title: ChIP-Seq reveals regulation of the heterochromatic mark, H3K9me3, in NAc following repeated cocaine administration

status: Public on Jan 18 2011

first: Li

last: Shen

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Repeated administration of the psychostimulant cocaine has been shown to produce persistent alterations in genome-wide transcriptional regulatory networks, chromatin remodeling activity and, ultimately, gene expression profiles in the brain’s reward circuitry. Virtually all previous investigations have centered on drug-mediated effects occurring throughout active euchromatic regions of the genome, such that very little is known concerning the impact of cocaine exposure on the regulation and maintenance of heterochromatin in adult brain. Here, we report that cocaine administration dramatically and dynamically alters heterochromatic histone H3 lysine 9 trimethylation (H3K9me3) in the nucleus accumbens (NAc), a key brain reward region. Furthermore, we demonstrate that repeated cocaine exposure induces persistent decreases in heterochromatization in this brain region, suggesting a potential role for heterochromatic regulation in the long-term actions of cocaine. To identify precise genomic loci affected by these alterations, chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-Seq) was performed on NAc. ChIP-Seq analyses confirmed the existence of the H3K9me3 mark mainly within inter-genic regions of the genome and identified specific patterns of cocaine-induced H3K9me3 regulation at repetitive genomic sequences. Cocaine-mediated decreases in H3K9me3 enrichment at specific genomic repeats (e.g., LI repeats) were further confirmed by the increased expression of LINE-1 and IAP retrotransposons in NAc. Such increases likely reflect global patterns of genomic de-stabilization in this brain region following repeated cocaine administration and open the door for future investigations into the epigenetic and genetic basis of drug addiction.

overall_design: Animals received daily i.p. injections of either 'saline' (7 treatments of saline) or 'repeated' cocaine (7 treatments of 20 mg/kg cocaine). 24 hours after the last dose, chromatin immunoprecipitation was performed utilizing previously validated methods. Each experimental condition was performed in either duplicate or triplicate (2 cocaine, 3 saline). Briefly, for each ChIP, bilateral 14-gauge NAc punches (anterior and posterior) were pooled from 5 mice (20 punches). Tissue was lightly fixed to cross-link DNA with associated proteins and the material was further sheared and immunoprecipitated using sheep anti-rabbit magnetic beads conjugated to an antibody that specifically recognizes H3K9me3. Resulting immunoprecipitated DNA and total (input) genomic DNA were prepared for ChIP-sequencing using an Illumina kit according to manufacturer’s instructions. 20 ng of starting material, as determined by PicoGreen concentrations, was used in each case.  Briefly, each sample underwent end repair followed by addition of an A base to the 3’ end. Proprietary adapters were then ligated to the ends, followed by size selection on a 3% agarose gel. The range of excision was 175-225 bp. Following DNA clean up, samples were amplified with 21 cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. 5 pM concentrations were used to generate clusters for sequencing analysis.

first: Ian

middle: S

last: Maze

first: Eric

middle: J

last: Nestler


title: Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA editing targets in transcript 3'UTRs

status: Public on Jan 23 2011

city: New York

first: Brad

last: Rosenberg

state: NY

address: 1 Gustave L Levy Place

department: Microbiology

country: USA

type: Expression profiling by high throughput sequencing

summary: Apolipoprotein B-editing enzyme, catalytic polypeptide-1 (APOBEC1) is a cytidine deaminase, initially identified by its activity in converting a specific cytidine (C) to uridine (U) in apolipoprotein B (apoB) mRNA transcripts in the small intestine. Editing results in translation of a truncated apoB isoform with distinct functions in lipid transport. To address the possibility that APOBEC1 edits additional mRNAs, we developed a transcriptome-wide comparative RNA-Seq screen. We identified and validated 32 previously undescribed mRNA targets of APOBEC1 editing, all of which are located in AU-rich segments of transcript 3′ untranslated regions (3′ UTRs).  Further analysis revealed several characteristic sequence features of editing targets, which were predictive for the identification of additional APOBEC1 substrates.  The identification of multiple mRNA editing substrates for APOBEC1 suggests additional functions for this cytidine deaminase beyond its characterized role in lipid absorption.

overall_design: Poly(A)+ RNA-Seq libraries were prepared from C57Bl6 Wild-type and congenic Apobec1-/- murine small intestinal epithelial cells (2 samples total).

middle: R

first: Claire

middle: E

last: Hamilton

first: Scott

last: Dewell

first: F

middle: N

last: Papavasiliou


title: Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals (meDIP)

status: Public on Jan 14 2011

city: Jerusalem

first: naomi

last: habib

address: Givat-Ram

department: Computer Scince

country: Israel

institute: Hebrew University

type: Methylation profiling by high throughput sequencing

summary:
Epigenetic information can be inherited through the mammalian germline, and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for genes in mice that responded to paternal diet. As part of this analysis, we chracterise the changes in sperm cytosine methylation in response to different diets.
Characterizing the RNA exression changes in livers of offspring mice in response to the paternal diet, comparing between low-protein diet and control-diet.

overall_design: Examination the effect of 3 different paternal diets, control diet, Caloric Restriction and low-protein diet, on sperm cytosine methylation.

first: Benjamin

last: Carone

first: Lucas

last: Fauquier

first: Naomi

last: Habib

first: Jeremy

middle: M

last: Shea

first: Caroline

last: Hart

first: Ruowang

last: Li

first: Christoph

last: Bock

first: Chengjian

first: Phillip

middle: D

last: Zamore

first: Alexander

last: Meissner

first: Zhiping

last: Weng

first: Hans

middle: A

last: Hofmann

first: Nir

last: Friedman

first: Oliver

last: Rando


title: Gene expression data of Sox17-GFP(+) mouse definitive endoderm before and after expansion on mesenchyme.

status: Public on Jan 12 2011

city: Cambridge

first: Julie

middle: Beth

last: Sneddon

state: MA

address: 7 Divinity Avenue

department: Department of Stem Cells and Regenerative Biology

institute: Harvard University

summary: Mouse embryonic stem cells containing a Sox17-GFP construct were differentiated using growth factors (Activin A and Wnt3A) to definitive endoderm.  Sox17-GFP(+) cells were sorted using fluorescence activated cell sorting and either used for total RNA harvest OR continued in culture in the presence of primary pancreatic mesenchymal cell lines.  At the end of 6 serial passages on mesenchyme, the Sox17-GFP(+) cells were again sorted and the RNA was harvested for arrays.

overall_design: Samples were prepared as described in summary, with technical duplicates for each of the following 3 categories: 1. Unpassaged (P0) endoderm, 2. Endoderm passaged 6 times (P6) on mesenchyme 1, and 3. Endoderm passaged 6 times (P6) on mesenchyme 2.

middle: B

first: Malgorzata

last: Borowiak

first: Douglas

last: Melton


title: A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (mRNA)

city: Nanchang

first: Lusheng

last: Huang

state: Jiangxi Province

address: No. 1101, Zhimin Avenue

country: China

institute: Jiangxi Agricultural University

summary: Pig is an important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-Seq) to generate a high-resolution map of the porcine transcriptome and miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from an F2 female full-sib pair with extreme phenotypes in growth and fat deposit. On the basis of the porcine annotated genes against the UCSC database, we identified 21,414 annotated genes in our RNA-Seq analysis and 48,045-122,931 novel transcript fragments, which could be clustered into 17,085-29,499 novel transcriptional active regions (nTARs). We found that ~18.8% of the detected known genes showed alternative splicing patterns, and alternative 3’ splicing was the most common type of alternative splicing events in pigs. We also detected that more than 22.7% of the known genes identified here were extended at their 5’ and/or 3’ end. We identified 2,796, 1,551 and 835 differentially expressed genes (DEGs), respectively, in AF, LI and LD between the two individuals.

overall_design: Examining the complexity of the pig transcriptome in three organs (liver, abdominal fat, longissimus dorsi muscle) from a female full-sib pair.

first: Congying

last: Chen


title: Native elongating transcript sequencing (NET-seq) of wild type Saccharomyces cerevisiae and of DST1, RCO1, SET1, SET2, EAF3 deletion strains

status: Public on Jan 19 2011

city: San Francisco

first: L. Stirling

middle: Stirling

last: Churchman

state: CA

address: 1700 Fourth St. Byers Hall - Room 404

institute: University of California-San Francisco

summary: We present an approach (native elongating transcript sequencing, NET-seq), based on deep sequencing of 3’ ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution. Application of NET-seq in Saccharomyces cerevisiae reveals that while promoters are generally capable of divergent transcription, the Rpd3S deacetylation complex enforces strong directionality to most promoters by suppressing antisense transcript initiation. Our studies also reveal pervasive polymerase pausing and backtracking throughout the body of transcripts. Average pause density shows prominent peaks at each of the first four nucleosomes, with the peak location occurring in good agreement with in vitro biophysical measurements. Thus nucleosome-induced pausing represents a major barrier to transcriptional elongation in vivo.

