title: Epstein-Barr Virus Exploits Intrinsic B-Lymphocyte Transcription Programs to Achieve Immortal Cell Growth

summary: Epstein-Barr Virus Nuclear Antigen 2 (EBNA2) gene regulation through the cell RBPJ transcription factor (TF) is essential for conversion of resting B-lymphocytes (RBLs) into Lymphoblastoid Cell Lines (LCLs). ChIP-seq investigation of EBNA2 and RBPJ sites in LCL DNA found EBNA2 at 5151 and RBPJ at 10,529 sites. EBNA2 was 72% localized with RBPJ, predominantly at intergenic and intronic sites and only 14% at promoter sites. EBNA2/RBPJ sites were enriched for Early B-cell Factor (EBF, 60%), RUNX(41%), ETS(35%), NF-ï«B(31%), and PU.1(17%) TF motifs. Using ENCyclopedia Of DNA Elements (ENCODE) LCL data, EBF, RELA, and PU.1 were found at 54%, 31%, and 17% of EBNA2 sites. K-Means clustering of EBNA2 site associated TFs found RELA-ETS, EBF-RUNX, EBF, ETS, RBPJ, and repressive RUNX ranked highest to lowest in nearly symmetric H3K4me1 signal distribution and nucleosome depletion, marks of active chromatin. Although quantitatively less, high level nearly symmetric H3K4me1 signals with nucleosome depletion at the same sites in RBLs was remarkably similar to LCLs, indicating that EBNA2 localizes into a pre-established RBL chromatin pattern, which likely evolved to enable RBL antigen-induced proliferation. EBF was critical for EBNA2 activation of the EBV LMP1 promoter. LCL HiC data mapped intergenic EBNA2 sites to EBNA2 up-regulated genes. Fluorescence In Situ Hybridization (FISH), conditional EBNA2 FISH, Chromatin Conformation Capture (3C), and 3C q-PCR, linked EBNA2/RBPJ enhancers 428 kb 5' of MYC to MYC. These data support the hypothesis that EBNA2 evolved to exploit the RBL transcription framework to drive B-lymphocyte proliferation in primary human infection.

overall_design: EBNA2 and RBPJ ChIP-seq from IB4 LCL

first: Bo

last: Zhao

first: Eris

last: Johannsen

first: Bradley

last: Bernstein

first: Elliott

last: Kieff


title: Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L (ChIP-Seq data)

status: Public on Jul 01 2011

city: Lausanne

first: Jacques

last: Rougemont

address: Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. Building on these data, we show here that Sch9, an AGC family kinase and direct substrate of TORC1, promotes ribosome biogenesis (ribi) and ribosomal protein (RP) gene expression via direct inhibitory phosphorylation of three transcription repressors, Stb3, Dot6 and Tod6. Dephosphorylation of these factors allows them to recruit the RPD3L histone deactelyase complex to ribi/RP gene promoters. Since rRNA and tRNA transcription are also under its control, Sch9 appears to be well positioned to coordinately regulate transcriptional aspects of ribosome biogenesis.

overall_design: ChIP-Seq of 8 S. cerevisiae strains treated with 1NM-PP1, a small molecule inhibitor for analog-sensitive kinases such as sch9-as.

first: Alexandre

last: Huber

first: Robbie

last: Loewith


title: Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L (mRNA-Seq data)

type: Expression profiling by high throughput sequencing

overall_design: mRNA-Seq of 8 S. cerevisiae strains treated with either DMSO alone or 1NM-PP1, a small molecule inhibitor for analog-sensitive kinases such as sch9-as.


title: Comparative analysis of gene expression changes upon Cabut or dE2F1/dDP overexpression in the Drosophila wing

status: Public on Jul 08 2011

city: Seattle

first: Laura

last: Buttitta

state: WA

address: 1100 Fairview Ave. N.

country: USA

institute: Fred Hutchinson Cancer Research Center

summary: Investigation of whole genome gene expression level changes in dissected Drosophila wings at the wandering L3 larval stage, 24h after pupa formation and 36h after pupa formation, expressing either UAS-Cabut or UAS-dE2F1 + UAS-dDP under control of apterous-gal4 with a tubulin driven temperature-sensitive gal80 transgene, compared to the parental strain lacking UAS transgenes.

overall_design:
A 36-chip study using total RNA recovered from four independently isolated samples of 10 dissected Drosophila wings at the indicated developmental stages expressing the indicated UAS-transgenes or the non-UAS-containing matched control strain. One sample (2D) did not pass our internal quality control and, therefore, was not included in the analysis.

The dE2F1+dDP data included here is further discussed in L. Buttitta, A.J. Katzaroff, B.A. Edgar (2010). A robust cell cycle control mechanism limits E2F-induced proliferation of terminally differentiated cells in vivo. Journal of Cell Biology vol. 189, 981-96 (PMID 20548101).
The Cabut data included here is further discussed in A.J. Katzaroff et al. (2011). The Krüppel-like-factor cabut has cell cycle regulatory properties similar to E2F.

middle: A

first: Alexia

middle: J

last: Katzaroff

first: Bruce

last: Edgar


title: Co-activation of GR and NF-kB leads to extensive rearrangemnet of their binding sites and target genes

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: Global identification of activated GR and p65 binding sites and target genes using ChIP-seq in HeLa B2 cells.

overall_design: generation genome-wide chromatin state-maps of GR, p65 and RNAPII in HeLa B2 cells under conditions 1) DMSO  (control); 2) TA 1µM 4hr; 3) TNFα 10ng/ml ; 4) TA 1µM 4hr at at third hour 10ng/ml TNF α  was added

first: Melysia

middle: T

last: McCalman

first: Nagesha

last: Rao

first: Panagiotis

last: Moulos

first: Kees-jan

last: Francoijs

first: Aristotelis

last: Chatziioannou

first: Fragiskos

middle: N

last: Kolisis

first: Michael

last: Alexis

first: Dimitra

last: Mitsiou

first: Hendrik

middle: G


title: [E-MTAB-460] Sanger_zebrafish_sequencing

status: Public on Jul 14 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

summary:
Abstract: Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues using the Illumina Genome Analyzer.  Study description: Zebrafish total RNA was extracted from adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 76 base reads on the Illumina Genome Analyzer.

ArrayExpress Release Date: 2011-01-28

Person Roles: submitter
Person Last Name: Service
Person First Name: Submission
Person Mid Initials:
Person Email: datahose@sanger.ac.uk
Person Phone:
Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: development_or_differentiation_design
Experimental Design: organism_part_comparison_design
Experimental Factor Name: ORGANISM_PART
Experimental Factor Type: organism_part


title: Regulation of nucleosome landscape and transcription factor binding at enhancers by BRG1

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Enhancers of transcription activate transcription via binding of sequence-specific transcription factors to their target sites in chromatin. In this report, we identify GATA1-bound enhancers genome-wide and find a global reorganization of the nucleosomes at these enhancers during differentiation of hematopoietic stem cells (HSCs) to erythrocytes. We show that the catalytic subunit BRG1 of BAF complexes localizes to these enhancers during differentiation and generates a longer nucleosome repeat length surrounding the GATA1 sites by shifting the flanking nucleosomes away. Intriguing, we find that the nucleosome shifting specifically facilitates binding of TAL1 but not GATA1, which subsequently activates transcription of target genes.

overall_design: Human hematopoietic stem cells (referred as CD34+ cells) were differentiated into erythroid lineage expressing the cell surface marker CD36 (referred as CD36+ cells). To study the function of ATP-dependent chromatin remodeling BAF complexes in the establishment of erythroid specific enhancers during differentiation, we mapped the genome-wide binding sites of GATA1 and TAL1, the key transcription regulators of erythroid differentiation, in CD36+ cells, then determined the genomic positions of the catalytic subunit BRG1 of the BAF complexes and the nucleosome landscapes, by ChIP-Seq and Mnase-Seq, respectively, for both HSCs and the differentiated cells. We compared changes in nucleosome landscapes with BRG1 binding at GATA1 and TAL1 binding sites and found that BRG1 binding is correlated with nucleosome shifting away from the binding sites, which is critical for TAL1 binding. To confirm that BRG1 is responsible for the nucleosome shift, we knocked down BRG1 in CD36+ cells and analyzed the nucleosome changes in the knockdown cells. The data indicated that inhibition of BRG1 caused a nucleosome shift towards the GATA1 or TAL1 sites, indicating that BRG1 is indeed responsible for the observed nucleosome shift.

first: Dustin

middle: E

last: Schones

first: Kairong

last: Cui

first: River

last: Ybarra

first: Daniel

last: Northrup

first: Qingsong

last: Tang

first: Luca

last: Gattinoni

first: Nicholas

middle: P

last: Restifo

first: Suming

last: Huang

first: Keji

last: Zhao


title: Unstressed HeLa cells and  ELAVL1/HuR knock down conditions: polyA RNA-Seq, small RNA-Seq, and PAR-CLIP

status: Public on Jun 30 2011

city: Berlin

first: Marvin

last: Jens

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Post-transcriptional gene regulation relies on hundreds of RNA binding proteins (RBPs) but the function of most RBPs is unknown. The human RBP HuR/ELAVL1 is a conserved mRNA stability regulator. We used PAR-CLIP, a method based on RNA-protein crosslinking, to identify transcriptome wide ~26,000 HuR binding sites. These sites were on average highly conserved, enriched for HuR binding motifs and mainly located in 3' untranslated regions. Surprisingly, many sites were intronic, implicating HuR in splicing. Upon HuR knock down, mRNA levels and protein synthesis of thousands of target genes was down regulated, validating functionality. HuR and miRNA binding sites tended to reside nearby but generally did not overlap. Additionally, HuR knock down triggered strong and specific up regulation of miR-7. In summary, we identified thousands of direct and functional HuR targets, found a human miRNA controlled by HuR, and propose a role for HuR in splicing.

overall_design:
PolyA mRNA was extracted from anti HuR siRNA treated and mock transfected HeLa cells to identify changes in mRNA expression and splicing. 2x100 paired end sequencing was performed according to the protocol on the Illumina HiSeq.

