title: H3K9/14Ac in TC-797 genome

city: boston

first: Chris

last: French

address: 75 francis st.

department: Pathology

institute: BWH

summary: The goal is to localize "active" histone marks known to bind BRD4-NUT in the NMC genome.  Characterization of the reference epigenome in humans by use of ChIP-Seq in the TC-797 human NMC cell line.

overall_design: ChIP-seq of untreated TC-797 cells using H3K9/14Ac antibodies versus IgG control.

first: Madeleine

last: Lemieux


title: Genetic and transcriptome analyses of early T-cell checkpoint failure and leukemia initiation in Rag1-deficient NOD mice

status: Public on Mar 07 2013

city: Pasadena

first: Mary

last: Yui

email: yui@caltech.edu, jingli@caltech.edu

address: 1200 E California Blvd

department: Biology

country: USA

institute: California Institute of Technology

type: Expression profiling by high throughput sequencing

summary: Both immunodeficient and wild type NOD mice exhibit defects in control of early T-cell development in the thymus. We show that Rag1-deficient NOD mice fail to enforce both the b-selection checkpoint and an earlier T-cell commitment checkpoint, based on genome-wide genetic and transcriptome analyses. A major QTL peak for the checkpoint breakthrough phenotype mapped to the diabetes susceptibility Idd9/11 region, as confirmed by congenic mouse analysis. Genome-wide RNA deep-sequencing revealed two classes of differences between NOD and B6 Rag1-deficient thymocytes: first, effects of genetic background prior to breakthrough, and second, effects of the breakthrough itself. These genotypes differentially express numerous signal transduction genes, prominently tyrosine kinase and actin-binding genes, some located within QTL regions. Emerging NOD breakthrough cells depart from the expected DN3 phenotype by expressing many stem cell-associated proto-oncogenes, such as Lmo2, Hhex, Lyl1, and Kit which are normally repressed earlier, and by illegitimate activation of post-b-selection genes like Cd2, Cd5, and Cd4. Co-expression of stem cell and T-cell genes persists in thymic lymphoma cells that emerge with high penetrance in these mice. These results imply that NOD thymocytes have defects that can collapse regulatory boundaries at two early T-cell checkpoints, which may predispose them to leukemia and autoimmunity.

middle: A

first: Ni

last: Feng

first: Jingli

last: Zhang

first: Chen

middle: Y

last: Liaw

first: Ellen

middle: V

last: Rothenberg


title: Lineage-specific functions of Bcl6  in immunity and inflammation are mediated through distinct biochemical mechanisms

status: Public on Mar 03 2013

city: New York

first: Katerina

last: Hatzi

state: NY

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transcription factor Bcl6 orchestrates the germinal center reaction through its actions in B and T cells, and regulates inflammatory signaling in macrophages. We report that genetic replacement by mutant Bcl6, which cannot bind corepressors to its BTB domain, disrupted  germinal center formation and immunoglobulin affinity maturation, due to a defect in B cell  proliferation and survival.  In contrast, BTB loss of function had no effect on T follicular helper cell differentiation and function, nor other T helper subsets.  Bcl6 null mice displayed a lethal inflammatory phenotype, whereas BTB mutant mice experienced normal healthy lives with no inflammation.  Bcl6 repression of inflammatory responses in macrophages was accordingly independent of the BTB domain repressor function.  Bcl6 thus mediates its actions through lineage-specific biochemical functions.

overall_design: ChIP-seq for Bcl6, SMRT and BCOR in germinal center B cells

first: Ari

last: Melnick


title: H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation [HIT-Seq]

status: Public on Mar 02 2013

city: Frederick

first: Xiaolin

last: Wu

state: MD

address: 8560 Progress Drive, C3001

department: Cancer Research Technology Program

institute: Frederick National Laboratory for Cancer Research/SAIC-Frederick Inc

summary: Histone modifications regulate chromatin-dependent processes, yet the mechanisms by which they contribute to specific outcomes remain unclear. H3K4me3 is a prominent histone mark that is associated with active genes and promotes transcription through interactions with effector proteins that include initiation factor TFIID. We demonstrate that H3K4me3-TAF3 interactions direct global TFIID recruitment to active genes, some of which are p53 targets. Further analyses show that (i) H3K4me3 enhances p53-dependent transcription by stimulating preinitiation complex (PIC) formation; (ii) H3K4me3, through TAF3 interactions, can act either independently or cooperatively with the TATA box to direct PIC formation and transcription; and (iii) H3K4me3-TAF3/TFIID interactions regulate gene-selective functions of p53 in response to genotoxic stress. Our findings indicate a mechanism by which H3K4me3 directs PIC assembly for the rapid induction of specific p53 target genes

overall_design: Examination of genome wide binding sites of TAF3 full length protein vs TAF3 PHD domain alone (Full vs PHD), with or without M880A mutation (WT vs mut) in mouse MEF cells using HITseq method (PNAS 2010, 107:3135-3140, PMID: 20133638)

first: Shannon

middle: M

last: Lauberth

first: Takahiro

last: Nakayama

first: Andrea

last: Ferris

first: Stephen

middle: H

last: Hughes

first: Robert

middle: G

last: Roeder


title: Loss of the DNA methyltransferase MET1 induces H3K9 hypermethylation at PcG target genes in Arabidopsis, and relocation of H3K27 trimethylation to transposons

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Profiling Genome-wide Chromatin Methylation with Engineered Posttranslation Apparatus within Living Cells

status: Public on Mar 04 2013

city: new york

first: Rui

last: Wang

state: new york

address: 1275 York Avenue

institute: MSKCC

summary: We have engineered the chromatin-modifying apparatus and formulated a novel technology, termed Clickable Chromatin Enrichment with parallel DNA sequencing (CliEn-seq), to probe genome-wide chromatin modification within living cells.

overall_design: Examine (E)-hex-2-en-5-ynylation mediated by engineered G9a Y1154A and GLP1 Y1211A in HEK293T cells.

first: Kabirul

last: Islam

first: Ying

last: Liu

first: Nathalie

last: Lailler

first: Minkui

last: Luo


title: H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq)

status: Public on Mar 05 2013

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation.

overall_design: MethylC-seq from naturally-occurring Arabidopsis accessions

middle: J

last: Schmitz

first: Taiji

last: Kawakatsu

first: Mark

last: Urich

first: Rosa

last: Castanon

last: Nery

first: Cesar

last: Barragan

first: Yupeng

last: He

first: Matthew

middle: D

last: Schultz

first: Huaming

last: Chen


title: High-throughput Sequencing of Small RNAs from Pollen and Silk and Characterization of miRNAs Involved in Pollen-Silk Interactions in Maize

city: Tai'an

first: Xiaoming

last: Li

state: Shandong

address: 61st ,Daizong Street

country: China

institute: Shandong Agriculutural University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we sequenced four small RNA libraries derived from mature pollens, in vitro germinated pollens, mature silks and pollinated silks of maize, respectively. In total, 161 known miRNAs belonging to 27 families and 82 novel miRNAs were identified. Of them, miRNAs involved in pollen-silk (pistil) interactions were analyzed. On the male side, miRNA differentially expressed between mature and germinated pollen were identified, some of them participate in pollen germination and tube growth. On the female side, silk-expressed miRNAs respond to pollination were also responsive to stresses, especially drought and fungal invasion. Furthermore, GO analysis of target genes revealed that members related to anxin signal transduction and gene expressional regulation were overrepresented.The results indicated that during pollen-silk interactions, miRNAs-mediated auxin signal transduction plays important roles, and miRNAs took part in complex transcriptional regulating network.

overall_design: Examination of 4 different tissues of maize to provide novel information for understanding the post-transcriptional regulations of pollen-pistil interactions

first: Xiansheng

last: Zhang


title: Interferon-mediated innate immune responses against malaria parasite liver stages

city: Seattle

first: Wonjong

last: Moon

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle BioMed

summary: Identification of innate immune responses in the livers of mice infected with liver-stage arresting, transgenic, Plasmodium yoelii parasites.

overall_design: Whole liver samples from mock and P. yoelli fabb/f- infected C57BL/6 and BALB/cJ mice. Samples were taken 1 and 3 days post infection

first: Jessica

last: Miller

first: Stefan

last: Kappe


title: DNA methylation profiling by HELP-seq in Dnmt1+/+ mouse embryonic fibroblasts

status: Public on Mar 01 2013

city: Heidelberg

first: James

middle: P

last: Reddington

address: Meyerhofstrasse 1

country: Germany

institute: EMBL

summary: DNA methylation and the Polycomb Repression System are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their genomic targeting. However, whether this role of DNA methylation is important in the context of transcriptional regulation is unclear. By genome-wide mapping of the Polycomb Repressive Complex 2 (PRC2)-signature histone mark, H3K27me3, in severely DNA hypomethylated mouse somatic cells, we show that hypomethylation leads to widespread H3K27me3 redistribution, in a manner that reflects the local DNA methylation status in wild-type cells. Unexpectedly, we observe striking loss of H3K27me3 and PRC2 from Polycomb-target gene promoters in DNA hypomethylated cells, including Hox gene clusters. Importantly, we show that many of these genes become ectopically expressed in DNA hypomethylated cells, consistent with loss of Polycomb-mediated repression. An intact DNA methylome is required for appropriate Polycomb-mediated gene repression by constraining PRC2 targeting. These observations identify a previously unappreciated role for DNA methylation in gene regulation and therefore influence our understanding of how this epigenetic mechanism contributes to normal development and disease.

overall_design: DNA methylation levels in Dnmt1+/+ mouse embryonic fibroblasts measured by HpaII tiny fragment Enrichment by Ligation-mediated PCR Sequencing (HELP-seq)

first: Richard

last: Meehan


title: mRNA-seq in DNA methylation deficient mouse embryonic fibroblasts

overall_design: comparison of Dnmt1+/+ vs Dnmt1-/- mouse embryonic fibroblasts by strand-specific mRNA-seq


title: Genome-wide transcription factor binding maps of  glioma-associated oncogene family zinc finger 3 (Gli3) in Second Heart Field (SHF) cells disected from Mouse Embryos.

