across species.

sample_organism:
Equus asinus
Equus caballus
Equus asinus x Equus caballus
Equus caballus x Equus asinus

overall_design: Examine allelic expression from individual samples of invasive trophoblast tissue of the chorionic girdle from gestation day 33-34 conceptuses of 5 horses, 3 donkeys, 6 mules, and 1 hinny.

first: Douglas

last: Antczak


title: Small RNA sequencing in maize hybrids and inbreds

city: Urbana

first: Wesley

middle: T

last: Barber

state: IL

address: 1201 W. Gregory Drive

department: Department of Crop Sciences

institute: University of Illinois at Urbana-Champaign

summary: Small RNAs (sRNAs) are hypothesized to contribute to hybrid vigor because they maintain genome integrity, contribute to genetic diversity, and control gene expression. We used Illumina sequencing to assess how sRNA populations vary between two maize inbred lines (B73, Mo17) and their hybrid. We sampled sRNAs from the seedling shoot apex and the developing ear, two rapidly growing tissues that program the greater growth of maize hybrids. We found that parental differences in siRNAs primarily originate from repeat regions. Although the maize genome contains greater number and complexity of repeats compared to Arabidopsis or rice, we confirmed that like these simpler plant genomes, 24-nt siRNAs whose abundance differs between maize parents also show a trend of downregulation following hybridization. Surprisingly, hybrid vigor is fully maintained when 24-nt siRNAs are globally reduced by mutation of the RNA-dependent RNA polymerase2 (RDR2) encoded by modifier of paramutation1 (mop1). We also discovered that 21-22nt siRNAs derived from a number of distinct retrotransposon families differentially accumulate between B73 and Mo17 as well as their hybrid. Thus, maize possesses a novel source of genetic variation for regulating both transposons and genes at a genomic scale, which may contribute to its high degree of observed heterosis.

overall_design:
sRNA libraries were derived from RNA isolated from the seedling shoot apex and developing ear tissues from B73, Mo17, B73xMo17 and Mo17xB73. The shoot apex was chosen because it is enriched for meristematic tissue where cell proliferation occurs, rates of organ initiation are determined, and organ size is specified. The developing ear was examined because it is enriched in meristematic tissue and is undergoing rapid growth, and also because the mature ear shows the highest degree of heterosis. Total RNA was isolated and separated on a 15% TBE-Urea polyacrylamide gel. Using a 10-bp ladder, the sRNA fraction representing 10-40-bp was excised. sRNA libraries were prepared according to Lu et al. (2007) or manufacturer's instructitions (Illumina). A combination of Perl scripts and FASTX toolkit scripts were used to remove adapters, collapse identical sequences and count reads per sequence.

Supplementary processed data text files contain the distinct sRNA sequences for all of the genotypes analyzed in that experiment. Abundance (reads per million) was calculated for each distinct sequence by dividing the number of reads of distinct sRNA in a library by the total number of sRNA reads for that library and multiplying this by 1 million.
Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.

first: Stephen

last: Moose

last: Hudson


title: Cell-type specific control of enhancer activity by H3K9 trimethylation

status: Public on May 28 2012

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)


title: Cis- and trans- regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. The majority of genes with both cis- and trans-effects are subjected to compensating interactions and stabilizing selection. Interestingly, chromatin modifications correlate with cis - and trans -regulation. In F1 allotetraploids, Arabidopsis arenosa trans factors predominately affect allelic expression divergence. Arabidopsis arenosa trans factors tend to upregulate Arabidopsis thaliana alleles, whereas Arabidopsis thaliana trans factors up- or down-regulate Arabidopsis arenosa alleles. In resynthesized and natural allotetraploids, trans effects drive expression of both homoeologous loci into the same direction. We provide evidence for natural selection and chromatin regulation in shaping gene-expression diversity during plant evolution and speciation.

sample_organism: Arabidopsis arenosa x Arabidopsis thaliana

overall_design: Examination of gene expression in 5 tetraploid Arabidopsis using mRNA-seq

first: Xiaoli

last: Shi

first: Danny

middle: W

last: Ng

first: Changqing

last: Zhang

first: Luca

last: Comai

first: Wenxue

last: Ye

first: Jeffrey

middle: Z


title: The transcriptional program controlled by Runx1 during early hematopoietic development (ChIP-seq data)

first: Anagha

last: Joshi

address: Wellcome trust/MRC building, Hills road

department: Dept. of haematology, CIMR

institute: University of cambridge

summary: Transcription factors have long been recognised as powerful regulators of mammalian development, yet it is largely unknown how individual key regulators operate within wider regulatory networks.  Here we have used a combination of global gene expression and chromatin-immunoprecipitation approaches across four ES-cell-derived populations of increasing haematopoietic potential to define the transcriptional programme controlled by Runx1, an essential regulator of blood cell specification.  Integrated analysis of these complementary genome-wide datasets allowed us to construct a global regulatory network model, which suggested that core regulatory circuits are activated sequentially during blood specification, but will ultimately collaborate to control many haematopoietically expressed genes.  Using the CD41/integrin alpha 2b gene as a model, cellular and in vivo studies showed that CD41 is controlled by both early and late circuits in fully specified blood cells, but initiation of CD41 expression critically depends on a later subcircuit driven by Runx1.  Taken together, this study represents the first global analysis of the transcriptional programme controlled by any key haematopoietic regulator during the process of early blood cell specification. Moreover, the concept of interplay between sequentially deployed core regulatory circuits is likely to represent a design principle widely applicable to the transcriptional control of mammalian development.