PARCLIP was performed as in Hafner et. Al 2010 but with an antibody against endogenous HuR (3A2, Santa Cruz, sc-5261) in unstressed HeLa cells. We used, independently, 4-thiouridine (4SU) and 6-thioguanosine (6SG) to assess a possible nucleotide bias. As our proteomics measurements required labeling of cells in a special medium we also performed PAR-CLIP on cells grown in SILAC medium. Altogether we performed three PAR-CLIP experiments: 4SU labeling in standard DMEM medium, 4SU labeling in SILAC medium (as a replicate) and 6SG labeling in SILAC medium.

Small RNA was extracted from anti HuR siRNA treated and mock transfected HeLa cells to identify changes in mRNA expression. Sequencing was performed on Illumina GAII using the standard sRNA 36cycle protocol.

first: Svetlana

last: Lebedeva

first: Kathrin

last: Theil

first: Bjoern

last: Schwanhaeusser

first: Matthias

last: Selbach

first: Markus

last: Landthaler

first: Nikolaus

last: Rajewsky


title: Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human Embryonic Stem cells (part 2)

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

summary: Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken a strand-specific RNA sequencing of multiple cellular RNA fractions (>18Gb) to uncover the transcriptional complexity of human ES cells. We have shown that human ES cells display a high degree of transcriptional diversity, with more than half? of active genes generating RNAs that differ from conventional gene models. We found evidence that more than >1000 genes express long 5’ and/or extended 3’ UTRs, which was confirmed by “virtual northern” analysis. Exhaustive sequencing the membrane-polysome and cytosolic/untranslated fractions of hESC was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. Finally, the impact of this newly defined transcriptional complexity on known gene-centric network models such as the Plurinet and the cell surface signalling machinery in human ES cells revealed a significant expansion of protein coding components at play, many of which alternative actions based on altered domain content.

overall_design: Human ES cells fractionated for mRNA, cytosolic polysome, membrane polysome

first: Gabriel

last: Kolle


title: Cell-type based analysis of microRNA profiles in the mouse brain

status: Public on Jun 29 2011

city: cold spring harbor

first: Miao

last: He

state: new york

address: 1 bungtown road

department: Neuroscience

institute: Cold Spring Harbor Laboratory

summary: MicroRNAs (miRNA) are implicated in brain development and function but the underlying mechanisms have been difficult to study in part due to cellular heterogeneity in neural circuits. To systematically analyze miRNA expression in neurons, we have established a miRNA tagging and affinity purification (miRAP) method that is targeted to cell types through the Cre-loxP binary system in mice. Our studies of the neocortex and cerebellum reveal the expression of a large fraction of known miRNAs with distinct profiles in glutamatergic and GABAergic neurons, and subtypes of GABAergic neurons.  We further detected putative novel miRNAs, tissue or cell type-specific strand selection of miRNAs, and miRNA editing.  Our method thus will facilitate a systematic analysis of miRNA expression and regulation in specific neuron types in the context of neuronal development, physiology, plasticity, pathology and disease models, and is generally applicable to other cell types and tissues.

overall_design: RNA was extracted from miRNA tagging samples(Ago2 IP or Myc IP), processed and sequenced on Illumina genome analyzer

first: Yu

last: Liu

first: Michael

last: Zhang

first: Gregory

last: Hannon

first: Z


title: Identification and analysis of pancreatic islet specific enhancers

city: Vancouver

first: Patrick

last: Plettner

state: BC

address: 100-570 West 7th Avenue

country: Canada

institute: BC Cancer Agency GSC

summary: We anticipated that the identification of cis-regulatory regions active in pancreatic islets would help increase our understanding of islet biology and the pathology of diabetes. Towards this end we used histone H3 lysine 4 monomethylation-based nucleosome predictions genome-wide, in conjunction with binding data for PDX1, FOXA2, MAFA, and NEUROD1, to identify 3,654 putative enhancers that are H3K4me1-enriched uniquely in islets as compared to 14 other tissue or cell-types. We show that these islet-specific enhancers are associated with genes with significantly higher islet specificity than genes associated with non-specific enhancers. Further, islet-specific enhancers were not enriched for typical active or repressive histone methylations in embryonic stem cells and liver, suggesting they are formed by de novo histone methylation during pancreas development. We also identify a subset of enhancers bivalently marked by both H3K4me1 and H3K27me3 in adult pancreatic islets. Further, we show that islet-specific enhancers triple- or quadruple- bound by PDX1, MAFA, NEUROD1 and/or FOXA2 are associated with genes with particularly high islet-specificity, and that these loci are enriched in regions with functional activity in islet cell types. Finally, we demonstrate that cytokines reduce H3K4me1 enrichment levels at selected triple- or quadruple-bound islet-specific enhancers, suggesting that epigenetic changes may contribute to cytokine-induced b-cell dysfunction.

overall_design: In conjunction with data from Hoffman et al Genome Research 2010, an analysis of histone modifications and transcription factor binding sites to identify enhancer regions

first: Brad

last: Hoffman

first: Pamela

last: Hoodless

first: Steven

last: Jones


title: ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19)

status: Public on Jul 13 2011

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 (Carrie Davis mailto:davisc@cshl.edu (experimental), Alex Dobin mailto:dobin@cshl.edu (computational), Felix Schlesinger mailto:schlesin@cshl.edu (computational), Tom Gingeras mailto:gingeras@cshl.edu (primary investigator), and Roderic Guigo's group mailto:rguigo@imim.es at the CRG). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

These tracks were generate by the ENCODE Consortium. They contain information about human RNAs > 200 nucleotides in length obtained as short reads off the Illumina GAIIx platform. Data is available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, we have also gather data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, RIKEN Institute) and Small RNA-Seq (<200 nucleotides, CSHL) and Pair-End di-TAG-RNA (PET-RNA, Genome Institute of Singapore) datasets available from the same biological replicates.

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:
We are using the published protocol http://www.ncbi.nlm.nih.gov/pubmed/19620212. This protocol generates directional libraries and reports the transcripts strand of origin. Exogenous RNA spike-ins (Round 5, pool 14), in development at National Institutes Standards Technology were added to each endogenous RNA isolate and carried through library construction and sequencing. The Illumina PhiX control library was also spiked-in at 1% to each completed human library just prior to cluster formation. Accompanying each RNA-Seq dataset is a "Production Document". This document contains details about the RNA isolations and treatments, library construction, spike-ins as well as quality control figures for individual libraries. The spike-in sequence and the concentrations can are available for download in the supplemental directory.
The libraries are sequenced on the Illumina platform to an average depth of ~200 million reads (100 million mate-pairs). The data are mapped against hg19 using Spliced Transcript Alignment and Reconstruction (STAR) written by Alex Dobin (CSHL). More information, about STAR including the parameters used for these data can be found at: http://gingeraslab.cshl.edu/STAR/.
Additionally, we provide the following processed "element" data files: de novo splice junctions, de novo transcripts, and contigs. These elements are assessed for reproducibility using a nonparametric irreproducible detection (IDR) rate script. The IDR values for each element are included in the files for end-users to threshold on. An IDR value of 0.1 means that the probability of detecting that element in a third experiment equivalent in depth to the the sum of the bioreplicates is 90%. In addition, we also compute expression values for annotated genes, transcripts and exons.

first: Carrie

last: Davis

first: Alex

last: Dobin

first: Felix

last: Schlesinger

first: Tom

last: Gingeras


title: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 5022 Genetic Medicine Building, CB#7264

department: Genetics

institute: UNC-Chapel Hill

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

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE19622
SuperSeries of: GSE25344
SuperSeries of: GSE25416
SuperSeries of: GSE30224
SuperSeries of: GSE30225
SuperSeries of: GSE30226

overall_design: Refer to individual Series


title: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [ChIP_seq].

summary:
The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq to map âopen chromatinâ. Over 870,000 DNaseI or FAIRE sites, which correspond largely to nucleosome depleted regions (NDRs), were identified across the seven cell lines, covering nearly 9% of the genome. The combination of DNaseI and FAIRE is more effective than either assay alone in identifying likely regulatory elements, as judged by coincidence with transcription factor binding locations determined in the same cells. Open chromatin common to all seven cell types tended to be at or near transcription start sites and encompassed more CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start sites, and contained DNA motifs recognized by regulators of cell-type identity. As one example of its ability to identify functional DNA, we show that open chromatin regions bound by CTCF are potent insulators. We identified clusters of open regulatory elements (COREs) that were physically near each other and whose appearance was coordinated among one or more cell types. Gene expression and RNA Pol II binding data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity. This publicly available atlas of regulatory elements may prove valuable in identifying non-coding DNA sequence variants that are causally linked to human disease.

