title: Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals [ChIP-seq]

summary: The mammalian circadian clock involves a transcriptional feedback loop in which CLOCK and BMAL1 activate the Period and Cryptochrome genes, which then feedback and repress their own transcription. We have interrogated the transcriptional architecture of the circadian transcriptional regulatory loop on a genome scale in mouse liver and find a stereotyped, time-dependent pattern of transcription factor binding, RNA polymerase II (RNAPII) recruitment, RNA expression and chromatin states. We find that the circadian transcriptional cycle of the clock consists of three distinct phases - a poised state, a coordinated de novo transcriptional activation state, and a repressed state. Interestingly only 22% of mRNA cycling genes are driven by de novo transcription, suggesting that both transcriptional and post-transcriptional mechanisms underlie the mammalian circadian clock. We also find that circadian modulation of RNAPII recruitment and chromatin remodeling occurs on a genome-wide scale far greater than that seen previously by gene expression profiling.

overall_design: Examination of 9 transcriptional regulators, 2 RNAPII and 6 histone modifications every 4hr during the circadian cycle in mouse liver


title: Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

status: Public on Aug 31 2012

city: Dallas

first: Joseph

middle: S

last: Takahashi

state: TX

address: 5323 Harry Hines Blvd., NA4.118

department: HHMI, Neuroscience

country: USA

institute: University of Texas Southwestern Medical Center

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series

first: Nobuya

last: Koike

first: Seung-Hee

last: Yoo

first: Hung-Chung

last: Huang

first: Vivek

last: Kumar

first: Choogon

last: Lee

first: Tae-Kyung

last: Kim


title: A Tetrahymena Piwi Bound to Mature tRNA 3' Fragments Activates the Exonuclease Xrn2 for RNA Processing in the Nucleus

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary:
Emerging evidence suggests that Ago/Piwi proteins function in the nucleus as well as the cytoplasm to control gene expression, but the mechanisms they employ in the nucleus remain poorly defined.
The Tetrahymena thermophila Ago/Piwi protein Twi12 is essential for growth and functions in the nucleus. We show that Twi12 interacts with the exonuclease Xrn2. Twi12 functions to stabilize and localize
Xrn2 in vivo, as well as activate its exonuclease activity in vitro. When Twi12 or Xrn2 are depleted, pre-rRNA processing intermediates accumulate and mature rRNA levels decline. RNA polymerase I and II
(RNAP I and II) transcripts also accumulate. Twi12 function depends on small RNA (sRNA) binding, which is required for its nuclear import. Twi12-bound sRNAs are Dicer-independent 3' tRNA fragments that
we propose may not be involved in sequence-specific base pairing to targets. Our findings suggest a role for tRNA fragments and an Ago/Piwi protein in global control of gene expression through interaction
with a conserved exonuclease.

overall_design:
One library is analyzed here: small RNAs associated with ZZF-tagged Twi12. Twi12 is the full-length version, which is extended by 17 amino acids at the N-terminus compared to the previously-reported Twi12.
Specifically, the 16-22 nt reads were analyzed here.

first: Gergana

last: Bounova

first: Elizabeth

last: Purdom

first: Terence

middle: P

last: Speed

first: Kathleen

last: Collins


title: Evolutionary Significance of DNA Methylation in Human and Chimpanzee Brains

status: Public on Sep 04 2012

city: Atlanta

first: Jia

last: Zeng

state: GA

address: Georgia Institute of Technology

department: School of Biology

institute: Georgia Institute of Technology

type: Methylation profiling by high throughput sequencing

summary: We compared the genome-wide patterns of DNA methylation in the brains of humans to those of our closest evolutionary relative, chimpanzees, using base-pair resolution whole-genome methylation maps of the prefrontal cortex.  Our data reveal that the prefrontal cortex is the most heavily methylated among the human tissues examined so far.  Nevertheless, hundreds of genes exhibit dramatically reduced levels of promoter DNA methylation in the human brain relative to the chimpanzee brain.  Many of these genes are associated with neurological disorders, psychological disorders, and cancers, and are enriched for functions related to cellular metabolic processes and protein binding.  Moreover, the majority of these genes exhibit higher expression in the human brain compared to the chimpanzee brain.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Profiling DNA methylation map in prefrontal cortex regions of postmortem brains of three humans and three chimpanzees

first: Zeng

last: Jia

first: Yi

last: Soojin


title: SOX2 gene regulates the transcriptional network of oncogenes and affects tumorigenesis of human lung cancer cells

city: Tianjin

last: LI

address: 94 Weijin Road

country: China

institute: NANKAI University

summary: Recent studies demonstrated that cancer stem cells (CSCs) have higher tumorigenesis properties than those of differentiated cancer cells and that transcriptional factor-SOX2 plays a vital role in maintaining the unique properties of CSCs; however, the function and underlying mechanism of SOX2 in carcinogenesis of lung cancer are still elusive. This study applied immunohistochemistry to analyze the expression of SOX2 in human lung tissues of normal individuals as well as patients with adenocarcinoma, squamous cell carcinoma, large cell and small cell carcinoma and demonstrated specific overexpression of SOX2 in all types of lung cancer tissues. This finding supports the notion that SOX2 contributes to the tumorigenesis of lung cancer cells and can be used as a diagnostic probe. In addition, obviously higher expression of oncogenes c-MYC, WNT1, WNT2 and NOTCH1 was detected in side population (SP) cells than in none side population (NSP) cells of human lung adenocarcinoma cell line-A549, revealing a possible mechanism for the tenacious tumorigenic potential of CSCs. To further elucidate the function of SOX2 in tumorigenesis of cancer cells, A549 cells were established with expression of luciferase and doxycycline inducible shRNA targeting SOX2. We found silencing of SOX2 gene reduces the tumorigenic property of A549 cells with attenuated expression of c-MYC, WNT1, WNT2 and NOTCH1 in xenografted NOD/SCID mice. By RNA-Seq method, additional 246 target cancer genes of SOX2 were revealed. These results present evidence that SOX2 may regulate the expression of oncogenes in CSCs to promote the development of human lung cancer.

overall_design: Examination of mRNA profiles in A549 cells with SOX2 silencing

last: Li

first: Si

last: Chen

first: Rong

last: Xiang


title: MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs

city: Stockholm

first: Johan

last: Reimegård

state: Solna

address: Tomtebodavägen 23A

country: Sweden

institute: Science for Life Laboratories

summary: We found 16 miRNAs in D. discoideum. Several were differentially expressed during growth and multicellular development.

overall_design: HTS of small RNAs was analyzed to identify miRNAs. Some of the miRNAs were then further verified using different experimental approaches.

first: Lotta

last: Avesson

first: Gerhart

last: Wagner

first: Fredrik

last: Söderbom


title: Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA.

city: Cold Spring Harbor

first: Joseph

last: Calarco

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

summary: Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information each generation by germline reprogramming. To assess the extent of germline reprogramming in plants, we sequenced the methylome of three haploid cell types from developing pollen: the sperm cell (SC), the vegetative cell, and their precursor the post-meiotic microspore.

overall_design: Whole genome bisulfite sequencing of FACS-purified sperm cells, vegetative nuclei and microspores

first: Filipe

last: Borges

first: Mark

last: Donoghue

first: Frédéric

last: Van Ex

first: Pauline

middle: E

last: Jullien

first: Telma

last: Lopes

first: Rui

last: Gardner

last: Berger

first: José

middle: A

last: Feijó

first: Jörg

middle: D

last: Becker

first: Robert

last: Martienssen


title: Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris using Xpression, an integrated tool for prokaryotic RNA-seq data processing

status: Public on Sep 01 2012

city: Seattle

first: Somsak

last: Phattarasukol

state: WA

address: 1705 NE Pacific St., HSC K-327

department: Microbiology

institute: University of Washington

summary: High-throughput sequencing of cDNA prepared from RNA, an approach known as RNA-seq, is coming into increasing use as a method for transcriptome analysis. Despite its many advantages, widespread adoption of the technique has been hampered by a lack of easy-to-use, integrated, open source tools for analyzing the nucleotide sequence data that are generated. Here we describe Xpression, an integrated tool for processing prokaryotic RNA-seq data. The tool is easy to use and is fully automated. It performs all essential processing tasks including nucleotide sequence extraction, alignment, quantification, normalization and visualization. Importantly, Xpression supports multiplexed and strand-specific nucleotide sequence data. It extracts and trims specific sequences from files and separately quantifies sense and antisense reads in the final results. Outputs from the tool can also be conveniently used in downstream analysis. In this paper, we show the utility of Xpression to process strand-specific RNA-seq data to identify genes regulated by CouR, a transcription factor that controls p-coumarate degradation by the bacterium Rhodopseudomonas palustris.

overall_design: Comparison of wild-type vs. couR mutant RNA-seq data to identify genes regulated by CouR. 2 wild-type replicates, 1 couR mutant replicate.

first: Caroline

last: Harwood


title: Maternal slimming reprograms metabolic gene expression in mice offspring  (mRNA-Seq)

status: Public on Aug 30 2012

city: Beijing

first: yanchang

last: wei

address: #1 Beichen West Rd

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Slimming is globally prevalent especially in young women, and it may contribute to the metabolic health of their offspring. Whereas some Lamarckian ideas about environmental inheritance have been dismissed, increasing evidence suggest that certain acquired traits can be transmitted to the next generation. It is therefore of great interest to determine how and to what extent a maternal lifestyle change contributes to their offspring. Here we show that enriched environment (EE) induced maternal slimming improves general health and reprograms metabolic gene expression in mice offspring. EE in mothers induced decreased body weight, adiposity, and improved glucose tolerance and insulin sensitivity. Relative to controls, their offspring exhibited improved general health such as reduced fat accumulation, enhanced metabolic parameters as well as glucose tolerance and insulin sensitivity. Maternal slimming altered the expression of 1,732 genes in the liver of offspring, with coherent downregulation of genes involved in lipid and cholesterol biosynthesis. Epigenomic profiling in offspring revealed numerous changes in cytosine methylation depending on maternal slimming, including hypermethylation of several genes involved in lipid biosynthesis, correlated with the downregulation of these genes. Maternal slimming also altered overall transcriptome patterns in mature oocytes, which contributes largely to the metabolic health and gene expression patterns in offspring. Overall, our studies suggest that maternal slimming have a beneficial role in regulating metabolic profiles in offspring, implying that it might be considered as a potential strategy to reverse the global prevalence of obesity and related metabolic syndromes.