overall_design: 4 samples: 3 samples of Runx1 transcription factor ChIP from the Runx1+/VE-cadherin+/CD41+ population, Runx1+/VE-cadherin+/CD41- population and Runx1+/VE-cadherin-/CD41+ population, and 1 Control (IgG).

first: Yosuke

last: Tanaka

first: Nicola

middle: K

last: Wilson

first: Sarah

last: Kinston

first: Shinichi

last: Nishikawa

first: Berthold

last: GÃ¶ttgens


title: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: The H3K27 demethylase Utx facilitates somatic and germ cell epigenetic reprogramming to pluripotency

first: Noa

last: Novershtern


title: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [BS-seq]

summary: Illumina-based whole genome bisulfite sequencing libraries for 4 RNA-directed DNA methylation mutants

overall_design: Examining DNA methylation levels in leaf tissue of RNA-directed DNA methylation mutants

first: Steve

last: Jacobsen


title: RNA Sequencing Analysis Generates Comprehensive Transcriptomic Landscape and Identifies PTK6 as a Novel Tumor Suppressor Gene in Esophageal Squamous Cell Carcinoma

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

summary: We performed the integrative transcriptome analysis of human esophageal squamous cell carcinoma (ESCC) using Illumina high-throughput sequencing. A total of 187 million 38bp sequencing reads were generated containing 7 billion bases for three pairs of matched patient-derived ESCC clinical specimens and their adjacent non-tumorous tissues. By investigating the digital gene expression profiling, we found 1425 genes significantly differentially expressed and detected more than 9000 SNPs across all six samples. We also identified protein tyrosine kinase 6 (PTK6) as a novel tumor suppressor gene, which is critical in ESCC development.

overall_design: Analysis of whole transcriptome from 3 paired patient-derived ESCC clinical specimens and their adjacent non-tumorous tissues.

first: Si

last: Lok

first: Xin-Yuan

last: Guan

first: Stephanie

last: Ma

first: Yun-Juan


title: Chromatin State Segmentation by HMM from ENCODE/Broad

status: Public on May 24 2012

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (mailto:jernst@mit.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track displays a chromatin state segmentation for each of nine human cell types (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?term=GM12878,H1-hESC,HepG2,HUVEC,HMEC,HSMM,K562,NHEK,NHLF). A common set of states across the cell types were learned by computationally integrating ChIP-seq data for nine factors plus input (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?term=CTCF,H3K4me1,H3K4me2,H3K4me3,H3K27ac,H3K9ac,H3K36me3,H4K20me1,H3K27me3,Input) using a Hidden Markov Model (HMM). In total, fifteen states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
ChIP-seq data from the Broad Histone (http://hgwdev.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeBroadChipSeq) track was used to generate this track. Data for nine factors plus input (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?term=CTCF,H3K4me1,H3K4me2,H3K4me3,H3K27ac,H3K9ac,H3K36me3,H4K20me1,H3K27me3,Input) and nine cell types (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?term=GM12878,H1-hESC,HepG2,HUVEC,HMEC,HSMM,K562,NHEK,NHLF) was binarized separately at a 200 base pair resolution based on a Poisson background model. The chromatin states were learned from this binarized data using a multivariate Hidden Markov Model (HMM) that explicitly models the combinatorial patterns of observed modifications (Ernst and Kellis, 2010). To learn a common set of states across the nine cell types, first the genomes were concatenated across the cell types. For each of the nine cell types, each 200 base pair interval was then assigned to its most likely state under the model. Detailed information about the model parameters and state enrichments can be found in (Ernst et al, accepted).
This is release 1 (Jun 2011) of this track, and it is based on the NCBI36/hg18 release of the Broad Histone (http://hgwdev.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeBroadChipSeq) track. This track has also been lifted over to GRCh37/hg19 (http://hgwdev.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHmm). It is anticipated that the HMM methods will be run on the newer GRCh37/hg19 Broad Histone (http://hgwdev.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone) data and will replace the lifted version.

first: Jason

last: Ernst

first: Manolis

last: Kellis

first: Bradley

last: Bernstein


title: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [leaves RNA-seq]

summary: Illumina TruSeq mRNA libraries for 4 RNA-directed DNA methylation mutants

overall_design: Examining mRNA levels in leaf tissue of RNA-directed DNA methylation mutants


title: Identification of wild soybean miRNAs and their target genes responsive to aluminum stress

status: Public on May 25 2012

city: Guangzhou

first: Hai

last: Nian

address: College of Agriculture, South China Agricultural University

department: College of Agriculture

institute: South China Agricultural University

summary: In this study, two small RNA libraries and two degradome libraries were constructed from roots of Al-treated and Al-free Glycine soja seedlings. For miRNA, a total of 7,287,655 and 7,035,914 clean reads in Al-treated and Al-free small RNAs libraries were generated, and 105 known miRNAs ,51 p3/p5 strands of known miRNA and 80 novel miRNAs were identified. Among them, expression of 34 miRNAs was responsive to Al stress. Through degradome sequencing, 82 and 11 genes were identified as tagerts of known and novel miRNAs obtained from this study, respectively. Gene Ontology (GO) annotations of target transcripts indicated that 52 out of 66 targets cleaved by conserved miRNA families may play role in regulation of transcription.