city: Chicago

first: Xinan

middle: "Holly"

last: Yang

state: IL

institute: universty of Chicago

summary: To investigate the heart development, the data were generated to examine the genome-wide Gli3 binding  in SHF disected from Mouse Embryos.

overall_design: Gli3 ChIP-Seq was compared to the input in SHF from mouse embryonic cells at E9.5.

first: Andrew

last: Hoffmann

first: Ivan

last: Moskowitz


title: Reduced Representation Bisulfite Sequencing in DNA methylation deficient mouse embryonic fibroblasts

overall_design: comparison of Dnmt1+/+ vs Dnmt1-/- mouse embryonic fibroblasts by Reduced Representation Bisulfite Sequencing


title: Hedgehog Molecular Networks in the Second Heart Field


title: Gene regulatory networks mediating canonical Wnt signal directed control of pluripotency and differentiation in embryo stem cells

city: Cambridge

first: Xiaoxiao

state: MA

address: 7 Divinity Ave.

department: Molecular and Cellular Biology

institute: Harvard University


title: ChIP-seq analysis of β-catenin in mouse embryonic stem cells treated with GSK3 inhibitor CHIR99021 under serum+LIF standard condition.

summary: The objective of this study was to identify the direct target genes of β-catenin acting downstream of canonical Wnt signaling in mouse embryonic stem cells (ESCs).Canonical Wnt signaling supports the pluripotency of mouse ESCs but also promotes differentiation of early mammalian cell lineages. To explain these paradoxical observations, we explored the gene regulatory networks at play. Canonical Wnt signaling is intertwined with the pluripotency network comprising Nanog, Oct4, and Sox2 in mouse ESCs. In defined media supporting the derivation and propagation of mouse ESCs, Tcf3 and β-catenin interact with Oct4; Tcf3 binds to Sox motif within Oct-Sox composite motifs that are also bound by Oct4-Sox2 complexes. Further, canonical Wnt signaling up-regulates the activity of the Pou5f1 distal enhancer via the Sox motif in mouse ESCs. When viewed in the context of published studies on Tcf3 and β-catenin mutants, our findings suggest that Tcf3 counters pluripotency by competition with Sox2 at these sites, and Tcf3 inhibition is blocked by β-catenin entry into this complex. Wnt pathway stimulation also triggers β-catenin association at regulatory elements with classic Lef/Tcf motifs associated with differentiation programs. The failure to activate these targets in the presence of a MEK/ERK inhibitor essential for mouse ESC culture suggests that MEK/ERK signaling and canonical Wnt signaling combine to promote mouse ESC differentiation.

overall_design: bCatenin ChIP-seq using anti-FLAG antibody and Streptavidin were otained from embryonic stem cells treated by CHIR99021 for 24 hours. Input without IP process were used as the control.

first: Shinsuke

last: Ohba

last: McMahon


title: Analysis of DNA methylation dynamics at Alu elements during human B cell activation

city: Research Triangle Park

first: Paul

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

summary: Paired-end sequencing of methylated DNA fragments in B cell subsets revealed widespread loss of methylation at Alu elements upon B cell activation.

overall_design: DNA methylation pattern was analyzed in purified naïve and germinal-center B cells derived from 1 patient

first: Anne

last: Lai


title: Rif1 Prevents Resection of DNA Breaks and Promotes Immunoglobulin Class Switching

city: NEW YORK

first: Thiago

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: DNA double-strand breaks (DSBs) represent a threat to the genome because they can lead to loss of genetic information and chromosome rearrangements. The DNA repair protein p53 binding protein 1 (53BP1) protects the genome by limiting nucleolytic processing of DSBs by a mechanism that requires its phosphorylation, but whether it does so directly is not known. Here we identify Rapl-interacting factor 1 (Rif1) as an Ataxia-Telangiectasia Mutated (ATM) phosphorylation-dependent interactor of 53BP1, and show that absence of Rif1 results in 5’-3’ DNA end resection in mice. Consistent with enhanced DNA resection, Rif1 deficiency impairs DNA repair in the G1 and S phases of the cell cycle, interferes with class switch recombination (CSR) in B lymphocytes, and leads to accumulation of chromosome DSBs.

overall_design: Study of Rif1 DNA-end protection activity against resection via analysis of single-stranded DNA binding protein RPA and Rad51 accumulation at sites of AID-induced DNA damage by ChIP-seq. All samples shown in Fig. 4 are included (controls and test samples, 7 samples in total).

first: Michela

last: Di Virgilio

first: Elsa

last: Callen

first: Arito

last: Yamane

first: Wenzhu

first: Mila

last: Jankovic

first: Alexander

last: Gitlin

first: Niklas

last: Feldhahn

first: Wolfgang

last: Resch

first: Brian

middle: T

last: Chait

first: André

last: Nussenzweig

first: Rafael

last: Casellas

first: Davide

middle: F

last: Robbiani

first: Michel

middle: C


title: macroH2A histone variants act as a barrier upon reprogramming towards pluripotency

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: Here we report that the histone variant macroH2A acts as a barrier to induced pluripotency. Using fibroblasts isolated from macroH2A double knockout mice, we observed enhanced reprogramming efficiency compared to fibroblasts from wild type animals. We further show that macroH2A isoforms act synergistically in this process. Genomic analysis in wild type fibroblasts reveals that macroH2A1 and H3K27me3 domains co-localize and occupy pluripotency genes. While the absence of macroH2A does not affect H3K27me3 in fibroblasts, macroH2A1 is highly enriched at a set of Utx target genes that are reactivated early during iPS reprogramming.

overall_design: Mononucleosomes from Dermal Fibroblasts (from wt and macroH2A1 and macroH2A2 double knockout mice) were isolated and ChIP'd with mH2A1, H3K27me3 and H3K27ac antibodies. DNA from Input and ChIP samples was purified and sequenced on Illumina's Hiseq.

first: Alexandre

last: Gaspar-Maia

first: Dan

last: Hasson


title: Differences in miRNA Detection Levels are Technology and Sequence Dependent

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

platform_organism:
Homo sapiens
synthetic construct

first: Shirley

last: Horn-Saban

first: Ester

last: Feldmesser


title: Human mitochondria hub of small RNAs: Analysis by deep Sequencing

city: Gandhinagar

first: Rajesh

last: Singh

state: GJ

address: Koba Inst Area

department: Cell Biology

country: India

institute: Indian Institute of Advanced Research

summary: We report here that human mitochondria contain small RNA including microRNA, piRNA, tRNA, rRNA, and RNA repeats. Mitochondria from human cells were purified and RNA isolated. Small RNAs were purified, library generated and analyzed by Illumina Hiseq 2000 system. The sequencing generated 19.5 and 17.7 million reads from HEK-293 and HeLa respectively. 91% and 97% sequences of HEK293 and HeLa respectively were annotated to various classes of small RNA. The total percentage of 4.21 and 2.58 sequences from HEK293 and HeLa respectively was found to be of miRNA. Further, we found only 1.2 % sequences from both the libraries aligned to mitochondrial genome. These results suggest that there is efficient transport of nuclear encoded small RNA to mitochondria. The small RNA in mitochondria may regulate critical cellular processes.

overall_design: Analyzing the smallRNA in human mitochondria from two human cell lines (HEK-293 and HeLa).

first: Lakshmi

last: Sripada

first: Dhanendra

last: Tomar


title: Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation.

overall_design: We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).

first: Gabriel

middle: E

last: Zentner

first: Steven


title: Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)


title: CDK8 ChIP-seq from HCT116 cells in normoxia and hypoxia

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: To test if CDK8 acts directly at HIF1A target genes, we performed ChIP-seq experiments in HCT116 cells under normoxic and hypoxic conditions.

overall_design: ChIP-seq for CDK8 versus Input under normoxia and 24hrs hypoxia (1% O2).


title: Genome-wide maps of Yan chromatin association

first: Ilaria

last: Rebay

address: 929 E. 57th St. GCIS W340M

department: Ben May Department

institute: University of Chicago

summary: High-resolution genome-wide binding of Yan used to confirm the presence of high-density regions seen in ChIP-chip

overall_design: ChIP-Seq of Yan protein in stage 11 Drosophila embryos

first: Jie

last: Zhang

first: Jemma

last: Webber

first: Lauren

last: Cote


title: H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation [ChIP-Seq]

first: Xiaolin

last: Wu

institute: Frederick National Laboratory for Cancer Research/SAIC-Frederick Inc

overall_design: Examination of TAF3, RNAPII, and H3K4me3 distribution in HCT116 cells.

first: Shannon

last: Lauberth

first: Takahiro

last: Nakayama

first: Andrea

last: Ferris

first: Stephen

last: Hughes

first: Robert

last: Roeder


title: Global analyses of how 3' UTR-isoform choice influences mRNA stability and translational efficiency

status: Public on Feb 28 2013

city: Stanford

first: Noah

last: Spies

address: 300 Pasteur Dr

institute: Stanford University

summary: We obtained global measurements of decay and translation rates for mammalian mRNAs with alternative 3' untranslated regions (3' UTRs).

overall_design: 1 3P-Seq sample from 3T3 cells and 1 3P-Seq sample from mouse ES cells; 2 2P-Seq steady state and 4 2P-Seq with actinomycin D; 6 polysome fraction 2P-Seq

first: Christopher

middle: B

last: Burge

first: David

last: Bartel


title: GRO-seq from HCT116 cells

summary: The majority of transcription studies examine steady-state RNA . However steady-state RNA is not a true reflection of the transcriptome, because the RNA levels are affected by both transcription rate and degradation rate. In this experiment we measured the amount of transcription occurring in HCT116 colon cancer cells, regardless of degradation, using GRO-seq (global nuclear run-on sequencing). This information demonstrates that many genes have a pile-up of transcriptionally-engaged polymerase near their 5'-end.