overall_design: Examination of the effect of 2 different maternal lifestyles, control and slimming, on the mRNA expression in the mature oocytes of the female mice. Naturally ovulated mature oocytes (MII stage) were collected from 3 control and 3 slimming female F0 founders (3 oocytes per mouse, 9 oocytes for each group).

first: Yanchang

last: Wei

first: Qing

middle: Y

last: Sun


title: Bromodomain-dependent stage-specific male genome programming by Brdt

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA


title: Bromodomain-dependent stage-specific male genome programming by Brdt [ChIP-Seq]

summary: Male germ cell differentiation is a highly regulated multistep process initiated by the commitment of progenitor cells into meiosis and characterized by major chromatin reorganizations in haploid spermatids. We report here that a single member of the double bromodomain BET factors, Brdt, is a master regulator of both meiotic divisions and post-meiotic genome repackaging. Upon its activation at the onset of meiosis, Brdt drives and determines the developmental timing of a testis-specific gene expression program. In meiotic cells, Brdt initiates a genuine histone acetylation-guided programming of the genome by activating essential meiotic genes and repressing a “progenitor cells” gene expression program, while “priming” a post-meiotic gene group for further activation. At post-meiotic stages, a global chromatin hyperacetylation gives the signal for Brdt’s first bromodomain to direct the genome-wide replacement of histones by transition proteins. Brdt is therefore a unique and essential regulator of male germ cell differentiation, which, by using various domains in a developmentally controlled manner, first drives a specific spermatogenic gene expression program, and later controls the tight packaging of the male genome.

overall_design: Examination of Brdt binding on chromatin in meiotic (spermatocytes) and post-meiotic (round spermatids) male germ cells from adult wild type mice and mice with a deletion of Brdt BD1 (first bromodomain).

first: Saadi

last: Khochbin

first: Emilie

last: Montellier

first: Jean

last: Imbert

first: Hélène

last: Holota

first: Fabrice

last: Lopez


title: RAMPAGE dataset for the human K562 cell line

city: Woodbury

first: Philippe

last: Batut

address: 500 Sunnyside Blvd.

institute: CSHL

summary: 5'-complete cDNA sequencing on ribosome-depleted total RNA from the human K562 cell line. Provides high-quality, genome-wide single-base resolution profiling of transcription start sites and their expression levels.

overall_design: This dataset represents a whole-genome, single-base resolution profiling of transcription start site (TSS) expression in the human K562 cell line. These profiles were established using RAMPAGE, a high-throughput, high-accuracy 5'-complete cDNA sequencing method implemented on the Illumina platform. The data was analyzed using custom scripts and algorithms that are all available upon request.

first: Alexander

last: Dobin

first: Charles

last: Plessy

first: Piero

last: Carninci

first: Thomas

middle: R

last: Gingeras


title: 96 mRRBS libraries: Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA

status: Public on Aug 29 2012

city: Cambridge

first: Kendell

last: Clement

address: 7 Divinity Ave.

institute: Harvard University

summary: Sequencing based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To further facilitate the mapping of DNA methylation, we describe a protocol for gel-free multiplexed reduced representation bisulfite sequencing (mRRBS) that reduces the workload dramatically and enables processing of 96 or more samples per week. mRRBS achieves similar CpG coverage as the original RRBS protocol, while the higher throughput and lower cost make it better suited for large-scale DNA methylation mapping studies including cohorts of cancer samples.

overall_design: Libraries of 96 human samples

first: Boyle

last: Patrick

first: Clement

last: Kendell

first: Gnirke

last: Andreas

first: Meissner

last: Alexander


title: RNA expression in Drosophila melanogaster mutants lacking HP1a

city: St. Louis

first: Nicole

middle: Christina

last: Riddle

state: MO

address: 1 Brookings Dr.; CB1137

department: Biology

institute: Washington University

summary: mRNA expression levels were determined by NGS for wildtype larvae as well as for larvae lacking HP1a [Su(var)205^04/Su(var)205^05 transheterozygotes].

overall_design: RNA samples from wildtype (OR) and HP1a mutant third instar larvae were examined, using duplicate biological samples and Illumina NGS.

middle: C

first: Sarah

last: Elgin


title: Genome-wide maps of Foxa2 binding sites in mouse embryonic stem cell-derived definitive endoderm cells

first: Chenhuan

last: Xu

address: 1 Beichen West Road

institute: Beijing Institute of Genomics

summary: Foxa2 is required for endoderm differentiation into hepatic lineage. The mechanism of activation for Foxa2 during this developmental process has not been elucidated yet. We established an in vitro system to guide ES cells differentiating into definitive endoderm (DE) cells and the following DE cells to early hepatic cells. ChIP-seq assays have been successfully performed to assess Foxa2 binding profile. Over 50% of Foxa2 target genes in DE cells were found being activated in hepatic cells which were at a stage later than DE stage. Therefore, our finding at genome-wide level proved Foxa2 serving as a pioneer factor at DE stage. Furthermore, Foxa2 could specifically induce H3K4me2 modifications to the promoter/enhancer regions of many hepatic genes to pre-mark the chromatin, and determine the hepatic lineage differentiation competence. Our study illustrated the wide existence of Foxa2’s pioneer factor function and uncovered the correlation between pioneer factor and chromatin pre-mark. These findings will be helpful for understanding the developmental process of hepatogenesis and efficiently controlling Foxa2 during hepatic induction for generating functional hepatocytes.

overall_design: Examination of Foxa2 binding sites in mESC-derived DE cells

first: Xiaowen

last: Lyu

first: Eric

middle: Z

last: Chen

first: Zhiying

last: He

first: Guangpeng

last: Li

first: Yue

last: Ma

first: Lijian

last: Hui

first: Bin

last: Xie

first: Yuan

last: Gao

first: Xiaoyan

last: Ding

first: Yiping

last: Hu

first: Ping

first: Jing-Dong

middle: J

last: Han

first: Xin

last: Wang


title: Chromatin accessibility, p300 and histone acetylation define PML-RARalpha- and AML1-ETO-binding sites

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: Chromatin accessibility is a key determinant of cell-type-specific gene expression. Here, we have investigated the chromatin architecture of different acute myeloid leukemia (AML) cells and the changes in accessibility when NB4 (APL) cells undergo the process of differentiation.

overall_design:
For nuclease-accessible site sequencing (NA-seq; Gargiulo et al. 2009), chromatin-accessible libraries were generated in different AML leukemic cells by using restriction enzymes NlaIII and HpaII. In the case of NB4 cells, accessibility was mapped both before and after treatment with all-trans retinoic acid (ATRA) for 48hr. Differences were observed between the two conditions, and chromatin accessibility was correlated with underlying epigenetic modifications. For validation purposes, NA-seq libraries (using the NlaIII enzyme) were generated in APL and AML M1 patient's blasts. All of the ChIP-seq (Martens et al. 2010) studies were performed in leukemic NB4 and SKNO-1 cells.

Supplementary file 'GSE30254_All_accessibleregions_ATRA_NB4_fseq.wig' includes data for Samples GSM749512, GSM749513, GSM749516, and GSM749517.
Supplementary file 'GSE30254_All_accessibleregions_untreated_NB4_fseq.wig' includes data for Samples GSM749510, GSM749511, GSM749514, and GSM749515.

first: Henk

middle: G

first: Joost

middle: H

last: Martens

first: Sadia

last: Saeed

first: Colin

last: Logie

first: Kees-Jan

last: Francoijs

first: Gian

middle: M

last: Frigè

first: Mauro

last: Romanenghi

first: Fiona

last: Nielsen

first: Lianne

last: Raats

first: Maryam

last: Shahhoseini

first: Martijn

last: Huynen

first: Lucia

last: Altucci

first: Saverio

last: Minnuci


title: LID ChIP-Seq in wild type, and H3K4me3 ChIP-Seq in wild type and lid RNAi Drosophila melanogaster

city: Barcelona

first: David

last: Rossell

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

summary: LID is a histone demethylase acting on H3K4me3, a mark related to transcription and found near the transcription start sites (TSS) of the genes. We analyzed where LID is localized and the effects of LID downregulation in the distribution of H3K4me3.

overall_design: Analysis of LID-binding sites in wild type, and of H3K4me3-binding sites in wild type and LID RNAi wing imaginal discs.

first: Marta

last: Lloret-Llinares

first: Fernando

last: Azorin


title: Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells

status: Public on Aug 28 2012

city: La Jolla

first: Kun

last: Zhang

state: CA

address: 9500 Gilman Dr Mailcode: 0412

department: Bioengineering

institute: University of California, San Diego

summary: In this work, we characterized the epigenomic integrity of 17 hiPSC lines derived from six different cell types with varied reprogramming efficiencies. We demonstrate that epigenetic aberrations are a general feature of the hiPSC state and are independent of the somatic cell source. Additionally, we determine that both shared and line-specific epigenetic aberrations in hiPSCs can directly translate into changes in gene expression in both the pluripotent and differentiated states.

overall_design:
Examination of differential methylation between iPSC and ESCs through differentiated states.
Examination of differential methylation between iPSC and somatic cell source and iPSC and ESCs.