overall_design: sample 1: Examination of small RNA in Al-free  wild soybean roots; sampple 2: Examination of small RNA in Al-treated wild soybena roots; sample 3: identification of miRNA targets in Al-free wild soybean roots; sample 4: identification of miRNA targerts in Al-treated wild soybean roots

first: Qiaoying

last: Zeng

first: Cunyi

last: Yang


title: RNA-seq-based analysis of the pathogen-induced defense transcriptome in Arabidopsis

city: Canberra

first: Stuart

last: Stephen

state: ACT

address: Black Mountain

department: Plant Industry

country: Australia

institute: CSIRO

summary: Pathogen infection triggers transcriptional reprogramming in host plants, however we still know little about the dynamics of the pathogen-induced defense transcriptome. The goal of this study was to investigate the dynamic reprogramming of the defense transcriptome in response to Fusarium oxysporum infection in Arabidopsis using RNA-seq technology and to provide a comprehensive analysis of genes underlying the innate immune response against the fungal pathogen. Our results suggest that the Arabidopsis transcriptome is reprogrammed to co-ordinately express multiple positive and negative regulators following pathogen infection to modulate defense gene expression and disease resistance. Our study identified a number of novel genes responsive to pathogen infection and provided a rich source of pathogen responsive genes for further functional characterization.

overall_design: Four samples (M1DPI, M6DPI, F1DPI and F6DPI; M=mock treated; F=Fusarium oxysporum infected; DPI=day post inoculation) were sequenced to identify pathogen responsive genes in each time point. Each sample was sequenced once, i.e. without biological replicate.

first: Qian-Hao

last: Zhu

first: Ming-Bo

last: Wang


title: CBX3 Regulates Efficient RNA Processing Genome Wide

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: University of California, San Diego

type: Genome binding/occupancy profiling by genome tiling array

summary: HP1 alpha, beta, and gamma play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, some HP1 family members may also participate in transcriptional regulation of genes. Recently, HP1 gamma binding to the bodies of a subset of genes has been observed in human and murine cells. However, the generality of this phenomenon and the role HP1 gamma may play in this context are unknown. Genome-wide localization analysis reveals broad and general HP1 gamma binding at actively transcribed genes, which strongly correlates with gene activity across multiple cell types. Unexpectedly, we find HP1 gamma binding is necessary for efficient RNA processing of its target genes. Loss of HP1 gamma results in defective recruitment of splicing factors including U1-70K, and leads to accumulation of unspliced nascent transcripts genome-wide. Therefore, our data argue that the primary role of HP1 gamma is to ensure efficient RNA processing in mammalian cells.

overall_design: Genome-wide localization and function of HP1 gamma in multiple cell types using ChIP-chip, ChIP-seq, and RNA-seq

first: Andrea

last: Smallwood

first: Gary

last: Hon

first: Fulai

last: Jin

first: Ryan

last: Henry

first: JoaquÃn

middle: M

last: Espinosa


title: Tn5 transposase-mediated library preparation of single-cell cDNAs for RNA-seq

city: London

first: Kenta

last: Yashiro

address: Charterhouse Square

department: Willaim Harvey research Institute

institute: Barts and The London School of Medicine and Dentistry, Queen Mary University of London

summary: Deep sequencing of single cell-derived genomic DNA and/or cDNAs brings novel insights into oncogenesis and embryogenesis. However, traditional library preparation for RNA-Seq requires multiple steps, including shearing the target DNA/RNA and following sequential enzymatic reactions, which result in consequent sample loss and stochastic variation at each step. Such variation may significantly affect the output from sequencing. We have found that a new technique of library preparation using hyperactive Tn5 transposase for the next-generation sequencer of Illumina's platform provided high-quality libraries from 100ng of short-length (average 700~800 bp) single-cell level cDNA. This new method reduced the number of steps in the protocol, which resulted in improved reproducibility and reduced variation among the specimens.

overall_design: Two methods of library preparation (sonication, tagmentation with hyperactive Tn5 transposase) were compared in the case of RNA-Seq for single-cell level cDNA. Technical triplicates were used.