overall_design: Examination of nascent transcripts in yeast and mutant strains

first: L

first: Jonathan

last: Weissman


title: Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

status: Public on Jan 10 2011

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

type:
Other
Expression profiling by array

summary: MicroRNAs (miRNAs) are a large family of 19-22nt non-coding RNAs that post-transcriptionally regulate their mRNA targets. Computational algorithms predict that over half of all genes are regulated by miRNAs, yet approaches for experimental identification of miRNA binding sites are now emerging.  To directly identify endogenous miRNA binding sites, we performed photo-crosslinking immunoprecipitation using antibodies against Ago2, followed by deep-sequencing of RNA tags (CLIP-seq) in mouse embryonic stem cells (mESCs). We also performed parallel CLIP-seq in Dicer null mESCs that lack mature miRNAs, allowing us to define whether the association of Ago2 with the identified sites was mediated by miRNAs. We include the exon-array expression data obtained from three sets of Dicer WT and Dicer Null mESCs.These data are used to determine genes that are differentially expressed between Dicer WT and Dicer Null conditions.

overall_design: Six samples (3 Dicer wild-type CLIP RNA libraries representing two biological replicates, 2 Dicer null CLIP RNA libraries, 1 short-RNA library from Dicer wild-type mESCs) were analyzed. Six total mESC samples were analyzed (3 Dicer WT, 3 Dicer Null). Expression values for probesets were summarized into a single per-gene value. The log fold change for Dicer_WT/Dicer_Null was defined as the difference between the mean expression in Dicer WT mESCs and the mean expression in the Dicer Null mESCs.

first: Anthony

middle: K

last: Leung

first: Amanda

middle: G

last: Young

first: Arjun

first: Grace

middle: X

last: Zheng

first: Andrew

last: Bosson

first: Cydney

last: Nielsen

last: Sharp


title: sRNA populations of 2 week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal F1 hybrids

city: Acton

first: Michael

last: Groszmann

state: ACT

address: Clunies Ross St

department: Agriculture

country: Australia

institute: CSIRO

type: Non-coding RNA profiling by high throughput sequencing

summary: We examined sRNA populations in the Arabidopsis ecotypes C24, Landsberg erecta (Ler), and their reciprocal hybrids which display strong intra-species heterosis.  The parental ecotypes had significant differences in their sRNA epigenomes and associated methylation profiles.  The hybrids differed greatly from the parents in their sRNA epigenomes including a marked reduction in 24nt sRNA associated with loci that differed in the frequency of 24nt sRNAs between the parents.

overall_design: Examination of sRNA populations from two-week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal hybrids.

first: Ian

last: Geraves

first: Elizabeth

last: Dennis

first: W

last: Peacock


title: A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing

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

overall_design: Refer to individual Series


title: Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models

city: Rechovot

first: Ram

last: Jaschek

address: P.O Box 26

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing


title: Regulation of Megakaryocytic differentiation in Cell Line Models by Dynamic Combinatorial Interactions of RUNX1 with Its Cooperating Partners

overall_design: Examination of RUNX1 binding in K562 cells, before and following TPA induction and CMK cells. Examination of GATA1 and FOS binding and H3K4me1 and H3K27me3 modification levels following TPA induction in K562 cells.

first: Niv

last: Pencovich


title: Diverse roles and interactions of the SWI/SNF chromatin-remodeling complex revealed using global approaches

city: Palo Alto

first: Ghia

last: Euskirchen

address: 1501 S. California Ave.

department: Genetics

institute: Stanford University

type: Genome binding/occupancy profiling by genome tiling array


title: Encyclopedia of C. elegans 3' UTRs and their regulatory elements - 454 sequencing of RACE clones

status: Public on Jan 21 2011

first: Kristin

middle: C

last: Gunsalus

department: Biology

institute: NYU Center for Genomics and Systems Biology

summary:
The 3' untranslated region (3'UTR) constitutes a major site of post-transcriptional regulation of gene expression. Sequence elements in the 3'UTR interact with trans-acting regulators such as microRNAs that affect translation and stability. The overall aim is to use a 3'RACE cloning-sequencing stragety to identify the 3'UTRs of C. elegans transcripts and explore their heterogeneity in different developmental stages and tissues.

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

overall_design: Use RACE clones to identify 3'UTR isoforms via deep sequencing.

first: Fabio

last: Piano

first: Marco

last: Mangone


title: Genome-wide profile of the SWI/SNF chromatin remodeling complex

summary: A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the biological processes in which chromatin remodeling proteins participate we globally mapped binding regions for several components of the SWI/SNF complex throughout the human genome using ChIP-Seq. SWI/SNF components were found to lie near regulatory elements integral to transcription (e.g. 5’ ends, RNA Polymerases II and III and enhancers) as well as regions critical for chromosome organization (e.g. CTCF, lamins and DNA replication origins). To further elucidate the association of SWI/SNF subunits with each other as well as with other nuclear proteins we also analyzed SWI/SNF immunoprecipitated complexes by mass spectrometry. Individual SWI/SNF factors are associated with their own family members as well as with cellular constituents such as nuclear matrix proteins, key transcription factors and centromere components implying a ubiquitous role in gene regulation and nuclear function. We find an overrepresentation of both SWI/SNF-associated regions and proteins in cell cycle and chromosome organization. Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated.

overall_design: ChIP-Seq analysis of the SWI/SNF subunits Ini1, Brg1, BAF155 and BAF170 in HeLa S3 cells

first: Raymond

last: Auerbach

first: Eugene

last: Davidov

first: Tara

last: Gianoulis

first: Joel

last: Rozowsky

first: Guoneng

last: Zhong

first: Nitin

last: Bhardwaj

first: Mark

last: Gerstein

middle: P

last: Snyder


title: Genome-wide analysis of RNAs associated with Lin28

city: Shanghai

first: Ling-Ling

last: Chen

address: 320 Yue-Yang Road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
We used immunoprecipitation to pulldown Lin28 associated RNA targets and used genome-wide high throughput deep sequencing to identified those Lin28-associated RNAs.
Keywords: Lin28 IP-RNAseq

overall_design: Examination of Lin28 immunoprecipitated RNA transcripts

first: Li

last: Yang

first: Goardon

last: Carmichael

first: Yingqun

last: Huang


title: An integrative analysis of the SOX2 response program in glioblastoma

city: HangZhou

first: Biaoyang

last: Lin

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

institute: ZheJiang University


title: Chip-Seq analysis of Sox2 protein genome-wide DNA binding sites in glioma cancer cells

summary: We report here our results of the genome wide target identification of SOX2 in GBM cells by ChIP-seq analysis.

overall_design: Identification of Sox2 DNA binding site in glioma cancer cells

first: Xuefeng

last: Fang


title: Expression analysis of melanoma harvested after GFP or SETDB1 expression

status: Public on Jan 07 2011

city: Karp 7

first: Yariv

last: Houvras

address: 1 Blackfan Circle

institute: Childrens Hospital Boston

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens


title: TDRD3 is an effector molecule for arginine methylated histone marks

status: Public on Jan 06 2011

city: Smithville

first: Yue

last: Lu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

summary: Specific sites of histone tail methylation are associated with transcriptional activity at gene loci. These methyl-marks are interpreted by effector molecules, which harbor protein domains that bind the methylated motifs and facilitate either active or inactive states of transcription. CARM1 and PRMT1 are transcriptional coactivators that deposit H3R17me2a and H4R3me2a marks, respectively. We used a protein domain microarray approach to identify the tudor domain-containing protein TDRD3 as a “reader” of these marks. Importantly, TDRD3 itself is a transcriptional coactivator. This coactivator activity requires an intact tudor domain. TDRD3 is recruited to an estrogen responsive element in a CARM1-dependent manner. Furthermore, ChIP-seq analysis of TDRD3 reveals that it is predominantly localized to transcriptional start site. Thus, TDRD3 is an effector molecule that promotes transcription by binding methylarginine marks on histone tails.

overall_design: ChIP seq analysis of TDRD3 in MCF7 cells

first: Yanzhong

last: Bedford


title: Architectural complexity of the polyadenylated intestinal transcriptome revealed by hybrid RNA sequencing

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

summary: We report the complexity of the polyadenylated transcriptome of the mouse intestinal tract assessed by a hybrid RNA-sequencing. We show that 90.72% of the polyA-derived unique reads map to known genes, but  9.28% of reads matched to nonannotated genomic regions.

overall_design: Screening and verification of non-annotated transcriptional units by different RNA-Seq protocols.

first: Ulrich

last: Klostermeier

first: Philip

last: Rosenstiel


title: Tissue-type specific estrogen signaling in breast and uterine cancer cells

status: Public on Jan 05 2011

city: Singapore

first: Cheng Wei

last: Chang

address: Genome Institute of Singapore Genome #02-01 60 Biopolis Street

department: Computational and Mathematical Biology 1

country: Singapore

institute: GIS

summary: Estrogen receptors play critical roles in both the normal physiological, and disease states of numerous tissues, including breast and uterus. Estrogen receptor alpha (ER) can activate or repress the expression of target genes upon estrogen stimulation. In order to better understand the transcriptional network of ER in breast  and uterus, we generated genome wide maps of  ER binding sites (ERBS) and gene expression profiles in breast cancer cells (MCF7 and T47D) and uterine cancer cells (ECC1 and Ishikawa) through ChIP-Seq and microarray techniques. Surprisingly, we identified large scale differences in the numbers of ERBS between these cell lines when treated with E2 (17-β estradiol). Besides identification of common and unique ERBS between breast and uterine cancer cell types., our data also suggest that both cell types could recruit a large set of common co-operating transcription factors (Co-TFs) and a few unique Co-TFs as well. Besides the genes that are commonly regulated between the different cell lines, there are a number of genes that are differentially regulated in different cell types. Gene pathway analyses of E2 target genes suggest that ER regulates many biological pathways and processes in both tissue-type dependent and independent manners. Our results showed that cell lines derived from same tissue display a greater similarity for both profiles of ERBS and gene expression, and that the differential profiles of ER and preferential recruitment of some Co-TFs are the main determinants for the differential regulation of E2 signaling in breast and uterine cancer cells.