first: Nongluk

last: Plongthongkum

first: Dinh

last: Diep

first: Athurva

last: Gore

first: Ho-Lim

last: Fung


title: microRNA-target RNA pairs revealed by Parallel analysis of RNA ends in Solanum lycopersicum

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

country: United Kingdom

institute: University of East Anglia

summary: Solanum lycopersicum RNA degradome sequencing

overall_design: Isolated polyadenylated RNA from total RNA extracts of Solanum lycopersicum, were ligated to 5'-adapter that includes an MmeI recognition site. The ligated products were purified again, reverse transcribed and cleaved with MmeI. The 5' fragments were purified from gel and ligated to a 3'- dsDNA adapter and PCR amplified. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

first: Gyorgy

last: Szittya

first: Irina

last: Mohorianu

first: Sara

last: Lopez-Gomollon

first: Frank

last: Schwach

first: Runchun

last: Jing

first: Tamas

last: Dalmay


title: EBNA1 ChIP-seq and MNase-seq in EBV-positive MUTU cell lines

city: New York

first: Aaron

last: Arvey

institute: Memorial Sloan-Kettering Cancer Center

summary: Epstein-Barr Virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B-lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome.  We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B-cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration.

overall_design: Six sequencing experiments were performed.  One EBNA1 ChIP-seq was controlled with IgG ChIP-seq.  Two MNase-seq biological replicates were each conrolled by input seq using the same cells subjected to MNase digestion.

first: Italo

last: Tempera

first: Fang

last: Lu

first: Priyankara

last: Wikramasinghe

first: Paul

last: Lieberman


title: Long non-coding RNAs from divergent transcription of protein-coding genes

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: A remarkable number of long non-coding RNA (lncRNA) species have been identified in mammalian cells, but the genomic origins of these molecules in individual cell types is poorly understood.  As a prerequisite to studying the transcriptional regulation of lncRNAs, we conducted a comprehensive analysis of the genomic origins of lncRNAs expressed in embryonic stem cells (ESCs).

overall_design: Polyadenylated RNA and total RNA depleted of ribosomal content was used for preparation of two independent  sequencing libraries

first: Alla

last: Sigova


title: Drosophila dKDM5/LID regulates H3K4me3 dynamics at the transcription start site of actively transcribed developmental genes

first: David

last: Rossell

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

overall_design: Refer to individual Series


title: Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans (Bisulfite-Seq)

status: Public on Aug 27 2012

first: Thomas

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

institute: University of Cambridge

summary: A major concern in common disease epigenomics is distinguishing causal from consequential epigenetic variation. One means of addressing this issue is to identify the temporal origins of epigenetic variants via longitudinal analyses. However, prospective birth-cohort studies are expensive and time-consuming. Here we report DNA methylomics of archived Guthrie cards for the retrospective longitudinal analyses of in utero-derived DNA methylation variation. We first validate two methodologies for generating comprehensive DNA methylomes from Guthrie cards. Then, using an integrated epigenomic/genomic analysis of Guthrie cards and follow-up samplings, we identify inter-individual DNA methylation variation that is present both at birth and three years later. These findings suggest that disease-relevant epigenetic variation could be detected at birth i.e. before overt clinical disease. Guthrie card methylomics offers a potentially powerful and cost-effective strategy for studying the dynamics of inter-individual epigenomic variation in a range of common human diseases.

overall_design: Bisulphite converted DNA was sequenced

first: H

last: Beyan

first: T

first: S

middle: V

last: Ramagopalan

first: K

last: Uvebrant

first: A

last: Nilsson

first: M

middle: L

last: Holland

first: C

last: Gemma

first: G

last: Giovannoni

first: B

middle: O

last: Boehm

last: Ebers

last: Lernmark

last: Cilio

first: R

last: Leslie

first: V

middle: K

last: Rakyan


title: Maternal slimming reprograms metabolic gene expression in mice offspring

first: yanchang

last: wei

type: Methylation profiling by genome tiling array


title: Id2a knockdown in zebrafish retina

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

summary: During vertebrate retinogenesis, the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways.  Moreover, there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways, which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non-autonomous role for the intrinsic HLH factor, Id2a, in regulating retinoblast proliferation and differentiation, with Id2a-deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia.  Here, we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis.  Id2a-deficient retinae possess elevated levels of Notch pathway component gene expression, while retinae overexpressing id2a possess reduced expression of Notch pathway component genes.  Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a-deficient retinae. In addition to regulating Notch pathway activity, through an RNA-Seq and differential gene expression analysis of Id2a-deficient retinae, we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a.  These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis.

overall_design: Two biological replicates for both Id2aMM and Id2aMO samples

first: Jeff

last: Gross

first: Rosa

last: Uribe

first: Edward

last: Marcotte


title: Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans

first: Thomas

last: Down


title: Genome wide maps of E2F7 binding in IMR90 cells

status: Public on Aug 25 2012

first: Ozlem

last: Aksoy

address: 415 East 68th Street

department: Watson School of Biological Sciences

summary: Oncogene-induced senescence is an anti-proliferative stress response program that acts as a fail-safe mechanism to  limit oncogenic transformation and is regulated by the retinoblastoma protein (RB) and p53 tumor suppressor  pathways. We identify the atypical E2F family member E2F7 as the only E2F transcription factor potently upregulated  during oncogene-induced senescence, a setting where it acts in response to p53 as a direct transcriptional  target. Once induced, E2F7 binds and represses a series of E2F target genes and cooperates with RB to efficiently  promote cell cycle arrest and limit oncogenic transformation. Disruption of RB triggers a further increase in E2F7,  which induces a second cell cycle checkpoint that prevents unconstrained cell division despite aberrant DNA  replication. Mechanistically, E2F7 compensates for the loss of RB in repressing mitotic E2F target genes.

overall_design: Examination of E2F7 binding in either growing or senescent IMR90 cells with different hairpins.

first: Agustin

last: Chicas

first: Scott

middle: W

last: Lowe

first: Xiaowo

last: Wang

first: Tianying

last: Zeng


title: Genome-wide maps of O-GlcNAc-Oct4 binding regions in ZHBTc4 F-Oct4 mouse embryonic stem cells

city: daejeon

first: Tae-Wook

last: Kang

address: 111 Gwahangno, Yuseong-gu

institute: KRIBB

summary: We report that Oct4 is modified by O-GlcNAc in stem cells. To find O-GlcNAc-Oct4 target genes, we ChIPed Oct4 with Flag(Oct4) antibody and then O-GlcNAc modified proteins are enriched by sWGA beads (succinylated wheat germ agglutinin (sWGA), which specifically binds O-GlcNAc). Results show that several genes implicated in pluripotency regulation are bound by O-GlcNAc-Oct4 in their gene region.

overall_design: 2 samples examined: Control (ChIP with anti-Flag(Oct4) and then reChIP with IgG), O-GlcNAc-Oct4 (ChIP with anti-Flag (Oct4) and then reChIP with sWGA)

first: Hong-Duk

last: Youn

first: Hyonchol

last: Jang

first: Tae

last: Kim

first: Seon-Young


title: The genetics and regulatory logic of alternative polyadenylation in human lymphoblastoid cells

city: Berkeley

first: Oh Kyu

last: Yoon

address: Stanley Hall rm 378

department: Molecular & Cell Biology

institute: UC Berkeley

summary: We set out to investigate genomic mechanisms by which alternative polyadenylation impacts gene expression and its variation across genetically distinct human individuals. We used 3’-end RNA-seq to maximize genome coverage and precision of transcript end positions, and to measure quantitative expression levels of transcript forms. The results shed light on the architecture of transcript ends and regulatory elements in human 3’ UTRs and the principles of genetic variation in 3’ length form usage.

overall_design: Survey of transcript 3' end positions in B-lymphocyte cell lines derived from six human individuals (two biological replicates each)

first: Oh-Kyu

first: Tiffany

last: Hsu

first: Rachel

middle: B

last: Brem


title: Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows

city: Dunsany

first: Cathriona

last: Foley

address: Grange

country: Ireland

institute: Teagasc

summary: All cows experience bacterial contamination and tissue injury in the uterus postpartum, instigating a local inflammatory immune response. However mechanisms that control inflammation and achieve a physiologically functioning endometrium, while avoiding disease in the postpartum cow are not succinctly defined. This study aimed to identify novel candidate genes indicative of inflammation resolution during involution in healthy beef cows. Previous histological analysis of endometrial inflammation showed a great degree of inflammation 15 days postpartum (DPP) which significantly decreased by 30 DPP. The current study generated a genome-wide transcriptomic profile of endometrial biopsies at both time points using mRNA-Seq. The pathway analysis tool GoSeq identified KEGG pathways enriched by significantly differentially expressed genes elevated at both time points. Novel candidate genes of inflammatory resolution were subsequently validated in additional postpartum animals using quantitative real-time PCR (qRT-PCR).

overall_design: Endometrial biopsies were collected as part of a previous study 15 and 30 days postpartum (DPP) from 13 mixed breed beef multiparous cows. The endometrial transcriptomic profiles from endometrial biopsies were assessed by mRNA-Seq (n=3) and candidate gene expression was measured by qRT-PCR (n=5) comparing 15 DPP to 30 DPP samples. Reads were mapped to the bovine genome with TopHat, Htseq-count summarized the number of aligned reads per exon and EdgeR normalized the data and returned significantly differentially expressed genes. GoSeq identified KEGG pathways enriched by significantly differentially expressed genes elevated at both time points.