first: Scott

last: Brouilette

last: Kuersten

first: Charles

last: Mein

first: Monika

last: Bozek

first: Anna

last: Terry

first: Kerith

middle: R

last: Dias

first: Leena

last: Bhaw-Rosun

first: Yasunori

last: Shintani

first: Steven

last: Coppen

first: Chiho

last: Ikebe

first: Vinit

last: Sawhney

first: Niall

last: Campbell

first: Masahiro

last: Kaneko

first: Nobuko

last: Tano

first: Hidekazu

last: Ishida

first: Ken

last: Suzuki


title: Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

status: Public on May 22 2012

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

institute: Max Planck Institute for Developmental Biology

type: Expression profiling by genome tiling array

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata

platform_organism:
Arabidopsis thaliana
Arabidopsis lyrata


title: Apple miRNAs and tasiRNAs with novel regulatory networks

first: Rui

last: Xia

address: 483 Wushan Rd, Tianhe

department: Horticulture

summary:
Background
miRNAs and their regulatory functions have been extensively characterized in model species but whether apple has evolved similar or unique regulatory features remains unknown.
Results
We performed deep sRNA-seq and identified 23 conserved, 10 less-conserved and 42 apple-specific miRNAs or families with distinct expression patterns. The identified miRNAs target 118 genes representing a wide range of enzymatic and regulatory activities. Apple also conserves two TAS gene families with similar but unique tasiRNA biogenesis profiles and target specificities. Importantly, we found that miR159, miR828 and miR858 can collectively target up to 81 MYB genes potentially involved in diverse aspects of plant growth and development. These miRNA target sites are differentially conserved among MYBs, which is largely influenced by the location and conservation of the encoded amino acid residues in MYB factors. Finally, we found that ten of the 19 miR828-targeted MYBs undergo siRNA biogenesis at the 3' cleaved, highly divergent transcript regions, generating over 100 sequence-distinct siRNAs that potentially target over 70 diverse genes as confirmed by degradome analysis.
Conclusion
Our work identified and characterized apple miRNAs, their expression patterns, targets and regulatory functions. We also discovered that three miRNAs and the ensuing siRNAs exploit both conserved and divergent sequence features of MYB genes to initiate distinct regulatory networks targeting a multitude of genes inside and outside the MYB family.

overall_design: Identification of apple miRNAs and their targets from four different tissues

first: Hong

last: Zhu

first: Zongrang

last: Liu

first: Eric

last: Beers

first: Yongqiang

last: An


title: ChIP-Seq of Pax7 and Pax3 in myoblasts

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary:
Examination of binding locations of Pax3 and Pax7 in primary myoblasts

UCSC track hub available at:
http://www.ogic.ca/projects/Soleimani_2012_Pax7_hub/hub.txt

For details on viewing the track hub in the UCSC Genome Browser:
http://altair.dartmouth.edu/ucsc/goldenPath/help/hgTrackHubHelp.html#View

overall_design: 3 Samples (Control, Pax7 ChIP, Pax3 ChIP)

first: Vahab

middle: D

last: Soleimani

first: Vincent

last: Punch

first: Yoh-ichi

last: Kawabe

first: Andrew

middle: E

last: Jones

first: Gareth

middle: A

last: Palidwor

first: Christopher

middle: J

last: Porter

first: Joe

last: Cross

first: Jaime

last: Caravajal

first: Christel

last: Kockx

first: Wilfred

last: van IJcken

first: Peter

last: Rigby

first: Frank

last: Grosveld

first: Michael

last: Rudnicki


title: Investigation into the Physiologies of Aeromonas veronii in vitro and Inside the Digestive-Tract of the Medicinal Leech using RNA-seq

city: Storrs

first: Joerg

last: Graf

state: CT

address: 91 North Eagleville Road

institute: University of Connectiuct

summary: In this study we used Illumina RNA-seq to identify genes expressed by A. veronii in mid-log phase growth in a rich medium and within the digestive tract of the medicinal leech. Our results shed light on the physiology of A. veronii during colonization of the leech gut.

overall_design: A comparison of Illumina RNA-seq of A. veronii in vivo versus in vitro.

first: Lindsey

last: Bomar


title: The transcriptional program controlled by Runx1 during early hematopoietic development

city: Cambridge

first: Anagha

last: Joshi


title: Oncogene-Mediated Alterations in Chromatin Conformation

status: Public on May 23 2012

city: New York

first: David

last: Soong

address: 1305 York Avenue

department: Institute for Computational Biomedicine

institute: Weill Cornell Medical College

summary: Emerging evidence suggests that chromatin adopts a non-random three-dimensional (3D) topology and that the organization of genes into structural hubs and domains affects their transcriptional status. How chromatin conformation changes in diseases such as cancer is poorly understood. Moreover, how oncogenic transcription factors, which bind to thousands of sites across the genome, influence gene regulation by globally altering the topology of chromatin requires further investigation. To address these questions, we performed unbiased high-resolution mapping of intra- and inter-chromosome interactions upon over-expression of ERG, an oncogenic transcription factor frequently over-expressed in prostate cancer as a result of a gene fusion. By integrating data from genome-wide chromosome conformation capture (Hi-C), ERG binding and gene expression, we demonstrate that oncogenic transcription factor over-expression is associated with global, reproducible and functionally coherent changes in chromatin organization. The results presented here have broader implications, as genomic alterations in other cancer types frequently give rise to aberrant transcription factor expression e.g., EWS-FLI1, c-Myc, n-Myc, PML-RARα.

