title: Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations

city: Singapore

first: Guoliang

address: 60 Biopolis Street, #02-01, Genome

department: Computational and Systems Biology

institute: Genome Institute of Singapore

summary: In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements. It is believed that their communication occurs within large discrete foci of aggregated RNA polymerases termed transcription factories in three-dimensional nuclear space. However, the dynamic nature of chromatin connectivity has not been characterized at the genome-wide level. Here, through a chromatin interaction analysis with paired-end tagging approach using an antibody that primarily recognizes the pre-initiation complexes of RNA polymerase II, we explore the transcriptional interactomes of three mouse cells of progressive lineage commitment, including pluripotent embryonic stem cells, neural stem cells and neurosphere stem/progenitor cells. Our global chromatin connectivity maps reveal approximately 40,000 long-range interactions, suggest precise enhancer?promoter associations and delineate cell-type-specific chromatin structures. Analysis of the complex regulatory repertoire shows that there are extensive colocalizations among promoters and distal-acting enhancers. Most of the enhancers associate with promoters located beyond their nearest active genes, indicating that the linear juxtaposition is not the only guiding principle driving enhancer target selection. Although promoter?enhancer interactions exhibit high cell-type specificity, promoters involved in interactions are found to be generally common and mostly active among different cells. Chromatin connectivity networks reveal that the pivotal genes of reprogramming functions are transcribed within physical proximity to each other in embryonic stem cells, linking chromatin architecture to coordinated gene expression. Our study sets the stage for the full-scale dissection of spatial and temporal genome structures and their roles in orchestrating development.

overall_design:
RNA polymerase II (RNAPII) guided chromatin interactions were discovered by Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing, in order to study genome-wise the enhancer-promoter interactions. Three cell lines, namely mouse embryonic stem cell E14, Neural stem cell NS5 and neuroshpere cells were grown under standard culture conditions and harvested at log phase. Harvested cells were cross-linked using 1% formaldehyde followed by neutralization with 0.2M glycine. Chromatin was isolated and subjected to ChIA-PET protocol as described in Fullwood et al, 2009. The ChIA-PET sequence reads were processed and analyzed using ChIA-PET Tool (Li et al, 2010)
Examine the distal transcriptional interactions in three murine cell lineages (RNA-Seq)

first: Yubo

last: Zhang

first: Chia-Lin

last: Wei


title: Identification of sex-biased genes in Drosophila using gonad RNAseq data

status: Public on Nov 04 2013

city: Sao Paulo

first: Maria

middle: D

last: Vibranovski

address: Rua do Matao, 277

department: Genetics and Evolutionary Biology

country: Brazil

institute: Universidade de Sao Paolo

type: Expression profiling by high throughput sequencing

summary:
Purpose: Accurate identification of sex-biased genes requires precise measurement of gene expression levels in gonads. This study is designed to provide such data for various Drosophila species to enhance studies of sex-biased gene expression and evolution across the genus.
Methods: Virgin flies were collected and aged 6-10 days before dissecting 2-3 replicates of testes or ovaries. Total RNA was extracted using the Arcturus® PicoPure® kit .  Illumina® TruSeq® RNA library kits were used to poly-A+ select and reverse-transcribe mRNA, shear cDNA into ~120 bp fragments, and produce libraries for 1x50 bp sequencing on an Illumina GAIIx or HiSeq2000. Illumina®’s Real Time Analysis v1.13 module processed images, called bases, and provided base qualities. Reads were mapped to the current reference genomes using Bowtie v2.1.0 (Langmead and Salzberg, 2012, Nat Meth) with default settings. Differentially expressed genes were detected using Cufflinks v 2.1.0 (Trapnell et al., 2010, Nat Biotech; default settings) or edgeR (Robinson et al., 2010, Bioinformatics; full-quantile GC-content normalization and full-quantile between-sample normalization). Genes were called differentially expressed at a Benjamini-Hochberg false discovery rate of 0.01.
Results: Thousands of male- and female-biased genes were detected for each species using both DE detection methods. These results provide a significant improvement in sensitivity of sex-biased gene detection relative to using whole-body RNA-sequencing data. These data provide a foundation for accurate identification of sex-biased genes throughout the Drosophila genus.

sample_organism:
Drosophila ananassae
Drosophila pseudoobscura
Drosophila yakuba

overall_design: Testis and ovary samples from Drosophila species were sequenced 1 x 50 bp in duplicate from 6-10 day old virgin, Wolbachia-free adult flies on an Illumina GAIIx or HiSeq2000.

first: Nicholas

middle: W

last: VanKuren


title: Porteresia transcriptome sequencing

status: Public on Nov 05 2013

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, we aim to present the complete transcriptome of Asian wild rice, Porteresia. We generated about 375 million high-quality reads for five different conditions (ranging from 65 to 90 million reads for each condition) using Illumina high-throughput sequencing GAII platform. We mapped the reads to Porteresia transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during conditions.

overall_design: We collected different tissue samples after various treatments (control, in water; salt450, in 450 mM sodium chloride solution; salt700, in 700 mM sodium chloride solution; submergence, submerged in water; salt+submergence, submerged in 450 mM sodium chloride solution) and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to Porteresia transcripts and reads per kilobase per million (RPKM) was calculated for each transcript in all the samples to measure their gene expression. Differential expression analysis was performed using DESeq software. The genes showing differential expression under various stress conditions were identified.

first: Garg

last: Rohini

first: Verma

last: Mohit

first: Agarwal

last: Shashank

first: Majee

last: Manoj

first: Jain

last: Mukesh


title: Integrated omics studies delineate the formation and dynamics of lipid droplets in Rhodococcus opacus PD630 for biofuel feedstock

city: Beijing

first: Jinhai

last: YU

address: Datun Road, NO. 15

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

summary:
Purpose: To delineate mechanisms underlying lipid storage in LDs, we compared the transcriptomes of cells cultivated under three lipid-accumulating conditions.
Methods: PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform. The sequence reads were mapped by using Bowtie followed by Cufflinks.
Results: Most genes were either expressed under all three conditions (6,759 genes) or under at least one condition (7,770 genes), but 1,177 genes were not expressed under any of these conditions. We observed a marked response 3 h after cells were transferred from NB to MSM; 56.99% of the genes were up-regulated and 30.32% were down-regulated, with 21.15% being up-regulated more than 2-fold and 9.36% being down-regulated more than 2-fold
Conclusions: Genes in category J (translation, ribosomal structure and biogenesis) were significantly up-regulated (p-value 5.05E-20, two-tailed Chi-square test), while genes in category K (transcription), G (carbohydrate transport and metabolism) and C (energy production and conversion) were down-regulated (p-values: 6.0E-07, 8.08E-06 and 4.56E-05, respectively, two-tailed Chi-square test). Increased expression of ribosomal proteins is consistent with number of genes (56.99%) up-regulated in the MSM3 treatment. This decrease in energy production and conversion is consistent with inhibition of cell division and lipid accumulation in MSM.

last: Yu

first: Yong

last: Chen

first: Hangxiao


title: H3K36me2_W.BG3.Solexa

status: Public on Nov 01 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
modENCODE_submission_6389
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina  NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown;  EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody H3K36me2 W (target is H3K36me2)

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: HOXC9-induced neuronal differentiation in human neuroblastoma BE(2)-C cells

status: Public on Nov 02 2013

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

country: USA

institute: Georgia Regents University

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

overall_design: Refer to individual Series


title: Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cells

city: Daejeon

first: Mirang

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: KRIBB(Korea Research Institute of Bioscience and Biotechnology

type: Methylation profiling by high throughput sequencing


title: Differential stress transcriptome landscape of historic and recently emerged hypervirulent strains of Clostridium difficile strains determined using RNA-seq

status: Public on Nov 06 2013

city: Brookings

first: Joy

last: Scaria

state: SD

department: Veterinary and Biomedical Sciences

institute: South Dakota State University

summary:
Purpose: To determine how divergent strains of C. difficile respond to environmental changes, the transcriptomes of two historic and two recently isolated hypervirulent strains were analyzed following nutrient shift and osmotic shock.

Methods: Following nutrient shift and osmotic shock, mRNA profile were determined using sequing of transcriptome in biological duplicates, using Illumina Hi-seq 2000.

Results: After applying the quality control steps,  for each sample, sequence reads were 90 nucleotides in length and the total number of reads per sample was ~ 26.6 million on average.  Expression of more than 90% CDS was detected under the three experimental conditions combined. About 20% of these genes were indentified to be differentially expressed at 1.5 fold or more.