first: Aspinas

last: Chapwanya

first: Christopher

last: Creevey

first: Fernando

last: Narciandi

first: Derek

last: Morris

first: Elaine

last: Kenny

first: Paul

last: Cormican

first: John

last: Callanan

first: Cliona

last: O’Farrelly

first: Kieran

last: Meade


title: Dual-mode modulation of Smad signaling by Smad-interacting protein Sip1 is required for myelination in the central nervous system

city: Dallas

first: Qing

middle: Richard

last: Lu

address: 5323 Harry Hines Boulevard

institute: UT southwestern medical center

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: CIRP, a cold-inducible RNA-binding protein, modulates circadian gene expression posttranscriptionally

status: Public on Aug 24 2012

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: University of Geneva

summary: In mammalian tissues circadian gene expression can be driven by local oscillators or systemic signals controlled by the master pacemaker in the suprachiasmatic nucleus. Here we show that simulated body temperature cycles, but not peripheral oscillators, can control the rhythmic expression of Cold-Inducible RNA binding Protein (CIRP) in cultured fibroblasts. In turn, loss-of-function experiments indicate that CIRP is required for high amplitude circadian gene expression. The transcriptome-wide identification of CIRP-bound RNAs by a biotin-streptavidin based CLIP-seq procedure revealed several CIRP-bound transcripts encoding circadian oscillator proteins. One of these, CLOCK, accumulated to particularly low levels in CIRP-depleted fibroblasts. Since ectopic expression of CLOCK improved circadian gene expression in these cells, we surmise that CIRP confers robustness to circadian oscillators via the regulation of CLOCK expression.

overall_design: Identification of CIRP-interacting RNA molecules in NIH3T3 cells and RNA expression in NIH3T3 cells treated with Control or CIRP siRNA after incubation of the cells at 33°C for 8 hours

first: Jörg

last: Morf

first: Kim

last: Schneider

first: Markus

last: Stratmann

first: Jun

last: Fujita

first: Felix

last: Naef

first: Ueli

last: Schibler


title: Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes

city: Zürich

first: Niklaus

last: Zemp

address: Universitätsstrasse 16

department: IBZ

institute: ETH Zurich

summary: Silene latifolia is a dioecious plant with heteromorphic sex chromosomes that have originated only ~10 MYA and is a promising model organism to study sex chromosome evolution in plants. Previous work suggests that S. latifolia XY chromosomes have gradually stopped recombining and the Y chromosome is undergoing degeneration as in animal sex chromosomes. However, this work has been limited by the paucity of sex-linked genes available. Here, we used 35 Gb of RNA-seq data from multiple males (XY) and females (XX) of a S. latifolia inbred line to detect sex-linked SNPs and identified more than 1700 sex-linked contigs (with X-linked and Y-linked alleles). Analyses using known sex-linked and autosomal genes, together with simulations indicate that these newly identified sex-linked contigs are reliable. Using read numbers, we then estimated expression levels of X-linked and Y-linked alleles in males and found an overall trend of reduced expression of Y-linked alleles, consistent with a widespread ongoing degeneration of the S. latifolia Y chromosome. By comparing expression intensities of X-linked alleles in males and females, we found that X-linked allele expression increases as Y-linked allele expression decreases in males, which makes expression of sex-linked contigs similar in both sexes. This phenomenon is known as dosage compensation and has so far only been observed in evolutionary old animal sex chromosome systems. Our results suggest that dosage compensation has evolved in plants and that it can quickly evolve de novo after the origin of sex chromosomes.

overall_design: 2 Samples (male and female) in triplicates

first: Alex

last: Widmer


title: 5-hmC in the brain: abundance in synaptic genes and differences at the exon-intron boundary (MRE-Seq)

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

summary:
5-hydroxymethylcytosine (5-hmC), a derivative of 5-methylcytosine (5-mC), is abundant in the brain for unknown reasons. We mapped the genomic distribution of 5-hmC and 5-mC in human and mouse tissues using glucosylation of 5-hmC coupled with restriction enzyme digestion, and interrogation on microarrays. We detected 5-hmC enrichment in genes with synapse-related functions in the brain.
We also identified significant, tissue-specific differential distributions of these DNA modifications at the exon-intron boundary, in both human and mouse.  This boundary change was mainly due to 5-hmC in the brain, but due to 5-mC in non-neural contexts. This pattern was replicated in multiple independent datasets, and the brain-specific change in 5-hmC was validated using single-molecule sequencing. Moreover, in the brain, constitutive exons contained higher levels of 5-hmC, relative to alternatively-spliced exons. Our study suggests a novel role for 5-hmC in RNA splicing and synaptic function in the brain

overall_design:
The β-glucosyltransferase (BGT) enzyme transfers a glucose molecule specifically to the hydroxymethyl group of 5-hmC, thus rendering it resistant to digestion by the methylation insensitive MspI enzyme at the ChmCGG target site;  5-hmC is thus detected by differential resistance to MspI-digestion with and without glucosylation of genomic DNA (gDNA).  HpaII (targets the same site, CCGG) cannot cut CmCGG or ChmCGG, and conceptually its difference with MspI digestion is a measure of both 5-mC and 5-hmC. Subtraction of 5-hmC from the HpaII-based estimate therefore measures 5-mC. These estimates were measured on respective Affymetrix whole-genome tiling arrays  (2.0 R )
MspI - APRIL_fc1.ch02_coverage.bed
Undigested DNA - APRIL_fc1.ch01_coverage.bed
GluMspI - APRIL_fc1.ch04_coverage_NONTARGET.bed
GluMspI - APRIL_fc1.ch04_coverage.bed
MspI - APRIL_fc1.ch02_coverage_NONTARGET.bed
Undigested DNA - APRIL_fc1.ch01_coverage_NONTARGET.bed
MspI - MARCH_fc1.ch02_coverage_NONTARGET.bed
Undigested DNA - MARCH_fc1.ch01_coverage_NONTARGET.bed
GluMspI - MARCH_fc1.ch04_coverage_NONTARGET.bed
GluMspI - MARCH_fc1.ch04_coverage.bed
MspI - MARCH_fc1.ch02_coverage.bed
Undigested DNA - MARCH_fc1.ch01_coverage.bed
MspI - MAY_fc1.ch02_coverage.bed
GluMspI - MAY_fc1.ch04_coverage_NONTARGET.bed
GluMspI - MAY_fc1.ch04_coverage.bed
Undigested DNA - MAY_fc1.ch01_coverage.bed
MspI - MAY_fc1.ch02_coverage_NONTARGET.bed
Undigested DNA - MAY_fc1.ch01_coverage_NONTARGET.bed

first: Tarang

last: Khare

first: Saulius

last: Klimasauskas

first: Arturas

last: Petronis


title: Identification of long ncRNAs using RNA-seq in Arabidopsis

status: Public on Aug 23 2012

city: No.12 Zhongguancun South Street, Haidian

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: We profiled Arabidopsis transcriptom using RNA-seq. Each RNA library yielded 223-250 million 101-bp single-end reads (235M on average). Using Tophat and Cufflinks, 30,199~30,650 assembled transcripts were identified in each of 4 samples. Of them, 1340 ones were derived from intergenic regions including 278 long intergenic ncRNAs (LincRNAs). Comparing with the 6,480 lincRNAs we identified by analysis of 200 tiling array data sets, 2,708 lincRNAs were also detected by RNA-seq.

overall_design: Transcriptom profiling in roots, leaves, flowers and siliques.

first: Shulin

last: Deng

first: Huan

last: Wang

first: Nam-Hai

last: Chua


title: A multiply redundant genetic switch locks in the transcriptional signature of T regulatory cells

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School


title: Genome-wide maps of FoxP3 binding in transduced CD4+ T cells

summary: The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability.

overall_design: We used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to assess how cofactors affect the genome-wide localization of FoxP3. Chromatin was prepared from primary CD4+ Tconv cells transfected with FLAG-FoxP3 alone or together with GATA1, immunoprecipitated with anti-FLAG, and the bound DNA determined by Illumina deep sequencing. Immunoprecipitation with anti-PolII, or whole cell extract, provided genome-wide controls for transcriptional start sites (TSSd) or for sequencing non-homogeneity, respectively.

first: Wenxian

last: Fu

first: Henry

last: Paik

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: The p23 molecular chaperone and GCN5 acetylase jointly modulate protein-DNA dynamics and open chromatin status.

city: Urbana

first: Brian

last: Freeman

state: Illinois

address: B107 CLSL  601 S. Goodwin Avenue

department: Department of Molecular & Integrative Physiology

institute: UIUC

summary: Dense mapping of individual DNase I cleavages from intact nuclei isolated from wild type, sba1Δ and gcn5Δ yeast using high-throughput sequencing.

overall_design: Open chromatin status of wild type, sba1-/- and gcn5-/- yeast strains were generated by Dnase-seq.

first: Elena

last: Zelin

first: Yang

last: Zhang

first: Oyetunji

middle: A

last: Toogun

first: Sheng

last: Zhong


title: Argonaute proteins couple chromatin silencing to alternative splicing

status: Public on Aug 22 2012

city: Paris

first: Eric

last: Batsche

address: 7-9, Quai Saint Bernard

department: B2A Biological Adaptation and Ageing - UMR8256 CNRS

institute: IBPS - Institut Biologie Paris Seine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel of archived human cancers

city: Stanford

first: Robert

middle: B.

last: West

address: 300 Pasteur Drive

department: Pathology

institute: Stanford School of Medicine

summary: Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs (lncRNAs), as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type specific biomarkers. However, despite the potential importance of lncRNAs to the cancer field, no comprehensive survey of lncRNA expression across various cancers has been reported. We used 3'-End Sequencing for Expression Quantification (3SEQ) to quantify transcript abundance across 64 solid tumors representing 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas, and sarcomas. We identified hundreds of transcripts from among the known 1,065 lncRNAs surveyed that show variability in transcript levels between the tumor types, and therefore, make potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types. We find that many of these differentially expressed cancer transcripts are also expressed in normal tissues. One such novel transcript specifically expressed in breast tissue was further evaluated using RNA in situ hybridization on a panel of breast tumors and shown to correlate with low tumor grade and estrogen receptor expression, thereby representing a potentially important new breast cancer biomarker. This study provides the first large survey of lncRNA expression within a panel of solid cancers and also identifies a number of novel transcribed regions differentially expressed across distinct cancer types that represent candidate biomarkers for future research.

overall_design:
3SEQ was performed on 64 formalin-fixed, paraffin-embedded (FFPE) human tumors representing 17 diagnostic cancer subtypes. Duplicate libraries were prepared for two of the tumors (ESS STT5520 and LMS STT516). 3SEQ was also performed on 27 normal human tissue samples. RNA-Seq was performed on 6 breast cancer cell lines for the examination of the breast-specific transcript on chr10.