overall_design: In order to explore common and distinctive features of ERα (estrogen receptor alpha) binding profiles between breast and uterus, we generated eight ChIP-Seq libraries for the four cell lines (MCF7, T47D, ECC1 and Ishikawa) under two different treatments (E2, ethanol). In addition, we generated four control libraries for the four cell lines. For all treatment libraries, we generated about 7-12 million unique tags each. ER antibody catalog number is (Santa Cruz,sc-543).

first: You

middle: F

last: Pan

first: Cheng

middle: W

first: Edwin

last: Cheung


title: Mus musculus intestine


title: LIM domain binding protein 1 regulates a transcriptional program essential for hematopoietic stem cell maintenance

status: Public on Jan 04 2011

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: We used ChIP-Seq to map Ldb1, Scl and Gata2 binding sites in mouse hematopoietic progenitor cells (HPCs). Together with functional studies using conventional and conditional Ldb1 deficient mouse models and bioinformatics analysis, we systematically determined a transcriptional program controlled by Ldb1 complexes in HSC maintenance.

overall_design: To evaluate the role of Ldb1 in hematopoietic stem cell maintenance.

last: LiQi

first: Kairong

last: Cui

first: Jan

middle: Y

last: Lee

first: Tsadok

last: Cohen

first: Marat

last: Gorivodsky

first: Itai

last: Tzchori

first: Yangu

last: Zhao

first: Sandra

last: Hayes

first: Emery

middle: H

last: Bresnick

first: Keji

first: H

last: Westphal

first: Paul

last: Love


title: ChIP-Seq sequencing of H3K9me2 in third instar Drosophila larvae

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

summary: This study describes the epigenetic profiling of the H3K9me2 in wt Drosophila larvae, as well as in Drosophila larvae for which the euchromatic catalytic enzyme depositing H3K9me2 (EHMT) is knocked out.

overall_design: ChIP-Seq profiling of H3K9me2 in wt and EHMT KO third instar Drosophila larvae

first: Jamie

last: Kramer

first: Korinna

last: Kochinke

first: Merel

last: Oortveld

first: Daniela

first: Eiko

last: deJong

first: J

middle: T

last: Westwood

first: Zoltan

last: Asztalos

last: Stunnenberg

first: Marla

last: Sokolowski

first: Krystyna

last: Keleman

first: Huiqing

last: Zhou

first: Hans

last: van Bokhoven

first: Annette

last: Schenck


title: Deep sequencing of the locust Locusta migratoria manilensis central nervous system transcriptome

city: Chongqing

first: Zhengyi

last: Zhang

address: Shapinba

institute: Chongqing University

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of nervous system in locust Locusta migratoria manilensis. By obtaining over 57,000,000 bases of sequence from central nervous system, we generated 101836 contigs and 69440 scaffolds. We finally get 41179 unigene with an average length of 570bp. There are 5519 unigenes beyond the length of 1000bp. Using BLAST searches of the NR, NT, Swiss-Prot, KEGG and COG databases we are able to identify 13552 unigene (E<0.0001). Comprehensive assessment of all the unigenes by comparing with the studied genes of other insects nervous system reveals that our unigene are broadly representative of the transcriptome of insect nervous system. Our data provides the most large-scale EST-project for locust nervous system, which greatly benefits the exploring of this insect. In addition, we identify a large number of novel nervous genes which can be used in systematic studies of locust and other insects.

overall_design: Examination of 1 sample

first: Zhiyu

last: Peng

first: Yanbing

last: Cheng

first: Yuxian

last: Xia


title: The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5 and Srf, Histone Modifications and MicroRNAs

status: Public on Jan 03 2011

city: Berlin

first: Silke

last: Sperling

state: Berlin

address: Lindenberger Weg 80

department: Cardiovascular Genetics

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine


title: Widespread targeted chromatin remodeling during the initial phase of somatic cell reprogramming [ChIP-Seq]

city: Boston

first: Richard

last: Koche

address: 185 Cambridge St.

institute: Broad Institute of Harvard and MIT

summary: Despite rapid progress in characterizing transcription factor-driven reprogramming of somatic cells to an induced pluripotent stem (iPS) cell state, many mechanistic questions still remain. To gain insight into the earliest events in the reprogramming process, we systematically analyzed the transcriptional and epigenetic changes that occur during early factor induction after discrete numbers of divisions. We observed rapid, genome-wide changes in the euchromatic histone modification, H3K4me2, at more than a thousand loci including large subsets of pluripotency or developmentally related gene promoters and enhancers. In contrast, patterns of the repressive H3K27me3 modification remained largely unchanged except for focused depletion specifically at positions where H3K4 methylation is gained. These chromatin regulatory events precede transcriptional changes within the corresponding loci. Our data provide evidence for an early, organized, and population-wide epigenetic response to ectopic reprogramming factors that clarify the temporal order through which somatic identity is reset during reprogramming.

overall_design: Covalent histone modifications were measured by ChIP-Seq during the initial phase in the reprogramming of mouse embryonic fibroblasts.

first: Zachary

last: Smith

first: Alexander

last: Meissner


title: Widespread targeted chromatin remodeling during the initial phase of somatic cell reprogramming


title: Integrative model of genomic factors for determining binding site selection by estrogen receptor alpha in MCF-7 cancer cells

first: Yuriy

middle: L

last: Orlov

address: 60 Biopolis Street

department: Computational Systems Biology

institute: Genome Institute of Singapore

summary: Using the estrogen receptor alpha (ERalpha) as a model ligand inducible transcription factor, we sought to explicitly define parameters that determine transcription factor binding site selection on a genomic scale in an inducible system that minimizes confounding chromatin effects by the transcription factor itself. By examining several genetic and epigenetic parameters, we find that an energetically favorable estrogen response element (ERE) motif sequence, evidence of occupancy of a "pioneering" transcription factor  FOXA1,  the presence of the enhancer mark, H3K4me1, and an open chromatin configuration (FAIRE) at the pre-ligand state provide specificity for ER binding. Genome-wide ChIP-sequencing was done in MCF-7 cancer cell line for the following histone H3 modifications: monomethylation H3K4me1, trimethylation H3K4me3, H3K9me3, H3K27me3, acetylation H3K9ac, H3K14ac. In addition sequencing of RNA Pol II was done at same treatment conditions (E2 and DMSO). In addition, we assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction.

overall_design: The analysis histone modifications in MCF-7 cancer cells was done by ChIP-seq data obtained either with E2 stimulation or without stimulation using vehicle as a control. Using the ERα binding sites defined by ChIP-seq (separate submission), we analyzed the population characteristics of the chromatin configuration of the ERα binding sites.  To this end, we performed ChIP-seq analysis for the occupancy configuration of each of the following marks before and after E2 exposure: RNA Pol II, the activation marks H3K4me1, H3K4me3, H3K9ac and H3K14ac, and the repression marks H3K9me3 and H3K27me3.   We assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The tag count of FAIRE fragments reflects the nucleosome depletion at any given site. RNA Pol II - Cat# ab5408, Abcam; H3K9me3 - Cat# ab8898, Abcam; H3K27me3 - Cat# 07-449, Upstate Biotechnology Inc.; H3K4me1 - Cat# ab8895, Abcam; H3K4me3 - Cat# ab8580, Abcam; H3K9ac - Cat# 07-352, Upstate Biotechnology Inc.; H3K14ac - Cat# 07-353, Upstate Biotechnology Inc.

first: Roy

last: Joseph

first: Say

last: Kong

first: Edison

last: Liu


title: Widespread targeted chromatin remodeling during the initial phase of somatic cell reprogramming [RRBS]

overall_design: Genome-scale DNA methylation was measured by reduced representation bisulfite sequencing (RRBS) during the initial phase in the reprogramming of mouse embryonic fibroblasts.


title: Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

status: Public on Jan 01 2011

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

summary: Aberrant DNA methylation (DNAm) was first linked to cancer over 25 years ago. Since then, many studies have associated hypermethylation of tumour suppressor genes and hypomethylation of oncogenes to the tumourigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) analysis have been developed, enabling unbiased analysis of cancer methylomes. Using MeDIP-seq, we report a sequencing-based comparative methylome analysis of malignant peripheral nerve sheath tumours (MPNST), benign Neurofibromas and normal Schwann cells. Analysis of these methylomes revealed a complex landscape of DNAm alterations. Contrary to the current dogma, significant global hypomethylation was not observed in the MPNST methylome. However, a highly significant (P<10-100) directional difference in DNAm was found in satellite repeats, suggesting these repeats to be the main target for hypomethylation in MPNST. Comparative analysis of the MPNST and Schwann cell methylomes identified 101,466 cancer-associated differentially methylated regions (cDMRs).  Analysis showed these cDMRs to be significantly enriched for two satellite repeat types (SATR1 and ARLα) and suggests an association between aberrant DNAm of these sequences and transition from healthy cells to malignant disease. Significant enrichment of hypermethylated cDMRs in CGI shores (P<10-60), non-CGI-associated promoters (P<10-4) and hypomethylated cDMRs in SINE repeats (P<10-100) was also identified. Integration of DNAm and gene expression data showed that the expression pattern of genes associated with CGI shore cDMRs was able to discriminate between disease phenotypes. This study establishes MeDIP-seq as an effective method to analyse cancer methylomes.