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: DNase-seq, FAIRE-seq, and ChIP-seq were performed on seven human cell lines: GM12878 (lymphoblastoid), K562 (leukemia), HepG2 (hepatocellular carcinoma), HelaS3 (cervical carcinoma), HUVEC (human umbilical vein endothelial cells), NHEK (keratinocytes), and   H1-ES (embryonic stem cells). For each cell line, two or three replicates were independently grown and split into three, one for each of the three experimental methods.  Control ChIP experiments were performed on five of the cell lines with NHEK and H1-ES being excluded due to lack of material.

first: Terrence

middle: S

first: Vishwanath

middle: R

last: Iyer

last: Crawford


title: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [FAIRE_seq]

first: Jason

middle: D

last: Lieb


title: Digital gene expression and global mapping of polyadenylation sites with PolyA-Seq

status: Public on Jun 25 2011

city: Dedham

first: Adnan

last: Derti

state: MA

address: 100 Alden Street

department: Bioinformatics

institute: personal

summary: We describe PolyA-Seq, a strand-specific method for high-throughput sequencing of the 3' ends of polyadenylated transcripts. PolyA-Seq is as accurate for digital gene expression as existing RNA sequencing approaches, and superior to microarrays. We used the approach to map polyadenylation (polyA) sites in 24 samples from normal tissues in human, rhesus, dog, mouse, and rat.

sample_organism:
Macaca mulatta
Homo sapiens
Canis lupus familiaris
Mus musculus
Rattus norvegicus

overall_design: Detection of polyA sites in a mixture of 24 tissues in human, mouse, rat, dog and rhesus. Samples included two replicates each of MAQC Human Brain Reference and MAQC Universal Human Reference. Two additional human sets of reads are included that were used to distinguish true polyA sites from internal priming sites.

first: Tomas

last: Babak


title: Application of Microdroplet PCR for Large-Scale Targeted Bisulfite Sequencing

city: La Jo

first: Traver

last: Hart

address: 10550 North Torrey Pines Road, MEM241B

department: Molecular & Experimental Medicine

institute: The Scripps Research Institute

type: Methylation profiling by high throughput sequencing

summary: Cytosine methylation of DNA CpG dinucleotides in gene promoters is an epigenetic modification that regulates gene transcription.  While many methods exist to interrogate methylation states, no current methods offer large-scale, targeted, single CpG resolution.  We report an approach combining bisulfite treatment followed by RainDance microdroplet PCR with next-generation sequencing to assay the methylation state of 50 genes in the regions 1 kb upstream and downstream of their transcription start sites.

overall_design: Wildtype and hypermethylated Jurkat DNA (New Englad Biolabs) was treated with bisulfite to convert all unmethylated cytosines to uracil.  Following bisulfite treatment, targeted amplification was carried out using a custom primer library and microdroplet PCR.  PCR product was sheared to 200 bp and ligated to sequencing adapters following standard protocols.  Sequencing was conducted with single-end 100 bp reads on an Illumina GAIIx for  wild type Jurkat DNA or Jurkat CpG DNA with a single sample per lane.

first: H

middle: K

last: Komori

first: Sarah

last: LaMere

first: Ali

last: Torkamani

first: G

first: Steve

last: Kotsopoulos

last: Warner

first: Michael

middle: L

last: Samuels

first: Jeff

last: Olson

last: Head

first: Phillip

last: Ordoukhanian

first: Pauline

last: Lee

first: Darren

last: Link

first: Daniel

last: Salomon


title: Two upland cotton tree fiber samples from different seasons

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

summary: Two fiber tissues harvested 10 days post anthesis from upland cotton trees grown under the same green house conditions except for different seasons of the year were used for RNA extraction. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer according to the manufacturer's instructions. The 35nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and several kinds of contaminants from the 35nt tags. All clean tag sequences with copy numbers were then summarized into a fasta format file.

overall_design: Fiber samples from different seasons were used for small RNA sequencing and data processing.

first: Xiang

last: Jin

first: Fangxing

last: Jia

first: Qin

last: Li

first: Yuxian


title: Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L

first: Jacques

last: Rougemont

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


title: Large-scale methylation domains mark a functional subset of neuronally expressed genes

status: Public on Jun 23 2011

city: Davis

first: Janine

last: LaSalle

address: Medical Microbiology and Immunology

institute: UC Davis

summary: DNA methylation is essential for embryonic and neuronal differentiation, but the function of most genomic DNA methylation marks are poorly understood. Generally the human genome is highly methylated (>70%) except for CpG islands and gene promoters. However, it was recently shown that the IMR90 human fetal lung fibroblast cells have large regions of the genome with partially methylated domains (PMDs, <70% average methylation), in contrast to the rest of the genome which is in highly methylated domains (HMDs, >70% average methylation). Using bisulfite conversion followed by high-throughput sequencing (MethylC-seq), we discovered that human SH-SY5Y neuronal cells also contain PMDs. We developed a novel hidden Markov model (HMM) to computationally map the genomic locations of PMDs in both cell types and found that autosomal PMDs can be over 9 Mb in length and cover 41% of the IMR90 genome and 19% of the SH-SY5Y genome. Genomic regions marked by cell line specific PMDs contain genes that are expressed in a tissue-specific manner, with PMDs being a mark of repressed transcription. Genes contained within N-HMDs (neuronal HMDs, defined as a PMD in IMR90 but HMD in SH-SY5Y) were significantly enriched for calcium signaling, synaptic transmission and neuron differentiation functions. Autism candidate genes were enriched within PMDs and the largest PMD observed in SH-SY5Y cells marked a 10 Mb cluster of cadherin genes with strong genetic association to autism. Our results suggest that these large-scale methylation domain maps could be relevant to interpreting and directing future investigations into the elusive etiology of autism.

overall_design: Examined DNA methylation in a human neuronal cell line and cerebral cortex

first: Diane

middle: I

last: Schroeder

middle: M


title: CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

city: Singapore

first: Lusy

last: Handoko

address: 60 Biopolis street 02-01

country: Singapore

institute: Genome Institute of Singapore

summary: We performed Chromatin Interaction Analysis by Paired-End-Tag sequencing to elucidate CTCF-mediated long range interactions. 1,480 cis and 336 trans interacting loci were identified with high reproducibility.  Associating these chromatin interaction loci with histone marks, RNA Pol II, p300 and Lamin B genome wide profiles, we uncover five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and may influence proper gene expression through extensive crosstalk between promoters and regulatory elements.

overall_design: Chromatin interaction analysis coupled with Pair End Tags of CTCF: ChIP using anti CTCF antibody, followed by close proximity ligations. ChIP-Seq was used map RNA Pol II, p300, Lamin B genome wide profiles

first: Han

last: Xu

first: Guoliang

first: Yijun

last: Ruan

first: Chia-Lin

last: Wei


title: PU.1 in normal erythroid progenitors and erythroleukemia cells

city: Bronx

first: Sandeep

middle: Nagaraj

last: Wontakal

state: NY

address: 1300 Morris Park Ave Chanin 402

department: Cell Biology

institute: Albert Einstein College of Medicine


title: Deep Transcriptional Profiling of Rice Using Illumina's Sequencing By Synthesis Technology

status: Public on Jun 22 2011

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technologies like ‘massively parallel signature sequencing (MPSS)’ and ‘Sequencing by Synthesis’ (SBS) to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). Illumina’s SBS technology can generate large amounts of sequence data in a short time at low cost compared to traditional Sanger sequencing based methods. Using the MPSS technology, we previously analyzed the transcriptomes of 72 rice tissues. To validate the sequencing results from MPSS technology, we employed SBS technology and constructed SBS libraries from 32 rice tissues (47 libraries including replications). For SBS library construction, we used the same mRNA samples and same restriction enzyme (DpnII) that were used for the construction of the MPSS libraries. These libraries include six abiotic-stress libraries, eight pathogen-infected libraries, five insect-damaged libraries, three developing seed libraries, and 10 untreated rice tissue libraries. This study was carried out with the following objectives; a) Identification and quantification of expressed genes in rice at all developmental stages of plant growth, response to biotic and abiotic stresses, and developing seeds; b) Compare SBS signatures with rice genomic sequence to identify novel transcripts; c) To validate the transcriptional data obtained through MPSS technology; and To create query and analysis tools to facilitate public use of and access to rice MPSS and SBS data and to display abundance and chromosomal locations of rice MPSS and SBS signatures. The SBS data will be available at http://mpss.udel.edu/rice_sbs/.


title: Transcriptional Regulation of Anabaena 7120 response to Nitrogen Deprivation

city: La Jolla

first: James

middle: W

last: Golden

address: 9500 Gilman Dr. MC 0116

department: Biological Sciences

institute: UCSD

summary: Here, we report the transcriptome of Anabaena sp. strain 7120, a cyanobacterium that forms specialized nitrogen-fixing cells called heterocysts. Our data suggests that cyanobacteria frequently have more complex transcripts than thought, with large 5' UTRs, numerous antisense transcripts, and multiple transcriptional start sites or processing sites.

overall_design: Four samples of total filament RNA were sequenced with Illumina 40bp reads using directional RNA sequencing (see the Illumina small RNA prep protocol). The samples are 0hr (vegetative cells grown in the presence of ammonia) and 6hr, 12hr, and 21hr cells (after nitrogen step down).

first: Britt

last: Flaherty

first: F

last: Van Nieuwerburgh

first: Steven

last: Head


title: Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

summary: DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated DNA obtained from early Xenopus tropicalis embryos demonstrates that this genome is heavily methylated during blastula and gastrula stages. Although DNA methylation is largely absent from transcriptional start sites marked with histone H3 lysine 4 trimethylation (H3K4me3), we find  both promoters and gene bodies of active genes robustly methylated. By contrast, DNA methylation is absent in large H3K27me3 domains, indicating these two repression pathways have different roles. Comparison with chromatin state maps of human ES cells reveals strong conservation of epigenetic makeup and gene regulation between the two systems. Strikingly, genes that are highly expressed in human pluripotent cells and in Xenopus embryos but not in differentiated cells exhibit relatively high methylation in both promoters and gene bodies in embryos. Therefore we tested the repressive potential of DNA methylation using transient and transgenic approaches and show that methylated promoters are robustly transcribed in blastula and gastrula-stage embryos, but not in oocytes or late embryos where methylated templates are repressed efficiently. These findings have implications for reprogramming and the epigenetic regulation of pluripotency and differentiation, suggesting a relatively open, pliable chromatin state in early embryos followed by re-established methylation-dependent transcriptional repression during organogenesis and differentiation.