overall_design: Nuclei were prepared from HCT116 cells (treated for 1hr with DMSO as control for additional GRO-seq experiments to be reported separately). Transcription run-on was performed (as per Core, L.J., Waterfall, J.J., and Lis, J.T. (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848) and nascent RNAs were purified and sequenced.

first: Mary

last: Allen


title: Adult stem cells in the human parasite Schistosoma mansoni

city: Urbana

first: James

last: Collins

address: 601 S. Goodwin

institute: University of Illinois at Urbana Champaign

summary: RNAseq experiments to identify gene expression changes following gamma irradiation

overall_design: Adult male Schistosoma mansoni (strain: NMRI) were subjected to 200 Gy of  gamma irradiation and cultured in vitro for 48hr hours.  After 48hr germ line tissues were removed and RNA was extracted from remaining somatic tissues.  Samples were processed for RNAseq using Illumina procedures.

first: Phillip

last: Newmark


title: Circular RNAs are a large class of animal RNAs with regulatory potency (PAR-CLIP)

city: Berlin

first: Marvin

last: Jens

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

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrueck Center for Molecular Medicine

summary: Circular RNAs (circRNAs) in animals are an enigmatic class of RNAs with unknown function. To systematically explore circRNAs, we sequenced and computationally analyzed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, with oftentimes tissue/developmental stage specific expression. Sequence analysis suggested important regulatory functions for circRNAs. Indeed, we discovered that human circRNA CDR1as is densely bound by miRNA effector complexes and harbors 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebra fish impaired midbrain development similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, indicating previously unrecognized regulatory potential of coding sequences.

overall_design: PARCLIP was performed as in Hafner et. al Cell 2010 with HEK293 cell lines stably expressing HIS/FLAG/HA-tagged AGO1 or AGO2. We used 4-thiouridine (4SU) to enhance the crosslink and generated cDNA libraries.

first: Markus

last: Landthaler

first: Mathias

last: Munschauer

first: Lea

last: Gregersen


title: Genome-wide analysis of acetylated H4K5 binding offers new insights into the acute and chronic effects of METH on gene expression in the dorsal striatum

city: Baltimore

first: Jean Lud

last: Cadet

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

summary: In contrast to the acute METH-induced transcriptional changes, chronic METH administration produces differential changes in IEG responses and blunts the striatal effects of a single METH injection (McCoy et al., 2011). These observations suggested that chromic METH might have caused changes in the molecular machinery that controls the acute effects of the drug. Gene transcription is regulated by complex interactions of transcription factors with regulatory elements [14,15]. During resting states, DNA is compacted in a way that interferes with the binding of transcription factors whereas DNA becomes more accessible during activation of cells by various stimuli [16]. DNA is indeed packaged into chromatin whose fundamental subunit, the nucleosome, is made of 4 core histones, histones H2A, H2B, H3, and H4 that form an octomer (2 of each histone) surrounded by 146 bp of DNA [17].  The N-tails of histones possess lysine residues that can be reversibly acetylated or deacetylated by several histone acetyltransferases (HATs) or by histone deacetylases (HDACs), respectively [18,19]. These changes promote alterations in gene expression by modifying chromatin conformation and enabling or inhibiting recruitment of regulatory factors onto DNA sequences [20].  Herein, we report that the acute, but not the chronic, transcriptional effects of METH are mediated, for the most part, by increased DNA binding of  histone H4  acetylated at lysine 5 (H4K5ac).    These results suggest that other factors, including histone and/or DNA methylation, might play a more important role in mediating the molecular effects of chronic METH exposure.

overall_design:
18 samples pooled as SS (4), SM (3), MS (3), MM (4), INPUT (4):
SS Saline pretreatment then saline treatment
SM Saline pretreatment then METH treatment
MS METH pretreatment then saline treatment
MM METH pretreatment then METH treatment
untreated

first: Jean

middle: L

first: Michael

last: McCoy

first: Subramaniam

last: Jayanthi

first: Bruce

last: Ladenheim

first: Irina

last: Krasnova

first: Elin

last: Lehrmann

first: Supriyo

last: De

first: Kevin

last: Becker

first: Christie

last: Brannock


title: Circular RNAs are a large class of animal RNAs with regulatory potency

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

overall_design: Refer to individual Series


title: Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli

city: Davis

first: Vadim

last: Mozhayskiy

address: One Shields Avenue

department: Genome Center

institute: UC Davis

summary:
We evolved Escherichia coli cells over 500 generations under five environments that include four abiotic stressors: osmotic, acidic, oxidative, n-butanol, and control
The goal of the experiment: Bacterial populations have a remarkable capacity to cope with extreme environmental fluctuations in their natural environments. In certain cases, adaptation to one stressful environment provides a fitness advantage when cells are exposed to a second stressor, a phenomenon that has been coined as cross-stress protection. A tantalizing question in bacterial physiology is how the cross-stress behavior emerges during adaptation and what the genetic basis of acquired stress resistance is.

overall_design: RNA profiles were obtained for six E. coli strains evolved for 500 generations under abiotic stressors; two technical replicates for each strain where sequenced by Illumina GAII analyzer

first: Martin

last: Dragosits

first: Semarhy

last: Quinones-Soto

first: Jiyeon

last: Park

first: Ilias

last: Tagkopoulos


title: Dynamics of yeast ISWI and CHD chromatin remodeler genomic association

first: Jorja

last: Henikoff

type: Genome variation profiling by high throughput sequencing

first: Gabriel

last: Zentner

first: Steven

first: Tsukiyama

last: Toshi


title: Quantitative, genome-wide analysis of eukaryotic replication initiation and termination

city: New York

first: Iestyn

last: Whitehouse

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

summary: Via the deep-sequencing of Okazaki fragments from Saccharomyces cerevisiae, we report the first comprehensive documentation of genome-wide replication directionality in any eukaryote; this permits the systematic analysis of both replication initiation and termination. We conduct a genome-wide analysis of origin competence and efficiency, and conclude that the majority of origins are competent to fire in each cell cycle and generally do so with high efficiency. Additionally, the spatial resolution of our data allow us to determine that leading-strand initiation generally occurs within the nucleosome-free region at origins. Using a strain in which late origins can be induced to fire early, we show that replication termination is a largely passive phenomenon that does not rely on cis-acting sequences or replication fork pausing and that the replication profile is determined largely by the kinetics of origin firing, allowing us to reconstruct chromosome-wide timing profiles from an asynchronous culture.

overall_design: 5 samples are included. Two are replicate, paired-end, wild-type samples sequenced via Illumina methodology. The raw data for these two are also deposited in the GEO repository under accession numbers GSM835650 and GSM835651. Two replicate, single-end, Sld2, Sld3, Dbf4, Dpb11, Cdc45 and Sld7 (SSDDCS) overexpression via galactose induction experiments are reported sequenced via Ion Torrent methodology. One single-end, Sld2, Sld3, Dbf4, Dpb11, Cdc45 and Sld7 (SSDDCS) normal expression control via glucose media experiment is reported sequenced via Ion Torrent methodology.

first: Duncan

last: Smith

first: Sean

last: McGuffee


title: The nucleoporin Nup170p is required for subtelomeric chromatin structure and gene silencing. [MNase-Seq]

city: Nanjing

first: Yakun

last: Wan

address: Sipailou #2

institute: Southeast University

summary: Transcriptionally silent heterochromatin preferentially localizes at the nuclear periphery, but, despite this, certain budding yeast genes relocate to the nuclear periphery following gene activation, implicating the nuclear envelope in both transcriptional activation and silencing. It is unclear how these distinct chromatin domains are established, maintained and distinguished from one another at the nuclear envelope. Here we report that nuclear pore complexes (NPCs) facilitate the transition between chromatin states by providing a platform to which chromatin-remodeling and chromatin-modifying complexes bind. In particular, we show that the RSC chromatin-remodeling complex associates with NPCs and that the nucleoporin Nup170p nucleates heterochromatin formation at telomeres through recruitment of Sir4p. Deletion of NUP170 altered subtelomeric chromatin structure, reduced SIR complex binding at telomeres, impaired telomeric silencing and abated telomere tethering. These results support a model in which telomeric heterochromatin formation occurs through telomere-NPC interactions that both promote Sir4p binding at telomeres and permit chromatin-remodeling complexes to mediate the transition between chromatin states.

overall_design: Examination of genome-wide nucleosome positions in WT and nup170∆ cells via next-generation sequencing of mononucleosomal DNA.

first: David

middle: W

last: Van de Vosse

first: Diego

last: Lapetina

first: Wei-Ming

last: Chen

first: Jung-Hsien

last: Chiang

first: John

last: Aitchison

first: Richard

last: Wozniak


title: A role for the nucleoporin Nup170p in chromatin structure and gene silencing

type: Genome binding/occupancy profiling by array

summary:
Embedded in the nuclear envelope, nuclear pore complexes (NPCs) not only regulate nuclear transport, but also interface with both transcriptionally active euchromatin and largely silenced heterochromatin, as well as the boundaries between these regions. It is unclear what functional role NPCs play in establishing or maintaining these distinct chromatin domains. Here we report that the yeast NPC protein Nup170p interacts with specific regions of the genome containing ribosomal protein and subtelomeric genes. At these locations, Nup170p functions to establish normal nucleosome positioning and as a repressor of transcription. We show that the function of Nup170p in subtelomeric gene silencing is linked to its association with the RSC chromatin-remodeling complex and the silencing factor Sir4p, and that the binding of Nup170p and Sir4p to subtelomeric chromatin is cooperative and necessary for the association of telomeres with the nuclear envelope. Our results establish the NPC as an active participant in the formation of peripheral heterochromatin.