Series supplementary files:

'GSE28866_raw_counts_54511_peaks_cancer_and_normal.txt': Raw_counts: Total 3SEQ reads in each peak for each sample. File includes read counts for 54,511 peaks for the 66 cancer libraries and the 27 normal libraries.

'GSE28866_36048_normalized_peaks_cancer_and_normal.txt': Normalized_peaks: Normalized 3SEQ expression data for the 36,048 filtered peaks for the 66 cancer libraries and the 27 normal libraries. Peaks were classified as coding, lncRNA (Rinn, Bartel, Hughes, Gencode_lnc), other known transcripts (ref_known_Gencode_nc, all_mrna, other known), downstream, intron, promoter, or novel_intergenic. Peaks determined to be differentially expressed in one of the 17 cancer subtypes using a series of 2-Class SAM analyses are noted along with the type of cancer showing upregulation. Expression data was normalized using the sequencing depth of each sample by scaling the data using the mean value of each sample. Data was further compressed to reduce outliers by taking the square root of each value.

first: Alayne

last: Brunner

first: Andrew

last: Beck

first: Badreddin

last: Edris

middle: T

last: Sweeney

first: Shirley

middle: X

last: Zhu

first: Rui

last: Li

first: Kelli

last: Montgomery

first: Sushama

last: Varma

first: Thea

last: Gilks

first: Xiangqian

last: Guo

first: Joseph

last: Foley

first: Daniela

last: Witten

first: Craig

middle: P

last: Giacomini

first: Ryan

last: Flynn

first: Jonathan

last: Pollack

last: Tibshirani

first: Howard

middle: Y

last: Chang

first: Matt

last: van de Rijn


title: High throughput sequencing of the mouse transcriptome within the VTA following exposure to emotional stress.

status: Public on Aug 21 2012

first: Li

last: Shen

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Using a novel stress paradigm, we generated emotionally stressed, physically stressed, and control animals.  We measured changes in mRNA expression using Illumina HiSeq2000 to obtain high-depth sequencing.  Interestingly, we observed a number of significantly up- and down-regulated mRNAs.  By identifying mRNAs that were regulated similarly in both emotionally and physically stressed mice, we hope to provide a list of potentially novel targets for therapeutic intervention in mood disorder.

overall_design: Examination of the transcriptome within the VTA in emotionally and physically (both susceptible and resilient) stressed C57BL/6J male mice.

first: Brandon

last: Warren

first: Vincent

last: Vialou

first: Carlos

last: Bolanos-Guzman


title: Transcriptome analysis of Drosophila neural stem cells reveals a transcriptional network for self-renewal.

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: Drosophila neuroblasts have emerged as a model for stem cell biology that is ideal for genetic analysis but is limited by the lack of cell-type specific gene expression data. Here, we describe a methodology to isolate large numbers of pure neuroblasts and differentiating neurons that retain both cell cycle and lineage characteristics. We determine transcriptional profiles by mRNA sequencing and identify 28 predicted neuroblast specific transcription factors, which can be arranged in a network containing hubs for Notch signaling, growth control and chromatin regulation. Overexpression and RNAi for these factors identify Klumpfuss as a regulator of self-renewal. We show that loss of Klu function causes premature differentiation while overexpression results in the formation of transplantable brain tumors. Our data represent a valuable resource for Drosophila developmental neurobiology and we describes methodology that can be applied to other invertebrate stem cell lineages as well.

overall_design: comparison of transcriptomes of Drosophila melanogaster larval neuroblasts and their differentiated daughter cells (neurons)

first: Heike

last: Harzer

first: Christian

last: Berger

first: Juergen

last: Knoblich


title: ASXL1 Mutations Promote Myeloid Transformation Through Loss of PRC2-Mediated Gene Repression

first: Richard

last: Koche

address: 185 Cambridge St.

institute: Broad Institute of Harvard and MIT

summary: Recurrent somatic ASXL1 mutations occur in patients with myelodysplasia (MDS), myeloproliferative neoplasms (MPN), and acute myeloid leukemia (AML), and are associated with adverse outcome. Despite the genetic and clinical data implicating ASXL1 mutations in myeloid malignancies, the mechanisms of transformation by ASXL1 mutations are not understood. Here we identify that ASXL1 mutations result in loss of PRC2-mediated histone H3 lysine 27 (H3K27) tri-methylation. Through integration of microarray data with genome-wide histone modification ChIP-Seq data we identify targets of ASXL1 repression including the posterior HOXA cluster that is known to contribute to myeloid transformation.  We demonstrate that ASXL1 associates with the Polycomb repressive complex 2 (PRC2), and that loss of ASXL1 in vivo collaborates with NRASG12D to promote myeloid leukemogenesis.

overall_design:
To assess the genome-wide effects of ASXL1 loss on chromatin state we performed chromatin immunoprecipitation followed by next generation sequencing (CHIP-seq) for histone modifications known to be associated with PcG (histone H3 lysine 27 trimethylation (H3K27me3)) or TxG activity (histone H3 lysine 4 trimethylation (H3K4me3)) in UKE1 cells expressing empty vector (EV) or 2 independent validated shRNAs for ASXL1.

This Series represents the ChIP-Seq data (not the microarray data referenced in the summary above).  The related micorarray data are available in GEO as GSE38692.

first: Omar

last: Abdel-Wahab

first: Mazhar

last: Adli

first: Bradley

last: Bernstein

first: Ross

last: Levine


title: Transcriptome of normal,paracancerous and cancerous colon tissues based on RNA-seq method

city: guangzhou

first: qianru

last: ai

address: xingang xi road No135

institute: igenomic

summary: To support our research of colon cancer in human genome, we conducted massively parallel pyrosequencing of mRNAs (RNA-seq) using normal,paracancerouse and cancerous human colon tissues. We obtained a total of 29.9M reads from normal,33.0M reads from paracancerous and 36.5M reads from cancerous.The RNA-seq data derived from the sample illustrated the differencially expreesion genes among normal,paracancerous and cancerous colon tissues of human.

overall_design: 3 samples examined: normal tissue, paracancerous tissue, cancerous tissue.

first: Wu

last: YA


title: Proliferation and Tumorigenesis of a Murine Sarcoma Cell Line in the Absence of Dicer

status: Public on Aug 20 2012

city: Cambridge

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

summary: MicroRNAs are a class of short ~22 nucleotide RNAs predicted to regulate nearly half of all protein-coding genes, including many involved in basal cellular processes and organismal development.  Although both increases and decreases in the levels of specific miRNAs have been shown to promote tumor development, a global reduction in miRNAs is commonly observed in various human tumors. However, complete loss has not been documented, suggesting an essential function for miRNAs in tumorigenesis.  Here we present the finding that transformed or immortalized Dicer-null somatic cells can be isolated readily in vitro, maintain the characteristics of Dicer-expressing controls and remain stably proliferative.  Furthermore, Dicer-null cells from a sarcoma cell line, though depleted of miRNAs, are competent for tumor formation.  Hence, miRNA levels in cancer may be maintained in vivo by a complex stabilizing selection in the intratumoral environment.

overall_design: Small RNAs from tumor cell lines (murine sarcoma KrasG12D, p53 -/-) with and without Dicer (Dicer f/-, Dicer -/-) were analyzed.

first: Arvind

last: Ravi

first: Allan

last: Gurtan

first: Madhu

middle: S

last: Kumar

first: Arjun

first: Christine

last: Chin

first: Victoria

last: Lu

first: Jacqueline

last: Lees

first: Tyler

last: Jacks

first: Phillip

last: Sharp


title: RNA sequencing of circulating tumour cells implicates WNT signaling in pancreatic cancer metastasis

status: Public on Aug 17 2012

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

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

overall_design: Refer to individual Series


title: Genome-wide map of transcription factor GATA1 occupancy during mitosis in G1E ER4+E2 cells

city: University Park

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Tissue-specific transcription patterns are preserved throughout cell divisions to maintain lineage fidelity. We investigated whether transcription factor GATA1 plays a role in transmitting hematopoietic gene expression programs through mitosis when transcription is transiently silenced. Live cell imaging revealed that a fraction of GATA1 is retained focally within mitotic chromatin. ChIP-seq of highly purified mitotic cells uncovered that key hematopoietic regulatory genes are occupied by GATA1 in mitosis. The GATA1 co- regulators FOG1 and TAL1 dissociate from mitotic chromatin, suggesting that GATA1 functions as platform for their postmitotic recruitment. Mitotic GATA1 target genes tend to re-activate more rapidly upon entry into G1 than genes from which GATA1 dissociates. A novel system designed to destroy GATA1 specifically during mitosis revealed that mitotic occupancy is required for rapid target gene reactivation. These studies suggest a requirement of mitotic “bookmarking” by GATA1 for the faithful propagation of cell type-specific transcription programs through cell division

overall_design: GATA1 occupancy profiles in mitotic G1E-ER4 +E2 cells generated by ChIP-sequencing. ChIP input DNA was sequenced as control. Previously reported (GSE18164) GATA1 occupancy in asynchrnous G1E-ER4 +E2 cells was analysed and compared with mitotic GATA1 occupancy.