Conclusions: Our results reveal that although C. difficile strains contain a large number of shared and strain specific genes, the majority of the differentially expressed genes were core genes.  We also detected a number of transcriptionally active regions that were not part of the primary genome annotation. Some of these are likely to be small regulatory RNAs.

overall_design: Differential stress transcriptomes of two historic (strain 630 and 196) and two recently emerged hypervirulent strains (stain R20291 and 32g58) of C. difficile was determined by deep sequencing, in duplicate, using Illumina Hi-Seq 2000.

first: Jenn-Wei

last: Chen

first: Mao

last: Chunhong

first: Yung-Fu

last: Chang


title: H2AV_9751.S2.GFP.RNAi.Solexa

first: DCC

last: modENCODE

summary:
modENCODE_submission_5596
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The goal of these experiments are to a) validate/confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome and b) evaluate their biological significance by assaying the impact of depletion on other proteins/marks. We are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, followed by Chromatin ImmunoPrecipitation (ChIP) assayed on genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H2AV 9751 (target is H2AV); dsRNA (RNAi_reagent) Fly_GFP_RNAi_2&oldid=76949

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

last: Shanower


title: Smc3_Q2580.D.mel 3rd Instar Larvae Nuclei.Solexa

summary:
modENCODE_submission_5568
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody Smc3 Q2580 (target is Smc3); Developmental Stage 3rd Instar Larvae

first: Greg

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

last: Pirrotta

last: Park


title: Genome-wide Profiling of NR2F2 (COUP-TFII) Binding in Human Endometrial Stromal Cells [ChIP-Seq]

city: Houston

first: Francesco

middle: J

last: DeMayo

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII; NR2F2) is an orphan nuclear receptor involved in cell-fate specification, organogenesis, angiogenesis and metabolism. Ablation of COUP-TFII in the mouse uterus causes infertility due to defects in embryo attachment and impaired uterine stromal cell decidualization. Although the function of COUP-TFII in uterine decidualization has been described in mice, its role in the human uterus remains unknown. To better elucidate the mechanisms with which COUP-TFII regulates target gene transcription, genome-wide COUP-TFII binding sites in human endometrial stromal cells (HESC) treated with deciduogenic hormones were identified using ChIP-seq. A total of 16,298 intervals (binding regions) for COUP-TFII were identified compared with the input in HESC chromatin with a very low false discovery rate (0.17%) using a stringent cutoff of p =1x10-10. Distribution of intervals showed that more than half (58.6%) of the COUP-TFII binding sites are located within 10 kb of gene boundaries. 7.5% of total intervals reside within the 10 kb promoter region. A total of 6,077 unique genes were identified to have COUP-TFII binding sites within 10 kb of their gene boundaries.

overall_design: Examination of NR2F2 binding in pooled primary human endometrial stromal cells from 6 healthy women upon decidualization with a hormone cocktail of cAMP, E2 and medroxyprogesterone acetate.

first: Xilong

last: Li

last: Large

first: Chad

last: Creighton

first: Rainer

middle: B

last: Lanz

first: Jae-Wook

last: Jeong

first: Steven

middle: L

last: Young

first: Bruce

middle: A

last: Lessey

first: Wilder

last: Palomino

first: Sophia

middle: Y

last: Tsai


title: POF (MO 459).D.mel 3rd Instar Larvae Nuclei.Solexa

first: DCC

last: modENCODE

summary:
modENCODE_submission_5121
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody POF (MO 459) (target is POF); Developmental Stage 3rd Instar Larvae

last: Karpen

last: Elgin

last: Gortchakov

first: Vincenzo

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: H2AV_9751.S2.H2AV_RNAi.Solexa

summary:
modENCODE_submission_5595
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The goal of these experiments are to a) validate/confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome and b) evaluate their biological significance by assaying the impact of depletion on other proteins/marks. We are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, followed by Chromatin ImmunoPrecipitation (ChIP) assayed on genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H2AV 9751 (target is H2AV); dsRNA (RNAi_reagent) CG5499_RNAi_2&oldid=76948

first: Gary

first: Sarah

first: Andrey

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

last: Pirrotta

last: Park


title: Accelerated growth in the absence of DNA replication origins

status: Public on Nov 03 2013

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

summary: DNA replication initiates at defined sites called origins, which serve as binding sites for initiator proteins that recruit the replicative machinery. Origins differ in number and structure across the three domains of life1 and their properties determine the dynamics of chromosome replication. Bacteria and some archaea replicate from single origins, whilst most archaea and all eukaryotes replicate using multiple origins. Initiation mechanisms that rely on homologous recombination operate in some viruses. Here we show that such mechanisms also operate in archaea. We have used deep sequencing to study replication in Haloferax volcanii. Four chromosomal origins of differing activity were identified. Deletion of individual origins resulted in perturbed replication dynamics and reduced growth. However, a strain lacking all origins has no apparent defects and grows significantly faster than wild-type. Origin-less cells initiate replication at dispersed sites rather than at discrete origins and have an absolute requirement for the recombinase RadA, unlike strains lacking individual origins. Our results demonstrate that homologous recombination alone can efficiently initiate the replication of an entire cellular genome. This raises the question of what purpose replication origins serve and why they have evolved.

overall_design: Measurement of replication dynamics (marker frequency analysis; MFA) for Haloferax volcanii strains, including wild-type, the laboratory strain, individual and combinations of replication origin deletions.

first: Michelle

last: Hawkins

first: Thorsten

last: Allers

first: Sunir

last: Malla

first: Martin

last: Blythe


title: JMJD2A-KDM4A_Q2541.D.mel 3rd Instar Larvae Nuclei.Solexa

first: DCC

last: modENCODE

summary:
modENCODE_submission_5115
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody JMJD2A-KDM4A Q2541 (target is JMJD2A/KDM4A); Developmental Stage 3rd Instar Larvae

last: Karpen

last: Elgin

last: Gortchakov

first: Vincenzo

first: Aki


title: Genome-scale DNA methylation maps of Zebrafish Muller glia during retina regeneration

city: Ann Arbor

first: Ana

middle: Rodrigues

last: Grant

state: MI

address: 100 Washtenaw Avenue

department: Computational Medicine & Bioinformatics

institute: University of Michigan

summary: Upon retinal injury, zebrafish Müller glia (MG) transition from a quiescent supportive cell to a progenitor cell (MGPC). This event is accompanied by the induction of key transcription and pluripotency factors. Because somatic cell reprogramming during iPSC generation is accompanied by changes in DNA methylation, especially in pluripotency factor gene promoters, we were interested in determining if DNA methylation changes also underlie MG reprogramming following retinal injury. Consistent with this idea, we found that genes encoding components of the DNA methylation/demethylation machinery were induced in MGPCs and that manipulating MGPC DNA methylation with 5-aza-2’-deoxycytidine altered their properties. A comprehensive analysis of the DNA methylation landscape as MG reprogram to MGPCs revealed that demethylation predominates at early times, while levels of de novo methylation increase at later times. We found that these changes in DNA methylation were largely independent of Apobec2 protein expression. A correlation between promoter DNA demethylation and injury-dependent gene induction was noted. In contrast to iPSC formation, we found that pluripotency factor gene promoters were already hypomethylated in quiescent MG and remained unchanged in MGPCs. Interestingly, these pluripotency factor promoters were also found to be hypomethylated in mouse MG.  Our data identify a dynamic DNA methylation landscape as zebrafish MG transition to a MGPC and suggest that DNA methylation changes will complement other regulatory mechanisms to ensure gene expression programs controlling MG reprogramming are appropriately activated during retina regeneration.

overall_design: Reduced representation bisulfite sequencing (MspI,~40-220bp size fraction) of zebrafish MG before and after injury. This dataset includes 4 replicated samples:  The MG samples report the genomic methylation of a quiescent state. The 4dpi MGPC sampes report the methylation of a dedifferentiated, proliferating progenitor.  The 2dpi morpholino samples report the genomic methylation of a dedifferentiated MGPC following a conrtol or Apobec2a,2b knockdown.

first: Curtis

last: Powell

middle: R

first: Eli

last: Cornblath

first: Daniel

last: Goldman


title: Solexa.BEAF-HB.14-16 hr OR embryo

summary:
modENCODE_submission_3954
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody BEAF-HB (target is BEAF32A and BEAF42B); Developmental Stage Embryo 14-16hr OR

first: Gary

first: Sarah

first: Andrey

last: Shanower

last: Tolstorukov

last: Kharchenko

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: Snyder_Pmex-5_HPL-2_YL472_yAd

summary:
modENCODE_submission_4641
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: YL472(official name : YL472 genotype : unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : It is actually extrachromosomal line by bombardment. made_by : Michelle Kudron in Reinke lab ); Developmental Stage: Young adult; Genotype: unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Young adult; Target gene hpl-2; Strain YL472(official name : YL472 genotype : unc-119(ed3) III; vrEx66 [pMEX-5::HPL-2:GFP:FLAG::HPL-2 3?UTR genotype : unc-119 (+)]) outcross : 0 mutagen : None tags : GFP::3xFlag description : It is actually extrachromosomal line by bombardment. made_by : Michelle Kudron in Reinke lab ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Snyder_lin-35_n745_EFL-1_Ab_L1

first: DCC

last: modENCODE

summary:
modENCODE_submission_4640
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: MT10430(official name : MT10430 genotype : lin-35(n745) I. ); Developmental Stage: L1 26dC; Genotype: lin-35(n745) I.; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L1 26dC; Target gene efl-1; Strain MT10430(official name : MT10430 genotype : lin-35(n745) I. ); temp (temperature) 20 degree celsius


title: Transcriptome sequencing of porcine hypothalamic samples

city: Madrid

first: Dafne

last: Pérez Montarelo

state: Madrid

address: Crta. de la Coruña Km 7.5

department: Animals Genetics

country: Spain

institute: INIA

summary:
Purpose: Identification of genes regulating growth and fatness traits in pig.
Methods: Hypothalamic transcriptome analysis through RNA-seq and differential expression analysis of divergent pigs for growth and fatness traits.
Results: Characterization of the transcripts expressed in the porcine hypothalamus and identification of differentially expressed genes, some of them located within previously described QTL regions.
Conclusions: Characterization of porcine hypothalamic transcriptome and identification of relevant genes and transcription factors related to the traits of interest.