This SuperSeries is composed of the SubSeries listed below.


title: Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition [PAR-CLIP]

status: Public on Feb 26 2013

first: Miguel

last: Brown

address: 1230 York Ave Box 186

summary: Human LIN28A and B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ~3,000 mRNAs at ~9,500 sites located in the 3’UTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines, and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. In HEK293 cells, LIN28 protein binding mildly stabilized target mRNAs and increased protein abundance. The top targets were its own mRNAs and those of other RBPs and cell-cycle regulators. Alteration of LIN28 protein levels also negatively regulated the abundance of some, but not all let-7 miRNA family members, indicating sequence-specific binding of let-7 precursors to LIN28 proteins and competition with cytoplasmic miRNA biogenesis factors.

overall_design: LIN28 protein PAR-CLIP

first: Hafner

last: Markus

first: Tuschl

last: Thomas


title: Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition [RNA-Seq]

overall_design: To assess whether miRNAs are regulated by LIN28B we analyzed the miRNA levels of LIN28B overexpressing and LIN28B-depleted cells using small RNA cDNA library sequencing. The RBP LIN28B was depleted by siRNAs and the expression levels was compared to mock-transfected HEK293 cells.

first: Markus

last: Hafner

first: Thomas

last: Tuschl


title: Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition


title: Differences in miRNA Detection Levels are Technology and Sequence Dependent [NGS]

first: Dena

last: Leshkowitz

summary: We undertook an integrative technological approach to compare miRNA detection capability of three high-throughput commercial platforms.

overall_design: We artificially introduced human precursor, 2’-O-methyl modified and mature spiked-in miRNAs in a controlled fashion into native human placenta total RNA.

first: Shirley

last: Horn-Saban

first: Yisrael

last: Parmet

first: Ester

last: Feldmesser


title: Specific miRNA Stabilization by Gld2-catalyzed Monoadenylation

status: Public on Feb 23 2013

city: Worcester

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: miRNAs are small non-coding RNAs that inhibit translation and promote mRNA decay.  The levels of mature miRNAs are the result of different rates of transcription, processing, and turnover. The non-canonical polymerase Gld2 has been implicated in the stabilization of miR-122 possibly by catalyzing 3’ monoadenylation, however, there is little evidence that this relationship is one of cause and effect.  Here, we biochemically characterize Gld2 involvement in miRNA monoadenylation and its effect on miRNA stability.  We find that Gld2 directly monoadenylates and stabilizes specific miRNA populations in human fibroblasts and that sensitivity to monoadenylation-induced stability depends on nucleotides in the miRNA 3‘ end.  These results establish a novel mechanism of miRNA stability and resulting post-transcriptional gene regulation.

overall_design: Sequencing of miRNAs to assess amount and 3' end monoadenylation state upon Gld2 knock-down.

first: Andrea

last: D'Ambrogio

first: Weifeng

last: Gu

first: Tsuyoshi

last: Udagawa

first: Joel

last: Richter


title: A global differential transcriptomic profiling of Mycobacterium gilvum PYR-GCK during pyrene and glucose metabolism, using RNA seq.

status: Public on Feb 22 2013

city: Ansan

first: Abimbola

middle: Comfort

last: Badejo

address: 1271 Sa3dong

country: South Korea

institute: Hanyang University

summary: We report the differential expression of a PAH degrading bacterium in different states of substrate induction.

overall_design: Separate substrate cultivation of the same batch of bacterial isolates; total RNA extraction, processing and sequencing; gene expression analysis using bioinformatics softwares and experimental validation using qRT-PCR.

first: KyoungHwa

last: Jung

first: SeKye

last: Kim

first: JinChoul

last: Chai

first: WonHyong

last: Chung

first: NamShin

first: HyoJoon

first: YoungGyu


title: High-throughput RNA sequencing analysis of WT, rdm16-2 and sta1 mutants

city: Shanghai

first: Lan

last: Yang

address: 300 Fenglin Road

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

summary: Using Illumina paired-end RNA-seq technology to examine the genome-wide gene expression and intron-retention events in WT, rdm16-2 and sta1

overall_design: RNA-seq analysis of 4-week-old leaves of WT, rdm16-2 and sta1 mutants

first: Chao-Feng

last: Huang

first: Jian-Kang

last: Zhu


title: Stranded RNA-seq of H9 cells

first: Li

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: We have used stranded RNA-seq to explore RNA editing in H9 cells

overall_design: Examination RNA editing with stranded RNA-seq

first: Shanshan

first: Jian-Feng

last: Xiang

first: Tian

last: Chen

first: Ling-Ling


title: Comparative Validation of the D. melanogaster Encyclopedia of DNA Elements Transcript Models

status: Public on Feb 25 2013

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: The model organism Encyclopedia of DNA Elements project (modENCODE) has produced a comprehensive annotation of D. melanogaster transcript models based on an enormous amount of high-throughput experimental data. However, some transcribed elements may not be functional, and technical artifacts may lead to erroneous inference of transcription. Inter-species comparison provides confidence to predicted annotation, since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function.  We have performed RNA-Seq and CAGE-Seq experiments on more than 80 samples from multiple tissues and stages of 15 Drosophila species, including 8 previously unsequenced genomes.  We have found strikingly conserved sequence, expression, and splicing for the vast majority of transcript models in modENCODE annotation (e.g. 99% exons of coding sequences (CDS), 88% exons of untranslated regions (UTR), and 87% splicing events), indicating that the transcriptome annotation is of very high quality.  We also describe dynamic transcriptome evolution within the Drosophila genus, including conserved promoter structure, labile positions of transcription start sites, and rapidly evolving RNA-editing events.  We demonstrate how this phylogenetic approach to DNA element validation will prove useful in the annotation of other high priority genomes, especially for genomes that are less compact than Drosophila (e.g. the vast majority of vertebrate genomes).

relation:
SuperSeries of: GSE19989
SuperSeries of: GSE20348
SuperSeries of: GSE20882
SuperSeries of: GSE28078
SuperSeries of: GSE31302
SuperSeries of: GSE43321
SuperSeries of: GSE66284

sample_organism:
Drosophila ananassae
Drosophila melanogaster
Drosophila mojavensis
Drosophila pseudoobscura
Drosophila simulans
Drosophila virilis
Drosophila yakuba
Drosophila eugracilis
Drosophila takahashii
Drosophila elegans
Drosophila ficusphila
Drosophila kikkawai
Drosophila bipectinata
Drosophila biarmipes
Drosophila rhopaloa

overall_design: Refer to individual Series (listed below).


title: Acinetobacter oleivorans DR1 : Wild type treated with tetracycline vs. harboring plasmid (pAST2) treated with tetracycline

status: Public on Feb 21 2013

city: Seoul

first: Hyerim

last: Hong

address: Korea Univ. Anam Campus, Anam-dong 5-ga, Seongbuk-gu

department: Environmental Science and Ecological Engineering

institute: Korea University

summary: Transcriptional profiling of A. oleivorans DR1 cells comparing tetracylcline-treated wild type cells with tetracycline-treated DR1 cell harboring pAST2.

overall_design: To identify genes important for tetracycline stress response in A. oleivorans DR1 and A. oleivorans DR1 harboring pAST2, the cells were grown to exponential phase (OD600 ~0.4) and treated with tetracycline (1μg/ml) over a period of 15 min.


title: Chip-seq for H3K27me3 and H3K4me3 in DNA methylation deficient mouse embryonic fibroblasts

status: Public on Feb 20 2013

city: Heidelberg

first: James

last: Reddington

address: Meyerhofstrasse 1

institute: EMBL

summary: DNA methylation and the Polycomb Repression System are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their genomic targeting. However, whether this role of DNA methylation is important in the context of transcriptional regulation is unclear. By genome-wide mapping of the Polycomb Repressive Complex 2 (PRC2)-signature histone mark, H3K27me3, in severely DNA hypomethylated mouse somatic cells, we show that hypomethylation leads to widespread H3K27me3 redistribution, in a manner that reflects the local DNA methylation status in wild-type cells. Unexpectedly, we observe striking loss of H3K27me3 and PRC2 from Polycomb-target gene promoters in DNA hypomethylated cells, including Hox gene clusters. Importantly, we show that many of these genes become ectopically expressed in DNA hypomethylated cells, consistent with loss of Polycomb-mediated repression. An intact DNA methylome is required for appropriate Polycomb-mediated gene repression by constraining PRC2 targeting. These observations identify a previously unappreciated role for DNA methylation in gene regulation and therefore influence our understanding of how this epigenetic mechanism contributes to normal development and disease.

overall_design: comparison of Dnmt1+/+ vs Dnmt1-/- mouse embryonic fibroblasts by ChIP-seq for H3K27me3 and H3K4me3

first: Richard

last: Meehan


title: Kdm2b maintains murine embryonic stem cell status  by recruiting PRC1 complex to CpG islands of developmental genes

city: Boston

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School


title: Histone methylation profiles of prospectively isolated mammary epithelial subpopulations

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary: In this study we mapped H3K27me3, H3K4me3 and H3K9me2 marks in three mammary epithelial subsets: MaSC/basal (MS), luminal progenitor (LP) and mature luminal (ML) in the steady-state. In addition, profiles were generated for H3K4me3 and H3K27me3 marks in the MaSC/basal and luminal populations from the glands of ovariectomized or mid-pregnant (12.5 days) mice as well as from control virgin mice.

overall_design: We used ChIPseq analysis to determine histone modification marks in the  MS, LP and ML subsets in the steady-state. We then determined the histone modification profiles of MS and sorted luminal (Lum) cells from pregnant (12.5 dP) or ovariectomized (OVX) mice and compared these with the profiles of control virgin mice in order to study the effect of hormones on the mammary epigenomes.