first: Stephan

last: Kadauke

first: Maheshi

last: Udugama

first: Jan

middle: M

last: Pawlicki

first: Jordan

middle: C

last: Achtman

first: Deepti

last: Jain

first: Yong

last: Cheng

first: Gerd

last: Blobel


title: Bbssk1 dependent gene expression in Beauveria bassiana

city: Hangzhou

first: zheng-liang

last: wang

address: Yu-hang-tang Road 388

department: Institute of Microbiology

institute: Zhejiang University

summary: Ssk1-type response regulator proteins are the core elements of histidine-to-aspartate systems that mediate fungal stress tolerance, a determinant to the biocontrol potential of fungal entomopathogens. We characterized for the first time the functions of Beauveria bassiana Ssk1 (Bbssk1) by analyzing multi-phenotypic changes in DBbssk1 and differentially expressed genes (DEGs) in the digital gene expression (DGE) libraries of DBbssk1 and wild-type constructed under osmotic stress. The results revealed 1003 DEGs, of which many associated with conidiation, xenotics transport, cell wall integrity, and protein and carbohydrate metabolism were greatly down-regulated.

overall_design: Total RNA obtained from Bbssk1 disruption mutant subjected to 0.5 M NaCl for 30 minutes compared to the wild type strain under the same stress treatment.

first: Zheng-Liang

last: Wang

first: Ming-Guang

last: Feng


title: RNA sequencing of circulating tumour cells implicates WNT signaling in pancreatic cancer metastasis (human data)

summary: Circulating tumour cells (CTCs) shed into blood from primary cancers include putative precursors that initiate distal metastases. While these cells are extraordinarily rare, they may identify cellular pathways contributing to the blood-borne dissemination of cancer. Here, we adapted a microfluidic device for efficient capture of CTCs from an endogenous mouse pancreatic cancer model and subjected CTCs to single-molecule RNA sequencing, identifying Wnt2 as enriched in CTCs. Expression of Wnt2 in pancreatic cancer cells suppresses anoikis, enhances anchorage-independent sphere formation, and increases metastatic propensity in vivo. The effect of Wnt2 is correlated with fibronectin upregulation, and it is mediated in part through non-canonical Wnt signaling and suppressed by inhibition of the Map3k7 (Tak1) kinase, an integrator of Wnt, BMP and TGF-beta signaling. In humans, formation of non-adherent tumour spheres by pancreatic cancer cells is associated with upregulation of multiple Wnt genes, and pancreatic CTCs revealed significant enrichment for non-canonical Wnt signaling in 5 of 11 cases. Thus, molecular analysis of CTCs may identify novel therapeutic targets to prevent the distal spread of cancer.

overall_design: Expression profiling of circulating tumor cells in human pancreatic cancer patients support a hypothesis that WNT signaling plays a role in pancreatic cancer metastasis.

first: Min

last: Yu

first: David

last: Ting

first: Shannon

middle: L

last: Stott

first: Fatih

last: Ozsolak

first: Paul

last: Suchismita

last: Ciciliano

first: Malgorzata

middle: E

last: Smas

first: Daniel

last: Winokur

first: Anna

middle: J

last: Gilman

first: Matthew

last: Ulman

first: Kristina

last: Xega

first: Gianmarco

last: Contino

first: Brinda

last: Alagesan

first: Brian

last: Brannigan

first: Patrice

last: Milos

last: Ryan

first: Lecia

middle: V

last: Sequist

first: Nabeel

last: Bardeesy

first: Sridhar

last: Ramaswamy

first: Mehmet

last: Toner

first: Shyamala

last: Maheswaran

last: Haber


title: Immune response of the Caribbean sea fan, Gorgonia ventalina exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing

city: Ithaca

first: Colleen

last: Burge

address: 215 Tower Road/E343 Corson Hall

department: Department of Ecology and Evolutionary Biology

institute: Cornell University

summary: Background.  Coral reef communities are undergoing marked declines due to a variety of stressors including climate change, eutrophication, sedimentation, and disease.  The sea fan coral, Gorgonia ventalina, is a tractable study system to investigate the hypothesis that stressors compromise immunity and lead to onset of disease. Functional studies in Gorgonia ventalina immunity indicate that several key pathways and cellular responses are involved in response to natural microbial invaders, although to date the functional and regulatory pathways remain largely un-neffectors, the primary line of defense in invertebrates.  This study used short-read sequencing (Illumina GAIIx) to identify genes involved in the response of G. ventalina to a naturally occurring Aplanochytrium spp. parasite.  Results. De novo assembly of the G. ventalina transcriptome yielded 90,230 contigs of which 40, 142 were annotated. RNA-Seq analysis revealed 210 differentially expressed genes in sea fans exposed to the Aplanochytrium parasite.  Differentially expressed genes involved in immunity include pattern recognition molecules, anti-microbial peptides, wound repair, and reactive oxygen species.  Gene enrichment analysis indicated eight biological processes were enriched representing 36 genes, largely involved with protein translation and energy production.  Conclusions.  This is the first report using high-throughput sequencing to characterize the host response of a coral to a natural pathogen.  Furthermore, we have generated the first transcriptome for a soft coral species.  G. ventalina is a non-model species for which few sequences had been previously described, and we were able to annotate a large number of genes and describe their potential roles in immune function. Expression analysis revealed genes important in invertebrate innate immune pathways, as well as those whose role is previously un-described in cnidarians. This resource will be valuable in characterizing G. ventalina immune response to infection and co-infection of pathogens in the context of environmental change.

overall_design: RNA seq experiment using Illumina GAIIx to compare sea fans exposed to an Aplanochytrium species compared to controls

first: Morgan

last: Mouchka

first: C

middle: D

last: Harvell

first: Steven

last: Roberts


title: Genome-wide distribution of 5-formylcytosine in ES cells is associated with transcription and depends on TDG

first: Dario

last: Beraldi

address: Robinson Way

institute: Cambridge Research Institute

summary:
Methylation of cytosine in DNA (5mC) is an important epigenetic mark that is involved in the regulation of genome function. During early embryonic development in mammals, the DNA methylation landscape is dynamically reprogrammed in part through active demethylation. Recent advances have identified key players involved in active demethylation pathways, including oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) by the TET family of enzymes and excision of 5fC by the base excision repair enzyme thymine DNA glycosylase (TDG). Here, we provide the first genome-wide distribution map of 5fC in mouse embryonic stem (ES) cells and evaluate potential roles for 5fC in differentiation.
Our method exploits the unique reactivity of 5fC to link a biotin tag for pulldown and high-throughput sequencing. Genome-wide mapping revealed 5fC enrichment in CpG islands (CGIs) of promoters and exons. CGI promoters in which 5fC was relatively more enriched than 5mC or 5hmC corresponded to transcriptionally active genes. Accordingly, 5fC-rich promoters had elevated H3K4me3 levels, a histone mark associated with active transcription, and were frequently bound by RNA Polymerase II. Downregulation of TDG led to accumulation of 5fC in CGIs in ES cells, which correlates with increased methylation in these genomic regions during differentiation and in mouse embryonic fibroblasts derived from TDG knockout embryos.
Collectively, our data suggest that 5fC plays a role in epigenetic reprogramming. The formation and removal of this cytosine modification are confined to specific genomic regions, which are in part controlled by TDG. Notably, 5fC excision in ES cells is necessary for the correct establishment of CGI methylation patterns during differentiation, and hence, for appropriate patterns of gene expression during development.

overall_design: We devised a method to map 5-formylcytosine (5fC) by linking a biotin tag to 5fC for pulldown and high-throughput sequencing. We mapped 5fC in the following samples of mouse embryonic stem cells (J1): Wild-type ES cells (two replicates); ES cells transfected with siRNA targeting TDG (two replicates); ES cells transfected with non-targeting siRNA (two replicates). One genomic input library was also sequenced to detect and correct biases in fragment enrichment.

first: Eun

last: Raiber

first: Gabriella

last: Ficz

first: Heather

last: Burgess

first: Miguel

last: Branco

first: Pierre

last: Murat

first: David

last: Oxley

first: Michael

last: Booth

first: Wolf

last: Reik

first: Shankar

last: Balasubramanian


title: The Akt-SRPK-SR axis constitutes a major pathway in transducing EGF signaling to regulate alternative splicing in the nucleus

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: Pre-mRNA splicing is regulated by developmental and environmental cues, but little is known about how specific signals are transduced in mammalian cells to regulate this critical gene expression step. Here, we report massive reprogramming of alternative splicing in response to EGF signaling.  By blocking individual branches in EGF signaling, we found that Akt activation plays a major role, while other branches, such as the JAK/STAT and ERK pathways, make minor contributions to EGF-induced splicing.  Activated Akt next branches to the SRPK family of kinases specific for SR proteins, rather than mTOR, by inducing SRPK autophosphorylation that switches the splicing kinases from Hsp70- to Hsp90-containing complexes.  This leads to enhanced SRPK nuclear translocation and SR protein phosphorylation. These findings reveal a major signal transduction pathway for regulated splicing and place SRPKs in a central position in the pathway, consistent with their reputed roles in a large number of human cancers.