overall_design: MethylCap (methylated DNA affinity capture with the MBD domain of MeCP2), 500mM and 700mM elution fractions of stage 9 (blastula) and stage 12.5 (gastrula) Xenopus tropicalis DNA

first: Simon

last: van Heeringen

last: Long

first: Arjen

last: Brinkman

first: Hendrik

last: Stunnenberg

first: Peter

last: Jones

first: Gert-Jan

middle: C

last: Veenstra


title: Genome-wide binding pattern of PU.1 in normal erythroid progenitors and erythroleukemia cells

summary: We find that the myeloid master regulatory transcription factor, PU.1, binds to >16,000 sites in both normal and leukemic erythroid cells. Of these bound sites, ~7,000 lie within 2kb of TSS of a gene, suggesting PU.1 may regulate a large number of genes in erythroid cells. Coupling this data with gene expression analysis, we show PU.1 directly regulates several critical signaling pathways in erythroid cells.

overall_design: Assaying PU.1 occupancy in normal and leukemic erythroid cells

first: Arthur

last: Skoultchi


title: Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells (ChIP-seq)

status: Public on Jun 21 2011

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

summary: Cellular differentiation entails reprogramming of the transcriptome from a pluripotent to a unipotent fate. This process was suggested to coincide with a global increase of repressive heterochromatin, which results in a reduction of transcriptional plasticity and potential. Here we report the dynamics of the transcriptome and an abundant heterochromatic histone modification, dimethylation of histone H3 at lysine 9 (H3K9me2), during neuronal differentiation of embryonic stem cells. In contrast to the prevailing model, we find H3K9me2 to occupy over 50% of chromosomal regions already in stem cells. Marked are most genomic regions that are devoid of transcription and a subgroup of histone modifications. Importantly, no global increase occurs during differentiation, but discrete local changes of H3K9me2 particularly at genic regions can be detected. Mirroring the cell fate change many genes show altered expression upon differentiation. Quantitative sequencing of transcripts reveals however that the total number of active genes is equal between stem cells and several tested differentiated cell types. Together, these findings reveal high prevalence of a heterochromatic mark in stem cells and challenge the model of low abundance of epigenetic repression and resulting global transcription in stem cells.  Instead cellular differentiation entails local rather than global changes in epigenetic repression and transcriptional activity.

overall_design: Our dataset comprises of 2 ChIP-seq samples using chromatin from embryonic stem (ES) cells and derived terminal neurons (TN)  which was immunoprecipitated, using antibodies against H3K27me3 and H3K4me2. For the same cells we generated H3K9me2 ChIP-chip samples in biological replicates. For ES cells, neurons and mouse embryonic fibroblasts (MEFs) we generated biological replicates of RNA-seq data.

first: Florian

last: Lienert

first: Fabio

last: Mohn

first: Vijay

last: Tiwari

first: Tuncay

last: Baubec

first: Tim

last: Roloff

first: Dimos

last: Gaidatzis

first: Michael

middle: B

last: Stadler

last: SchÃ¼beler


title: Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells (RNA-seq)


status: Public on Jun 16 2011

city: Rockville

first: Ravi

last: Sanka

state: Maryland

address: 9704 Medical Center Drive

institute: JCVI

summary: To better understand the effect of temperature on mycotoxin biosynthesis, RNA-Seq technology was used to profile the Aspergillus flavus transcriptome under different temperature conditions. This approachallowed us to quantify transcript abundance for over 80% of fungal genes including 1,153 genes that were differentially expressed at 30°C and 37°C. Wleven of the 55 secondary metabolite clusters were up-regulated at the lower temperature, including aflatoxin biosynthesis genes, which were among the most highly up-expressed genes. On average, transcript abundance for the 30 aflatoxin biosynthesis genes was 3,300 times greater at 30°C as compared to 37°C. The results are consistent with the view that high temperature negatively affects aflatoxin production by turning down transcription of the two key transcriptional regulators, aflR and aflS. Subtle changes in the expression levels of aflS to aflR appear to control transcription activation of the aflatoxin cluster.

overall_design: 2 samples examined: from the fungus grown at 30°C and 37°C

first: Jiujiang

last: Yu

first: Natalie

last: Fedorova

first: Beverly

last: Montalbano

first: Deepak

last: Bhatnagar

first: Thomas

last: Cleveland

first: Joan

last: Bennett

first: William

last: Nierman


title: DNA sequencing of selected Globobulimina pseudospinescens organisms

status: Public on Jun 20 2011

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

institute: Radboud University

type: Genome variation profiling by high throughput sequencing

summary:
We introduce FACIL (http://www.cmbi.ru.nl/FACIL), a fast, reliable tool to evaluate nucleic acid sequences for non-standard codes that detects alternative genetic codes even in species distantly related to known organisms. Results are visualized in a Genetic Code Logo. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens. These are particularly challenging data, as the genome is highly fragmented and incomplete. Approximately 10,000 single-cell Globobulimina pseudospinescens organisms were isolated by hand from Gullmar Fjord Sweden sediment. After washing, total DNA was extracted and sequenced by Illumina sequencing. The reads were assembled using Edena.

To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens, an organism without any sequenced relatives in the databases. These are particularly challenging data, as the genome is highly fragmented and incomplete.

overall_design: DNA isolated from approximately 10,000 single-cell Globobulimina pseudospinescens organisms

first: Bas

last: Dutilh

first: Rasa

last: Jurgelenaite

first: Radek

last: Szklarczyk

first: Sacha

middle: A

last: van Hijum

first: Harry

last: Harhangi

first: Markus

last: Schmid

first: Bart

last: de Wild

first: Kees-Jan

last: Francoijs

first: Hendrik

first: Marc

last: Strous

first: Mike

last: Jetten

first: Huub

middle: J

last: Op den Camp

first: Martijn

last: Huynen


title: Ascaris suum transcriptome (RNA-Seq) data

city: Aurora

first: Jianbin

last: Wang

state: CO

address: 12801 East 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

summary: Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris.  miRNAs are synthesized immediately following fertilization in utero, prior to pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to Ascaris’ life cycle and parasitism.

overall_design: We generated transcriptomes from Ascaris germline and embryos for de-novo assembly as well as cDNA expression profiles. Two types of libraries were prepared: 1) sheared, full-length cDNA synthesized using a combination of oligo-dT and random hexamer priming and 2) cDNA prepared from RNA first chemically sheared and then double-stranded cDNA prepared using ramom hexamer priming.

first: Richard

last: Davis


title: Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates

city: London

first: Guillermo

last: Carbajosa

address: 4 Newark Street

department: Diabetes

institute: Blizard Institute

summary: Here, we demonstrate that Nematostella vectensis, Ciona intestinalis, Apis mellifera, and B. mori, show two distinct populations of genes differentiated by gene-body CpG density. Genome-scale DNA methylation profiles for A. mellifera spermatozoa reveal CpG-poor genes are methylated in the germ line, as predicted by the depletion of CpGs. We find an evolutionarily conserved distinction between CpG-poor and -rich genes: the former are associated with basic biological processes, the latter with more specialized functions. This distinction is strikingly similar to that recently observed between euchromatin-associated genes in Drosophila that contain intragenic histone 3 lysine 36 trimethylation (H3K36me3) and those that do not, even though Drosophila doesnât display CpG density bimodality or methylation. We confirm that a significant number of CpG-poor genes in N. vectensis, C. intestinalis, A. mellifera and B. mori are orthologs of H3K36me3- rich genes in Drosophila. We propose that over evolutionary time, gene-body H3K36me3 has influenced gene-body DNA methylation levels, and consequently the gene-body CpG density bimodality characteristic of invertebrates that harbor CpG methylation.

overall_design: Examination of DNA methylation in Apis Mellifera sperm

first: Vardhman

last: Rakyan


title: Deep sequencing of small RNAs in the Xenopus tropicalis gastrula

status: Public on Jun 18 2011

city: Santiago

first: Juan

last: Larrain

address: Alameda 340

department: Cell and Molecular Biology

country: Chile

institute: P. Universidad Catolica de Chile

summary: Transposable elements comprise a large proportion of animal genomes. Transcripts of transposable elements are a source for the synthesis of endogenous siRNAs and piRNAs. In order to determine if small RNAs mapped to expressed Tc1-like elements are present during early Xenopus tropicalis development, we used Illumina (Solexa) to sequence small RNAs from gastrula-stage embryos. We obtained about 17 million reads that mapped perfectly to the genome. Small RNAs mapped to selected transposable elements were characterized and the expression of selected small RNAs was experimentally verified during development. This is the first deep sequencing experiment for small RNAs in the Xenopus tropicalis gastrula.

overall_design: Analysis of small RNAs expressed in the Xenopus tropicalis gastrula.

first: Fernando

last: Faunes

first: Natalia

last: Sanchez

first: Mauricio

last: Moreno

first: Gonzalo

last: Olivares

first: Dasfne

last: Lee-Liu

first: Leonardo

last: Almonacid

first: Alex

last: Slater

first: Tomas

last: Norambuena

first: Ryan

last: Taft

first: John

last: Mattick

first: Francisco

last: Melo


title: Ascaris suum Small RNA-Seq data

overall_design: We constructed and analyzed 51 libraries from discrete regions of gametogenesis and synchronized stages of embryo development in the parasitic nematode Ascaris, using three types of small RNA libraries preparation methods: 1) 28 libraries of 18-34 or 18-40 nt RNAs with a 5’ monophosphate (5’ monophosphate libraries), 2) 4 libraries of 18-34 nt RNAs with a 5’ monophosphate but treated with periodate to enrich for small RNAs with 3’ end modifications (5’ monophosphate, 3’ end modified), and 3) 19 libraries of 18-28 or 18-40 nt RNAs with a 5’ triphosphate, diphosphate, or monophosphate (5’ allphosphate). These libraries enabled us to identify different small RNAs, characterize their different 5’ and 3’ ends, and their expression profiles through gametogenesis and embryogenesis.