first: Bhupinder

last: Pal

first: Toula

last: Bouras

first: François

last: Vaillant

first: Julie

last: Sheridan

first: Kun

last: Jiang

first: Kelsey

last: Breslin

first: Matthew

last: Young

first: Naiyang

last: Fu

last: Ritchie

first: Geoffrey

last: Lindeman

first: Gordon

middle: K

last: Smyth

first: Jane

last: Visvader


title: Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of lineage genes [ChIP-Seq]

first: Li

summary: Polycomb group (PcG) proteins play important roles in repressing lineage-specific genes and maintaining the undifferentiated state of mouse embryonic stem cells (mESCs). However, the mechanisms by which PcG proteins are recruited to their targets are largely unknown. Here, we show that the histone demethylase Kdm2b is highly expressed in mESCs and regulated by the pluripotent factors Oct4/Sox2 directly. Depletion of Kdm2b in mESCs causes de-repression of lineage-specific genes and induces early differentiation. The function of Kdm2b depends on its CXXC-ZF domain, which mediates Kdm2b’s genome-wide binding to CpG islands (CGIs). Kdm2b interacts with the core components of the Polycomb repressive complex 1 (PRC1) and recruits the complex to the CGIs of early lineage-specific genes. Thus, our study not only reveals a novel Oct4/Sox2-Kdm2b-PRC1-CGI regulatory axis and its function in maintaining undifferentiated state of mESCs, but also demonstrates a critical function of Kdm2b in recruiting PRC1 to the CGIs of lineage-specific genes to repress their expression.

overall_design: In this dataset, we include the ChIP-seq data of Kdm2b, Ezh2 and Ring1b in both control and Kdm2b knock down mouse embryonbic stem cells.

first: Jin

last: He

first: Ma

last: Wan

first: Olena

last: Taranova

first: Hao

last: Wu

first: Yi

last: Zhang


title: Genome-wide mapping of Flag-Evi1Δ324 in SKOV-3 ovarian carcinoma cells

city: Singapore

first: Ahmed

last: Sayadi

state: Singapore

address: 61 biopolis

country: Singapore

institute: Genome Institute of Singapore

summary: Discovery of Evi1Δ324 genomic occupancy and target genes

overall_design: ChIP-enriched DNA and input DNA were analyzed by Solexa sequencing.

first: E

middle: A

last: Bard-Chapeau

first: A

first: C

last: Wei

first: N

last: Jenkins

last: Copeland


title: De novo characterization of foliar transcriptome in Chenopodium amaranticolor and analysis of the differentially expressed genes during the stage of hypersensative response induced by distinct plant viruses

city: Beijing

first: WEIMIN

last: LI

address: No.12 Zhongguancun St.

institute: Biotechnology Research Institute, CAAS

summary: The hypersensitive response (HR) system of Chenopodium spp. confers broad-spectrum virus resistance. However, scant knowledge exists at the genomic level for Chenopodium, thus impeding the advanced molecular research of this attractive feature. Hence we took advantage of RNA-seq to survey the foliar transcriptome of C. amaranticolor, one Chenopodium species being widely used as laboratory indicator for pathogenic viruses, in order to facilitate the characterization of the HR-type of virus resistance. In a single run, we obtained 39,868,984 reads with 3,588,208,560 bp, which were assembled into 112,453 unigenes (3,848 clusters and 108,605 singletons). BlastX search against the NCBI NR database identified 62,482 sequences with a cut-off E-value above 10-5. Assembled sequences were annotated with gene descriptions, GO, COG and KEGG terms. A dataset containing 738 resistance gene analogs and sequences represent 6 key signaling proteins within the R proteins-directed signaling pathway was generated. Additionally, using RNA-Seq digital gene expression analysis, we investigated the gene expression profiles over the stage of HR induced by Tobacco mosaic virus and Cucumber mosaic virus in C. amaranticolor leaves, and identified numerous candidate genes specifically or commonly regulated by these two distinct viruses at early and late stages of the HR. Specifically, the dynamic changes of the differently expressed genes enriched in the pathway of plant-pathogen interaction were analyzed. To our knowledge, this is the first study to elucidate the genetic makeup of Chenopodium spp., providing a starting-point for future functional genomics studies on Chenopodium.

overall_design: Analysis of the differentially expressed genes over the stage of hypersensative response induced by viruses in C. amaranticolor

first: Yongqiang


title: Degradome sequencing reveals an endogenous microRNA target in C. elegans

status: Public on Feb 19 2013

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

institute: Seoul National University

summary: Total poly(A) RNAs from wild-type adult stage worms were subjected to high-throughput sequencing using an Illumina platform to detect RNA cleavage fragment.

overall_design: Wild-type (N2) C. elegans

first: June

middle: H

last: Park

last: Nam


title: mRNA-Seq of whole adult females and males, and miixed sex embryos, from multiple Drosophila species

first: Brian

last: Oliver

summary: We performed transcriptional profiling of sexed whole adults and mixed sex embryos of eight Drosophila species.  These data were used in a comparative transcriptomics analysis of multiple Drosophila species to define functional elements conserved throughout the Drosophila genus.

sample_organism:
Drosophila eugracilis
Drosophila takahashii
Drosophila elegans
Drosophila ficusphila
Drosophila kikkawai
Drosophila bipectinata
Drosophila biarmipes
Drosophila rhopaloa

overall_design: For each species, wild-type inbred strains were analysed.  Each sample represents an independent pool of flies (30 flies for adult samples, 200-300 ml for embryos).

first: David

last: Sturgill

first: Zhen-Xia

last: Chen

first: Artyom

last: Kopp

first: Stephen

last: Richards


title: The histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia

city: Cold Spring Harbor

first: Shinpei

last: Kawaoka

address: 1 Bungtown road

institute: Cold Spring Harbor Laboratory

summary: MLL-fusions are potent oncogenes that initiate aggressive forms of acute leukemia. As aberrant transcriptional regulators, MLL-fusion proteins alter gene expression in hematopoietic cells through interactions with the histone H3 lysine 79 (H3K79) methyltransferase DOT1L. Notably, interference with MLL-fusion cofactors like DOT1L is an emerging therapeutic strategy in this disease. Here we identify the histone H2B E3 ubiquitin ligase RNF20 as an additional requirement for MLL-fusion-mediated leukemogenesis. Suppressing the expression of Rnf20 in diverse models of MLL-rearranged leukemia leads to inhibition of cell proliferation; under tissue culture conditions as well as in vivo. Rnf20 knockdown leads to reduced expression of MLL-fusion target genes, including Hoxa9 and Meis1; effects that resemble Dot1l-inhibition. Using ChIP-seq, we found that H2B ubiquitination (H2Bub) is enriched in the body of MLL-fusion target genes, correlating with sites of H3K79 methylation and transcription elongation. Furthermore, we found that Rnf20 is required to maintain local levels of H3K79 di-methylation by Dot1l at Hoxa9 and Meis1. These findings support a model whereby co-transcriptional recruitment of Rnf20 at MLL-fusion target genes leads to amplification of Dot1l-mediated H3K79 methylation, thereby rendering leukemia cells dependent on Rnf20 to maintain their oncogenic transcriptional program.

overall_design: Examination of gene expression profiles upon RNF20 RNAi in MLL-AF9 acute myeloid leukemia cells

first: Christopher

last: Vakoc


title: The transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola

city: Honolulu

first: Yangrae

last: Cho

state: HI

address: 3190 Maile Way, St John 317

department: Plant and Environmental Protection Sciences

institute: University of Hawaii at Manoa

summary: Alternaria brassicicola is a successful saprophyte and necrotrophic plant pathogen.  Several A. brassicicola genes have been characterized as virulence factors affecting pathogenesis of Brassica species.  To study regulatory mechanisms of pathogenesis, we mined 421 genes in silico encoding putative transcription factors in a machine-annotated, draft genome sequence of A. brassicicola.  Targeted gene disruption mutants for 114 of the genes with proteins predicted to contain at least one putative zinc-finger domain were produced and functionally analyzed.  Six of these genes were associated with pathogenesis.  Disruption mutants corresponding to five of the genes were ≥50% less virulent than the wild type. Unexpectedly, the mutants of one gene (designated Amr1) were 100% more virulent.  Amr1 is a homolog of Cmr1, a transcription factor previously found to regulate melanin biosynthesis in several fungi.  Gene deletion mutants (Δamr1) were created and their phenotypes characterized.  The Δamr1 mutants utilized pectin as a carbon source more efficiently than the wild type, were melanin-deficient, and more sensitive to UV light and glucanase digestion.  The Amr1 protein was localized in the nuclei of hyphae and in highly melanized conidia during the late stage of plant pathogenesis.  RNA-seq analysis revealed that three genes in the melanin biosynthesis pathway, along with the deleted Amr1 gene, were not expressed in the mutants.  In contrast, many hydrolytic enzyme-coding genes were expressed at much higher levels in the mutants than in the wild type during pathogenesis.  The results of this study suggested that only a small number of transcription factors with zinc finger domains are needed to maintain strong virulence.  Furthermore, a gene important for survival in nature negatively affected virulence, probably by less efficient use of pectin.  We speculate that the functions of the Amr1 gene are important to the success of A. brassicicola as a competitive saprophyte and plant parasite

overall_design: gene expression profile comparisons between wild type and a transcription factor mutant during the late stage of host infection

first: Robin

last: Ohm


title: Stallion sperm transcriptome as revealed by microarray analysis and RNA sequencing

city: College Station

first: Pranab

middle: Jyoti

last: Das

address: Room 314B Bldg. 1197

department: Department of Veterinary Integrative BioSciences

institute: Texas A&M University

summary:
Purpose: In order to understand the functional significance of sperm transcriptome in stallion fertility, the aim of this study was to generate a detailed body of knowledge about the sperm RNA profile that defines a normal fertile stallion.
Methods: The 50 bp single-end ABI SOLiD raw reads were directly aligned with the horse reference sequence EcuCab2 using ABI aligner software (NovoalignCS version 1.00.09, novocraft.com) which uses multiple indexes in the reference genome, identifies candidate alignment locations for each primary read, and allows completion of the alignment.
Results: Next generation sequencing (NGS) of total RNA from the sperm of two reproductively normal stallions generated about 70 million raw reads and more than 3 Gb of sequence per sample; over half of these aligned with the EcuCab2 reference genome. Altogether, 19,257 sequence tags with average coverage ≥1 (normalized number of transcripts) were mapped in the horse genome.
Conclusion: The sequence of stallion sperm transcriptome is an important foundation for the discovery of transcripts of known and novel genes, and non-coding RNAs, thus improving the annotation of the horse genome sequence draft and providing markers for evaluating stallion fertility.