overall_design: Examination of methylation profiles in malignant, benign and normal tissue

first: Andrew

last: Feber

first: Lu

first: Nadege

last: Presneau

first: Bernadine

last: Idowu

first: Thomas

last: Down

first: Vardhman

last: Rakyan

first: Elia

last: Stupka

middle: E

last: Teschendorff

first: Gary

last: Schroth

first: Adrienne

last: Flanagan

first: Stephan

last: Beck


title: Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes (Illumina sequencing data)

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies that underlie signal- and time-dependent transitions of gene expression. Using a combination of genome-wide and gene-specific approaches, we provide evidence that rather than representing off/on transitions, Toll-like receptor 4 (TLR4)-dependent activation of nearly all immediate/early (I/E) and late response genes results from a sequential process in which signal-independent factors, exemplified by Gabpa, initially establish basal levels of gene expression that are then amplified by signal-dependent transcription factors. Promoters of I/E genes are distinguished from those of late genes by the use of distinct sets of signal-dependent transcription factors, preferential binding of TBP and basal enrichment for RNA Pol II immediately downstream of transcriptional start sites. Global nuclear run-on (GRO) sequencing and total RNA sequencing further indicates that TLR4 signaling markedly increases efficiency of transcriptional elongation of nearly all I/E genes, while RNA splicing is largely unaffected. NCoR/SMRT co-repressor complexes are unexpectedly found to be associated with H3K4me3-positive promoters of TLR4-responsive genes that exhibit a broad range of basal expression levels, implying a dynamic, rather than static role in regulation of gene expression. Collectively, these findings reveal mechanisms underlying temporally distinct patterns of TLR4-dependent gene activation required for homeostasis and effective immune responses.

overall_design: ChIP-Seq, Total RNA-Seq, Gro-Seq, and gene expression profiling was performed in macrophages treated with Kdo2 Lipid A. Control samples for H3K4me3 in Macrophages and B cells, in addition to control microarray data are included in GEO accession# GSE21512. FASTA files are available for older experiments that lack quality read information (i.e. no FASTQ file)

first: Laure

last: Escoubet-Lozach

first: Minna

middle: U

last: Kaikkonen

first: Jean

last: Lozach

first: Sven

last: Heinz

first: Nathanael

last: Spann

first: Andrea

last: Crotti

first: Josh

last: Stender

first: Serena

last: Ghisletti

last: Glass


title: Fast forward genetics: mutation mapping and identification using next-generation sequencing and enrichment of bulk segregant pools

status: Public on Dec 31 2010

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

type: Genome variation profiling by high throughput sequencing

summary: Phenotype-driven forward genetic experiments are among the most powerful approaches for linking biology and disease to genomic elements. Although widely used in a range of model organisms, positional cloning of causal variants is still a very laborious process. Here, we describe a novel universal approach, named fast forward genetics that combines traditional bulk segregant techniques with next-generation sequencing technology and targeted genomic enrichment, to dramatically improve the process of mapping and cloning multiple mutants in a single experiment. In a two-step procedure the mutation is first roughly mapped by ‘light’ sequencing of the bulk segregant pool, followed by genomic enrichment and deep-sequencing of the mutant pool for the linked genomic region. The latter step allows for simultaneous fine-mapping and mutation discovery. We successfully applied this approach to three Arabidopsis mutants, but the method can in principle be applied to any model organism of interest and is largely independent of the genome size. Moreover, we show that both steps can be performed in multiplex using barcoded samples, thereby increasing efficiency enormously.

overall_design:
Inducible overexpression of the RETINOBLASTOMA-RELATED (RBR-OE) gene in Arabidopsis roots causes the complete differentiation of stem cells and premature differentiation of daughter cells, leading to a full exhaustion of the primary root meristem. In order to identify regulators of RBR function in cell differentiation, RBR-OE plants in the Columbia background (Col0) were treated with EMS mutagenesis and a set of genetic suppressors of RBR-OE, which restores root growth capacity, were isolated. In this study, we used one the identified suppressor lines, which segregated as a recessive mutation. Mapping populations were generated by outcrossing to Ler ecotype. Seedlings from the F2 population were grown for 15 days post germination (dpg). A pool of 60 seedlings each with a clear suppressor phenotype (homozygous for suppressor mutation) and of 60 seedlings showing RBOE phenotype (Heterozygous for the suppressor mutation) were prepared and genomic DNA was isolated with the RNeasy Plant Mini Kit from QIAGEN according to manufacturer's protocol.
The other two, mutants 136 and 193 were obtained in fluorescence based mutant screen and a QCmarker based mutagenesis, respectively. Mutants were generated by chemical mutagenesis (EMS) in Colombia (Col) genetic background. Mutants were subsequently crossed to the Landsberg (Ler) ecotype to create the mapping populations. Bulk-segregant pools of about 200 mutant as well as wild-type plants were generated for every mutant line.

first: Isaac

middle: J

last: Nijman

first: Rene

last: Benjamins

first: Anja

last: van Dijken

first: Alfredo

last: Cruz Ramirez

first: Ben

last: Scheres

first: Edwin

last: Cuppen


title: Identification of transcription factor Srf binding sites and histone 3 actetylated regions in mouse cardiomyocytes

first: Silke

last: Sperling

summary: We investigated the cardiac transcription network driven by the DNA-binding key factor Srf in combination with epigenetic marks of histone 3 acetylation (H3ac). Srf has been shown to play a key role in cardiac cell growth and muscle gene regulation. However, we still have limited understanding of the global transcription network driven by this factor in a direct or indirect manner. Moreover, we lack knowledge to which extent epigenetic marks such as histone modifications interfere with the regulation of direct targets. To gain insights into the transcriptional regulatory network two independent chromatin immunoprecipitation (ChIP) samples were profiled. DNA fragments bound to Srf or modified with acetylated histone 3 in mouse cardiomyocytes (HL1-cells) were sequenced using ultra-high throughput DNA sequencing.

overall_design: ChIP-seq profile of a transcription factor (Srf) and a histone modification (H3ac)

middle: R


title: Deep sequencing of organ- and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae)

city: Brisbane

first: Alexandre

middle: Santos

last: Cristino

state: Queensland

address: 79 QBI Building

department: The Queensland Brain Institute

institute: The University of Queensland

summary: microRNAs (miRNAs) have been reported as key regulators in the post-transcriptional process in eukaryotic cells. In insects most of the studies have been reported in holometabolans while only recently two hemimetabolans  (Locusta migratoria and Acyrthosiphonpisum) have had their miRNAs identified. Therefore, the study on miRNAs of the evolutionarily basal hemimetabolan  Blattella germanica, may provide valuable insights on the structural and functional evolution of miRNAs. Small RNA libraries of the cockroach B. germanica were built from the whole body of the last instar nymph, and the adult ovaries. The high throughput Solexa sequencing resulted in approximately 11 and 8 million reads for the whole-body and ovaries, respectively. Bioinformatic analyses identified 38 known miRNAs as well as 11 known miRNA*s. We also found 411 miRNA candidates conserved in other insects and 1017 candidates specific of B. germanica. The positive correlation between Solexa data and real-time quantitative PCR showed that reads can be used as quantitative method. Novel miRNA candidates were validated by decreasing levels of expression in dicer-1 RNAi knockdown individuals. The comparison of the two libraries indicates that whole-body nymph contain more known miRNAs than ovaries, whereas the adult ovaries are enriched with novel miRNA candidates. Our study has identified many known miRNAs and novel miRNA candidates in the basal hemimetabolan insect B. germanica, and most of the specific sequences were found in ovaries. Deep sequencing data reflect miRNA abundance and Dicer-1 RNAi assay is a reliable method to validate novel miRNAs.

overall_design: Small RNAs were sequenced whole body of the last instar nymph and adult ovaries of the cockroach Blattella germanica.

middle: S

first: Erica

middle: D

last: Tanaka

first: Mercedes

last: Rubio

first: Maria-Dolors

last: Piulachs

first: Xavier

last: Belles


title: Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes

first: Christopher

last: Benner

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

overall_design: Refer to individual Series


title: Global Deterministic and Stochastic Allelic Specific Gene Expression in Single Blastomeres of Mouse Early Embryos

city: Foster City

first: Catalin

last: Barbacioru

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

summary:
Here we modified a single cell whole transcriptome amplification method to make it capable of amplifying cDNAs as long as 3kb efficiently and unbiasedly. We combined this modified single cell cDNA amplification method with Applied Biosystems next generation sequencing SOLiD™ System to set up a single cell whole transcriptome assay.  The modified amplification strategy allows us to amplify full-length cDNAs for most of the expressed genes. We show that it is feasible to get digital gene expression profiles at single cell resolution. This allows us to ask fundamental biological questions that could not be addressed previously and to understand transcriptome complexity at the resolution of a single cell.
Oocyte, Two-cell, Four-cell, and 8-cell stage embryos were recovered from MF1 females mated with MF1 male mice (Nagy et al. 2003). The zona pellucida was removed by treatment with acidic tyrode solution. The individual blastomeres were separated by gentle pipeting using a glass capillary.