first: Benjamin

last: Czech

first: Gregory

last: Hannon


title: Small RNA and degradome sequencing in Medicago truncatula roots (Glomus intraradices colonized and non-colonized)

city: Esch-Belval

first: Patrick

last: May

state: Luxembourg

address: 7, avenue des Hauts-Fourneaux

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

overall_design: Refer to individual Series

first: Devers

last: Emanuel

first: Anja

last: Branscheid

first: Franziska

last: Krajinski


title: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [DNase_seq].

city: Chapel Hill

first: Terry

last: Furey

address: 5022 Genetic Medicine Building, CB#7264

institute: UNC-Chapel Hill

summary:
The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq to map âopen chromatinâ. Over 870,000 DNaseI or FAIRE sites, which correspond largely to nucleosome depleted regions (NDRs), were identified across the seven cell lines, covering nearly 9% of the genome. The combination of DNaseI and FAIRE is more effective than either assay alone in identifying likely regulatory elements, as judged by coincidence with transcription factor binding locations determined in the same cells. Open chromatin common to all seven cell types tended to be at or near transcription start sites and encompassed more CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start sites, and contained DNA motifs recognized by regulators of cell-type identity. As one example of its ability to identify functional DNA, we show that open chromatin regions bound by CTCF are potent insulators. We identified clusters of open regulatory elements (COREs) that were physically near each other and whose appearance was coordinated among one or more cell types. Gene expression and RNA Pol II binding data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity. This publicly available atlas of regulatory elements may prove valuable in identifying non-coding DNA sequence variants that are causally linked to human disease.

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: DNase-seq, FAIRE-seq, and ChIP-seq were performed on seven human cell lines: GM12878 (lymphoblastoid), K562 (leukemia), HepG2 (hepatocellular carcinoma), HelaS3 (cervical carcinoma), HUVEC (human umbilical vein endothelial cells), NHEK (keratinocytes), and   H1-ES (embryonic stem cells). For each cell line, two or three replicates were independently grown and split into three, one for each of the three experimental methods.  Control ChIP experiments were performed on five of the cell lines with NHEK and H1-ES being excluded due to lack of material.

first: Terrence

last: Crawford


title: Degradome sequencing in Medicago truncatula roots (Glomus intraradices colonized and non-colonized)

summary: Identification of microRNA targets in M. truncatula roots

overall_design: Degradome sequencing of mycorrhizal and non-mycorrhiza M. truncatula roots

first: Emanuel

last: Devers


title: Small RNA sequencing in Medicago truncatula roots (Glomus intraradices colonized and non-colonized)

summary: Identification of microRNA expressed in M. truncatula roots

overall_design: Small RNA sequencing of mycorrhizal and non-mycorrhiza M. truncatula roots


title: Integrating 5 Hydroxymethylcytosine into the Epigenetic Landscape of Human Embryonic Stem Cells

status: Public on Jun 24 2011

city: Atlanta

first: Keith

last: Szulwach

state: GA

address: 615 Michael Street, Whitehead Suite 301

department: Human Genetics

institute: Emory University

summary: Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the role of 5-hmC in the epigenomic landscape of pluripotent cells, here we profile the genome-wide 5-hmC distribution and correlate it with the genomic profiles of 11 diverse histone modifications and six transcription factors in human ES cells. By integrating genomic 5-hmC signals with maps of histone enrichment, we link particular pluripotency-associated chromatin contexts with 5-hmC. Intriguingly, through additional correlations with defined chromatin signatures at promoter and enhancer subtypes, we show distinct enrichment of 5-hmC at enhancers marked with H3K4me1 and H3K27ac. These results suggest potential role(s) for 5-hmC in the regulation of specific promoters and enhancers. In addition, our results provide a detailed epigenomic map of 5-hmC from which to pursue future functional studies on the diverse regulatory roles associated with 5-hmC.

overall_design: Genome wide enrichment profile of 5-hmC in H1 human embryonic stem cells

first: Peng

last: Jin

first: Chuan

last: He


title: The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

city: Utrecht

first: Erik

last: Splinter

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: 3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps of the active and inactive X-chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial re-folding of the inactive X into a conformation resembling the active X, without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X-chromosome independently of transcription.

overall_design: Five or six 4C viewpoints were applied on the mouse female wild type active X-chromosome, the wild type inactive X-chromosome, the conditional Xist X-chromosome and the Xist knock out X-chromosome

first: Elzo

last: de Wit

first: Elphege

last: Nora

first: Petra

last: Klous

first: Harmen

last: van de Werken

first: Yun

last: Zhu

first: Lucas

last: Kaaij

first: Wilfred

last: van Ijcken

first: Joost

last: Gribnau

first: Edith

last: Heard

first: Wouter

last: de Laat


title: Deep Small RNA Sequencing from the Nematode Ascaris Reveals Conservation, Functional Diversification, and Novel Developmental Profiles

first: Jianbin

last: Wang

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


title: Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells

first: Dirk

last: Schuebeler

type: Genome binding/occupancy profiling by genome tiling array


title: Small non-coding RNA expression in murine germ cells

status: Public on Jun 10 2011

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: In order to monitor the changes in small RNAs expression during mouse spermatogenesis. Type A spermatogonia, pachytene spermatocytes and round spermatids were isolated following collagenase treatment of testes and trypsin digestion of isolated seminiferous tubules using unit gravity sedimentation in a bovine serum albumin gradient. The small RNA fraction (18-36nt) was cloned and sequenced from total RNA of each cell type.

overall_design: Three types of mouse germ cells small RNAs were used for high throughput sequencing analysis

first: Haiyun

last: Gan


title: RNA-Seq analysis of microRNA expression profiles in mouse primary CFU-E late erythroid progenitors and Ter119+ mature erythroblasts

status: Public on Jun 09 2011

city: Cambridge

first: Lingbo

last: Zhang

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research and MIT Department of Biology

summary: Using RNA-seq technology, we quantitatively determined the expression profile of microRNAs during mouse terminal erythroid differentiation. CFU-E erythroid progenitors were isolated from E14.5 fetal liver as the Ter119, B220, Mac-1, CD3 and Gr-1 negative, C-Kit positive and 20% high CD71 population. Mature Ter119+ erythroblasts were isolated from E14.5 fetal liver as C-Kit negative and Ter119 positive population. Consistent with nuclear condensation and global gene expression shut down during terminal erythroid differentiation, we found that the majority of microRNAs are downregulated in more mature Ter119+ erythroblasts compared with CFU-E erythroid progenitors.

overall_design: Examination of microRNA expression profiles in 2 cell types

first: Johan

last: Flygare


title: Degeneration of penicillin production in ethanol-limited chemostat cultivation of Penicillium chrysogenum: A systems biology approach

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

summary: In microbial production of non-catabolic products, a loss of production capacity upon long-term cultivation (for example, chemostat), a phenomenon called strain degeneration, is nearly always observed. In this study, a systems biology approach (monitoring changes from gene to produced flux) was used to study degeneration of penicillin production by Penicillium chrysogenum in ethanol-limited chemostat fermentations where the biomass specific penicillin production rate decreased 10-fold within 30 generations. Results showed that the copy number of penicillin gene clusters and expression levels of central metabolism showed little decrease. With respect to penicillin production, major changes were observed: a strong downregulation of the cysteine pathway in agreement with its nearly 10-fold flux reduction. Also, levels of ACVS and IPNS, two penicillin pathway enzymes, and the penicillin transport capacity decreased many fold. This indicates that degeneration is caused by changed regulation of post-translational modifications or an increased protein degradation rate of these proteins. Continued subcultivation of a degenerated culture resulted in partial recovery of the biomass specific penicillin production rate, however, it was still 5-fold lower than the peak biomass specific penicillin production rate.

overall_design: Prolonged chemostat cultivations up to 500 hours (30 generations) with ethanol as the sole limiting carbon source were performed because degeneration is found to be more pronounced with ethanol as a limiting sole carbon source compared to glucose. Measurements included genome level (number of penicillin gene clusters), genome-wide transcriptome, protein levels of penicillin pathway enzymes, number of peroxisomes (microbodies where part of the penicillin pathway occurs), metabolome (of central metabolism, nucleotides, penicillin pathway intermediates including intracellular PAA and PenG) and fluxome.

first: Tania

last: Veiga Dos Innocentes

first: Rutger

last: Douma

first: Walter

last: van Gulik


title: ChIP-seq for CTCF and Rad21 in Rag1−/− pro-B cells

status: Public on Jun 07 2011

first: Ali

last: Torkamani

address: 3344 North Torrey Pines Court Suite 300

institute: TSRI

summary: Genome-wide ChIP data of CTCF and Rad21 binding in Rag1−/− pro-B cells

overall_design: CTCF and Rad21 binding in Rag1−/− pro-B

first: Ann

last: Feeney

first: A

first: S

last: Degner


title: MicroRNA sequence and expression analysis in breast tumors by deep sequencing [miRNA sequence data]

city: New York

first: Thalia

last: Farazi

address: 1230 York Ave, BOX 186

department: Lab of RNA Molecular Biology

institute: Rockefeller University

summary: MicroRNAs (miRNAs) regulate many genes critical for tumorigenesis. We profiled miRNAs from 11 normal breast tissues, 17 non-invasive, 151 invasive breast carcinomas, and 6 cell lines by in-house-developed barcoded Solexa sequencing. miRNAs were organized in genomic clusters representing promoter-controlled miRNA expression and sequence families representing seed-sequence-dependent miRNA-target regulation. Unsupervised clustering of samples by miRNA sequence families best reflected the clustering based on mRNA expression available for this sample set. Clustering and comparative analysis of miRNA read frequencies showed that normal breast samples were separated from most non-invasive ductal carcinoma in situ and invasive carcinomas by increased miR-21 (the most abundant miRNA in carcinomas) and multiple decreased miRNA families (including mir-98/let-7), with most miRNA changes apparent already in the non-invasive carcinomas. In addition, patients that went on to develop metastasis demonstrated increased expression of mir-423, and triple negative breast carcinomas were most distinct from other tumor subtypes due to up-regulation of the mir-17~92 cluster. However, absolute miRNA levels between normal breast and carcinomas did not reveal any significant differences. We also discovered two polymorphic nucleotide variations among the more abundant miRNAs miR-181a (T19G) and miR-185 (T16G), but we did not identify nucleotide variations expected for classical tumor suppressor function associated with miRNAs. The differentiation of tumor subtypes and prediction of metastasis based on miRNA levels is statistically possible, but is not driven by deregulation of abundant miRNAs, implicating far fewer miRNAs in tumorigenic processes than previously suggested.