overall_design: Reproductively fertile Stallion sperm transcriptome as revealed by  RNA sequencing

first: Terje

last: Raudsepp


title: ALKBH5 is a New Mammalian RNA Demethylase

status: Public on Feb 15 2013

city: Chicago

first: zhike

last: lu

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: N6-methyladenosine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as a new mammalian demethylase that oxidatively removes the m6A modification in mRNA in vitro and inside cells. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the assembly of mRNA processing factors in nuclear speckles. Alkbh5-deficient male mice are characterized by impaired fertility resulting from apoptosis that affects meiotic metaphase-stage spermatocytes. In accordance with this defect, we have identified in mouse testes 1552 differentially expressed genes which cover broad functional categories and include spermatogenesis-related mRNAs involved in the p53 functional interaction network. We show that Alkbh5-deficiency impacts the expression levels of some of these mRNAs, supporting the observed phenotype. The discovery of this new RNA demethylase strongly suggests that the reversible m6A modification plays fundamental and broad functions in mammalian cells.

overall_design: RNA-seq in two cell types

first: Guanqun

last: Zheng

first: Zhike

last: Lu


title: RNA-Sequencing Analysis of High Glucose Treated Monocytes Reveals Novel Transcriptome Signatures and associated Epigenetic Profiles

city: Duarte

first: Nancy

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: We report high throughput transcriptomic profiling with RNA-Sequencing (RNA-Seq) to uncover network responses in human THP-1 monocytes treated with high glucose (HG).

overall_design: Examination of differential expression between normal and high glucose condition in THP1 cells.

first: Rama

last: Natarajan

first: Feng

last: Miao

first: Zhuo


title: Avian resistance to Campylobacter jejuni colonization is associated with an intestinal immunogene expression signature identified by mRNA sequencing.

city: Dublin

first: Sarah

last: Connell

address: College Green

country: Ireland

institute: Trinity College Dublin

summary: RNAseq analysis of caecal tissue from 14 C. jejuni-susceptible and 14 C. jejuni-resistant birds from a single population of infected chickens was conducted in order to identify gene expression associated with resistance to colonization. Significantly higher expression of genes involved in the innate immune response, cytokine signaling, B cell and T cell activation and immunoglobulin production, as well as the renin-angiotensin system was observed in resistant birds.

overall_design: A population of 255 Barred Rock chickens were orally inoculated with C. jejuni and their caecal colonization levels estimated 48 hours post-inoculation. Caecal samples from 14 birds with no colonization and the 14 birds with the highest colonization were selected for mRNA sequencing.

first: S

first: C

last: O'Farrelly


title: Long non-coding RNAs regulate adipogenesis (Illumina RNA-Seq)

city: Cambridge

first: Cole

last: Trapnell

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Adipogenesis involves the regulation of hundreds of genes by several well-studied proteins, but the role of long, noncoding RNAs in this process has not been defined.  We track the regulation of hundreds of lncRNAs during adipocyte differentiation, and find several that are essential for this process.

overall_design: We extractedbrown and white primary adipocytes and pre-adipocytes and profiled lncRNA expresssion via mRNA-Seq.  We also profiled cultured, differentiated adipocytes to verify that we could recapitulate the adipocyte expression profile in preparation for a loss-of-function screen for essential adipogenic lincRNAs.

first: Lei

last: Sun

first: Loyal

last: Goff

first: Ryan

last: Alexander

first: Alice

last: Lo

first: Manolis

last: Kellis

first: Harvey

last: Lodish

first: John

last: Rinn


title: An inherently bi-functional subset of Foxp3+ Treg/T-helper cells is controlled by the transcription factor Eos

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: At sites of inflammation, certain Foxp3+ Tregs have the ability to alter their phenotype and become pro-inflammatory helper/effector cells, without losing Foxp3 expression.  We show that this functional reprogramming is controlled by the transcription factor Eos (Ikzf4), an obligate co-repressor for Foxp3.  The ability to reprogram was restricted to a specific subset of Foxp3+ Tregs, arising as early as the thymus and identifiable by short half-life of Eos at rest, characteristic cell-surface markers (CD38+CD69+CD103NEG) and a distinct pattern of DNA methylation.  Mice made selectively deficient in this subset of Eos-labile Tregs became markedly impaired in their ability to cross-present new antigens and prime CD8+ T cells.  Downregulation of Eos and consequent Treg reprogramming was prevented by the immunoregulatory enzyme IDO, via activation of the aryl hydrocarbon receptor (AhR).  Thus, the Foxp3+ lineage contains a committed subset of Tregs that are constitutively primed for conversion into biologically important helper cells.

overall_design: Cells from thymus or spleen were incubated for 1 hr with cycloheximide (CHX), then CD4+GFP+ Tregs were FACS-sorted into Eos-labile (CD38+CD103NEG) and Eos-stable (CD103+CD38NEG) subsets.  Control CD4+GFPNEG (non Treg) cells were sorted from spleen.  Genome-wide differential methylation analysis was performed using Reduced Representation Bisulfite Sequencing (RRBS).  The genomic DNA from each sample was digested with the methylation-insensitive restriction enzyme MspI (restriction site, CCGG) and ligated to Illumina sequencing adaptors containing methylated cytosine residues. The ligated MspI fragments were size-selected, treated with sodium bisulfite, and amplified by PCR. The PCR products were purified and sequenced using Illumina HiSeq 2000 sequencer with a read length of 100bp.

first: David

last: Munn


title: RNA-Sequencing and promoter chromatin profiles analysis of High Glucose Treated Monocytes

first: Nancy

last: Chen

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

overall_design: Refer to individual Series


title: Bisulfite-Seq profiling of undifferentiated ESCs, and in vitro derived primordial germ cells (iPGCs)

status: Public on Feb 14 2013

city: Los Angeles

last: Vincent

address: 621 Charles E Young Dr. S

department: MCDB

institute: UCLA

summary: We report that in vitro derived PGCs undergo genome-wide DNA demethylation and that this demethylation does not require Tet1/Tet2

overall_design: Examination of methylation in ESCs, iPGCs, and Tet2-/- iPGCs depleted of Tet1 by shRNA lentiviruses

first: Amander

last: Clark


title: Long non-coding RNAs regulate adipogenesis


title: Ptf1a binding sites in a pancreatic cell line which mimics embryonic day E10.5 pancreas progenitors.

city: Copenhagen N

first: Anne

last: Grapin-Botton

address: Blegdamsvej3 B

department: DanStem

country: Denmark

institute: University of Copenhagen

summary: Pancreatic specific transcription factor1a (Ptf1a) immunoprecipitated chromatin from 266.6 cells produced 26 million tags with the Illumina high throughput sequencing technology. Many of the mapped tags were genes which were found to be differentially expressed at E10.5 in the microarray experiments comparing Ptf1a heterozygotes versus null mutant mice (study GSE26816). As Ptf1a is a bHLH transcription factor, it recognizes an E Box on the chromatin CANNTG. Since it belongs to a transcription factor complex, one of which recognizes the binding site TGGGAA,  we also found this sequence one, two or three helical turns of DNA away from the E-box where peaks were detected.

overall_design: Ptf1a chromatin immunoprecipitation of cross-linked pancreatic cells, 266.6, to compare with the expressed genes in Ptf1a +/- vs -/- E10.5 pancreatic dorsal buds.

last: Thompson


title: Transcriptional regulation by H3K122 acetylation in the lateral surface of the histone octamer

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

summary: We characterize the acetylation of H3K122 for the first time. Towards this we mapped the genomic distribution of H3K122Ac, identified the enzyme introducing H3K122Ac, and addressed the functional contribution H3K122Ac to transcription. We found that H3K122Ac is associated with chromatin marks and genomic regions associated with active transcription and is catalysed by p300/CBP and can be regulated by estrogen signaling in MCF-7. Moreover H3K122Ac stimulates transcription as dermined by in vitro  transcription assays

overall_design: ChIP seq study

first: Philipp

last: Tropberger

first: Robert

last: Schneider


title: DNA methylation of hematopoietic stem cells during ontogeny and after enforced proliferative history

first: Isabel

last: Beerman

address: 200 Longwood Ave, WAB 156

institute: Boston Childrens Hospital

summary: Genome-scale DNA methylation profiles at nucleotide resolution covering the vast majority of CpG islands and a representative sampling of conserved non-coding elements, transposons and other genomic features generated using high-throughput reduced representation bisulfite sequencing (RRBS) for murine hematopoietic stem cells during ontongeny and after enforced prolferative history.

overall_design: Analysis of hematopoietic stem cell methylation during ontogeny and after undergoing enforced proliferative history


title: The Cytokines IL-21 and GM-CSF have Opposing Regulatory Roles in the Apoptosis of Conventional Dendritic Cells