overall_design: We used stable isogenic, normal benign prostate epithelial cell lines (RWPE1) that differ with respect to ERG3 over-expression. To test whether ERG over-expression is associated with global changes in chromatin structure, we performed unbiased chromatin interaction mapping using the Hi-C technique from both RWPE1-ERG and RWPE1-GFP cells, with biological replicates. Successful fill-in and ligation were determined as previously reported by testing for a known interaction between two distant genomic loci located on chromosome 6. The Hi-C libraries were paired-end sequenced using an Illumina GAIIx platform. Following alignment to the human genome (hg18) and filtering to remove un-ligated and self-ligated DNA, we identified intra-chromosomal (or cis-) and inter-chromosomal (or trans-) interactions in both RWPE1 cell lines. To characterize ERG binding and ERG-mediated gene expression changes in these cells, we performed chromatin-immunoprecipitation combined with high-throughput sequencing (ChIP-seq) and RNA sequencing (RNA-seq). ERG was bound to 6,398 sites in RPWE1-ERG cells. Based on paired-end RNA-seq data from both cell lines, 1,266 genes were differentially expressed between RWPE1-ERG and RWPE1-GFP cell lines.

middle: S

last: Rickman

first: Daivd

first: Benjamin

last: Moss

first: Juan

last: Mosquera

first: Jan

last: Dlabal

first: Stéphane

last: Terry

first: Theresa

middle: Y

last: MacDonald

first: Joseph

last: Tripodi

first: Karen

last: Bunting

first: Vesna

last: Najfeld

first: Francesca

last: Demichelis

first: Ari

last: Melnick

first: Olivier

last: Elemento

first: Mark

last: Rubin


title: Transcriptional Dominance of Pax7 in Adult Myogenesis Is Due to High-Affinity Recognition of Homeodomain Motifs

first: Theodore

last: Perkins

first: Vahab

last: Soleimani

first: Vincent

middle: G

last: Punch

first: Yoh-ichi

last: Kawabe

first: Andrew

last: Jones

first: Gareth

last: Palidwor

first: Christopher

last: Porter

first: Joe

last: Cross

first: Jaime

last: Caravajal

first: Cristel

last: Kockx

first: Wilfred

middle: F

last: van IJcken

first: Peter

last: Rigby

first: Frank

last: Grosveld

first: Michael

last: Rudnicki


title: Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

status: Public on May 20 2012

city: Rehovot

first: Eilon

last: Sharon

address: 234 Herzl Street

department: Computer Science And Applied Mathematics

institute: Weizmann Institute of Science

summary: Despite extensive research, our understanding of the rules according to which cis-regulatory sequences are converted into gene expression is limited We devised a method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters and applied it to measure the effect of systematic changes in the location, number, orientation, affinity and organization of transcription-factor binding sites and nucleosome-disfavoring sequences. Our analyses reveal a clear relationship between expression and binding-site multiplicity, as well as dependencies of expression on the distance between transcription-factor binding sites and gene starts which are transcription-factor specific, including a striking ~10-bp periodic relationship between gene expression and binding-site location. We show how this approach can measure transcription-factor sequence specificities and the sensitivity of transcription-factor sites to the surrounding sequence context, and we compare the activity of 75 yeast transcription factors. Our method can be used to study both cis and trans effects of genotype on transcriptional, post-transcriptional and translational control.

overall_design: Expression profiling of 6500 synthetic promoters in yeast (Saccharomyces cerevisiae). The results were achieved using a method for obtaining pooled and highly accurate expression measurements (closely related to MPRA).  In short, the synthetic promoters, which contain unique barcodes, are inserted upstream to a yellow florescence reporter gene, the cells are sorted by their florescence level (using FACS) to expression bins, the promoters in each expression bin are amplified and are send to parallel sequencing (SOLiD) to determine the percent of cells of each promoter in each expression bin; finally an mean expression value is extracted from the raw results. The measurements contain two replicates of exponentially growing yeast cells in SC-Gal-URA (synthetic complete media with 2% galactose and without uracil).

first: Yael

last: Kalma

first: Ayala

last: Sharp

first: Tali

last: Raveh-Sadka

first: Michal

last: Levo

first: Danny

last: Zeevi

first: Leeat

last: Keren

first: Zohar

last: Yakhini

first: Adina

last: Weinberger

first: Eran

last: Segal


title: The transcriptome sequencing of yak (Bos grunniens)

status: Public on May 18 2012

city: shenzhen

first: zhiyong

last: huang

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

institute: BGI-Shenzhen, Shenzhen 518083, China

summary: Deep sequencing of mRNA from 6 organs of yak (Bos grunniens)

overall_design: Analysis of ploy(A)+ RNA of brain,heart,liver,lung,spleen, and stomach of yak (Bos grunniens)

first: Qiang

last: Qiu

first: Guojie

last: Zhang


title: Base Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

status: Public on May 17 2012

city: Dallas

first: Gary

middle: Chung

last: Hon

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

summary: The study of 5-hydroxylmethylcytosines (5hmC), the sixth base of the mammalian genome, as an epigenetic mark has been hampered by a lack of method to map it at single-base resolution.   Previous affinity purification-based methods could not precisely locate 5hmC nor accurately determine its relative abundance at each modified site.  We here present a genome-wide approach for mapping 5hmC at base resolution. Application of this new method to the embryonic stem cells not only confirms widespread distribution of 5hmC in mammalian genome, but also reveals a strong sequence bias and strand asymmetry at sites of 5hmC.  Additionally, the relative abundance of 5hmC varies significantly depending on the types of functional sequences, suggesting different mechanisms for 5hmC deposition and maintenance.  Furthermore, we observe high levels of 5hmC and reciprocally low levels of 5mC at transcription factor binding sites, revealing a dynamic DNA methylation process at cis-regulatory elements.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Base resolution sequencing of 5 hydroxymethylcytosine in human and mouse embryonic stem cells

first: Keith

last: Szulwach


title: KAP1 regulates gene networks controlling B lymphoid cell differentiation and function

city: Milan

first: Francesca

middle: R.