overall_design: Transcriptome sequencing of 10 hypothamic samples of two groups of divergent pigs for growth and fatness (five per group).

last: Pérez-Montarelo

first: Ana

middle: I

last: Fernández Ávila


title: Global and local perturbation of the tomato microRNA pathway by a trans-activated DICER-LIKE 1 mutant

city: Bet Dagan

first: Tzahi

last: Arazi

state: ISRAEL

address: Institute of Plant Sciences, ARO the Volcani Center

department: Institute of Plant Sciences

country: Israel

institute: ARO - Volcani Center

type: Non-coding RNA profiling by high throughput sequencing

summary: DICER-like 1 (DCL1) is a major player in micro RNA (miRNA) biogenesis and accordingly, its few known loss-of-function mutants are either lethal or display arrested seedling development. Consequently, generation of dcl1 mutants by reverse genetics and functional analysis of DCL1 in late-developing organs are challenging. Here, these challenges were resolved through the unique use of trans-activated RNA interference. Global, as well as organ-specific tomato DCL1 (SlDCL1) silencing was induced by crossing the generated responder line (OP:SlDCL1IR) with the appropriate driver line. Constitutive trans-activation knocked down SlDCL1 levels by ~95%, resulting in severe abnormalities including post-germination growth arrest accompanied by decreased miRNA and 21-nucleotide small RNA levels, but prominently elevated levels of 22- nucleotide small RNAs. The elevation in the 22- nucleotide small RNAs was correlated with specific upregulation of SlDCL2b and SlDCL2d, which are likely involved in their biogenesis. Leaf- and flower-specific OP:SlDCL1IR trans-activation inhibited blade outgrowth, induced premature bud senescence and produced pale petals, respectively, emphasizing the importance of SlDCL1-dependent small RNAs in these processes. Together, our results establish OP:SlDCL1IR as an efficient tool for analyzing processes regulated by SlDCL1-mediated gene regulation in tomato.

overall_design: Examination of small RNA populations in control (35S:LhG4) and SlDCL1 silenced seedlings (35S>>SlDCL1IR) 2 biological replicates each

first: T

first: M

last: Kravchik

first: R

last: Sunkar


title: Characterization of chromosomal architecture in Arabidopsis thaliana by Chromosome Conformation Capture

city: Zurich

first: Stefan

last: Grob

address: Zollikerstrasse 107

department: Institute of Plant Biology

country: Switzerland

institute: University of Zurich

summary: Background: The packaging of long chromatin fibres in the nucleus poses a major challenge, as it must fulfil both physical and functional requirements. Until recently, insight into the chromosomal architecture of plants was mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalised description of nuclear organization.  Results: Employing circular chromosome conformation capture (4C), this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organisation of chromosomes is reflected in the genome-wide interactome. In addition, we studied the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 (hk4s) maintained a pericentromere-like interaction profile and interactome despite its euchromatic surrounding.  Conclusion: Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria:   (i) heterochromatin and euchromatin represent two distinct interactomes, (ii) interactions between chromosomes correlates with the linear position on the chromosome arm, and (iii) distal chromosome regions have a higher potential to interact with other chromosomes.

overall_design: This study includes circular chromosome conformation capture (4C) sequencing information of 13 samples, present in two batches, each present in duplicates (A and B). The individual 4C sequencing information can be retrieved by the 4C primer sequence, given in the 4C primer information file.


title: ChIP-seq analysis of genome wide Brg1 binding in mouse primary keratinocytes

city: Bradford

first: Michael Y

last: Fessing

address: Richmond Road

institute: University of Bradford

summary: We analyzed Brg1 binding genomeiwide in freshly isolated newborn mouse epidermal keratinocytes using ChIP-seq technology

overall_design: Mouse epidermal keratinocytes were isolated form the newborn C57Bl6 mice and Brg1 binding in their chromatin was analyzed using ChIP-seq technology on Hi-Seq 2500 machine

first: Andrei

middle: N

last: Mardaryev

first: Joanne

last: Yarker

first: Krzysztof

last: Poterlowicz

first: Andrey

last: Sharov

first: Vladimir

last: Botchkarev

first: Michael


title: High-resolution chromosomal maps of Xist RNA reveal a two-step spreading mechanism during X-inactivation

city: Farmington

middle: F

last: Pinter

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health

summary: The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes. During XCI, Xist coats the future inactive X (Xi) and recruits Polycomb Repressive Complex 2 (PRC2) to the X-inactivation center (Xic). Currently unclear is how Xist spreads silencing on a 150 Mb scale. Here we generate high-resolution maps of Xist binding across a developmental time course using CHART-seq. In female cells undergoing XCI de novo, Xist follows a two-step mechanism in which it initially targets gene-rich islands before spreading to intervening gene-poor domains. Xist is depleted from genes that escape XCI but frequently concentrates near escapee boundaries. Xist binding was linearly proportional to PRC2 density and H3 lysine 27 trimethylation (H3K27me3), suggesting co-migration of Xist and PRC2. Interestingly, when the Xi is acutely stripped of Xist in post-XCI cells, Xist recovers quickly within both gene-rich and -poor domains on a time scale of hours instead of days, suggesting a previously primed Xi chromatin state. We conclude that Xist spreading takes on distinct stage-specific forms: During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and -poor regions.

overall_design:
Capture hybridization analysis of RNA targets (CHART) and input samples of (differentiating) mouse embryonic stem (ES) cells and immortalized mouse embryonic fibroblasts (MEF) using paired-end 75 nt reads on Illumina HiSeq2500, with 2 replicates per sample (# of samples). RNA-seq of the same cell lines with 50 nt reads on Illumina HiSeq2000, with 2 replicates per sample (2 samples, 4 datasets total).

CHIP-seq: Data from GSE36905 was aligned and processed as CHART-seq samples. Resulting coverage tracks (EZH2/K27me3) are linked directly to GSE48649 (bedGraphs linked below).

first: Matthew

last: Simon

first: Rui

last: Fang

first: Kavitha

last: Sarma

last: Rutenberg-Schoenberg

first: Sarah

middle: K

last: Bowman

first: Barry

last: Kesner

first: Verena

last: Maier

first: Robert

middle: E

last: Kingston

first: Jeannie

middle: T

last: Lee


title: Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cells (Methylation BeadChip)

first: Mirang

last: Kim

summary: DNA methylation and hydroxymethylation have been implicated in normal development and differentiation, but our knowledge about the genome-wide distribution of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) during cellular differentiation remains limited. Using in vitro model system of gradual differentiation of human embryonic stem (hES) cells into ventral midbrain-type neural precursor (NP) cells and terminally into dopamine (DA) neurons, we explored changes in 5mC or 5hmC patterns during lineage commitment. We used three techniques, 450K DNA methylation array, MBD-seq, and hMeDIP-seq, and found combination of these methods can provide comprehensive information on the genome-wide 5mC or 5hmC patterns. We observed dramatic changes of 5mC patterns during differentiation of hES cells into NP cells. Although genome-wide 5hmC distribution was more stable than 5mC, coding exons, CpG islands and shores showed dynamic 5hmC patterns during differentiation. In addition to the role of DNA methylation as a mechanism to initiating gene silencing, we also found DNA methylation as a locking system to maintain gene silencing. More than 1,000 genes including mesoderm development related genes acquired promoter methylation during neuronal differentiation even though they were already silenced in hES cells. Finally, we found that activated genes lost 5mC in transcription start site (TSS) but acquired 5hmC around TSS and gene body during differentiation. Our findings may provide clues for elucidating the molecular mechanisms underlying lineage specific differentiation of pluripotent stem cells during human embryonic development.