overall_design: RNA-Seq from 24 single mouse blastomeres from oocytes, 2-cell, 4-cell and 8-cell stages.

first: Fuchou

last: Tang

first: Kaiqin

last: Lao

first: M

middle: A

last: Surani


title: Genome-wide gene expression profiling of human narcolepsy

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

country: Italy

institute: UCSC

summary: Study objectives: The objectives of this study was perform the global gene expression profiling aimed at identifying differentially expressed genes in the circulating lympho-monocytes of NRLCP patients affected by Narcolepsy with Cataplexy (NRLCP). Based on the tight association to the HLA-DQB1*0602 haplotype in caucasians, it could be hypotesized an immunological dysregulation underlying the pathogenesis of the disease.  Design: 10 NRLCP patients with 10 healthy controls were compared. Total RNA isolated from blood specimens was analyzed using microarray technology followed by statistical data analysis to detect genome-wide differential gene expression between patients and controls. Functional analysis of the genelist was performed in order to interpret the biological significance of the data.  Results: 173 genes showed significant (p<0.01) differential expression between the two tested conditions. The biological interpretation allowed to categorize differentially expressed genes into main functional groups including includes genes involved in brain development, which could be possibly regarded as peripheral markers of the disease, along with molecular markers of the NRLCP-related dysmetabolic syndrome and immuregulatory molecules. Moreover a striking correlation within selected HLA haplotypes and HLA gene expression was detected, indicating an allele-specific trend of gene expression for the DQB1, DQA1 and DRB4 genes across all the tested subject, regardless of the disease status.  Conclusions: the molecular profile associated to NRLCP suggested that molecular markers of neural, metabolic and immunological dysregulation can be detected in blood of NRLCP patients. Moreover, the allele-specific HLA gene expression could suggest a possible direct role of MHCII as a co-factor in the disease etio-pathogenesis

overall_design: A case-control study was performed comparing 10 narcoleptic patients (both sexes, mean age 50, median age 50) with 10 age- and sex-matched healthy controls


title: Small RNA sequencing in mouse cardiomyocytes after siRNA mediated knockdown of Srf

summary: We performed two independent siRNA mediated knockdowns of Srf (Srf si1 & Srf si2) and an unspecific siRNA (siNon) in mouse cardiomyocytes HL-1 cells. Small RNAs were sequenced by Illumina/Solexa next-generation (single-end) sequencing technology. The sequence reads were mapped to the mouse reference genome (NCBI v37, mm9) using MicroRazerS. MicroRazerS searches for the longest possible prefix-match of each read, i.e. the longest possible contiguous match starting at the first base. Hence, it is robust to possible adapter sequence at the 3' end of a read and requires no adapter trimming.

overall_design: Small RNA-seq profiles of two siRNA mediated knockdowns of Srf and an unspecific siRNA in mouse cardiomyocytes


city: Cambridge

first: Steve

last: Bilodeau

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Histone profile for wild type MEF and secondary MEF with Dox-inducible vectors for Klf4, Sox2 and Oct4 (KSO).

overall_design: ChIP-Seq data for H3K4me3, H3K27me3 and H3K9me3

first: Richard

last: Young


title: Nucleotide composition-linked divergence of vertebrate core promoter architecture

status: Public on Dec 30 2010

first: Gert Jan

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

institute: Radboud University

summary: Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists, however for most of these motifs the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. We have used oligo-capping in combination with deep sequencing to determine transcription start sites in Xenopus tropicalis. To systematically predict regulatory elements we have developed a de novo motif finding pipeline using an ensemble of computational tools. A comprehensive comparison of human and amphibian promoter sequences revealed both similarities and differences in core promoter architecture. Some of the differences stem from a highly divergent nucleotide composition of Xenopus and human promoters. Whereas the distribution of some core promoter motifs is conserved independent of species-specific nucleotide bias, the frequency of another class of motifs correlates with the single nucleotide frequencies. This class includes the well-known TATA box and SP1 motifs, which are more abundant in Xenopus and human promoters, respectively. While these motifs are enriched above the local nucleotide background in both organisms, their frequency varies in step with this background. These differences are likely adaptive as these motifs can recruit TFIID to either CpG island or sharply initiating promoters. Our results highlight both conserved and diverged aspects of vertebrate transcription, most notably showing co-opted motif usage to recruit the transcriptional machinery to promoters with diverging nucleotide composition. This shows how sweeping changes in nucleotide composition are compatible with highly conserved mechanisms of transcription initiation.

overall_design: ChIP-seq profiles of TBP in Xenopus tropicalis stage 12 embryos and TSS-seq profiles of Xenopus oocytes and stage 12 embryos

first: Simon

last: van Heeringen

first: Waseem

last: Akhtar

first: Ulrike

middle: G

last: Jacobi

first: Robert

last: Akkers

first: Yutaka

last: Suzuki

first: Gert


title: High-throughput sequencing of small RNA during metamorphosis in the Japanese flounder (Paralichthys olivaceus)

status: Public on Dec 23 2010

city: Shanghai

first: Yuanshuai

last: Fu

address: College of Fisheries and Life Science, Shanghai Ocean University

department: College of Fisheries and Life Science

institute: Shanghai Ocean University

summary: Many known miRNAs in fish come from zebrafish and fugu whose genome sequence data are available. The Japanese flounder undergoes typical metamorphosis which is characterized by major morphological, functional, and behavioral changes during growth due to this metamorphosis from larva to juvenile. Metamorphosis is a biological process by which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's body structure through cell growth and differentiation. Here, the high-throughput sequencing was adopted to identify the miRNAs during metamorphosis in the Japanese flounder. We found abundant microRNAs during metamorphosis in the Japanese flounder.

overall_design: Small RNAs were sequenced from metamorphosis stages of Japanese flounder

first: Zhiyi

last: Shi


status: Public on Jan 25 2011

first: Guoliang

last: Li

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

department: Computational and Systems Biology

summary: Using the estrogen receptor alpha (ERalpha) as a model ligand inducible transcription factor, we sought to explicitly define parameters that determine transcription factor binding site selection on a genomic scale in an inducible system that minimizes confounding chromatin effects by the transcription factor itself. By examining several genetic and epigenetic parameters, we find that an energetically favorable estrogen response element (ERE) motif sequence, evidence of occupancy of a "pioneering" transcription factor FOXA1, the presence of the enhancer mark, H3K4me1, and an open chromatin configuration (FAIRE) at the pre-ligand state provide specificity for ER binding. Genome-wide ChIP-sequencing was done in MCF-7 cancer cell line for the following histone H3 modifications: monomethylation H3K4me1, trimethylation H3K4me3, H3K9me3, H3K27me3, acetylation H3K9ac, H3K14ac. In addition sequencing of RNA Pol II was done at same treatment conditions (E2 and DMSO). In addition, we assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction.

overall_design: The analysis histone modifications in MCF-7 cancer cells was done by ChIP-seq data obtained either with E2 stimulation or without stimulation using vehicle as a control. Using the ERα binding sites defined by ChIP-seq (separate submission), we analyzed the population characteristics of the chromatin configuration of the ERα binding sites. To this end, we performed ChIP-seq analysis for the occupancy configuration of each of the following marks before and after E2 exposure: RNA Pol II, the activation marks H3K4me1, H3K4me3, H3K9ac and H3K14ac, and the repression marks H3K9me3 and H3K27me3. We assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The tag count of FAIRE fragments reflects the nucleosome depletion at any given site. RNA Pol II - Cat# ab5408, Abcam; H3K9me3 - Cat# ab8898, Abcam; H3K27me3 - Cat# 07-449, Upstate Biotechnology Inc.; H3K4me1 - Cat# ab8895, Abcam; H3K4me3 - Cat# ab8580, Abcam; H3K9ac - Cat# 07-352, Upstate Biotechnology Inc.; H3K14ac - Cat# 07-353, Upstate Biotechnology Inc.

first: Roy

last: Joseph

first: Say

last: Kong

first: Yuriy

last: Orlov

first: Edison

last: Liu


title: Formation, regulation and evolution of 3' UTRs in Caenorhabditis elegans

status: Public on Dec 24 2010

first: calvin

last: jan

address: 9 Cambridge center

institute: WIBR/MIT/HHMI

summary: Much of posttranscriptional mRNA regulation occurs through cis-acting sequences in mRNA 3´ untranslated regions (UTRs), which interact with specific proteins and ribonucleoprotein complexes that modulate translation, mRNA stability and subcellular localization.  Studies in Caenorhabditis elegans have revealed indispensable roles for 3´UTR-mediated gene regulation, yet most C. elegans genes have lacked annotated 3´UTRs.  Here we describe a high-throughput method to reliably identify 3´ ends of polyadenylated RNAs.  This method, called poly(A)-position profiling by sequencing (3P-Seq), was used to determine the UTRs of C. elegans.  Compared to standard methods also recently applied to C. elegans UTRs, 3P-Seq identified 8775 additional UTRs while excluding thousands of shorter UTR isoforms that do not appear to be authentic.  Analysis of this expanded and corrected dataset indicated that the high A/U content of C. elegans 3´UTRs facilitated genome compaction, since the elements specifying cleavage and polyadenylation, which are A/U-rich, can more readily emerge in A/U rich regions.  Indeed, 30% of the protein-coding genes have mRNAs with alternative, partially overlapping end regions that generate another 10,000 cleavage and polyadenylation sites that had gone largely unnoticed and represent potential evolutionary intermediates of progressive UTR shortening.  Moreover, a third of the convergently transcribed genes utilize palindromic arrangements of bidirectional elements to specify UTRs with convergent overlap, which also contributes to genome compaction by eliminating regions between genes.  Although nematode 3´UTRs have median length only one-sixth that of mammalian 3´UTRs, they have twice the density of conserved microRNA sites, in part because additional types of seed-complementary sites are preferentially conserved.  These findings reveal the influence of cleavage and polyadenylation on the evolution of genome architecture and provide resources for studying posttranscriptional gene regulation.