overall_design: 21 barcoded sequencing runs, including 185 unique samples and 54 samples in replicate (6 in triplicate and the remaining in duplicate). The details of each sample can be found in Supplementary Tables S1 and S2.

first: Hugo

last: Horlings

first: Jelle

last: ten Hoeve

first: Aleksandra

last: Mihailovic

first: Hans

last: Halfwerk

first: Pavel

last: Morozov

first: Miguel

last: Brown

first: Markus

last: Hafner

first: Fabien

last: Reyal

first: Marieke

last: van Kouwenhove

first: Bas

last: Kreike

first: Daoud

last: Sie

first: Volker

last: Hovestadt

first: Lodewyk

last: Wessels

first: Marc

last: van de Vijver

first: Thomas

last: Tuschl


title: Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development

city: Philadelphia

first: Ravi

last: Gupta

state: PA

address: 3601 Spruce Street

department: Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program

institute: The Wistar Institute

summary: Mammalian development is an intricate process regulated by multiple gene isoforms and their epigenetic states, which are yet undefined. Using integrative massive parallel sequencing and bioinformatics approach, we built genome-wide inventory of transcript variants, their promoters and histone modification states during normal development, using mouse cerebellum as model system. The data we integrated consists of 29,589 (4,792 novel) promoters that transcribe 61,525 (12,796 novel) distinct mRNAs, corresponding to 14,508 protein-coding and 9,862 non-coding genes. While 68% of the multi-transcript genes exhibit alternative splicing, 78% use alternative transcriptional events that are regulated during cerebellar development through H3K4me3 and H3K27me3. The data presented highlight the magnitude of alternative promoters and transcriptional termination as major source of transcriptome diversity along with alternative splicing. We also show that alternative promoters differentially activated during normal cerebellar development are aberrantly used in medulloblastoma, emphasizing the importance of studying gene regulation and function at the isoform-level.

overall_design:
Study of transcriptome diversity in cerebellar development.
We performed mRNA-seq and ChIP-seq experiments. mRNA-seq were performed on total RNA isolated from two P0, P5, P15 and adult cerebellum using 10 microgram of total RNA as the starting material for sequencing library prep. For each stage, mRNA-seq data was obtained from two lanes of a flowcell. For ChIP-seq experiments, solubilized chromatin was prepared by pooling multiple cerebellum tissues (3-18) and then ChIP-enriched DNA (using anti-RNAP II, anti-H3K4me3, anti-H3K27me3, or negative control IgG antibodies) were isolated. 10 microgram of ChIP-enriched DNA was used to prepare the ChIP-seq library for sequencing in a single lane.

first: Sharmistha

last: Pal

first: Hyunsoo

last: Kim

first: Priyankara

last: Wickramasinghe

first: Valérie

last: Baubet

first: Louise

last: Showe

first: Naida

last: Dahmane

first: Ramana

middle: V

last: Davuluri


title: RNA-Seq of mouse eye and retina tissues from wild type and Nrl transcription factor knockout mice

city: Cleveland

first: Debarshi

last: Mustafi

state: OH

address: 2109 Aldelbert Rd

department: Pharmacology

institute: Case Western Reserve University

summary:
The initial aim of this work was to understand the pathophysiology of Enhanced S-cone Syndrome (ESCS) that leads to retinal degeneration. Although ESCS was identified in humans decades ago and since then the causative genes have been elucidated, our understanding of the accompanying retinal degeneration is still poorly understood. Knockout of the Nrl transcription factor in mice produces a retina overpopulated with S-cone like photoreceptors along with absence of rod photoreceptors and recapitulates many of the phenotypic features seen in human ESCS patients. We wanted to study this murine model through a combinatorial genetic and structural approach to improve understanding of the disease process that leads to photoreceptor degeneration and blindness, potentially guiding future therapies.
By using RNA-Sequencing (RNA-Seq) to examine mature wild type and Nrl-/- ocular tissues, we were able to determine global changes in their transcriptomes. The massively parallel RNA-sequencing experiment revealed new insight into the transcriptional mis-regulation in the ESCS murine model and revealed a change in gene expression in putative proteins involved in photoreceptor phagocytosis. Key photoreceptor ligands necessary for phagocyotsis, Tub and Tulp1, were down-regulated in the Nrl-/- retina. Down regulation of key retinoid metabolic genes, coupled with down-regulation of Tub and Tulp1, suggested a potential mechanism involving defective phagocytosis underlies the photoreceptor degeneration seen in ESCS.

overall_design:
We report RNA-Seq experiments of whole eye and retinal tissues from wild type and Nrl transcription factor knockout mice on the C57BL/6 background.
Examine two different ocular tissues in two mouse models of varying photoreceptor populations

first: Brian

last: Kevany

first: Mark

last: Adams

first: Krzysztof

last: Palczewski


title: miRNAs high throughput sequencing profiling of basals cells and columnar cells

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: The airway mucociliary epithelium is consituted of three main cell types : columnar ciliated  plus secretory cells and basal cells. Columnar cells are represented by a great majority of ciliated cells. We used Cell sorting by FACSaria to separate basal cells from ciliated and secreting columnar cells. Then, we performed microRNA high throughput sequencing to investigate the specific signature of microRNA of basal and columnar cells.

overall_design: miRNAs high throughput sequencing profiling of human nasal mucosa: basals cells (B) and columnars (C) cells for 3 donors.

first: B

last: Marcet

first: P

last: Barbry

first: K


title: MicroRNA sequence and expression analysis in breast tumors by deep sequencing

first: Thalia

last: Farazi

summary:
MicroRNAs (miRNAs) regulate many genes critical for tumorigenesis. We profiled miRNAs from 11 normal breast tissues, 17 non-invasive, 151 invasive breast carcinomas, and 6 cell lines by in-house-developed barcoded Solexa sequencing. miRNAs were organized in genomic clusters representing promoter-controlled miRNA expression and sequence families representing seed-sequence-dependent miRNA-target regulation. Unsupervised clustering of samples by miRNA sequence families best reflected the clustering based on mRNA expression available for this sample set. Clustering and comparative analysis of miRNA read frequencies showed that normal breast samples were separated from most non-invasive ductal carcinoma in situ and invasive carcinomas by increased miR-21 (the most abundant miRNA in carcinomas) and multiple decreased miRNA families (including mir-98/let-7), with most miRNA changes apparent already in the non-invasive carcinomas. In addition, patients that went on to develop metastasis demonstrated increased expression of mir-423, and triple negative breast carcinomas were most distinct from other tumor subtypes due to up-regulation of the mir-17~92 cluster. However, absolute miRNA levels between normal breast and carcinomas did not reveal any significant differences. We also discovered two polymorphic nucleotide variations among the more abundant miRNAs miR-181a (T19G) and miR-185 (T16G), but we did not identify nucleotide variations expected for classical tumor suppressor function associated with miRNAs. The differentiation of tumor subtypes and prediction of metastasis based on miRNA levels is statistically possible, but is not driven by deregulation of abundant miRNAs, implicating far fewer miRNAs in tumorigenic processes than previously suggested.

This SuperSeries is composed of the SubSeries listed below.

first: Hugo

last: Horlings

first: Jelle

last: ten Hoeve

first: Aleksandra

last: Mihailovic

first: Hans

last: Halfwerk

first: Pavel

last: Morozov

first: Miguel

last: Brown

first: Markus

last: Hafner

first: Fabien

last: Reyal

first: Marieke

last: van Kouwenhove

first: Bas

last: Kreike

first: Daoud

last: Sie

first: Volker

last: Hovestadt

first: Lodewyk

last: Wessels

first: Marc

last: van de Vijver

first: Thomas


title: microRNAs-449 control vertebrate multi-ciliogenesis by repressing Notch signalling

first: Kevin

last: Lebrigand

sample_organism:
Xenopus laevis
Homo sapiens

platform_organism:
Xenopus laevis
Homo sapiens


title: microRNAs signatures of Xenopus laevis embryo epidermis at stage 11 (non ciliated) and 26 (ciliated) using high throughput sequencing

summary:
Epidermis of Xenopus embryos forms a mucociliary epithelium constituted of basal, scattered, secreting and ciliated cells and is histologically similar to human airway mucociliary epithelium.
We compared microRNAs signatures of epidermis of Xenopus embryos at stage 11.5 (gastrula, non ciliated epidermis) and at stage 26 (tailbud, ciliated epidermis).