overall_design: Examination of genome-wide DNA methylation in 3 cell types (human embryonic stem, neural precursor, and dopamine neuron cells)

first: Young-Kyu

last: Park

first: Tae-Wook

last: Kang

first: Sang-Hun

first: Yong-Hee

last: Rhee

first: Jong-Lyul

first: Hee

first: Seon-Young

first: Daeyoup

first: Doheon

first: Yong

middle: S


title: Polysome-associated mRNA profiling of cancer cells in response to CXCL12 and IGF1

city: New York

first: Xin

last: Jin

state: New York

address: 417 East 68th Street

department: Cancer Biology and Genetics

institute: Memorial Sloan-Kettering Cancer Center

summary: CXCL12 and IGF1 are key secreting molecules produced by cancer-associated fibroblasts in breast cancer. These factors promote the survival of disseminated cancer cells in the bone marrow. To assess the combined responses elicited by CXCL12 and IGF1, we examined the translating transcriptome of cancer cells in response to these two factors by Translating Ribosome Affinity Purification (TRAP)-RNAseq.

overall_design: MDA-MB-231 cells were engineered to express an EGFP-tagged version of ribosomal protein L10a. This allows the retrieval of polysome-associated mRNA by anti-GFP pull down (TRAP) and profiling the translating transcriptome by RNAseq. EGFP-L10a+ cancer cells were serum starved (0.2% serum) for 24 hours, and then treated with CXCL12 (30ng/mL) + IGF1 (10ng/mL) or CXCL12 (300ng/mL) + IGF1 (100ng/mL) for 6hrs. Two biological replicates were profiled for each condition.

first: Xiang

middle: H

last: Zhang

first: Joan

last: Massague


title: HOXC9-induced neuronal differentiation in human neuroblastoma BE(2)-C cells [ChIP-seq analysis]

first: Justin

last: Choi

summary: Cell differentiation is an essential process of normal development by which a stem cell or progenitor cell becomes a post-mitotic, specialized cell with unique morphology and function. Also, it has long been recognized that differentiation is associated with a marked reduction in DNA damage response at the global level. The molecular basis for the coordination between cell cycle exit, acquirement of specialized structure and function, and attenuation of DNA damage response during differentiation is not well understood. We have conducted a genome-wide analysis of the HOXC9-induced neuronal differentiation program in human neuroblastoma cells. Gene expression profiling reveals that HOXC9-induced differentiation is associated with transcriptional regulation of 2,395 genes, which is characterized by global upregulation of neuronal genes and downregulation of cell cycle and DNA repair genes. Remarkably, genome-wide mapping demonstrates that HOXC9 occupies 40% of these genes, including a large number of genes involved in neuronal differentiation, cell cycle progression and DNA damage response. These findings suggest that HOXC9 directly activates and represses the transcription of distinct sets of genes to coordinate the cellular events characteristic of neuronal differentiation.

overall_design: Two independent preparations of BE(2)-C/Tet-Off/Myc-HOXC9 cells cultured in the absence of doxycycline for 6 days were used for chromatin immunoprecipitation (ChIP) against Myc-tagged HOXC9 and massively parallel sequencing by Illumina Genome Analyzer IIx.

first: Han-Fei

last: Ding

first: Jane

first: Jeong-Hyeon


title: Translating transcriptome of cancer cells in situ in mesenchymal-rich tumor microenvironment

summary: A mesenchymal rich stroma such as cancer-associated fibroblasts (CAFs) in breast tumors favors the selection of cancer clones with enhanced bone metastatic ability. To determine the cancer cell transcriptomic response to the mesenchymal stroma, we supplemented experimental mammary tumours with or without exogenous mesenchymal cells. We used bone marrow-derived human mesenchymal stem cells (MSCs) as a source of mesenchymal stroma, as MSCs have been shown to undergo CAF-like differentiation. We engineered the cancer cells to express an EGFP-tagged version of ribosomal protein L10a (EGFP-L10a). This allows the retrieval of cancer cell specific transcripts rapidly from whole tumor lysates by translating ribosome affinity purification (TRAP) and direct profiling of cancer cell gene expression patterns when they are in situ.

overall_design: EGFP-10a+ MDA-MB-231 cells were orthotopically injected into the mammary fat pad with or without 1:1 ratio of MSCs. The mammary tumors were retrieved for TRAP-RNAseq profiling after 3 weeks.


title: Genome-wide localization of NF-E2 p45 in mouse primary megakaryocytes.

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Center for Radioisotope Science

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: ChIP-seq assay was performed with anti-p45 antibody using in vitro cultured primary megakaryocytes to identify direct p45 target genes in megakaryocytes.  This analysis revealed genes that regulate platelet function, which were not known previously to be p45-regulated.

overall_design: ChIP was performed using a day-3 primary culture of megakaryocytes from E13.5 fetal livers of wild-type mice with an anti-p45 antibody.

first: Rie

last: Fujita

first: Satoshi

last: Fujii

first: Akinori

last: Sarai

first: Hiroyuki

last: Aburatani

first: Emery

last: Bresnick

first: Masayuki

last: Yamamoto


title: Methylomic analysis identifies the involvement of migration and adhesion genes in the ageing of primary haematopoietic stem cells

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

institute: UCL Cancer Institute

summary: we utilize Nano-MeDIP-seq for the analysis of the LT-HSC methylome and, for the first time, simultaneously interrogate the methylome and transcriptome of a homogeneous population of primary murine HSCs, in order to define the underlying causes of changes in HSC functionality during normal ageing.

overall_design: We isolated and phenotyped primary LT-HSCs from young, middle-aged and old mice and subjected them to comprehensive methylome (MeDIP-seq) and transcriptome (RNA-seq) analysis.

first: Oluwatosin

last: Taiwo

first: Warren

last: Emmett

first: Tiffany

last: Morris

first: Dominique

last: Bonnet

first: Tomas

last: Adejumo

first: Daniel

last: Pearce

first: Stephan

last: Beck


title: Deep sequencing of HetR-bound DNA reveals novel HetR targets in Anabaena sp. strain PCC 7120

status: Public on Oct 31 2013

city: La Jolla

first: James

last: Golden

state: CA

department: Biology

institute: UCSD

summary: We employed chromatin pull-down and deep sequencing to globally identify HetR DNA targets in vivo at 6 hours after fixed-nitrogen deprivation. We identified novel DNA binding targets of tagged HetR-6xHis and defined a consensus HetR binding site from these HetR target sequences.

overall_design: Chromatin pull down of hetR mutant strain UHM103 carrying pAM4375, which expresses HetR-6xHis, and a wild-type control. One dataset was collected.

first: Britt

last: Flaherty


title: Transcriptomes of isolated rice gametes characterized by deep sequencing:  Evidence for distinct sex-dependent chromatin and epigenetic states before fertilization

city: Davis

first: Venkatesan

last: Sundaresan

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

summary: The formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes.  In flowering plants, the embryo sac embedded within the ovule contains the egg cell, while the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. We isolated living egg cells, sperm cells, and pollen vegetative cells from rice, and identified transcripts for ~36,000 genes by deep sequencing.  The three transcriptomes are highly divergent, with about three quarters of those genes differentially expressed in the different cell types.  Distinctive expression profiles were observed for genes involved in chromatin conformation, including an unexpected expression in the sperm cell of genes associated with active chromatin.  Furthermore, both the sperm cell and the pollen vegetative cell were deficient in expression of key RNAi components. Differences in gene expression were also observed for genes for hormonal signaling and cell cycle regulation. The egg cell and sperm cell transcriptomes reveal major differences in gene expression to be resolved in the zygote, including pathways affecting chromatin configuration, hormones and cell cycle.  The sex-specific differences in expression of RNAi components suggest that epigenetic silencing in the zygote might act predominantly through female-dependent pathways.  More generally, this study provides a detailed gene expression landscape for flowering plant gametes, enabling the identification of specific gametic functions and their contributions to zygote and seed development.

overall_design: The gene expression profiles of the three gametic cells, egg cell (EC), sperm cell (Sp) and vegetative cell (Ve) were compared via RNA-seq using three biological replicates for each. Differential expression (DE) analysis was performed using edgeR and the resulting DE genes were assessed for Gene Ontology term enrichment.

first: Sarah

last: Anderson

first: Cameron

last: Johnson

last: Jones

first: Liza

last: Conrad

first: Xiaoping

last: Gou

first: Scott

middle: D

last: Russell


title: Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Metazoan gene expression is often regulated after the recruitment of RNA polymerase II (Pol II) to promoters, through the controlled release of promoter-proximally paused Pol II into productive RNA synthesis. Despite the prevalence of paused Pol II, very little is known about the dynamics of these early elongation complexes or the fate of short transcription start site-associated (tss) RNAs they produce. Here, we demonstrate that paused elongation complexes can be remarkably stable, with half-lives exceeding 15 minutes at genes with inefficient pause release. Promoter-proximal termination by Pol II is infrequent and released tssRNAs are targeted for rapid degradation. Further, we provide evidence that the predominant tssRNA species observed are nascent RNAs held within early elongation complexes. We propose that stable pausing of polymerase provides a temporal window of opportunity for recruitment of factors to modulate gene expression and that the nascent tssRNA represents an appealing target for these interactions.

overall_design: This submission includes 13 raw data files. Four samples (chromatin, soluble, mock-treated, and Rrp40-depleted) are represented by two biological replicate raw data files, while five samples (cells, DMSO, FP, mock-treated + FP, and Rrp-40depleted + FP) are represented by single raw data files.