overall_design: Examination of EGF induced AKT-SRPK-SR pathway in the regulation of splicing in HEK293T cells with RASL-seq

first: Zhihong

last: Zhou

first: Jinsong

last: Qiu

first: Wen

last: Liu

first: Yu

first: Ryan

last: Plocinik

first: Hairi

last: Li

first: Qidong

last: Hu

first: Gourisanker

last: Ghosh

first: Joseph

last: Adams

middle: G

last: Rosenfeld


title: Gene expression in the developing aleurone and starchy endosperm of wheat

status: Public on Aug 15 2012

city: Lismore

first: Susan

middle: Alana

last: Gillies

state: NSW

address: Miliatary  Rd

department: Plant Science

country: Australia

institute: Southern Cross University

summary: This reports the transcript profiling of the aleurone and starchy endosperm layers of wheat seed over 3 time points critical in the development of the aleurone layer. Wheat is a critical food source globally. The aleurone layer develops from the starchy endosperm and is a concentrated source of vitamins and minerals, essential for the germination of the plant embryo. However the molecular mechanisms behind the development of this layer remain poorly understood. Here we present the first direct systematic comparison of the transcriptomes of the aleurone and starchy endosperm tissues of the wheat seed (Triticum aestivum) at time points critical to the development of the aleurone layer of 6, 9 and 14 days post anthesis. Gene expression patterns reflect the changing role of these tissues in seed development. Illumina sequencing gave 25 to 55 million sequence reads per tissue, of the trimmed reads, 70 – 81% mapped to reference expressed sequence transcripts. To quantify transcript abundance, RNA-Seq normalisation was performed to generate RPKM values, these were used in comparative analyses between the tissues at each time point using Kals Z-test. Sequences with significantly different RPKM values were categorised on the basis of tissue and time point expression and functionally annotated using standardised gene ontology vocabularies, revealing two very distinct tissues. In conclusion we show the relationships between and the fundamental biological reprogramming of the two major biologically and economically significant tissues of the wheat seed over time. Understanding these changes in gene expression profiles is essential to mining the potential these tissues hold for human nutrition and contributing to foundational and systems biology of this important crop.

overall_design: Examines the transcript profile of aleurone and starchy endoperm tissues at 6,9 and 14DPA. A minimum of 5 individual seeds from 3 separate spikes from three individual plants were pooled for each tissue preparation.

middle: A

first: Robert

last: Henry

first: Agnelo

last: Futardo


title: Core transcriptional regulatory circuit controlled by the TAL1 complex in human T-cell acute lymphoblastic leukemia

status: Public on Aug 16 2012

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research


title: Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

city: Lebanon

first: xiaoyang

last: zhang

address: 1 Medical Center Driver

institute: Dartmouth Medical School

summary: Genome-wide association studies (GWASs) have identified thousands of single nucleotide polymorphisms (SNPs) associated with human traits and diseases. But because the vast majority of these SNPs are located in the noncoding regions of the genome their risk promoting mechanisms are elusive. Employing a new methodology combining cistromics, epigenomics and genotype imputation we annotate the noncoding regions of the genome in breast cancer cells and systematically identify the functional nature of SNPs associated with breast cancer risk. Our results demonstrate that breast cancer risk-associated SNPs are enriched in the cistromes of FOXA1 and ESR1 and the epigenome of H3K4me1 in a cancer and cell-type-specific manner. Furthermore, the majority of these risk-associated SNPs modulate the affinity of chromatin for FOXA1 at distal regulatory elements, which results in allele-specific gene expression, exemplified by the effect of the rs4784227 SNP on the TOX3 gene found within the 16q12.1 risk locus.

overall_design: Examination of histone modification H3K4me2 in untreated and E2 treated cells

first: Xiaoyang

last: Zhang


title: RNA sequencing of circulating tumour cells implicates WNT signaling in pancreatic cancer metastasis (mouse data)

first: Ben

last: Wittner

overall_design: Expression profiling of primary tumor, circulating tumor cells and ascites in a mouse model of pancreatic cancer suggested WNT signaling plays a role in pancreatic cancer metastasis. Induction of Wnt2 signaling in mouse pancreatic NB508 cells supported the hypothesis.

first: Min

last: Yu

first: David

middle: T

last: Ting

first: Shannon

last: Stott

first: Fatih

last: Ozsolak

first: Paul

last: Suchismita

first: Jordan

last: Ciciliano

first: Malgorzata

last: Smas

first: Daniel

last: Winokur

first: Anna

last: Gilman

first: Matthew

last: Ulman

first: Kristina

last: Xega

first: Gianmarco

last: Contino

first: Brinda

last: Alagesan

first: Brian

middle: W

last: Brannigan

first: Patrice

last: Milos

last: Ryan

first: Lecia

last: Sequist

first: Nabeel

last: Bardeesy

first: Sridhar

last: Ramaswamy

first: Mehmet

last: Toner

first: Shyamala

last: Maheswaran

last: Haber


title: Effects of drought on gene expression in Maize reproductive and leaf meristem tissue revealed by RNA-seq

status: Public on Aug 14 2012

city: Blacksburg

first: Akshay

last: Kakumanu

state: Virginia

address: 101H Price Hall, Virginia Tech

department: PPWS

institute: Virginia Tech

summary:
Purpose: To study the effects of drought at the transcriptomic level on two different actively dividing maize tissue: the ovaries, and the leaf meristem

Methods: The Illumina reads were mapped to the maize B73 reference genome using Tophat followed by transcriptome reconstruction using Cufflinks. The FPKM valuse were extracted from cufflinks output and an R package called Limma was used to identify differentially expressed genes under drought under both tissues

Results and Conclusions: Different processes which were differentially expressed under drought in both tissues were identified and analyzed in detail. A working hypothesis was formulated to account for the observed susceptibility of the reproductive tissue when compared to the robust response of the vegetative tissue. This analysis also servers as a basis for future study on drought-induced embryo abortion.

overall_design: Maize (Zea mays) plants of inbred line B73 were grown in the green house under well watered and drought stress conditions until they reached the reproductive stage (at the onset of silk emergence).  For the drought stress two to three days after irrigation was withheld, the plants were hand pollinated, and 24 hours after pollination measurements and samples were collected for transcriptome analysis. At the end of the drought period (1DAP) the basal leaf meristem of the three youngest leaves and the ovary tissues were sampled for Illumina deep sequencing.  Samples were labeled as well watered control leaf meristem (MLC), well watered control ovaries/ "cob" (MCC), drought stressed leaf meristem (MLD) and drought stressed ovary tissue (MCD). There are 8 libraries in total including one biological replicate for each condition.

first: Andy

last: Pereira

first: Ruth

last: Grene


title: Complexity of expression from transiently transfected plasmids

city: Prague 4

first: Radek

last: Malik

address: Videnska 1083

department: Dep. of Epigenetics Regulations

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

summary: Transient plasmid transfection is common approach for studies in cultured mammalian cells. To examine behavior of transfected plasmids, we analyzed their transcriptional landscape by deep sequencing. We found that plasmids generate different levels of transcripts virtually everywhere. Spurious transcription may have undesirable effects as some co-transfected plasmids inhibited expression of luciferase reporters in a dose-dependent manner. In one case, we attributed this effect to kan/neo resistance cassette, which generated a unique population of edited sense and antisense small RNAs. The unexpected complexity of expression of transiently transfected plasmids highlights the importance of appropriate experimental controls.

overall_design: HEK293 cells (human origin) transiently transfected with 4 various plasmids

first: Jana

last: Nejepinska

first: Martin

last: Moravec

first: Petr

last: Svoboda


title: Transcriptome-wide Regulation of Splicing and mRNA Localization by Muscleblind Proteins

city: Gainesville

first: Eric

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: The Muscleblind-like (Mbnl) family of RNA-binding proteins plays important roles in muscle and eye development and in Myotonic Dystrophy (DM), where expanded CUG or CCUG repeats functionally deplete Mbnl proteins. We identified transcriptome-wide functional and biophysical targets of Mbnl proteins in brain, heart, muscle, and myoblasts using RNA sequencing and crosslinking/immunoprecipitation-sequencing approaches. This analysis identified several hundred splicing events whose regulation depended on Mbnl function, in a pattern indicative of functional interchangeability between Mbnl1 and Mbnl2. A nucleotide resolution RNA map associated repression or activation of exon splicing with Mbnl binding near either 3' splice site or near the downstream 5' splice site, respectively. Transcriptomic analysis of sub-cellular compartments uncovered a global role for Mbnls in regulating localization of mRNAs encoding membrane, synaptic and other proteins in both mouse and Drosophila cells, and Mbnls also contribute to protein secretion. These findings hold several new implications for DM pathogenesis.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: To assess global functions of Muscleblind proteins, RNA-Seq was performed using WT and Mbnl1 KO brain, heart, and muscle (5 mice each). Additionally, C2C12 mouse myoblasts were depleted of Mbnl1, Mbnl2, or both. Subcellular fractionation experiments were performed to analyze mRNA localization following depletion of Mbnl1 and Mbnl2 in C2C12 mouse myoblasts, and following depletion of Mbnl in Drosophila S-2R+ cells. CLIP-Seq was also performed against Mbnl1 in mouse brain, heart, muscle, and C2C12 myoblasts. Finally, ribosome footprinting was performed with C2C12 mouse myoblasts that were depleted of Mbnl1, Mbnl2, or both.

first: Neal

last: Cody

first: Sonali

last: Jog

first: Michela

last: Biancolella

first: Thomas

first: Daniel

last: Treacy

first: Shujun

last: Luo

first: Gary

middle: P

last: Schroth

first: David

last: Housman

first: Sita

last: Reddy

last: Lécuyer

first: Christopher

middle: B

last: Burge


title: Chromatin Accessibility Reveals Insight into Androgen Receptor Activation and Transcriptional Specificity

city: Durham

first: Alok

last: Tewari

address: 101 Science Drive

institute: Duke University

summary: Using DNase-seq, mRNA-seq and publicly available ChIP-seq data sets, we examined the role of chromatin accessibility (DNase-seq) in androgen receptor binding to the genome (ChIP-seq) and AR-mediated transcriptional changes (mRNA-seq). Our data reveals genome-wide changes in chromatin structure that correspond to AR binding and  differential gene expression.  A focused examination of DNase-seq data around androgen receptor motifs within androgen receptor ChIP-seq peaks reveals distinct patterns of protection from DNaseI cleavage.