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Interleukin-21 (IL-21) has broad actions on T- and B-cells, but its actions in innate immunity are poorly understood. Here we show that IL-21 induced apoptosis of conventional dendritic cells (cDCs) via STAT3 and Bim, and this was inhibited by granulocyte-macrophage colony-stimulating factor (GM-CSF). ChIP-Seq analysis revealed genome-wide binding competition between GM-CSF-induced STAT5 and IL-21-induced STAT3. Expression of IL-21 in vivo decreased cDC numbers, and this was prevented by GM-CSF. Moreover, repetitive α-galactosylceramide injection of mice induced IL-21 but decreased GM-CSF production by natural killer T (NKT) cells, correlating with decreased cDC numbers. Furthermore, adoptive-transfer of wild-type CD4+ T cells caused more severe colitis with increased DCs and interferon (IFN)-γ-producing CD4+ T cells in Il21r-/-Rag2-/- mice (which lack T cells and have IL-21-unresponsive DCs) than in Rag2-/- mice. Thus, IL-21 and GM-CSF exhibit cross-regulatory actions on gene regulation and apoptosis, regulating cDC numbers and thereby the magnitude of the immune response.

overall_design: Total 6 samples were examined. Splenic dendritic cells were treated with IL-21 and/or GM-CSF studying STAT3 and STAT5B binding in the genome

first: Chi-Keung

last: Wan

first: Jangsuk

last: Oh

first: Elizabeth

last: Wong

first: Rosanne

last: Spolski

first: Lu

last: Wang

first: Zu-Xi

last: Yu

first: Brian

last: Kelsall

first: Warren

last: Leonard


title: Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

status: Public on Feb 13 2013

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research


title: Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection

city: Munich

first: Lukas

last: Windhager

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität Munich

summary: During viral infections cellular gene expression is subject to rapid alterations induced by both viral and antiviral mechanisms. In this study, we applied metabolic labeling of newly transcribed RNA with 4-thiouridine (4sU-tagging) to dissect the real-time kinetics of cellular and viral transcriptional activity during lytic murine cytomegalovirus (MCMV) infection. Microarray profiling on newly transcribed RNA obtained from different times during the first six hours of MCMV infection revealed discrete functional networks of cellular genes regulated with distinct kinetics at surprising temporal resolution. Most of these were undetectable in total RNA, either due to low temporal sensitivity of standard gene expression profiling using total RNA, or due to rapid (viral) counter-regulation. Furthermore, metabolic labeling and purification of newly transcribed RNA detailed the real-time kinetics and regulation of viral gene expression in absence of any interfering virion-associated RNA. Both qRT-PCR and next-generation sequencing of newly transcribed RNA demonstrated an unexpected peak of viral gene expression during the first two hours of infection including transcription of immediate early, early and even well characterized late genes. Interestingly, this peak was subject to rapid gene silencing (independent of the multiplicity of infection) with similar transcriptional activity only reached late in infection. For some genes, e.g. m152, this resulted in massive down-regulation of transcriptional activity by 6 hours post infection, which was not even reversed late in infection. Our findings thus highlight the importance of transcriptional activity during the first few hours of CMV infection and hint at novel mechanisms governing the kinetics of viral gene expression. In conclusion, studying real-time transcriptional activity during lytic CMV infection provides intriguing new insights into the regulation of cellular and viral gene expression.

overall_design: In total 13 samples were examined: 3 samples of total RNA (mock, 25, 48 hours past MCMV infection), 3 samples pre-existing RNA (mock, 25, 48 hpi), and 7 samples newly-transcribed RNA (mock, 1-2, 5-6, 11-12, 18-19, 24-25, 47-48 hpi)

first: Lisa

last: Marcinowski

first: Michael

last: Lidschreiber

first: Martina

last: Rieder

first: Jens

last: Bosse

first: Bernd

last: Rädle

first: Thomas

last: Bonfert

first: Ildiko

last: Györy

first: Olivia

last: Prazeres da Costa

first: Philip

last: Rosenstiel

first: Caroline

last: Friedel

first: Ralf

last: Zimmer

first: Zsolt

last: Ruzsics

first: Ulrich

last: Koszinowski

first: Lars

last: Dölken


title: Modulation of gene expression by ZNF143, THAP11 and NOTCH1 via overlapping binding sites in mammalian cells

city: Strasbourg

first: PHILIPPE

last: CARBON

address: 15 rue René Descartes

department: UPR9002 ARN du CNRS

country: France

institute: IBMC

summary: In this study we investigated the genome wide DNA binding profile of ZNF143 and ICN1 in human and murine cells. We also analyzed the expression profile in human cells after overexpression or knockdown of ZNF143.

overall_design: To identify ZNF143 targets we performed ChIP-seq on 4 human cells lines and 3 murine cell types. We also identified, by ChIP-seq, ICN1 binding sites in HPB-ALL cells. To identify directly regulated genes by ZNF143, we analyzed, by RNA-seq, the expression profile after knockdown and overexpression of the transcription factor.

first: R

last: NGONDO-MBONGO

first: E

last: MYSLINSKI

first: P


title: Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes [ChIP-Seq]

first: Richard

last: Young

summary: The master transcription factors Oct4, Sox2 and Nanog bind enhancer elements and recruit the Mediator co-activator to activate much of the gene expression program of embryonic stem cells (ESCs). We report here that the ESC master transcription factors and Mediator form “super-enhancers” at most genes known to control the pluripotent state, including those encoding the master transcription factors themselves. These super-enhancers consist of extraordinarily large genomic domains occupied by exceptional amounts of Oct4, Sox2, Nanog, Klf4, Esrrb and Mediator.  Super-enhancers stimulate considerably higher transcription than typical enhancers in vivo and in reporter vectors.  Reduced levels of Oct4 or Mediator cause preferential loss of expression of super-enhancer-associated genes relative to other genes, suggesting how changes in gene expression programs might be accomplished during development.  In other more differentiated cells, super-enhancers containing cell-type-specific master transcription factors are also found at genes that define cell identity.  These results implicate super-enhancers in the control of mammalian cell identity and differentiation.

overall_design: ChIP-Seq and controls associated with Super-Enhancers in murine cell types

first: Jamie

last: Newman

first: Steve

last: Bilodeau

first: Alan

last: Mullen

first: Jessica

last: Reddy

first: Warren

last: Whyte

first: David

last: Orlando

first: Brian

last: Abraham

first: Denes

last: Hnisz


title: Next Generation Sequencing   Analysis of Wild Type and 53BP1-/- Transcriptomes in B lymphocytes

status: Public on Feb 12 2013

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Absence of 53BP1 influences the profile of DNA rearrangements in B lymphocytes.To determine whether the differences in translocation partner choice were due to differences in transcription, we compared the transcriptome of 53BP1 deficient and wild-type B cells by RNA-Seq and Polymerase II chromatin immunoprecipitation sequencing (ChIP-Seq).

overall_design: Analysis of total mRNA and PolII loading in the presence or absence of 53BP1 in activated B lymphocytes

first: Mila

last: Jankovic

first: Niklas

last: Feldhahn

first: Israel

last: Silva

first: Kyong-rim

last: Kieffer-Kwon

first: Arito

last: Yamane

first: Wolfgang

last: Resch

first: Isaac

last: Klein

first: Davide

last: Robbiani

first: Rafael

last: Casellas

first: Michel

last: Nussenzweig


title: Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

status: Public on Feb 11 2013

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: In the Metazoan germline, piwi proteins and associated piwi-interacting RNAs (piRNAs) provide a defense system against the expression of transposable elements. In the cytoplasm, piRNA sequences guide piwi complexes to destroy complementary transposon transcripts by endonucleolytic cleavage. However, some piwi family members are nuclear, raising the possibility of alternative pathways for piRNA-mediated regulation of gene expression. We found that Drosophila Piwi is recruited to chromatin, co-localizing with RNA polymerase II on polytene chromosomes. Knockdown of Piwi in the germline increases expression of transposable elements that are targeted by piRNAs, whereas protein-coding genes remain largely unaffected. De-repression of transposons upon Piwi depletion correlates with increased occupancy of RNA polymerase II on their promoters. Expression of piRNAs that target a reporter construct results in a decrease in Pol II occupancy and an increase in repressive H3K9me3 marks and HP1 on the reporter locus. Our results indicate that Piwi identifies targets complementary to the associated piRNA and induces transcriptional repression by establishing a repressive chromatin state when correct targets are found.

overall_design:
Examination of mRNA levels, Pol II occupancy,  and chromatin repressive state in D. melanogaster ovaries upon Piwi knockdown and Piwi mutation.
This records present the sequencing data related to Piwi knockdown study portion.

first: Adrien

last: Le Thomas

first: Alicia

last: Rogers

first: Alexandre

last: Webster

first: Susan

last: Liao

first: Edward

middle: M

last: Perkins

first: Junho

last: Hur

first: Alexei

last: Aravin

first: Katalin

last: Tóth


title: An intricate interplay between astrocytes and motor neurons in ALS

city: New York

first: Sean

last: O'Keeffe

address: 701 West 168th Street

institute: Columbia University

summary: Amyotrophic Lateral Sclerosis (ALS) results from the selective and progressive degeneration of motor neurons. Although the underlying disease mechanisms remain unknown, glial cells have been implicated in ALS disease progression. Here we examine the effects of glial cell/motor neuron interactions on gene expression, using the hSOD1G93A mouse model of ALS. We detect striking cell autonomous and non-autonomous changes in gene expression in co-cultured motor neurons and glia, revealing that the two cell types profoundly affect each other. In addition, we found a remarkable concordance between the cell culture data, expression profiles of whole spinal cords, and of acutely isolated spinal cord cells, during disease progression in the G93A mouse model, providing validation of the cell culture approach. Bioinformatics analyses identified changes in the expression of specific genes and signaling pathways that may contribute to motor neuron degeneration in ALS, among which are TGF-b signaling pathways.

overall_design: RNA-seq profiles of: 1) 43 Sandwich culture samples at 3 different time points (3, 7 and 14 days), in duplicate, in different combinations of genetic background WT/SOD1_G93A mutant glia and WT/SOD1_G93A mutant neurons; 2) 16 spinal cord samples at 4 different time points, WT and SOD1_G93A mutant.