first: Telmo

last: Henriques

last: Gilchrist

first: Sergei

last: Nechaev

first: Michael

last: Bern

first: Ginger

last: Muse

first: Adam

last: Burkholder

first: David

last: Fargo


title: Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells (RNA-seq)

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary:
PRDM proteins belong to the SET domain protein family, which is involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcriptional regulation remain to be delineated.
In this study, we find that Prdm5 is highly expressed in mouse embryonic stem (mES) cells and exploit this cellular system to characterize molecular functions of Prdm5. By combining proteomics and next-generation sequencing technologies, we identify Prdm5 interaction partners and genomic occupancy.
We demonstrate that although Prdm5 is dispensable for mES cell maintenance, it directly targets genomic regions involved in early embryonic development and affects the expression of a subset of developmental regulators during cell differentiation.
Importantly, Prdm5 interacts with Ctcf, cohesin, and TFIIIC and cooccupies genomic loci. In summary, our data indicate how Prdm5 modulates transcription by interacting with factors involved in genome organization in mouse embryonic stem cells.

overall_design: For each condition (ATRA-induced differentiation model and LIF cytokine deprivation) three replicate are available for both Prdm5 wt mES cells and Prdm5 KO mES cells, for a total of 12 samples

first: Giorgio

middle: G

last: Galli

first: Matteo

last: Carrara

first: Chiara

last: Francavilla

first: Kristian

last: de Lichtenberg

first: Jesper

middle: V

last: Olsen

first: Anders

last: Lund


title: Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells

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

overall_design: Refer to individual Series


title: Heterochronic meiotic misexpression in an interspecific yeast hybrid

city: Durham

first: Devjanee

last: Swain Lenz

state: NC

address: 130 Bioscience Drive

institute: Duke University

summary: Changes in gene regulation rapidly accumulate between species and may contribute to reproductive isolation through misexpression of genes in interspecific hybrids. Hybrid misexpression, defined by expression levels outside the range of both parental species, is thought to be a result of cis- and trans-acting regulatory changes that interact in the hybrid, or arise from changes in the relative abundance of various tissues or cell types due to defects in developmental. Here, we show that misexpressed genes in a sterile interspecific Saccharomyces yeast hybrid result from a heterochronic shift in the timing of the normal meiotic gene expression program. By tracking nuclear divisions, we find that S. cerevisiae initiates meiosis earlier than its closest known relative, S. paradoxus, yet both species complete meiosis at the same time. Although the hybrid up- and down-regulates genes in a similar manner to both parents, the hybrid meiotic program occurs earlier than both parents. The timing shift results in a heterochronic pattern of misexpression throughout meiosis I and the beginning of meiosis II. Coincident with the timing of misexpression, we find an increase in the relative abundance of opposing cis and trans-acting changes and compensatory changes, as well as a transition from predominantly trans-acting to cis-acting expression divergence over the course of meiosis. However, misexpression does not appear to be a direct consequence of cis- and trans-acting regulatory divergence. Our results demonstrate that hybrid misexpression in yeast results from a heterochronic shift in the meiotic gene expression program.

sample_organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

overall_design: We analyzed three biological replicates of the parental yeast strains, S. cerevisiae and S. paradoxus, and four replicates of their hybrid over four developmental time points.  Two hybrid replicates contain MATa from S. cerevisiae and MATalpha from S. paradoxus.  The other two hybrid replicates are reciprocal crosses.  The developmental time points are T0, which serves as a control, and is the moment cells enter sporulation media.  M1 is the beginning of meiosis I.  M1/M2 is the overlap of the end of meiosis I and the beginning of meiosis II.  M2 is the end of meiosis II.

first: Linda

last: Riles

first: Justin

middle: C

last: Fay


title: Changes in the expression of miR-381 and miR-495 are inversely associated with the expression of the MDR1 gene and development of multi-drug resistance

status: Public on Oct 29 2013

city: Canberra

first: Stephen

middle: John

last: Ohms

state: Australian Capital Territory

address: Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

summary: Multidrug resistance (MDR) frequently develops in cancer patients exposed to chemotherapeutic agents and is usually brought about by over-expression of P-glycoprotein (P-gp) which acts as a drug efflux pump. MiRNAome profiling using next-generation sequencing identified differentially expressed microRNAs (miRs) between parental K562 cells and MDR K562 cells (K562/ADM) induced by chronic adriamycin treatment.

overall_design: MiRNAome profiling in untreated K562 cells and K562 cells exposed to long-term adriamycin treatment

first: Yan

last: Xu

middle: J

first: Zhen

last: Li

first: Qiao

last: Wang

first: Guangming

last: Gong

first: Yiqiao

last: Hu

first: Zhiyong

last: Mao

first: M

last: Shannon

first: Jun

last: Fan


title: Zfp322a regulates mouse ES cell pluripotency and enhances reprogramming efficiency [ChIP-Seq]

city: Singapore

first: Qiang

last: Wu

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: Embryonic stem (ES) cells derived from the inner cell mass (ICM) of blastocysts are characterised by their ability to self-renew and their potential to differentiate into many different cell types. Recent studies have shown that zinc finger proteins are crucial for maintaining pluripotent ES cells. Mouse zinc finger protein 322a (Zfp322a) is expressed in the ICM of early mouse embryos. However, little is known regarding the role of Zfp322a in the pluripotentcy maintenance of ES cells. Here, we report that Zfp322a is required for ES cell identity since depletion of Zfp322a directs ES cells towards differentiation. Chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays revealed that Zfp322a binds to Oct4 and Nanog promoters and regulates their transcription. These data along with the results obtained from our ChIP-seq experiment showed that Zfp322a is an essential component of the ES cell transcription regulatory network. Targets which are directly regulated by Zfp322a were identified by correlating the gene expression profile of Zfp322a RNAi-treated ES cells with the ChIP-seq results. These experiments revealed that Zfp322a inhibits ES cell differentiation by suppressing MAPK pathway. Additionally, Zfp322a is found to be a novel reprogramming factor that can replace Sox2 in the classical Yamanaka’s factors (OSKM). It can be even used in combination with Yamanaka’s factors and that addition leads to a higher reprogramming efficiency and to acceleration of the onset of the reprogramming process. Together, our results demonstrate that Zfp322a is a novel essential component of the transcription factor network which maintains the identity of ES cells.

overall_design: E14 mES cells were immunoprecipitated with Zfp322a antibody or IgG from rabbit.

first: Hui

last: Ma

first: Hui-Min

last: Ng

first: Xiuwen

last: Teh

first: Hu

first: Yun-Hwa

last: Lee

first: Yew-Mei

last: Chong

first: Yuin-Han

last: Loh

first: James

last: Collins

first: Bo

last: Feng

first: Henry

last: Yang


title: Effects of MBD3 depletion on nucleosome occupancy in MCF-7 cells

city: RTP

first: Takashi

last: Shimbo

address: 111 TW Alexander Dr.

institute: NIH/NIEHS

summary: We and others have identified that MBD3/NuRD localizes at active promoters and enhancers, suggesting an active role of NuRD at open chromatin region. Because NuRD includes nucleosome remodelers, CHD3 and CHD4, we hypothesized that NuRD regulates nucleosome organization at open chromatin region. To test this idea, we performed micrococcal nuclease digestion followed by massively parallel sequencing (MNase-seq) in MBD3 knockdowned MCF-7 cells. We observed the decrease of nucleosome occupancy at promoters and enhancers in MBD3 knockdowned cells. Our results suggest a regulatory role of MBD3/NuRD at open chromatin region.

overall_design: Mapped nucleosome positioning in control (shLuc) and MBD3 knockdowned MCF-7 cells, in duplicate.

first: Sara

middle: A

last: Grimm

first: Paul

last: Wade


title: Zfp322a regulates mouse ES cell pluripotency and enhances reprogramming efficiency


title: Deep sequencing of the porcine endometrial transcriptome on day 12 of pregnancy

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

summary: The porcine conceptus undergoes rapid differentiation and expansion of its trophoblastic membranes between Days 11 and 12 of gestation. Concomitant with trophoblast elongation, production of conceptus estrogen, the porcine embryonic pregnancy recognition signal increases. Conceptus attachment to the uterine surface epithelium starts after Day 13 initiating epitheliochorial placentation. To analyze the transcriptome changes in the endometrium in the course of maternal recognition of pregnancy (MRP), deep sequencing of endometrial RNA samples of Day 12 pregnant animals (n=4) and corresponding non-pregnant controls (n=4) was performed using Illumina RNA-Seq. Between 30 and 35 million sequence reads per sample were produced and mapped to the porcine genome (Sscrofa10.2). Analysis of read counts revealed 2,593 differentially expressed genes (DEG). Expression of selected genes was validated by the use of quantitative real-time RT-PCR. Bioinformatics analysis identified several functional terms specifically overrepresented for up-regulated or down-regulated genes. Comparison of the RNA-Seq data from Days 12 and 14 of pregnancy was performed at the level of all expressed genes, of the DEG, and at the level of functional categories. This revealed specific gene expression patterns, reflecting the different functions of the endometrium during these stages, i.e. recognition of pregnancy and preparation for conceptus attachment. Genes related to mitosis, immune response, epithelial cell differentiation and development, proteolysis, and prostaglandin signaling and metabolism are discussed in detail. In conclusion, this study identified comprehensive transcriptome changes in porcine endometrium associated with MRP and initiation of implantation and a number of genes and pathways potentially involved in regulation of these processes.