overall_design: 2 technical replicates of a pool of 50 explants for each stage 11.5 (non ciliated)  and 26 (ciliated) of Xenopus laevis development

first: B

last: Marcet

first: P

last: Barbry

first: K


title: Histone modifications of Arabidopsis thaliana (aerial tissue)

status: Public on Jun 06 2011

city: Los Angeles

first: Chongyuan

last: Luo

address: 695 Charles E Young Drive South

institute: University of California Los Angeles

summary: Bioinformatics powered correlative analysis of epigenomic patterns is an effective method to help derive biological hypotheses that can be tested genetically or biochemically. To accommodate the variety and complexity of epigenomic and transcriptomic patterns, ANchored COrrelative Patterns (ANCORP) was developed as a platform to integrate and intuitively visualize a large number of genome-wide profiles. With global profiles of 9 histone modifications mapped by ChIP-seq and a strand-specific RNA-seq dataset, we have applied the ANCORP-genetics pipeline for hypothesis building and testing in order to understand how global transcription may be regulated by epigenetic pathways such as histone modifications. It was found that intragenic antisense RNAs were depleted from genes with strong gene-body H3K36me2 mark and cytosine methylation enrichments but were significantly overrepresented in H3K4me3/H3K27me3 bivalent genes. Moreover, gene body H3K36me2 and DNA methylation anti-correlated with multiple active chromatin marks including H3K4me2/3, H3K9Ac and H3K18Ac. These observations lead us to hypothesize that H3K36me2 and DNA methylation may synergistically repress active chromatin marks in gene bodies and subsequently inhibit transcription of the antisense strand. Mutant analyses revealed that Polymerase Associated Factors (PAF) may be universally required for modulating NAT abundance whereas the role for the 5mC and H3K36me marks are more locus specific. H3K36me and PAF may either repress or permit the accumulation NATs depending on the chromatin state context in a particular transcription unit. Interestingly, the activation of antisense RNA in sdg8-2 or elf8-1 mutants does not associate with any increase of histone marks in gene bodies that are known to correlate with gene activation. Our results suggest that ANCORP-genetics is an effective approach to uncover epigenetic regulatory mechanisms by leveraging on the rapid advances in sequencing technologies and the resultant wealth of genome-wide information.

overall_design: Global profiling of nine histone modifications and transcriptome in aerial tissue of Arabidopsis thaliana

first: David

last: Sidote

first: Randall

last: Kerstetter

first: Todd

last: Michael

first: Eric

last: Lam


title: miRNAs high throughput sequencing profiling of regenerating human airway epithelial cells

summary:
The regeneration of the airway mucociliary epithelium involves several sequential events including migration, proliferation, polarization and final differentiation (i.e ciliogenesis).
The airway mucociliary epithelium is consituted of three main cell types : ciliated cells, secretory cells and basal cells. We used microRNA microrrays to investigate the signature of microRNA during the four step of regeneration of the airway epithelium.

overall_design: Four time points (ALI-D0, ALI-D7, ALI-D14, ALI-D21) of regeneration of the airway epithelium for 3 donors.


title: Activator protein-2γ is a critical determinant of estrogen receptor interactome formation and gene transcription in breast cancer [ChIP-Seq]

status: Public on Jun 03 2011

city: Singapore

first: SI KEE

last: TAN

address: 60 Biopolis Street #02-01 Genome

department: Cancer biology and Pharmacology

institute: Genomic Institute of Singapore

summary: Estrogen receptor α (ERα) is key player in the progression of breast cancer. ERα binds to DNA and mediates long-range chromatin interactions throughout the genome, but the underlying mechanism in this process is unclear. Here, we show that AP-2 motifs are highly enriched in the ERα binding sites (ERBS) identified from the recent ChIA-PET of ERα. More importantly, we demonstrate that AP-2γ (also known as TFAP2C), a member of the AP-2 family which has been implicated in breast cancer oncogenesis, is recruited to chromatin in a ligand-independent manner and co-localized with ERα binding events. Furthermore, pertubation of AP-2γ expression disrupts ERα DNA binding, long-range chromatin interactions, and gene transcription. Using ChIP-seq, we show that AP-2γ and ERα binding occurs in close proximity on a genome-wide scale. The majority of these shared genomic regions are also occupied by the pioneer factor, FoxA1. AP-2γ is required for efficient FoxA1 binding and vice versa. Finally, we show that most ERBS associated with long-range chromatin interactions are co-localized with both AP-2γ and FoxA1. Together, our results suggest AP-2γ is an essential factor in ERα-mediated transcription, primarily working together with FoxA1 to facilitate ERα binding and long-range chromatin interactions.

overall_design: Genome-wide binding analysis of AP-2γ and FoxA1 in MCF-7 with and without E2 (estradiol) stimulation using ChIP-Seq.

first: Si

last: Tan

first: Zhenhua

last: Lin

first: Cheng

last: Chang

first: Edwin

last: Cheung


title: High-throughput sequencing of small RNAs in Heliconius melpomene

status: Public on Jun 02 2011

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

institute: University of East Anglia

summary:
Background: Heliconius butterflies are an excellent model system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus and several genes in this region show expression pattern differences across races. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. It seems likely that miRNAs could act as downstream regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races.
Results: We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs appeared to be differentially expressed between colour pattern races and this was tested further in different developing pupal wing stages using Northern blots. These revealed that differences in expression were due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified miR-193 and miR-2788; located 2380bp apart in an intergenic region. A search for miRNAs in all available H. melpomene BAC sequences (~2.5Mb) did not reveal any other miRNA genes and no novel miRNAs were predicted. There were several regions where other small RNA sequences assembled to the HmYb region and appeared to be differentially expressed.These might represent other regulatory RNAs.
Conclusions: Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages. Two miRNAs were located in the HmYb region. Future work will examine the expression of these miRNAs in different colour pattern races and identify miRNA targets among wing patterning genes.

sample_organism:
Heliconius melpomene rosina
Heliconius melpomene melpomene

overall_design:
High-throughput sequencing of Heliconius melpomene endogenous small RNAs.
Size fractionated small RNA from total RNA extracts of two different Heliconius melpomene races (Heliconius melpomene melpomene and Heliconius melpomene rosina) were isolated from wing tissue using miRVana kit. 100µg RNA from 11  individuals of different developmental stages was pooled for each race as follows: 4.1% larval stage <1; 2% larval stage 1-1.75; 2.9% larval stage  2-2.5; 22% larval stage 2.75-3; 19% larval stage > 3; 25% early pupae; 25%  mid-melanin pupae. Sequences were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

first: Alison

last: Surridge

first: Nicola

last: Nadeau

first: Luana

last: Maroja

first: Chris

last: Jiggins

first: Sara

last: Lopez-Gomollon

first: Tina

last: Rathjen

first: Tamas

last: Dalmay


title: Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells (ChIP-seq)

status: Public on Jun 01 2011

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

institute: Baker Heart and Diabetes Institute

summary: We report that hyperglycemia-mediated induction of genes and pathways associated to endothelial dysfunction occur through modulation of acetylated H3K9/K14 inversely correlated with methyl-CpG content.

overall_design: Examination of H3K9/K14 histone acetylation and DNA methylation in hyperglycemic conditions.

first: Luciano

last: Pirola

first: Aneta

last: Balcerczyk

first: Richard

last: Tothill

first: Izhak

last: Haviv

first: Antony

last: Kaspi

first: Sebastian

last: Lunke

first: Tom

last: Karagiannis

first: Stephen

last: Tonna

first: Adam

last: Kowalczyk

first: Bryan

last: Beresford-Smith

first: Mark

last: Zieman

first: Ma

last: Kelong

first: Zhang

last: Hongyu

first: Sun

last: Jinfeng

first: Jingde

last: Zhu


title: 5-hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells.

status: Public on Jun 13 2011

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: Hydroxymethylcytosine (5hmC) was recently found to be abundantly present in certain cell types including embryonic stem cells. The function of 5hmC is poorly understood. Here we have generated a genome-wide map of 5hmC in human embryonic stem cells (hESCs) by hydroxymethyl-DNA immunoprecipitation followed by massively parallel sequencing (hmeDIP-seq).  We found that 5hmC is enriched over enhancers as well as gene bodies, suggesting a potential role of 5hmC in gene regulation.  Consistent with localization of 5hmC at enhancers, 5hmC was significantly enriched in histone modifications associated with enhancers such as H3K4me1 and H3K27ac.   5hmC was enriched in other protein-DNA interaction sites such as OCT4 and NANOG binding sites.  Furthermore we found that 5hmC regions tend to be GC-skewed (excess G over C on one strand of DNA).   These findings suggest that 5hmC may be targeted to certain genomic regions based both on gene expression and sequence composition.

overall_design: 2 experiments, 2 controls

first: Steven

middle: E

last: Jacobsen


title: L3MBTL2 protein acts in concert with PcG protein mediated monoubiquitination of H2A to establish a repressive chromatin structure [ChIP-Seq data].

city: Palo Alto

first: Philip

last: Cayting

address: 1501 S California Ave

department: Genetics

institute: Stanford University

summary: Human MBT domain-containing protein L3MBTL2 was found to be an integral component of a protein complex that we termed Polycomb Repressive Complex 1-like 3 (PRC1L3) given the presence of the PcG proteins RING1, RING2 and PCGF6. L3MBTL2 binds chromatin in a histone modification-independent manner and is required for the repressive function of PRC1L3. PRC1L3 also contains E2F6 and CBX3, two factors with well‐established functions in transcriptional repression. Genome‐wide profiling identified several hundred genes that are simultaneously bound by L3MBTL2 and E2F6, preferentially around transcriptional start sites. Importantly, these genes are largely distinct from those targeted by other E2Fs or L3MBTL, another MBT‐domain containing protein that interacts with RB1. H3K27 or H3K9 methylation, two chromatin modifications implicated in gene silencing, are not present on all L3MBTL2 target genes. L3MBTL2-specific RNAi results in altered target gene expression patterns and affects the differentiation program of hematopoietic cells. Our data suggest that repression of transcription via chromatin modulation, reflective of PRC1 function, can be achieved by multiple players and does not necessarily require the presence of histone lysine methylation marks.