overall_design: Nine samples (10 sequencing runs) from various mixed and specific stages of wild-type Caenorhabditis elegans and glp-4 mutant adults.

first: Calvin

last: Jan

first: Robin

middle: C

last: Friedman

first: J

last: Ruby

first: David

last: Bartel


title: X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila males (Untreated)

status: Public on Dec 22 2010

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: MSL (Male-specific lethal) complex increases transcription on the single X chromosome of Drosophila males in order to equalize expression of X-linked genes between males (XY) and females (XX). The increase in transcript levels correlates with MSL- dependent acetylation of histone H4 at K16 within the bodies of active genes, but identification of the transcriptional step affected has not been possible. In this study, we use global run-on sequencing (GRO-seq) to examine the specific effect of MSL complex on RNA Polymerase II (RNAP II) on a genome-wide level. Results indicate that MSL complex enhances transcription by facilitating the progression of RNAP II across the bodies of active X-linked genes. Improving transcriptional output downstream of typical gene-specific control may explain how dosage compensation can be imposed on the diverse set of genes along an entire chromosome.

overall_design: Global Run-On Sequencing (GRO-Seq) reads, i.e., RNA-Seq of nascent RNA transcripts, from D. Melanogaster SL2 cells.  Two biological replicates were analyzed.

first: Erica

last: Larschan

first: Eric

middle: P

last: Bishop

middle: V

last: Kharchenko

first: Leighton

last: Core

first: John

last: Lis

first: Mitzi

middle: I

last: Kuroda


title: HIF-1synergizes with glucocorticoids to promote BFU-E progenitor self-renewal

status: Public on Dec 21 2010

first: Whitehead

last: Institute

department: Genome Technology Core

summary: With the aim of finding small molecules that stimulate erythropoiesis earlier than erythropoietin and that enhance CFU-E production, we studied the mechanism by which glucocorticoids increase CFU-E formation. Using BFU-E and CFU-E progenitors purified by a new technique, we demonstrate that glucocorticoids stimulate the earliest (BFU-E) progenitors to undergo limited self-renewal, which increases formation of CFU-E cells > 20-fold. Interestingly, glucocorticoids induce expression of genes in BFU-E cells that contain promoter regions highly enriched for hypoxia-induced factor 1 alpha (HIF1a) binding sites. This suggests activation of HIF1a may enhance or replace the effect of glucocorticoids on BFU-E self-renewal. Indeed, HIF1a activation by a prolyl hydroxylase inhibitor (PHI) synergizes with glucocorticoids and enhances production of CFU-Es 170-fold. Since PHIs are able to increase erythroblast production at very low concentrations of glucocorticoids, PHI-induced stimulation of BFU-E progenitors thus represents a conceptually new therapeutic window for treating Epo-resistant anemia.

overall_design: RNA-Seq was performed on enriched populations of BFU-E, CFU-E and Ter119+ as well as BFU-E enriched cells treated with Dex and DMOG

first: Johan

last: Flygare

first: Violeta

last: Estrada

first: Chanseok

last: Shin

first: Sumeet

last: Gupta

first: Harvey

middle: F

last: Lodish


title: Genome-wide identification of Polycomb-associated RNAs by RIP-seq

first: Mark

last: Borowsky

address: 185 Cambridge Street

institute: MGH

summary: Large-scale analyses have revealed that 60-90% of the mammalian genome is transcriptionally active. Because <2% of sequences have protein-coding potential, why so much cellular energy is expended on RNA synthesis is a major question in the post-genomic era. The hypothesis that RNA may serve as recruiting platforms for chromatin modifiers has gained ground with discoveries linking long ncRNAs, such as RepA, Xist, and Tsix, to locus-specific targeting of Polycomb proteins to the X-chromosome. Long ncRNAs have also been associated with Polycomb proteins at human HOX loci. Here, we ask if RNA targeting may be a general feature of regulation for mouse Polycomb repressive complex 2 (PRC2). We develop a method to capture the 'PRC2 transcriptome' by combining RNA immunoprecipitation (RIP) with deep sequencing (seq). RIP-seq of mouse embryonic stem cells identifies >3000 RNAs in the PRC2 transcriptome. Approximately 14% of RNAs originate from previously described PRC2-binding sites and many are promoter-associated. The transcriptome includes a large number of unannotated noncoding and antisense RNAs, with the X-chromosome exhibiting a high density of PRC2 RNAs. Imprinted genes and other disease genes, including those involved in cancer, are also well-represented. Functional validation of select candidates confirms RNA-PRC2 interactions in vivo and recruitment of Polycomb proteins in cis. Thus, RNA cofactors may be one general mechanism, among others, for targeting mammalian PRC2. Given PRC2's essential roles during stem cell renewal, development, and cancer, the PRC2 transcriptome described herein will provide a valuable resource for regenerative medicine and cancer biology.

overall_design: Identification and characterization of RNAs associated with PRC2 complex in mouse embryoinc stem cells

first: Jing

last: Zhao

first: Johnny

last: Kung

first: Toshiro

last: Ohsumi

first: Jeannie

last: Lee


title: Genome-wide maps of HNF4a and HNF4g binding state in HepG2 cells.

city: Meguro

first: Kenji

last: Daigo

state: Tokyo

department: Research Center for Advanced Science and Technology

country: Japan

institute: University of Tokyo

summary: Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor which has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady state remains to be elucidated. Here we report the native HNF4α isoforms, phosphorylation status and complexes in the steady state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semi-quantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and Hepatocyte nuclear factor-4γ was found. A biochemical and genome-wide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here is important for an accurate understanding of transcriptional regulation.

overall_design: Examination of HNF4alpha binding sites with domain-specific antibodies and HNF4gamma binding sites in HepG2 cell.

first: Takeshi

last: Kawamura

first: Yoshihiro

last: Ohta

first: Riuko

last: Ohashi

first: Satoshi

last: Katayose

first: Toshiya

last: Tanaka

first: Hiroyuki

last: Aburatani

first: Makoto

last: Naito

first: Tatsuhiko

last: Kodama

first: Sigeo

last: Ihara

first: Takao

last: Hamakubo


title: miRNA expression profiling in embryonic chicken heart

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

institute: Leiden University Medical Center

summary: MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique explicitly suitable for profiling of known and novel microRNAs. A modification to the small-RNA expression kit (SREK, Ambion) library preparation method for the SOLiD sequencing platform is described to generate microRNA sequencing libraries that are compatible with the Illumina Genome Analyzer. High quality sequencing libraries can successfully be prepared from as little as 100 ng small RNA enriched RNA. An easy to use perl-based analysis pipeline called E-miR was developed to handle the sequencing data in several automated steps including data format conversion, 3' adapter removal, genome alignment and annotation to non-coding RNA transcripts. Both the sample preparation and E-miR pipeline were successfully used to determine cardiac enriched microRNA expression in stage 16 chicken embryos.

overall_design: Comparing miRNA expression profiles for whole Chicken Embryo and isolated Heart tubes at developmental stage HH16

first: Yavuz

last: Ariyurek

first: Gertjan

last: van Ommen

first: Johan

last: den Dunnen

first: Peter-Bram

last: t Hoen


title: Genome-wide maps of Sin3A and Sin3B binding in C2C12 myoblasts and differentiated myotubes

city: New York

first: Brian

last: Dynlacht

department: Cancer Institute

institute: NYU Medical Center

summary: Sin3A and Sin3B bind to distinct and overlapping target sites. Sin3 proteins bind to distinct sites in cycling myoblasts whereas there is a converge of Sin3A and Sin3B proteins to sites in differentiated myotubes. We identified a subset of Sin3 target genes involved in muscle differentiation and physiology and showed that conditional  ablation of Sin3 proteins in vivo in mouse results in sarcomere defects

overall_design: Examination of Sin3A and Sin3B binding during myogenesis

first: Chris

last: van Oevelen

first: Christopher

last: Bowman

first: Patrick

last: Asp

first: Jemmie

last: Cheng

first: Fabio

last: Parisi

first: Mariann

last: Micsinai

first: Yuval

last: Kluger


title: Role of Prdm14 in mouse embryonic stem cells: ChIP-seq and RNA-seq analyses

city: Stanford

first: Ziyang

last: Ma

address: 269 Campus Dr, Room 3130

institute: Stanford University

summary: Prdm14 is a PR-domain and zinc-finger protein whose expression is restricted to the pluripotent cells of an early embryo, embryonic stem cells (ESCs), and germ cells. Here we show that Prdm14 safeguards mouse ESC maintenance by preventing induction of extraembryonic endoderm (ExEn) fates. Conversely, Prdm14 overexpression impairs ExEn differentiation during embryoid body (EB) formation. Prdm14 occupies and represses genomic loci encoding ExEn differentiation factors, while also binding to and promoting expression of genes associated with ESC self-renewal. Prdm14-bound genomic regions significantly overlap those occupied by Nanog and Oct4, are enriched in a chromatin signature associated with distal regulatory elements, and contain a unique DNA-sequence motif recognized by Prdm14 in vitro. Our work identifies Prdm14 as a new member of mouse ESC (mESC) transcriptional network, which plays a dual role as a context-dependent transcriptional repressor or activator at distal silencers and enhancers.

overall_design:
[ChIP-seq] Genome-wide mapping of Prdm14 binding sites in mouse embryonic stem cells:
A FLAG-HA tagged Prdm14 (FH-Prdm14) mESC line was established. FLAG-HA double ChIP (ChIP with FLAG antibody followed by ChIP with HA antibody) was performed with FH-Prdm14 mESCs (Prdm14-ChIPseq) and as a negative control, wildtype mESCs (FLAG-HA_ChIPseq).
H3K4me1 ChIPseq in mouse ES cells. Using published H3K4me1 data, we found there is a correlation between Prdm14 binding and H3K4me1 marks. So we obtained our own H3K4me1 data, using the wildtype mESCs.