overall_design: In total, 8 samples were analyzed, 4 biological replicates for pregnant animals (samples from 4 different animals) and 4 biological replicates for cyclic controls (samples from 4 different animals)

first: Anastazia

last: Samborski

first: Alexander

last: Graf

last: Krebs

first: Barbara

last: Kessler

first: Susanne

last: Ulbrich


title: Dynamic transcriptomes during human erythroid differentiation and development

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

summary: To explore the mechanisms controlling erythroid differentiation and development in human, we analyzed the genome-wide transcription dynamics that occurs during the differentiation of HESCs into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. Undifferentiated HESCs as well as erythroid cells at three developmental stages-ESER (embryonic stage), FLER (fetal stage) and PBER (adult stage)-were analyzed. Our findings revealed that the number of expressed genes decreased during the differentiation, while the total expression intensity increased. At the 3 transitions (HESC-ESER, ESER-FLER and FLER-PBER), differential expression of many types of genes was observed at every transition. These differentially expressed genes were involved in maintaining the pluripotency of stem cells, early erythroid specification, rapid cell growth and enucleation potential. In addition, differentially expressed genes were found to constitute networks and central nodes at each transition. Clusters of genes in some chromosomal regions switched between expression and silence. We also discovered that differentially expressed genes constituted networks and central nodes of them in each transition. Our studies provide a fundamental basis for further investigation of erythroid differentiation and development.

overall_design: Compare the transcriptome of embryonic stem cells and three erythroid cell types at different developmental stages

first: Songnian

last: Hu

first: Xiangdong

last: Fang


title: High-resolution mapping of the spatial organization of Caulobacter crescentus chromosome by chromosome conformation capture in conjunction with next-generation sequencing (Hi-C)

status: Public on Oct 30 2013

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

summary: Chromosomes must be highly compacted and organized within cells, but how this is achieved in vivo remains poorly understood. We report the first use of Hi-C to map the structure of bacterial chromosomes at a high, unprecedented resolution. Analysis of Hi-C data and polymer modeling indicates that the Caulobacter crescentus chromosome consists of multiple, largely independent spatial domains likely comprised of supercoiled plectonemes arrayed into a bottlebrush-like fiber. These domains are stable throughout the cell cycle and re-established concomitantly with DNA replication. We provide strong evidence that domain boundaries are established by highly-expressed genes and the formation of plectoneme-free regions. Additionally, we use Hi-C to demonstrate that supercoiling, the histone-like protein HU, and SMC act at different length-scales and in complementary ways to organize and structure chromosomes within cells.

overall_design: Hi-C experiments were performed on untreated wild type swarmer cells and drug-treated swarmer cells (Novobiocin or Rifampicin) of Caulobacter crescentus CB15N. Hi-C were also performed on swarmer cells of smc knock-out and hup1hup2 knock-out mutants of Caulobacter crescentus. Time-course Hi-C were performed on a synchronous population of Caulobacter crescentus at 5, 10, 30, 45, 60 and 75 minutes after synchronization.  The progression of DNA replication during the cell cycle was followed by total genomic DNA sequencing.

first: T

middle: B

first: M

last: Laub

last: Imakaev

first: L

last: Mirny


title: RNA Polymerase-II-generated DNA supercoils destabilize nucleosomes

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: The twin supercoiled domain model posits that, as RNA Polymerase II (Pol II) transcribes a gene, it generates negative and positive supercoils upstream and downstream respectively, but little is known about the functional consequence in vivo of the resulting torsional strain. Here we provide a method for high resolution mapping of DNA supercoils using next-generation sequencing, and show that the level of supercoiling is correlated with gene expression in Drosophila cells. Inhibition of topoisomerases, enzymes that relieve torsional strain, leads to accumulation of supercoils surrounding gene bodies and of Pol II at the transcription start sites. Topoisomerase I inhibition results in increased nascent RNA transcripts with Topoisomerase II inhibition shows little change in nascent RNA levels. Despite these different effects on transcription, inhibition of either enzyme results in increased nucleosome turnover within gene bodies, suggesting that torsional stress contributes to destabilizing nucleosomes ahead of Pol II.

overall_design: 12 paired-end samples and 8 single-end samples were sequenced and analyzed.

first: Sheila

last: Teves

first: Steven


title: Canonical Nucleosome Organization at Promoters Forms During Genome Activation

city: Shanghai

first: Yong

last: Zhang

address: 1239 Siping Road

institute: Tongji University

summary: The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.

overall_design: MNase-seq to generate nucleosome organization in mouse embryonic stem cell (J1)

first: Nadine

middle: L

last: Vastenhouw

first: Jianxing

last: Feng

first: Kai

last: Fu

first: Chenfei

last: Wang

first: Ying

last: Ge

first: Andrea

last: Pauli

last: van Hummelen

last: Schier

first: Xiaole

last: Liu


title: Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Pattern

first: Lan

last: Yang

address: 300 Fenglin Road

institute: Institute of Plant Physiol & Ecology, Chinese Academy of Sciences


title: Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a “cleavable complex”. To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment affected transcription initiation, elongation, termination, splicing and enhancer activity. Following removal of camptothecin, transcription spread as a wave from the 5’-end of genes with no recovery of transcription apparent from RNA polymerases stalled in the body of genes. As a result, camptothecin preferentially inhibited the expression of large genes such as proto-oncogenes, and anti-apoptotic genes while smaller ribosomal protein genes, pro-apoptotic genes and p53 target genes showed relative higher expression. In addition, a set of mitotic regulator genes and histone genes were inhibited in a size-independent manner. Cockayne syndrome group B fibroblasts showed a very similar RNA synthesis recovery profile to normal fibroblasts suggesting that transcription-coupled repair is not involved in the repair of transcription-blocking TOP1 lesions. These findings of the effects of camptothecin on transcription have important implications for its anti-cancer activities and may aid in the design of improved combinatorial treatments involving Top1 poisons.

overall_design: Analysis of the effect of Camptothecin (CPT) on transcription. Normal fibroblasts and Cockayne syndrome group B fibroblasts were exposed to CPT for 60 minutes, after which a washout was performed. Nascent RNA was labeled using bromouridine for 15 minutes starting at time points: 1) 15 minutes before the washout; 2) Immediately after the washout; 3) 15 minutes after the washout. Test samples are compared to control cells that were not exposed to CPT.

first: Artur

last: Veloso

first: Benjamin

last: Biewen

first: Michelle

last: Paulsen

first: Leonardo

last: Carmo de Andrade Lima

first: Jayendra

last: Prasad

first: Karan

last: Bedi

first: Thomas

last: Wilson


title: Comparative characterization of microRNA profiles of different genotypes of Toxoplasma gondii

city: Lanzhou

first: Min-jun

last: Xu

state: Gansu

address: 1 Xujiaping, Yanchangbu

department: State Key Laboratory of Veterinary Etiological Biology

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences

summary: The present study characterized comparatively the miRNA profiles of three different genotypes of T. gondii, identified genotype-shared miRNAs and strain-specific miRNAs.

overall_design: Compared the miRNA expression profiles of five T. gondii strains

first: Xingquan

last: Zhu

first: Minjun


title: Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells (ChIP-seq)

first: Raffaele

last: Calogero

overall_design: ChIP-Sequencing of fragments enriched by immunoprecipitation of Prdm5 in wild type mouse embryo fibroblasts (MEF) in duplicate. Background noise details obtained by ChIP-Sequencing of Prdm5 lacz/lacz MEF, in duplicate.

first: Giorgio

last: Galli

first: Matteo

last: Carrara

first: Chiara

last: Francavilla

first: Kristian

last: de Lichtenberg

first: Jesper

last: Olsen

first: Anders

last: Lund


title: Stem cell quiescence acts as a tumor suppressor mechanism in hair follicle initiated squamous tumors

status: Public on Oct 28 2013

city: Boulder

first: Zhaojie

last: Zhang

state: CO

address: 2300 Arapahoe Ave

institute: University of Colorado at Boulder

summary: In many organs, adult stem cells are uniquely poised to serve as cancer cells of origin. In the epidermis, hair follicle stem cells (HFSCs) cycle through stages of quiescence (telogen) and proliferation (anagen) to drive hair growth. Within the hair follicle, HFSCs are capable of initiating squamous cell carcinoma, yet it is unclear how the hair cycle contributes to tumorigenesis. The data presented here show that HFSCs are unable to initiate tumors during the quiescent phase of the hair cycle, indicating that the mechanisms that keep HFSCs dormant are dominant to gain of oncogenes (Ras) or loss of tumor suppressors (p53). Instead, prolonged oncogenic stimuli only exert their effects when HFSC quiescence mechanisms are removed by normal HFSC activation. Furthermore, Pten activity is necessary for quiescence based tumor suppression, since Pten deletion alleviates this stem cell specific ability without affecting proliferation per se.