last: Santoni de Sio

address: via Olgettina 58

department: SR-TIGET

institute: San Raffaele Scientific Institute


title: ChIP-seq analysis of KAP1 and H3K9me3 modifications in mouse spleen B cells

summary: Chromatin remodeling is fundamental for B cell differentiation. Here, we explored the role in this process of KAP1, the cofactor of KRAB-ZFP transcriptional repressors. B lymphoid-specific Kap1 knockout mice displayed reduced numbers of mature B cells, lower steady-state levels of antibodies and accelerated rates of decay of neutralizing antibodies following viral immunization. Transcriptome analyses of Kap1-deleted B splenocytes revealed an upregulation of PTEN, the enzymatic counter-actor of PIK3 signaling, and of genes encoding DNA damage response factors, cell-cycle regulators and chemokine receptors. ChIP/seq studies established that KAP1 bound at or close to a number of these genes, and controlled chromatin status at their promoters. Genome-wide, KAP1-binding sites avoided active B cell-specific enhancers and were enriched in repressive histone marks, further supporting a role for this molecule in gene silencing in vivo. Likely responsible for tethering KAP1 to at least some of these targets, a discrete subset of KRAB-ZFPs is enriched in B lymphocytes. This work thus reveals the role of KRAB/KAP1-mediated epigenetic regulation in B cell development and homeostasis.

overall_design: Examination of KAP1 binding sites and H3K9me3 enriched regions in KAP1 wild type and KO mouse B splenocytes.

first: Adamandia

last: Kapopoulou

first: Didier

last: Trono


title: Identification of miRNA-like RNAs in a plant pathogen fungus Sclerotinia sclerotiorum by High-throughput sequencing

city: Wuhan

first: Jiasen

last: Cheng

address: Shizishan Street#1

institute: Huazhong Agricultural University

summary: This study provides a first large-scale cloning and characterization of Sclerotinia sclerotiorum milRNAs and milRNAs candidates. Two microRNA-like RNAs (milRNAs) and 42 milRNA candidates were identified by sequence analysis. These milRNAs and candidates provide new insights into the functional roles of small RNAs and adds new resources for the study of plant pathogenic fungi.

overall_design: We constructed a small RNA library from Sclerotinia sclerotiorum.

first: Daohong

last: Jiang


title: Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3' UTRs and Near Stop Codons

first: Christopher

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

summary: Here, we use a novel technique for locating regions of N6-adenosine methylation (m6A) throughout the transcriptome and present a profile of m6A sites in the mouse brain. Our use of methylated RNA immunoprecipitation combined with RNA-seq (MeRIP-Seq) identifies thousands of RNAs which contain m6A sites. In addition, we find that regions of m6A formation are particularly enriched near stop codons, which might provide clues into the potential funciton of this highly prevalent RNA modificaiton.

overall_design: Examination of m6A sites in murine brain RNA and human embryonic kidney cells.

first: Kate

last: Meyer

first: Yogesh

middle: V

last: Saletore

first: Olivier

last: Elemento

first: Paul

last: Zumbo

first: Samie

last: Jaffrey


title: Next-generation sequencing reveals HIV-1-mediated suppression of T cell activation and RNA processing and the regulation of non-coding RNA expression in a CD4+ T cell line

status: Public on May 16 2012

city: Seattle

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

summary: We sequenced the total mRNA from infected cells and detected differences in the expression of both host mRNA. We detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi providing new possible markers of virus-induced T cell cytopathology. By 24 hpi the expression of over 50% of detectable host loci was also altered indicating widespread alteration of host processes including RNA processing, splicing, and transport to an extent not previously reported. In addition next-generation sequencing provided insights into the expression of non-coding RNAs including microRNA host genes.

overall_design: We isolated polyadenylated RNA from SUPT1 cells infected with HIV-1 strain LAI at 12 and 24 hours post-infection (3 replicates for each time point). As controls we isolated polyadenylated RNA from mock-infected cells at 12 and 24 hours post-infection (2 replicates at 12 hours post-infection, 3 replicates at 24 hours post-infection).

first: Stewart

middle: T

last: Chang

first: Pavel

last: Sova

first: Xinxia

last: Peng

first: Jeffrey

last: Weiss

first: G

middle: L

last: Law

first: Robert

last: Palermo


title: A map of nucleosome positions in yeast at base-pair resolution

city: Evanston

first: Ji-Ping

last: Wang

address: 2006 Sheridan Road

institute: Northwestern University

summary: The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function, yet existing methods for mapping nucleosomes do not provide the necessary single base pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centers based on chemical modification of engineered histones. The resulting map locates nucleosome center positions genome-wide in unprecedented detail and accuracy. It reveals novel aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing, and the higher order structure of the chromatin fiber itself.