[RNA-seq] Global RNAseq analysis of Prdm14 knockdown in mouse embryonic stem cells:
Analysis of poly(A)+ RNA from mESCs treated with non-targeting control siRNA and Prdm14 siRNA.

first: Joanna

last: Wysocka


title: A unique chromatin signature uncovers early developmental enhancers in humans

status: Public on Dec 15 2010

first: Alvaro

last: Rada

address: 269 Campus Drive, CCSR Building

department: Chemical and Systems Biology

summary: Cell fate transitions involve integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of the genomic sequences that control the earliest steps of human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs) unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, and monomethylation of histone H3 at lysine 4 (H3K4me1). In addition, the elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized enhancers active in hESCs, and are generally located proximally to genes expressed in hESCs and in the epiblast. In contrast, the elements within the second class, which we termed “poised enhancers”, are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3) and are linked to genes inactive in hESCs and involved in orchestrating early steps in mammalian development, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of these elements acquires a chromatin signature associated with active enhancers. Remarkably, when assayed in zebrafish embryos, human poised enhancer elements are able to direct cell type and stage specific expression patterns characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that enhancers are epigenetically pre-marked and suggest a heretofore unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the unique chromatin signature associated with poised enhancers allowed us to uncover over 2,000 putative developmental regulatory sequences, thereby creating an invaluable resource for future studies and isolation of transient, rare cell populations representing early steps of human development.

overall_design:
For GSM602289-90: RNA-seq experiments in human ESC and neuroectodermal (NEC) speheres

For GSM602291-303: Genome-wide analysis of p300, H3K4me3, H3K4me1, H3K27me3 and H3K27ac in human embryonic stem cells (ESC) and neuroectoderm cells (NEC). Additionally, in H9 ESC ChIP-seq were alsoe obtained for BRG1 and FAIRE-seq was also performed.

last: Rada-Iglesias


title: Proteomic analysis of native hepatocyte nuclear factor-4{alpha} (HNF4{alpha}) isoforms, phosphorylation status, and interactive cofactors.

first: Kenji

last: Daigo

summary:
Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor which has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady state remains to be elucidated. Here we report the native HNF4α isoforms, phosphorylation status and complexes in the steady state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semi-quantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and Hepatocyte nuclear factor-4γ was found. A biochemical and genome-wide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here is important for an accurate understanding of transcriptional regulation.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.

first: Takeshi

last: Kawamura

first: Yoshihiro

last: Ohta

first: Riuko

last: Ohashi

first: Satoshi

last: Katayose

first: Toshiya

last: Tanaka

first: Hiroyuki

last: Aburatani

first: Makoto

last: Naito

first: Tatsuhiko

last: Kodama

first: Sigeo

last: Ihara

first: Takao

last: Hamakubo


title: Selective chemical labeling reveals intragenic enrichment of 5-hydroxymethylcytosine in mouse cerebellum

status: Public on Dec 12 2010

city: Atlanta

first: Keith

last: Szulwach

state: GA

address: 615 Michael Street, Whitehead Suite 301

institute: Emory University

summary: 5-Methylcytosine (5-mC) is an important DNA modification found in eukaryotes that impacts gene regulation and disease pathogenesis. Recently, 5-hydroxymethylcytosine (5-hmC), another form of DNA modification, has been identified in substantial amounts in certain mammalian cell types; however, its roles as well as its distribution in mammalian genomes are unknown. Here we present a selective chemical labeling method for 5-hmC by utilizing T4 bacteriophage BGT-glucosyltransferase to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5-hmC, which in turn can chemically incorporate a biotin group for detection, affinity enrichment, and sequencing of 5-hmC in mammalian genomes. Using this highly effective method, we demonstrate that 5-hmC is present in human cell lines beyond those previously recognized. We also find a gene expression level-dependent enrichment of intragenic 5-hmC in mouse cerebellum and an age-dependent acquisition of this modification in specific gene bodies linked to neurodegenerative disorders

overall_design: Identification of 5hmC enriched genmoic regions in mouse cerebellum

first: Chuan

middle: H

last: Peng Jin


title: Genome-wide maps of Tamoxifen resistance MCF7 cell line

status: Public on Dec 20 2010

city: Columbus

first: Fei

last: Gu

state: Ohio

department: Molecular Virology, Immunology & Medical Genetics

institute: The Ohio State University

summary: We report the ER alpha regulatory network of Tamoxifen resistance MCF7 cell line using the Chromatin immunoprecipitated high-throughput sequencing technology (ChIP-seq). By Integrating the gene expression data (previously reported) with the ChIP-seq data, we generated ER alpha regulatory network and pathways. For ER alpha regulatory network, hub TFs with enriched motifs were identified from ER alpha peak together with PolII peaks. We then scan the position weight matrix (PWM) of ER alpha peak region of certain gene to find out the regulatory relationship between hub TF and normal TF. For regulatory pathway, genes were grouped base on their expression value at 4 different time point. Then the hub TF that plays important role in each time point of each group was identified. This study provides a framework for the application of ChIP-seq and gene expression data for the construction of ER alpha regulatory network.

overall_design: 4 different ChIP-seq dataset in Tamoxifen resistance MCF7 cell line

first: Hang-Kai

last: Hsu

first: Pei-Yin

first: Jiejun

last: Wu

first: Yilin

last: Ma

first: Jeffrey

last: Parvin

first: Tim

last: Huang

first: Victor

middle: X

last: Jin


title: Polycomb preferentially targets stalled promoters of coding and non-coding transcripts

city: 4058 Basel

first: Daniel

last: Enderle

state: Basel Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

summary: The Polycomb group (PcG) and Trithorax group (TrxG) of proteins are required for stable and heritable maintenance of repressed and active gene expression states. Their antagonistic function on gene control, repression for PcG and activity for TrxG, is mediated by binding to chromatin and subsequent epigenetic modification of target loci. Despite our broad knowledge about composition and enzymatic activities of the protein complexes involved, our understanding still lacks important mechanistic detail and a comprehensive view on target genes. In this study, we use an extensive data set of ChIP-seq, RNA-seq, and genome-wide detection of transcription start sites (TSSs) to identify and analyze thousands of binding sites for the PcG proteins and Trithorax from a Drosophila S2 cell line. In addition to finding a preference for stalled promoter regions of annotated genes, we uncover many intergenic PcG-binding sites coinciding with non-annotated transcription start sites. Interestingly, this set includes previously unknown promoters for primary transcripts of microRNA genes, thereby expanding the scope of Polycomb control to non-coding RNAs essential for development, apoptosis and growth.

overall_design: Chromatin from S2 cells was immunoprecipitated using antibodies against Pc, Ph, Psc, Trx-C or H3K4me3. In parallel, we isolated RNA from S2 cells and generated global gene expression profiles by RNA-seq. We also surveyed the Drosophila genome for yet non-annotated transcription start sites (TSSs) using a newly adapted protocol for Illumina sequencing (termed 5’-MACE) with RNA isolated from S2 cells and embryos.

first: Christian

last: Beisel

first: Michael

middle: B

last: Stadler

first: Moritz

last: Gerstung

first: Prashanth

last: Athri

first: Renato

last: Paro


title: Altered antisense-to-sense transcript ratios in breast cancer: Sage-Seq

status: Public on Dec 10 2010

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we describe consistent and significant differences in the distribution of sense and antisense transcripts between normal and neoplastic breast tissues. Many of the differentially expressed antisense transcripts likely represent long ncRNAs. A subset of genes that mainly generate antisense transcripts in normal but not cancer cells is involved in essential metabolic processes. These findings suggest fundamental differences in global RNA regulation between normal and cancer cells that might play a role in tumorigenesis.

overall_design: Global transcriptome profilings of 12 samples in normal and 9 samples in cancer from clinical breast tissue using Sage-Seq.

first: Maruyama

last: Reo

first: Michail

last: Shipitsin

first: Sibgat

last: Choudhury

first: Zhenhua

first: Alexei

last: Protopopov

first: Jun

last: Yao

first: Pang-Kuo

last: Lo

first: Marina

last: Bessarabova

first: Alex

last: Ishkin

first: Yuri

last: Nikolsky

first: Xiaole

last: Liu

first: Saraswati

last: Sukumar


title: Altered antisense-to-sense transcript ratios in breast cancer: ASSAGE

overall_design: Global strand-specific transcriptome profilings of 2 samples in cancer and 1 sample in normal from clinical breast tissue using asymmetrical strand-specific analysis of gene expression (ASSAGE).

last: Wu


title: Ovary small RNA

status: Public on Dec 13 2010

first: Nicolas

last: Robine

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
We sequenced small RNA from total RNA samples in two siRNA-pathway mutants in fly ovaries.