overall_design: Small RNAs were cloned from Trizol-lysed cells sorted from mouse skin and sequenced with the Illumina HiSeq2000.

first: Rui

last: Yi

first: William

last: Lowry


title: Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Patterns [BS-Seq]

first: Lan

last: Yang

summary: A forward genetics screen led to the identification of the putative chromatin regulator EDM2 as a cellular anti-silencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite PHD finger domain that recognizes both active H3K4 and repressive H3K9 methylation marks at the intronic repeat elements in genes such as the histone H3K9 demethylase gene IBM1, and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes.Our results thus increase the understanding of anti-silencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin.

overall_design: Col-0 and edm2-4 total genomic DNAs are extracted from leaves and then subjected to bisulfite convertion and sequencing in accordance with standard protocol.

first: Jian-Kang

first: Honggui

last: La

first: Mingguang

last: Lei


title: Transcription-dependent positioning of Structural Maintenance of Chromosome complexes across the genome: RNA-Seq

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The Structural Maintenance of Chromosomes (SMC) complexes regulate the chromosome structures essential for proper genome regulation and cell viability.  In mammals, the coordinated actions of the SMC complexes condensin I, condensin II and cohesin regulate dynamic chromosome structures throughout the cell cycle, but it is not clear how these complexes are positioned across the genome.  We report here that condensin I, condensin II and cohesin occupy active euchromatic regions of the embryonic stem cell genome, but not heterochromatic regions.  Like cohesin, we find that condensin II is deposited at active genes by the SMC loading factor Nipbl.  The recruitment of Condensin II to active genes is dependent on their transcriptional activation.  Subsequent transcriptional elongation by RNA polymerase II distributes condensin II across gene bodies.  During mitosis, condensin I occupies the same set of active genes occupied by condensin II during interphase.  Thus, SMC complexes are positioned in the genome by transcription-dependent processes, indicating that condensin-dependent condensation mechanisms are preferentially utilized in euchromatic regions.

overall_design: RNA-seq in mES cells after known-down of Smc1, CapH2 or Smc2.

first: Jill

last: Dowen

first: David

last: Orlando


title: Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Patterns [RNA-Seq]

overall_design: Col-0 and edm2-4 total RNA are extracted from leaves and then polyA mRNAs are isolated for mRNA-seq.

last: Zhu


title: Uracil DNA glycosylase (UNG) loss enhances DNA double strand break formation in human cancer cells exposed to pemetrexed

city: Cleveland

first: Peter

last: Scacheri

state: OH

address: 2109 Adelbert Rd.

institute: Case Western Reserve University

summary: To test the effects of uracil DNA glycosylase (UNG) loss on the formation of double strand breaks (DSBs) by the anti-cancer agent pemetrexed, we performed ChIP-seq for serine 139-phosphorylated H2AX (gammaH2AX), a marker of DSBs, in human cells wild-type or deficient for UNG in combination with pemetrexed treatment.  UNG deficiency results in an increase in DSBs upon pemetrexed treatment, and we found that pemetrexed treatment induces DSBs at different genomic locations in UNG wild-type and knockout cells.  Similar results were observed upon cisplatin treatment of UNG wild-type and knockout cells, and the genomic locations of DSBs were distinct between pemetrexed-treated and cisplatin-treated samples.  Taken together, our results suggest differential mechanisms for DSB formation in UNG-competent and UNG-deficient cells.

overall_design: The genomic distribution of gammaH2AX in UNG WT and KO cells treated with pemetrexed or cisplatin was determined by ChIP-seq

first: Lachelle

last: Weeks

first: Gabriel

last: Zentner

first: Stanton

last: Gerson


title: Evaluation of TRAP-sequencing technology with a versatile conditional mouse model

city: Solna

first: Jan

middle: M

last: Stenman

address: Box 240

country: Sweden

institute: Ludwig Institute for Cancer Research Ltd

summary: Evaluation of TRAP-sequencing by comparing transcriptomes and translatomes of different organs and distinct cell populations.

overall_design: E14.5 brain and kidney transcriptome and translatome profiling of organs or distinct cell populations from these organs was performed using the Illumina TruSeq RNA technology.

first: Mike

last: Hupe

first: Minerva

middle: X

last: Li


title: Gene Expression Profile for knocking down Tet1 in pre-iPSCs culturing in Vc medium.

status: Public on Oct 27 2013

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

summary: Tet1 is a hydroxylase known for its role in the conversion of 5-methylcytosines (5mC) to 5-hydroxymethylcytosines (5hmC) involved in the possible active demethylation process and gene expression regulation. As somatic cell reprogramming involves the re-activation of pluripotency genes and the silencing of somatic ones, it remains unclear the role of Tet1 in the reprogramming process. Here, we performed RNAseq for WT and knocking down Tet1 in two pre-iPSCs cell lines, pre2-2 and pre3.

overall_design: Using two pre-iPSCs cell lines: pre2-2 and pre3, cultured by mES medium(+lif), transfected siCtrl/siTet1 siRNA or non-treatment, then, after 16h, the medium were replaced by mES(+lif) medium plus Vc(50ug/ml), total RNA was extracted after another 32h later for RNAseq.

first: Duanqing

last: Pei

first: Guo-Liang

last: Xu


title: MBD3 localization by ChIP-seq

first: Takashi

last: Shimbo

summary: Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. We identified the localization of MBD3, a component of Mi-2/NuRD complex, in two breast cancer cell lines (MCF7 and MDA-MB-231) using ChIP-Seq. MBD3 showed cell-type specific localization with overlap across cell lines being less than 50%. MBD3 localized across gene bodies, peaking around the transcription start site (TSS).  Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have roles in fine tuning expression for active genes. These data represent an important first step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and gene expression.

overall_design: Identification of MBD3 localization in human breast cancer cell lines

first: Huidong

last: Shi

first: Paul

last: Wade

first: Ying

last: Du


title: Transcriptional regulation in pluripotent stem cells by Methyl CpG binding protein 2 (MeCP2)

status: Public on Oct 25 2013

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

summary: Rett syndrome (RTT) is one of the most prevalent female mental disorders. De novo mutations in methyl CpG binding protein 2 (MeCP2) are a major cause of RTT. MeCP2 regulates gene expression as a transcription regulator as well as through long-range chromatin interaction. Because MeCP2 is present on the X chromosome, RTT is manifested in a X-linked dominant manner. Investigation using murine MeCP2 null models and post-mortem human brain tissues has contributed to understanding the molecular and physiological function of MeCP2. In addition, RTT models using human induced pluripotent stem cells derived from RTT patients (RTT-iPSCs) provide novel resources to elucidate the regulatory mechanism of MeCP2. Previously, we obtained clones of female RTT-iPSCs that express either wild type or mutant MECP2 due to the inactivation of one X chromosome. Reactivation of the X chromosome also allowed us to have RTT-iPSCs that express both wild type and mutant MECP2. Using these unique pluripotent stem cells, we investigated the regulation of gene expression by MeCP2 in pluripotent stem cells by transcriptome analysis. We found that MeCP2 regulates genes encoding mitochondrial membrane proteins. In addition, loss of function in MeCP2 results in de-repression of genes on the inactive X chromosome. Furthermore, we showed that each mutation in MECP2 affects a partly different set of genes. These studies suggest that fundamental cellular physiology is affected by mutations in MECP2 from very early fetal development and that a therapeutic approach targeting to unique forms of mutant MeCP2 is needed.

overall_design: RNA samples from normal ESCs/iPSCs, RTT-iPSCs and MeCP2 KD iPSCs were obtained. Gene expression of those cells were analyzed.

first: In-Hyun

last: Park


title: Differential gene expression in Malaysian and Wine/European yeast isolates

city: Berkeley

first: Rachel

last: Brem

address: 176 Stanley Hall # 3220

institute: University of California, Berkeley

summary: Comparative-genomic studies have reported widespread variation in levels of gene expression within and between species. In the vast majority of cases, the phenotypic and evolutionary relevance of regulatory change is unknown. We haveu sed a wild Malaysian population of S. cerevisiae as a testbed in the search to identify organismal correlates of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron.

overall_design: Analysis of differential gene expression between three Malaysian and two Wine/European isolates and allele-specific expression within three Malaysian x Wine/European hybrids.

first: Hana

middle: N

last: Lee

first: Yulia

last: Mostovoy

first: Tiffany

middle: Y

last: Hsu

first: Amanda

last: Chang


title: Estrogen induces global reorganization of chromatin structure in human breast cancer cells

city: Indianapolis

first: Lang

state: IN

address: 410 West 10th Street HITS 5003 lab

department: Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics

institute: Indiana School of Medicine, Indiana University

summary: In the cell nucleus, each chromosome is confined to a chromosome territory. This spatial organization of chromosomes plays a crucial role in gene regulation and genome stability.   Recently an additional level of organization has been discovered at the chromosome scale: the spatial segregation into open and closed chromatin to form two genome-wide compartments. Although considerable progress has been made in our knowledge of chromatin organization, a fundamental issue remains the understanding of its dynamic, especially in cancer.   To address this issue, we performed genome-wide mapping of intra- and interchromosomal interactions (Hi-C) over the time after estrogen (E2) stimulation of breast cancer cells. To biologically interpret these interactions, we integrated with estrogen receptor alpha (ER alpha) binding events, gene expression and multiple epigenetic marks. We show that E2 induces a global reorganization of genome. More specifically, gene-rich chromosomes as well as areas of open and highly transcribed chromatins are moved spatially closer, thus enabling genes to share transcriptional machinery and regulatory elements. At a lower scale, differentially interacting loci are enriched for cancer proliferation and E2 related genes. We also observe that these differentially interacting loci are correlated with higher ER alpha binding events and gene expression.

overall_design:
5 time points: before E2 (0h) and after E2 (0.5h, 1h, 4h and 24h). For each time point, there are two lanes per sample and two biological replicate samples.
Please note that a processed data file corresponds to the merging of 2 replicates, and  that there are 2 lanes per replicates (4 files in total per processed data file).