overall_design: 7 total ChIP-seq datasets; one L3MBTL2 dataset done in duplicate in K562 cells; one E2F6 dataset done in duplicate in K562 cells; one H3K27me3 replicate dataset in K562 cells.

first: Alina

last: Cao

first: Peggy

last: Farnham


title: mRNA-seq of Human Airway Epithelial Cells

city: Boston

first: Avrum

last: Spira

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

summary: mRNA expression was profiled from pooled bronchial airway epithelial cell brushings (n=3 patients/pool) obtained during bronchoscopy from healthy never (NS) and current smokers (S) and smokers with (C) and without (NC) lung cancer

overall_design: 4 samples were sequened, each representing a pool of 3 patients.  The phenotypes of the 4 samples were as follows: healthy non-smoker, healthy smoker, smoker without lung cancer and smoker with lung cancer.

first: Jennifer

last: Beane


title: Activator protein-2γ is a critical determinant of estrogen receptor interactome formation and gene transcription in breast cancer

first: SI KEE

last: TAN

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

overall_design: Refer to individual Series


title: mRNA sequencing from ego-1(om84) and control L3, L4, and adult C. elegans hermaphrodites

city: Stanford

first: Jay

last: Maniar

address: 300 Pasteur Dr L302

summary: Cellular RdRPs play a critical role in the development of many organisms.  Using high-throughput small RNA and messenger RNA sequencing we found that the Caenorhabditis elegans RdRP, EGO-1, is required to produce small RNAs antisense to a number of germline-expressed genes through several developmental stages.  We found that these genes fall into distinct classes including genes required for kinetochore and nuclear pore assembly, as well as the production of histone-modifying and centromeric proteins.  We also found several RNAi-related genes to be targets of EGO-1.  Finally, we show a strong correlation between the loss of small RNAs and the rise of mRNA levels in ego-1 mutant animals.

first: Andrew

middle: Z

last: Fire


title: 5'-monophosphate-independent small RNA sequencing from ego-1(om84) and control L3, L4, and adult C. elegans hermaphrodites


title: Widespread Expression of piRNA-like Molecules in Somatic Tissues

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: Piwi-interacting RNA (piRNA) are small RNA abundant in the germline across animal species. In fruit flies and mice, piRNA were implicated in maintenance of genomic integrity by transposable elements silencing. Outside of the germline, piRNA have only been found in Drosophila ovarian follicle cells. Previous studies further reported the presence of multiple piRNA-like small RNA (pilRNA) in fly heads and a small number of pilRNA in mouse tissues and human NK cells. Here, by analyzing high-throughput small RNA sequencing data in more than 130 fruit fly, mouse and rhesus macaque samples, we show widespread presence of pilRNA displaying all known characteristics of piRNA in multiple somatic tissues of these three species. In mouse pancreas and macaque epididymis, pilRNA abundance was compatible with piRNA abundance in the germline. Using in situ hybridizations, we further demonstrate pilRNA co-localization with mRNA expression of Piwi-family genes in all macaque tissues. These findings indicate that piRNA-like molecules might play important roles outside of the germline.

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: Small RNA expression profiles were examined in five rhesus macaque tissues (testis, epididymis, prostate, seminal vesicles, cortex) and one mouse tissue (epididymis).

first: Zheng

last: Yan

first: Wei

last: Chen

first: Philipp

last: Khaitovich


title: Genome-wide analysis of GATA1, GATA2, RUNX1, FLI1 and SCL binding in primary human megakaryocytes

first: Samuel

middle: David

last: Foster

state: Cambridgeshire

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

department: Department of Haematology

institute: Cambridge Institute for Medical Research

summary: We have mapped the binding sites for the five key regulators GATA1, GATA2, RUNX1, FLI1 and TAL1/SCL in primary human megakaryocytes. Statistical analysis identified subsets of enriched as well as depleted combinatorial binding patterns. In particular simultaneous binding by all 5 factors was highly enriched and occurred in the vicinity of many genes known to be involved in blood and megakaryocyte development. Knock down in zebrafish of 8 of these genes with no previously known role in hematopoiesis, revealed all to be essential for thrombocyte and/or erythroid development. Combinatorial analysis of multi-factor ChIP-Seq datasets coupled with a high-throughput in vivo screen therefore offers a powerful strategy to identify novel essential regulators of complex mammalian differentiation processes.

overall_design: 5 transcription factors and rabbit-IgG in megakaryocytes.

first: Marloes

last: Tijssen

first: Ana

last: Cvejic

first: Rebecca

last: Hannah

first: Anagha

last: Joshi

first: Xiaonan

last: Wang

first: Dana

last: Bellissimo

first: Willem

middle: H

last: Ouwehand

first: Berthold

last: Gottgens


title: Human Large Airway Epithelial Cells from healthy never and current smoker and smokers with and without lung cancer

first: Avrum

last: Spira


title: Deep-sequencing of total RNA from manually dissected wild-type and kyp-2m/KYPp Arabidopsis embryos

city: Glarus

first: Marc

middle: William

last: Schmid

address: Hauptstrasse 34

institute: MWSchmid GmbH

summary: This dataset provide deep-profiling of the embryonic transcriptome of total RNA at an early developmental stage (2-to-4 cells stage) and at the globular stage in Arabidopsis. Embryos were derived from either a cross between a Landsberg erecta (Ler) maternal parent and a Columbia (Col0) paternal parent or a cross between a kyp-2 Ler maternal parent and a Columbia paternal parent. Embryos were manually dissected ensuring no contamination with maternal seed coat or endosperm.

overall_design: 6 samples: crosses between Ler and Col, or kyp-2 (Ler) and Col; Ler seed coat at 2-4cells embryo stage # SC_2.

first: Célia

last: Baroux

first: Michael

last: Raissig

first: Ueli

last: Grossniklaus

last: Wittig

last: Rosenstiel


title: Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough

status: Public on May 27 2011

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

type: Expression profiling by genome tiling array

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough


title: Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes

status: Public on May 31 2011

city: Cambridge

first: Kinyui Alice

last: LO

address: 77 Massachusetts Ave.

department: Biological Engineering

institute: MIT

summary: We use ChIP-seq to discover the genome-wide sites of acetylation of lysine 56 of the histone H3 (H3K56), which is a target of three histone modifying enzymes with known roles in diabetes and insulin resistance, in human adipocytes derived from mesenchymal stem cells. Surprisingly, we find that a very large fraction of genes show some level of acetylation on H3K56, but the highest levels of acetylation are associated with genes previously reported to be involved  in type 2 diabetes.  Using computational methods, we propose that the transcription factor E2F4 may be involved in recruiting histone modifying enzymes to these sites.  We confirm this prediction by measuring the binding of E2F4 using ChIP-seq. We also examine the binding of two other proteins using ChIP-Seq:  HSF-1 and C/EBPα .  HSF-1 is a master regulator of stress responses, and is a target of the same histone modifiers as H3K56.  We find a high degree of overlap between HSF-1 binding and H3K56 acetylation even in cells that are not stressed.  By contrast, C/EBPα , which is not known to be modified by these enzymes, shows much less overlap with the sites of H3K56 acetylation.   Our results represent the first mapping of the regulatory code of human adipocytes.

overall_design: Examination of H3K56 acetylation sites and E2F4,C/EBPα and HSF-1 binding sites in human adipocytes.

first: Kinyui

last: Lo

first: Ernest

last: Fraenkel


title: Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough (RNA-Seq)

summary: 5' RNASeq of mRNA from DvH in defined lactate/sulfate media (LS4D)

platform_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: One lane of sequence each for two different protocols applied to independently grown cells under similar conditions

first: Adam

last: Deutschbauer

first: Jennifer

last: Kuehl

middle: P

last: Arkin


title: Expression profile of 16C ovarian follicle cells

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: We use DSN normalized RNA-seq to transcriptionally profile FACS sorted 16C ovarian follicle cells. These data provide insights into the developmental control of gene expression programmed gene amplificaton.

overall_design: Follicle cells were isolated from whole ovaries by trypsinization and filtering and stained with Hoescht. 16C follicle cells were isolated by FACS sorting based on DNA content (Hoescht). RNA was extracted with TRIzol reagent and 100ng of total RNA and used to generate a total library. This library was then subjected to DSN normalization prior to Illumina based sequencing.

first: Jane

last: Kim

first: Jared

last: Nordman

first: Fang

last: Xie

first: Helena

last: Kashevsky

first: Thomas

last: Eng

first: Sharon

last: Li

first: David

last: MacAlpine

middle: L


title: Systematic bias in high-throughput sequencing data and its correction by BEADS

status: Public on May 25 2011

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

institute: University of Cambridge

summary: ChIP-seq and input sequence data used in the development and evaluation of the BEADS normalization method.

overall_design: Examination of ChIP and input sequence reads across the worm genome

first: Julie

last: Ahringer

first: Isabel

last: Latorre

first: Ming-Sin

last: Cheung


title: ORC2, RNAPII, and tetra-acetylated histone H4 ChIP-chip egg chambers and RNA-Seq 16C ovarian follicle cells


title: High-throughput sequencing of small RNAs from different developmental stages of tomato fruits

first: Simon

last: Moxon

summary: Comparison of endogenous small RNA profiles from different developmental stages of tomato fruits

overall_design: Size fractionated small RNA from total RNA extracts was ligated to adaptors, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

first: Runchun

last: Jing

first: Irina

last: Mohorianu

first: Frank

last: Schwach

first: Vincent

last: Moulton

first: Tamas

last: Dalmay