overall_design:
Examination of chromatin accessibility (DNase-seq), AR binding (AR ChIP-seq), and transcription (mRNA-seq) in LNCaP cells before and after 12 hours of 1 nM R1881 treatment
This Series represents the RNA-Seq data only. Exon microarray data generated under the same conditions is available through GSE15805.  The DNase-seq data is publicly available through GSE32970 as well as the UCSC genome browser (genome.ucsc.edu) under Regulation::ENCODE DNase/FAIRE::Duke DNaseI HS:LNCaP and LNCaP + Andro.  The accession numbers for the ChIP-seq experiments used are GSE14097 and GSE28126.


title: Drosophila melanogaster 0-1hr embryo

status: Public on Aug 10 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_755
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton-S; Tissue: embryo; Replicate type: biological; Developmental Stage: embryonic 0-1hr; Sex: NA;  EXPERIMENTAL FACTORS: Strain: Canton-S

last: Lai


title: Drosophila melanogaster 6-10hr embryo

summary:
modENCODE_submission_754
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton-S; Tissue: embryo; Replicate type: biological; Developmental Stage: embryonic 6-10hr; Sex: NA;  EXPERIMENTAL FACTORS: Strain: Canton-S


title: Drosophila melanogaster small RNA sequence: female heads

summary:
modENCODE_submission_750
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton-S; Tissue: adult head tissue; Replicate type: biological; Developmental Stage: adult; Sex: female;  EXPERIMENTAL FACTORS: Strain: Canton-S


title: Transcriptome Sequencing of Life Stages and Tissues of the Yellow Fever Mosquito Ae. aegypti

first: Zhijian

last: Tu

state: VA

address: 309 Engel Hall

department: Biochemistry

summary: RNA-Seq was used for transcriptome sequencing of 11 samples covering various life stages and tissues from the yellow fever mosquito Ae. aegypti.

overall_design: RNA was isolated from described samples for RNA-Seq. Samples included four embryonic time points from 0-12 hr, larvae, pupae, adult males, 0-1 day old ovaries, ovaries from 24 post blood fed females, and 24 hr post blood fed female carcass (ovaries extirpated). Raw data not available for GSM847403, GSM847404, GSM847405, and GSM847406


title: Drosophila melanogaster 3rd Instar Larvae

summary:
modENCODE_submission_748
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton-S; Tissue: L3 larvae; Replicate type: biological; Developmental Stage: 3rd Instar Larvae; Sex: NA;  EXPERIMENTAL FACTORS: Strain: Canton-S


title: Rapid Genome-Scale Mapping of Chromatin Accessibility in Tissue

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh). The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue. Combined with massive parallel sequencing TACh identifies accessible regions that are associated with euchromatic features and accessibility at transcriptional start sites correlates positively with levels of gene transcription.

overall_design: Idetification of accessible chromatin in forzen adult mouse liver tissue

first: Lars

last: Grontved

first: Gordon

last: Hager

last: Levens


title: Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication

first: Yan

last: chenghai

address: Yuhangtang Road 866

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

overall_design: Refer to individual Series

first: Yu

last: Wang

first: Longjiang

last: Fan


title: Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [degradome]

summary:
The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips.
A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family.
Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.

overall_design: The 5' end of the 3' degraded mRNAs with polyA tails  were collected and generated from seedlings at four-leaves stage of O.rufipogon by degradome highthoughput sequecing using Illumina GAII


title: Drosophila melanogaster Pupae 2-4 days

summary:
modENCODE_submission_757
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton-S; Tissue: pupae; Replicate type: biological; Developmental Stage: Pupae 2-4d; Sex: NA;  EXPERIMENTAL FACTORS: Strain: Canton-S

first: Eric


title: Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [small RNA]

summary: The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips.  A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.

overall_design: Non-coding small RNA were generated from three different tissues of O.rufipogon by sequecing using Illumina GAII


title: Muscleblind-Like 2 mediated alternative splicing in the developing bain by mRNA sequencing

first: Ranjan

last: Batra

state: California

address: 2880 Torrey Pines Scenic Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary:
We have identified Mbnl2 mediated splicing events and mRNA expression regulation by comparing WT and Mbnl2 ΔE2/ΔE2 mouse hippocampii using Affymetrix Mouse Exon Junction Array and mRNA sequencing.

The splicing microarray data has already been submitted under GSE37908 which also includes a re-analysis of RNA-seq data.

The TableS1.xls contains Splicing microarray analysis data of Mbnl2+/+ vs. MBNL2 ΔE2/ΔE2 knockout hippocampus.
The TableS2.xls files contain RNA-Seq, Gene Ontology, HITS-CLIP and CIMS summary of Mbnl2+/+ vs. MBNL2 ΔE2/ΔE2 knockout hippocampus.
The file contents are descibed in the 'TableS1_S2_readme.pdf' and data processing details are included in the 'data_processing_readme.pdf' file.

The Mbnl2_TableS2.xls contains data from exon junction microarrays for splicing analysis between WT and Mbnl2 delta2 mice. It also contains RNA-seq based splicing analysis between WT and Mbnl2 delta2 mice. Mbnl2_TableS2 further contains common targets between the two analyses, Gene Ontology and finally the HITS-CLIP data. CLIP tag summary describes read numbers for the three biological replicates. CLIP sig peaks contains significant HITS-CLIP unique reads/peaks after processing the data (BED files). Finally, CIMS analysis describes the Mbnl2 binding motif.

overall_design: 9 total samples were analyzed; 6 for RNA-seq: brains from 3 WT and 3 MBNL2   E2/  E2 female mice, all 2-3 months of age, and 3 for HITS-CLIP: brains from 3 WT BL6 female mice, all 2-3 months of age.

first: Batra

last: Ranjan

first: Zhang

last: Chaolin


title: Global Changes in Chlamydomonas Gene Expression Regulated by Carbon Dioxide and CIA5/CCM1

city: Ames

first: Martin

middle: H.

last: Spalding

state: IA

address: 1210 Molecular Biology Building

department: Department of Genetics, Development and Cell Biology

institute: Iowa State University

summary: We used RNA-Seq to query the Chlamydomonas reinhardtii transcriptome for regulation by CO2 concentration and by the transcription regulator CIA5(CCM1). Both CO2 concentration and CIA5 are known to play roles in induction of an essential CO2-concentrating mechanism (CCM), but the degree of interaction and the extent of global regulation beyond the CCM were not previously understood. We compared the transcriptome of a wild type strain vs. a cia5 strain under 3 CO2 supply conditions: high CO2 (H-CO2; 5%); low CO2 (L-CO2; 0.03 to 0.05%); and very-low CO2 (VL-CO2; <0.02%). Our goals were to: 1) reveal candidate genes that, through changes in their expression, distinguish multiple acclimation states induced by H-CO2, L-CO2, and VL-CO2; 2) reveal genes regulated directly or indirectly by CIA5; and 3) reveal genes responding to the interaction between CIA5 and changes in CO2 concentration. Our results revealed a small group of genes as encoding putative Ci transporters based on their expression patterns. The results also showed a massive and much broader impact on global gene regulation by CIA5/CCM1, which directly or indirectly affected 15% of the Chlamydomonas genome. The transcriptomes under L-CO2 and VL-CO2 conditions were not significantly different, suggesting that these two acclimation states must be controlled by mechanisms operating beyond transcript abundance.

overall_design: Both 137c wild type (cc125) and cia5 mutant were induced for 4 hours induction under H-CO2 (5%), L-CO2 (300~500 ppm), and VL-CO2 (100~200 ppm) conditions. 2 biological replicates were done for each strain -CO2 combination.

first: Wei

last: Fang

first: Yaqing

last: Si

first: Stephen

last: Douglass

last: Casero

first: Sabeeha

last: Merchant

first: Matteo

last: Pellegrini

first: Peng

last: Liu

middle: H


title: Drosophila melanogaster Canton-S small RNA sequence: Adult Female Body

status: Public on Aug 09 2012

first: DCC

last: modENCODE

summary:
modENCODE_submission_2555
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Developmental Stage: Adult female; Genotype: wild type; Sex: Female; EXPERIMENTAL FACTORS: Strain Canton S; Tissue Female body; Replicate type: biological;

last: Lai


title: Global Gene Expression Profiling in Litopenaeus stylirostris

city: San Marcos

first: DENISE

last: GARCIA

address: 333 S. Twin Oaks Valley Rd.

department: Biological Sciences

institute: California State University, San Marcos

summary: The primary goal of this project is to monitor host  global gene expression patterns in response to viral infection in the shrimp, Litopenaeus stylirostris.

overall_design: Specific Pathogen Free (SPF) L. stylirostris were obtained from High Health Aquaculture (Honolulu, Hawaii) and kept in environmentally controlled tanks.  For control, animals were injected with saline (30 ul) between the second and third tergal plates of the lateral side of the tail using a 1 ml tuberculin syringe.  Infected individuals were inoculated with homogenate created from IHHNV infected shrimp tissue.  After 24 hours, the shrimp were sacrificed and tissue was collected from the ventral and flash frozen in liquid nitrogen and stored in the -80 ºC freezer. Libraries of sequence tags were generated via the Long-SAGE kit (Invitrogen®, Carlsbad, CA) until the ditag PCR preparation step and directly pyrosequenced by 454 Roche.

first: Suzanne

last: Hizer

first: Dominika

last: Rainey

first: Letitia

last: Jones

first: Yessenia

middle: R

last: Miranda

first: Denise

middle: K

last: Garcia