Information about data merging is provided in the title of the sample. For instance :
0h_replicate_1_lane 1
0h_replicate_1_lane 2
0h_replicate_2_lane_1
0h_replicate_2_lane_2
are merged to generate the processed data hic_0h-all-1M.IC.csv.gz.

Several bin sizes are provided for the same processed data:
hic_0h-all-1M.IC.csv.gz
hic_0h-all-2M.IC.csv.gz
hic_0h-all-4M.IC.csv.gz
hic_0h-all-500k.IC.csv.gz
are the same processed data, but with different bin sizes.

first: Raphael

last: Mourad

first: Liran

last: Juan

first: Pei-Yin


title: Semiconductor based DNA sequencing of histone modification states

first: Christine

middle: S

last: Cheng

address: 7 Cambridge Center

institute: Broad Institute of MIT and Harvard

summary:
The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing and targeted re-sequencing.
Here, we demonstrate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP-seq on the Ion Torrent platform.
We leverage this method for epigenetic profiling of tumor tissues.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of histone modifications in mouse dendentic cells stimulated with LPS, matched melanoma derived cell line, melanoma tumor tissue

first: Ido

last: Amit


title: Novel kinase fusion oncogenes in post-Chernobyl radiation-induced pediatric thyroid cancers

city: New York

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Exposure to ionizing radiation during childhood markedly increases the risk of developing papillary thyroid cancer. We identified non-overlapping somatic driver mutations in all 26 cases of post-Chernobyl thyroid cancers we studied through candidate gene assays and next generation RNA-sequencing. We found that 22/26 harbored fusion oncogenes arising primarily through intrachromosomal rearrangements. Altogether 23/26 of the oncogenic drivers identified in this cohort aberrantly activate MAPK signaling, including the two novel somatic rearrangements ETV6-NTRK3 and AGK-BRAF. Two other tumors harbored distinct fusions leading to overexpression of the nuclear receptor PPARγ. A lower prevalence of fusion oncogenes was found in a cohort of pediatric thyroid cancers from children from the same geographical regions that were not exposed to radiation. Radiation-induced thyroid cancers are a paradigm of tumorigenesis driven by fusion oncogenes that activate MAPK signaling or, less frequently, a PPARγ-driven transcriptional program.

overall_design: Examination of transcriptome profiles and genetic somatic changes in thyroid cancer.

first: Julio

last: Ricarte-Filho

first: Sheng

last: Li

first: Maria

last: Garcia-Rendueles

first: Cristina

last: Montero-Conde

first: Francesca

last: Voza

first: Jeffrey

last: Knauf

first: Adriana

last: Heguy

first: Agnes

last: Viale

first: Tetyana

last: Bogdanova

first: Geraldine

last: Thomas

first: James

last: Fagin


title: Hierarchical mechanisms for transcription factor-mediated reprogramming of fibroblasts to neurons

status: Public on Oct 24 2013

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: Here we reveal a hierarchical mechanism in the direct conversion of fibroblasts into induced neuronal (iN) cells mediated by the transcription factors Ascl1, Brn2, and Myt1l.

overall_design: Examination of global transcriptional changes and mapping genome-wide transcription factors occupancy at distinct time points during the transdifferentiation process

first: Orly

last: Wapinski

first: Howard

last: Chang

first: Marius

last: Wernig


title: Comparative transcriptome analysis of geographically distinct virulent and attenuated Babesia bovis

status: Public on Oct 23 2013

city: Pullman

first: Audrey

middle: Oi-ting

last: Lau

state: Washington State University

department: Veterinary Microbiology & Pathology

institute: Washington State University

summary: Geographical distinct virulent Babesia bovis strains have similar gene expression changes as they go through attenuation.

overall_design: Pair end RNA-sequencing reads on three biological replicate sample pairs of virulent parent and attenuated derivative Babesia bovis strain isolated in Argentina.


title: Sub-Cellular Transcriptomics – Dissection of the mRNA composition in the axonal compartment of sensory neurons

city: Rehovot

first: Avraham

last: Yaron

department: Department of Biological Chemistry

institute: Weizmann Institute of Science

summary: RNA localization is a regulatory mechanism that is conserved from bacteria to mammals. Yet, little is known about the mechanism and the logic that govern the distribution of RNA transcripts within the cell. Here we present a novel organ culture system, which enables the isolation of RNA specifically from NGF dependent re-growing peripheral axons of mouse embryo sensory neurons. In combination with massive parallel sequencing technology, we determine the sub-cellular localization of most transcripts in the transcriptome. We found that the axon is enriched in mRNAs that encode secreted proteins, transcription factors and the translation machinery. In contrast, the axon was largely depleted from mRNAs encoding transmembrane proteins, a particularly interesting finding, since many of these gene products are specifically expressed in the tip of the axon at the protein level. Comparison of the mitochondrial mRNAs encoded in the nucleus with those encoded in the mitochondria, uncovered completely different localization pattern, with the latter much enriched in the axon fraction. This discovery is intriguing since the protein products encoded by the nuclear and mitochondrial genome form large co-complexes. Finally, focusing on alternative splice variants that are specific to axonal fractions, we find short sequence motifs that are enriched in the axonal transcriptome. Together our findings shed light on the extensive role of RNA localization and its characteristics.

overall_design: For each RNA sample, Spinal Cords\ DRGs were dissected from 40 E13.5 embryos and cultured for 48H. Total RNA was extracted from whole DRG and Peripheral axons. Poly-A enriched. In duplicates, using GAIIx. Read length - 80nt.

first: Adi

last: Minis


title: Transcriptional super-enhancers connected to cell identity and disease

first: Richard

last: Young

summary: Super-enhancers are large clusters of transcriptional enhancers that drive expression of genes that control and define cell identity. Improved understanding of the roles super-enhancers play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying super-enhancers across the spectrum of human cell types. We describe here the population of transcription factors, cofactors, chromatin regulators and core transcription apparatus that occupy super-enhancers in embryonic stem cells (ESCs) and evidence that super-enhancers are highly transcribed. We then use epigenomic data to produce a catalogue of super-enhancers in a broad range of human cell types. These super-enhancer domains are associated with genes encoding master transcription factors and other components that play important roles in the biology of these cells. Interestingly, sequence variation associated with a broad spectrum of diseases is especially enriched in the super-enhancers of disease-relevant cell types. Furthermore, we find that cancer cells generate super-enhancers at oncogenes and other genes that play important roles in tumor pathogenesis. We discuss these insights and their implications for future study of human health and disease.

overall_design:
ChIP-Seq for transcription factors in mouse embryonic stem cells and H3K27ac in Jurkat T-ALL cell line
RNA-Seq for mouse embryonic stem cells

first: Brian

last: Abraham

first: Denes

last: Hnisz

first: Ashley

first: Alla

last: Sigova

first: Violaine

last: Saint-Andre

first: Heather

last: Hoke

first: Peter

last: Rahl

first: Jamie

last: Newman

first: Lee

last: Lawton

first: Warren

last: Whyte


title: Genome-wide map of p53 binding sites by ChIP-seq in  human lymphoblastoid cell lines  treated with nutlin-3

city: Research Triangle Park

first: Xuting

last: Wang

address: 111 TW Alexander Dr

institute: NIEHS/NIH

summary: We have used chromatin immune-precipitation with parallel sequencing (ChIP-Seq) technology to identify genome-wide p53 binding in human lymphoblastoid cell lines treated with a MDM2 inhibitor nutlin-3

overall_design: ChIP-Seq analysis of p53 binding sites in human lymphoblastoid cells treated with nutlin-3 or vehicle

first: Michelle

middle: R

last: Campbell

first: Dan

last: Su

first: Douglas

last: Bell