This submission comes from a modENCODE project. 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: Small RNAs were sequenced from D. melanogaster Canton S ovaries. Raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt.

first: Eric

last: Lai

first: Katsutomo

last: Okamura


title: Genome-wide mapping of the transcription factor GABP-alpha binding in human CD34+CD133+ hematopoietic progenitor cells.

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: We used ChIP-Seq to map GABP-alpha binding sites in human hematopoietic progenitor cells (HPCs). Coupled with functional assays using GABP-alpha deficient mouse model and bioinformatics analysis, we systematically determined a transcriptional module controlled by GABP in HPCs.

overall_design: Examination of the role of GABP in hematopoietic stem cells

first: Shuyang

last: Yu

first: Keji

last: Zhao

first: Hai-Hui

last: Xue


title: Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: Among its many roles in development, retinoic acid determines the anterior-posterior identity of differentiating motor neurons by activating Retinoic Acid Receptor (RAR)-mediated transcription. RAR is thought to bind the genome constitutively, and only induce transcription in the presence of the retinoid ligand. However, little is known about where RAR binds to the genome or how it selects target sites. We tested the constitutive RAR binding model using the retinoic acid-driven differentiation of mouse embryonic stem cells into differentiated motor neurons.  We find that retinoic acid treatment results in widespread changes in RAR genomic binding, including novel binding to genes directly responsible for anterior-posterior specification, as well as the subsequent recruitment of the basal polymerase machinery. Finally, we discovered that the binding of transcription factors at the embryonic stem cell stage can accurately predict where in the genome RAR binds after initial differentiation. We have characterized a ligand-dependent shift in RAR genomic occupancy at the initiation of neurogenesis. Our data also suggests that enhancers active in pluripotent embryonic stem cells may be preselecting regions that will be activated by RAR during neuronal differentiation.

overall_design: The differentiation of ventral motor neurons is induced by treating embryonic stem cell cultures with retinoic acid. Here, ChIP-seq is used to profile the genome-wide occupancy of RAR isofroms both immediately prior to and during exposure of the cells to retinoic acid. ChIP-seq is also used to profile the genomic occupancy of Pol2 with phosphorylated serine 5 (Pol2-S5P) and phosphorylated serine 2 (Pol2-S2P) after exposure to retinoic acid.

first: Esteban

middle: O

last: Mazzoni

first: Scott

last: McCuine

first: Richard

last: Young

first: Hynek

last: Wichterle

first: David

middle: K

last: Gifford


title: modENCODE_White Lab: genome-wide ChIP data of Su[var]3-9 from E0-12h on Illumina Genome Analyzer.

status: Public on Dec 09 2010

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Su[var]3-9 from E0-12h generated by ChIP and analyzed on Illumina Genome Analyzer.

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:
A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody.

This submission represents the ChIP-seq component of the study

last: Negre

first: Nicholas

last: Bild


title: ENCODE Cold Spring Harbor Labs Long RNA-seq

status: Public on Dec 28 2010

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

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

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Altered antisense-to-sense transcript ratios in breast cancer

city: Boston

first: Kornelia

last: Polyak

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


title: modENCODE_White Lab: genome-wide ChIP data of anti-Bonus-[GP37] from E16-24h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor anti-Bonus-[GP37] from E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer.

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

first: Nicolas


title: modENCODE_White Lab: genome-wide ChIP data of GFP from R13-E1-6h-Set2 on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor GFP from R13-E1-6h-Set2 generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: Comparison of the bovine embryonic transcriptomes using RNA-Seq

city: Madison

first: Wen

last: Huang

state: WI

address: 1675 Observatory Dr. Room 634

department: Department of Dairy Science

institute: University of Wisconsin - Madison

summary: Transcriptomes of bovine IVF embryos showing distinct developmental statuses were sequenced

overall_design: Two GA lanes for each of the two samples being compared

first: Hasan

last: Khatib


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Kr-D2 from E16-24h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Kr-D2 from E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: modENCODE_White Lab: genome-wide ChIP data of GFP from 5T-8-16h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor GFP from 5T-8-16h generated by ChIP and analyzed on Illumina Genome Analyzer.

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


title: A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (small RNA)

city: Nanchang

first: Lusheng

address: No. 1101, Zhimin Avenue

institute: Jiangxi Agricultural University

summary: Pig is the important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-seq) to generate a high-resolution map of the porcine miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from a F2 female full-sib pair with extreme phenotypes on growth and fat deposit. Through small RNA sequencing and on the basis of miRbase15.0, we detected a total of 184 mature miRNAs and 164 unique porcine novel miRNAs. Some conserved miRNAs, such as miR-122, miR-1, miR-206 and let-7 family showed high expression level in this study. Finally, we identified 10, 20 and 63 differentially expressed miRNAs, respectively, in LI, LD and AF. This high resolution and comprehensive transcriptome analysis significantly enhances the current genome annotation of pigs.

overall_design: examining the complexity of pig transcriptome in three organs from a female full-sib pair

first: Congying

last: Chen


title: Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto


title: Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation (ChIP-Seq)

summary: The rate of RNA polymerase II (pol II) elongation can influence splice site selection in nascent transcripts, yet the extent and physiological relevance of this kinetic coupling between transcription and alternative splicing is not well understood. We performed experiments to perturb pol II elongation and then globally compared alternative splicing patterns with genome-wide pol II occupancy. RNA binding and RNA processing functions were significantly enriched among the genes with pol II elongation inhibition-dependent changes in alternative splicing. Under conditions that interfere with pol II elongation, including cell stress, increased pol II occupancy was detected in the intronic regions flanking the alternative exons in these genes, and these exons generally became more included. A disproportionately high fraction of these exons introduced premature termination codons that elicited nonsense-mediated mRNA decay (NMD), thereby further reducing transcript levels. Our results provide evidence that kinetic coupling between transcription, alternative splicing and NMD affords a rapid mechanism by which cells can respond to changes in growth conditions, including cell stress, to coordinate the levels of RNA processing factors with mRNA levels.

overall_design: To monitor pol II distributions, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) was performed using an anti-pol II antibody (4H8) and cross-linked chromatin preparations from Jurkat cells, treated with or without pol II elongation inhibitor 5,6-dichloro-1-β-D-ribofuranosyl-benzimidazole (DRB) at 10 and 25 ug/ml respectively prior to phorbol 12-myristate 13-acetate (PMA) stimulation, for 5000+ alternative splicing events.

first: Joanna

middle: Y

last: Ip

first: Dominic

last: Schmidt

first: Arun

last: Ramani

first: Jonathan

last: Ellis

first: Andrew

last: Fraser

first: Duncan

middle: T

last: Odom

first: Benjamin

middle: J

last: Blencowe


title: EpiChip: Gene-by-gene quantification of epigenetic modification levels

status: Public on Dec 07 2010

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Rd

institute: University of Warwick

summary: Using datasets for the H3KAc histone modification in Th2 cells and an accompanying IgG control, we present an analysis strategy termed 'EpiChip' that alternates between single gene and global data distribution levels and allows a clear distinction between experimental background and signal.

overall_design: Examination of H3KAc histone modifications in one cell type plus an IgG control.


title: Digital gene expression tag profiling of digit morphologies in bats

status: Public on Dec 06 2010

first: Zhe

last: Wang

address: 3663 Zhongshan North Road

institute: East China Normal University

summary: As the only truly flying mammals, bats use their unique wing formed from elongated digits connected by membranes to power their flight. The forelimb of bats consists of four elongated digits (digits II-V) and one shorter digit (digit I) that is morphologically similar to the hindlimb digits. Elongation of bat forelimb digits is thought to results from changes in the temporal and spatial expression of a number of developmental genes. As a result, comparing gene expression profiles between short and elongated digit morphologies of the fore- and hindlimbs may elucidate the molecular mechanisms underlying digit elongation in bats. Here, we performed a large-scale analysis of gene expression of forelimb digit I, forelimb digits II-V, and all five hindlimb digits in Myotis ricketti using digital gene expression tag profiling approach. Results of this study not only implicate several developmental genes as robust candidates underlying digit elongation in bats, but also provide a better understanding of the genes involved in autopodial development in general.

overall_design: A large-scale analysis of gene expression of 3 different parts of autopods in Myotis ricketti using digital gene expression tag profiling approach.

first: Dong

last: Dong

first: Rebecca

middle: L

last: Young

first: Shuyi

last: Zhang


title: [E-MTAB-407] GENCODE PCR-Seq Batch II

status: Public on Dec 04 2010

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

summary:
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. This is batch II, based on annotation from April 2009.

ArrayExpress Release Date: 2010-10-28

Publication Title: GENCODE: producing a reference annotation for ENCODE
Publication Author List: Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R

Person Roles: submitter
Person Last Name: Kokocinski
Person First Name: Felix
Person Mid Initials:
Person Email: fsk@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

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:
Experimental Design: co-expression_design
Experimental Design: high_throughput_sequencing_design
Experimental Design: organism_part_comparison_design
Experimental Factor Name: ORGANISM_PART
Experimental Factor Type: organism_part