overall_design: 6 samples were analyzed with high throughout parallel sequencing.  All samples were created using the same chemical mapping protocol except with varying reaction times.  The different reaction times did not make any significant difference in the nucleosome maps so all the data, for the 6 samples, were combined into one data set for the paper and are all considered replicates.  The 6 samples are as follows: 1. 20 minute reaction time (single-end sequencing) 2. 20 minute reaction time (single-end sequencing) 3. 1 minute reaction time (single-end sequencing) 4. 1.5 minute reaction time (single-end sequencing) 5. 20 minute reaction time (paired-end sequencing) 6. 1.5 minute reaction time (paired-end sequencing)

first: Kristin

last: Brogaard

first: Liqun

last: Xi

first: Jonathan

last: Widom


title: Dynamic Deposition of the Histone H3.3 Variant Accompanies Developmental Remodeling of Arabidopsis Transcriptome (ChIP-Seq)

city: Singapore

first: Pierre-Étienne

last: Jacques

address: 60 Biopolis Street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

summary: In animals, replication coupled histone H3.1 can be distinguished from replication independent histone H3.3. H3.3 variants are enriched at active genes and their promoters. Furthermore, H3.3 is specifically incorporated upon gene activation. Histone H3 variants evolved independently in plants and animals and it is unclear whether different replication independent H3.3 variants developed similar properties in both phyla. We studied Arabidopsis H3 variants in order to find core properties of this class of histones. Here we present genome-wide maps of H3.3 and H3.1 enrichment and the dynamic changes of their profiles upon cell division arrest. We find H3.3 enrichment to positively correlate with gene expression and to be biased towards the transcription termination site. While heterochromatic regions are mostly depleted of H3.3, H3.1 shows a more even distribution along the genome. We report that in planta, dynamic changes in H3.3 profiles are associated with the extensive remodeling of the transcriptome that occurs during cell differentiation. We propose that H3.3 dynamics are linked to transcription and are involved in resetting covalent histone marks at a genomic scale during plant development. Similarities between plant and animal H3.3 deposition profiles indicate that H3 variants likely result from functionally convergent evolution.

overall_design: Analysis of 2 different histone H3 variants and transcriptome in 2 conditions.

first: Heike

last: Wollmann

first: Sarah

last: Holec

first: Keith

last: Alden

first: Neil

last: Clarke

first: Frédéric

last: Berger


title: Dynamic Deposition of the Histone H3.3 Variant Accompanies Developmental Remodeling of Arabidopsis Transcriptome (mRNA-Seq)


title: Platypus fibroblast and ovary transcriptomes

city: Lausanne

first: Philippe

last: Julien

address: Batiment Genopode

department: CIG

country: Switzerland

institute: University of Lausanne

summary: As a result of sex chromosome differentiation from ancestral autosomes, male mammalian cells only contain one X chromosome. It has long been hypothesized that X-linked gene expression levels have become doubled in males to restore dosage balance between the X and autosomes, and that the resulting X overexpression in females then drove the evolution of X inactivation (XCI). However, this model has never been directly tested and patterns and mechanisms of dosage compensation across different mammals and birds generally remain little understood. We have traced the evolution of dosage compensation using extensive transcriptome data from males and females representing all major mammalian lineages and birds. Our analyses suggest that the X has become globally upregulated in marsupials but probably not in placental mammals, where instead at least a subset of autosomal genes interacting with X-linked were downregulated. Thus, different driving forces may underlie the evolution of XCI and the highly efficient equilibration of X expression levels between the sexes observed for both of these lineages. In the egg-laying monotremes and birds, which have homologous sex chromosome systems, partial upregulation of the X (Z in birds) evolved but is largely restricted to the heterogametic sex, which provides an explanation for the partially sex-biased X (Z) expression and lack of global inactivation mechanisms in these lineages. Our findings suggest that dosage reductions imposed by sex chromosome differentiation events in amniotes were resolved in strikingly different ways.

overall_design: 3 samples (ovary, fibroblast male, fibroblast female) from different platypus individuals are analysed.

first: David

last: Brawand

first: Magali

last: Soumillon

first: Anamaria

last: Necsulea

first: Angelica

last: Liechti

first: Tasman

last: Daish

first: Frank

last: Grützner

first: Henrik

last: Kaessmann


title: Dynamic Deposition of the Histone H3.3 Variant Accompanies Developmental Remodeling of Arabidopsis Transcriptome

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length

status: Public on May 15 2012

city: Basel

first: Andreas

last: Gruber

address: Klingelbergstrasse 50-70

department: Biozentrum

institute: University of Basel


title: Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: CLIP

summary: Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome‐wide both binding sites of 3' end processing factors CPSF‐160, CPSF‐100, CPSF‐73, CPSF‐30, Fip1, CstF‐64, CstF-64tau, CF Im25, CF Im59, and CF Im68 and 3' end processing sites in HEK293 cells. We found that although binding sites of these factors generally cluster around the poly(A) sites most frequently used in cleavage, CstF‐64/CstF-64tau and CF Im proteins have much higher positional specificity compared to CPSF components. Knockdown of CF Im68 induced a systematic use of proximal polyadenylation sites, indicating that changes in relative abundance of a single 3' end processing factor can modulate the length of 3' untranslated regions transcriptome-wide, and suggesting a mechanism behind the previously observed increase in tumor cell invasiveness upon CF Im68 knockdown.

overall_design: We performed PAR-CLIP experiments for 3' end processing factors including CPSF-30, CPSF-73, CPSF-100, CPSF-160, Fip1, CF Im25, CF Im59, CF Im68, CstF-64, and CstF-64tau.

first: Georges

last: Martin

first: Walter

last: Keller

first: Mihaela

last: Zavolan


title: ERa-dependent E2F transcription can mediate resistance to estrogen deprivation in human breast cancer

city: Nashville

first: Todd

middle: W

last: Miller

state: TN

address: 2220 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt Univ


title: Degradome sequencing from S. castellii

status: Public on May 14 2012

city: San Francisco

middle: Eric

last: Weinberg

address: 600 16th Street, GH S572F

institute: University of California, San Francisco

summary: The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 Å crystal structure of Kluyveromyces Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RNA duplexes autonomously loaded by recombinant KpAGO. Despite their diverse sequences, guide-RNA nucleotides 1-8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2'-hydroxyl groups pre-organizing the backbone of nucleotides 2-8 in a near-A-form conformation. Compared with prokaryotic Argonautes, KpAGO has numerous surface-exposed insertion segments, with a cluster of conserved insertions repositioning the N domain to enable full propagation of guide-target pairing. Compared with Argonautes in inactive conformations, KpAGO has a hydrogen-bond network that stabilizes an expanded and repositioned loop, which inserts an invariant glutamate into the catalytic pocket. Mutation results and analogies to Ribonuclease H indicate that insertion of this glutamate finger completes a universally conserved catalytic tetrad, thereby activating Argonaute for cleavage.

overall_design: High-throughput sequencing of cellular RNAs containing both a 5'-monophosphate group and a poly(A) tail. To identify Argonaute-dependent cleavage tags, sequencing libraries were prepared from Δxrn1 and Δxrn1 Δago1  strains.

middle: P

last: Bartel


title: Structure of yeast Argonaute with guide RNA

sample_organism:
Naumovozyma castellii
Vanderwaltozyma polyspora


title: Bacteria-derived small RNAs that co-purify with KpAGO

overall_design: Employ high-throughput sequencing of small RNAs extracted from soluble or crystalline K. polysporus Ago1(207-1251) that had been purified from E. coli

first: Kotaro

last: Nakanishi

first: Dinshaw

last: Patel


title: Radicicol treatment of Drosophila cells

first: Cem

last: Sievers

address: Mattenstrasse

institute: ETH Zurich

summary: Drosophila S2 cells were treated with Heat-shock protein 90 (Hsp90) inhibitor radicicol for 15min, 30min and 1h. Poly(A) RNA was isolated and sequenced.

overall_design: Kinetics of transcriptional response to Hsp90 inhibition

first: Renato

last: Paro


title: RNA-seq from ENCODE/Caltech (Mouse)

status: Public on May 10 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Georgi K. Marinov mailto:georgi@caltech.edu (data coordination/informatics/experimental), Diane Trout mailto:diane@caltech.edu (informatics) Brian Williams mailto:bawilli_91125@yahoo.com (experimental)). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly (Mortazavi et al., 2008). RNA-seq is performed by reverse-transcribing an RNA sample into cDNA, followed by high-throughput DNA sequencing, which was done here on the Illumina HiSeq sequencer. The transcriptome measurements shown on these tracks were performed on polyA selected RNA (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?term=longPolyA&type=rnaExtract) from total cellular RNA (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?term=cell&type=localization). PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis and then converted into cDNA by random priming and amplified. Paired-end 2x100 bp reads were obtained from each end of a cDNA fragment. Reads were aligned to the mm9 human reference genome using TopHat (Trapnell et al., 2009), a program specifically designed to align RNA-seq reads and discover splice junctions de novo. All sequence and alignments files are available at http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=mm9&g=wgEncodeCaltechRnaSeq.

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell/mouse). Cells were lysed in RLT buffer (Qiagen RNEasy kit), and processed on RNEasy midi columns according to the manufacturer's protocol, with the inclusion of the "on-column" DNAse digestion step to remove residual genomic DNA. A quantity of 75 µgs of total RNA was selected twice with oligo-dT beads (Dynal) according to the manufacturer's protocol to isolate mRNA from each of the preparations. A quantity of 100 ngs of mRNA was then processed according to the protocol in Mortazavi et al. (2008), and prepared for sequencing on the Illumina GAIIx or HiSeq platforms according to the protocol for the ChIP-Seq DNA genomic DNA kit (Illumina). Paired-end libraries were size-selected around 200 bp (fragment length). Libraries were sequenced with the Illumina HiSeq according to the manufacturer's recommendations. Paired-end reads of 100 bp length were obtained.
Reads were mapped to the reference mouse genome (version mm9 with or without the Y chromosome, depending on the sex of the cell line, and without the random chromosomes in all cases) using TopHat (version 1.3.1) (http://tophat.cbcb.umd.edu/). TopHat was used with default settings with the exception of specifying an empirically determined mean inner-mate distance and supplying known ENSEMBL version 63 splice junctions.

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first: Georgi

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first: Gordon

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first: Katherine

last: Fisher

first: Gilberto

last: De Salvo

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last: Mortazavi

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