first: Hemali

middle: P

last: Phatnani

first: Tom

last: Maniatis


title: Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of polycomb-target genes

city: Heidelberg

first: James

last: Reddington

address: Meyerhofstrasse 1

institute: EMBL


title: TGF-beta/Smad2/3 signaling directly regulates several miRNAs in mouse ES Cells and early embryos

city: Oxford

first: Carme

last: Camps

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics/ U. of Oxford

summary:
Purpose: We aimed to identify miRNAs which are induced by the Activin/Nodal effectors, P-Smad2/3, in order to further our understanding of how P-Smad2/3 controls downstream gene expression in mouse ES cells to regulate crucial biological processes.
Methods: We used a previously developed Tetracycline-On (Tet-On) system (TAG1) to manipulate the levels of P-Smad2/3 in mouse ES cells and performed an Illumina deep-sequencing screen to identify miRNAs which followed the P-Smad2/3 pathway.
Results: We filtered the deep-seq data to identify a list of 28 miRNAs which showed a >1.25 fold increase in response to P-Smad2/3 induction and a >1.25 fold decrease in response to P-Smad2/3 repression.
Conclusions: Our study represents a comprehensive global profiling of miRNA expression in response to changes in P-Smad2/3 levels in mouse ES cells.

overall_design: miRNA profiles of TAG1 cells which were untreated (control), SB-431541 treated (P-Smad2/3 repressed), or Dox treated (P-Smad2/3 induced), were generated using Illumina GAII.

first: Nicholas

last: Redshaw

first: Jiannis

last: Ragoussis

first: Vasso

last: Episkopou


title: Probing the off-target effect of EGFP siRNA and pro-siRNA in the HeLa-d1EGFP cell line

city: Boston

first: Linfeng

last: Huang

state: Massachusetts

address: 200 Longwood Avenue

department: PCMM

institute: Boston Children's Hospital

summary: We have develped a novel method of making siRNAs (named pro-siRNA for prokaryotic siRNA). To evaluate off-targeting of pro-siRNA, we compared the mRNA expression profiles of HeLa-d1EGFP cells transfected with 4 nM EGFP siRNAs and pro-siRNAs by microarray.

overall_design:
We used microarray to study the off-target effect of siRNAs in the HeLa-d1EGFP cell line. After transfection of siRNAs for 24 hrs, RNA were extracted using Trizol. Deep sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530).
HeLa-d1EGFP cells are HeLa cells stably expressing d1EGFP gene. EGFP siRNA is a siRNA made by chemical synthesis. EGFP100 and EGFPFL are pro-siRNAs made from either a 100 bp hairpin or a full length hairpin targeting EGFP coding sequence.

first: Jingmin

last: Jin

first: Larry

last: McReynolds

first: Judy

last: Liebmerman


title: A comprehensive view of the transcriptome during development of the mouse cerebral cortex

status: Public on Feb 10 2013

first: J Raphael

last: Gibbs

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

summary: The complexity of the mature adult brain is a result of both developmental processes and experience-dependent circuit formation. One way to look at the process of brain development is to examine gene expression changes, and previous studies have used microarrays to address this in a global manner. However, the transcriptome is more complex than gene expression levels alone, as both alternative splicing and RNA editing occur to generate a more diverse set of mature transcripts. The aim of the current study was to develop a high-resolution transcriptome dataset of mouse cortical development using RNA sequencing (RNA-Seq), thus assaying exon usage and RNA editing as well as overcoming some of the inherent limitations of microarrays. We found a large number of differentially expressed genes, but also altered splicing and RNA editing between embryonic and adult cerebral cortex. Each dataset was validated both technically and biologically, and in each case tested we found our RNA-Seq observations to have high predictive validity. We propose this dataset, and the accompanying analysis, to be a helpful resource in the understanding of changes in gene expression during development.

overall_design: Three young adult cerebral cortices four embryonic  cerebral cortices

first: Allissa

last: Dillman

first: David

middle: N

last: Hauser

first: J

middle: R

first: Michael

last: Nalls

first: Melissa

last: McCoy

first: Alice

last: Kaganovich

first: Iakov

last: Rudenko

first: Dagmar

last: Galter

first: Mark

last: Cookson


title: NO-mediated transcriptional response in C. elegans

first: Ivan

last: Gusarov

state: NY

address: 450E 29th street

department: Biochemistry

institute: NYU School of Medicine

summary: We used next generation sequensing to determine C.elegans genes induced by Nitroc Oxide (NO) treatment

overall_design: Compare expression profile of NO treated and untreated control.


title: ChIP-Seq of Sox2 and Brn2 in ESCs, NPCs, and differentiating ESCs

last: Lodato

institute: Whitehead Institute

summary: We analyzed the genome-wide binding of Sox2 and POU factor partner factors, Oct4 in ESCs (using published datasets PMID:18692474 and GSM307137, GSM307154, GSM307155) and Brn2 in NPCs. We found that Sox2 and Oct4 co-occupied a large subset of promoters and enhancers in ESCs, but that Sox2 and Brn2 co-occupy predominantly enhancers.  Further, we overexpressed Brn2 in differentiating ESCs and showed that ectopic Brn2 recruited Sox2 to NPC-specific targets, resulting in skewed differentiation towards the neural lineage.

overall_design: Examination of transcription factor binding in ESCs, NPCs, and differentiating ESCs by ChIP-Seq.

first: Rudolf

last: Jaenisch

first: Laurie

last: Boyer


title: The role of Ldb1 in hemangioblast development: genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis

status: Public on Feb 09 2013

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

institute: The Weatherall Institute of Molecular Medicine

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

overall_design: Refer to individual Series


title: Multiple roles for Piwi in silencing Drosophila transposons

city: Cold Spring Harbor

first: Nikolay

middle: V

last: Rozhkov

email: nik.rozhkov@gmail.com, rozhkov@cshl.edu

address: 1 Bungtown Rd.

institute: CSHL

summary: Silencing of transposons in the Drosophila ovary relies on three Piwi-family proteins, Piwi, Aubergine (Aub), and Ago3, acting in concert with their small RNA guides, the piRNAs.  Aub and Ago3 are found in the germ cell cytoplasm, where they function in the ping-pong cycle to consume transposon mRNAs.  The nuclear Piwi protein is required for transposon silencing in both germ and somatic follicle cells, yet the precise mechanisms by which Piwi acts remain largely unclear.  We investigated the role of Piwi by combining cell-type specific knockdowns with measurements of steady state transposon mRNA levels, nascent RNA synthesis, and small RNA abundance.  In somatic cells, Piwi loss lead to concerted effects on nascent transcripts and transposon mRNAs, indicating that Piwi acts through transcriptional gene silencing (TGS).  In germ cells, Piwi loss showed disproportionate impacts on steady state RNA levels, indicating that it also exerts an effect on post-transcriptional gene silencing (PTGS). Piwi knockdown affected levels of germ cell piRNAs presumably bound to Aub and Ago3, perhaps explaining its post-transcriptional impacts.  Overall, our results indicate that Piwi plays multiple roles in the piRNA pathway, in part enforcing transposon repression through effects on transcription but also participating in germ cell piRNA biogenesis.

overall_design: Piwi function in transcriptional and post-transcriptional transposon silencing was probed using deep-sequencing of small RNAs, steady-state and nascent transcripts, and DNA associated with H3K9me3 chromatin mark. In all cases comparison of two samples was performed: Tj- or nos-driven knock down of piwi to respective knock down of white gene (control sample). RNA-seq dataset has two replicates.

first: Molly

last: Hammell

first: Gregory

middle: J

last: Hannon


title: The genome and transcriptome of Panagrellus redivivus is shaped by the harsh demands of a free-living lifestyle

status: Public on Feb 07 2013

city: Minneapolis

first: Marissa

last: Macchietto

address: 117 Pleasant Street SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Minneapolis

summary: Nematodes comprise an abundant and diverse invertebrate phylum with members inhabiting nearly every ecological niche. Panagrellus redivivus (the ’microworm’) is a free-living nematode frequently used to understand the evolution of developmental and behavioral processes given its phylogenetic distance to Caenorhabditis elegans. Here we report the de novo sequencing of the genome, transcriptome, and small RNAs of P. redivivus. Using a combination of automated gene finders and RNA‑seq data, we predict 24249 genes and 32676 transcripts. Small RNA analysis revealed 248 micro RNA hairpins, of which 63 had orthologs in other species. Fourteen miRNA clusters containing 42 miRNA precursors were found. P. redivivus has a full complement of genes for regulation of dauer formation despite the apparent absence of dauer juveniles in this species. The RNAi and programmed cell death pathways are largely conserved. Analysis of protein family domain abundance revealed that P. redivivus has experienced a striking expansion of BTB domain‑containing proteins and an unprecedented expansion of the cullin scaffold family of proteins involved in multi‑subunit ubiquitin ligases, suggesting proteolytic plasticity and/or tighter regulation of protein turnover. The eukaryotic release factor (eRF1) protein family has also been dramatically expanded and suggests an ongoing evolutionary arms race with viruses and transposons. The P. redivivus genome provides a resource to advance our understanding of nematode evolution and biology and to further elucidate the genomic architecture leading to free-living lineages, taking advantage of the many fascinating features of this worm revealed by comparative studies.

overall_design: Mixed-stage poly-A selected RNA

first: Jagan

last: Srinivasan

first: Adler


title: In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation [RNA-seq]

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: Numerous studies have described the altered expression and the causal role of miRNAs in human cancer. However, to date efforts to modulate miRNA levels for therapeutic purposes have been challenging to implement. Here, we find that Nucleolin (NCL), a major nucleolar protein, post-transcriptionally regulates the expression of a specific subset of miRNAs, including miR-21, miR-221, miR-222, and miR-103, causally involved in breast cancer initiation, progression and drug-resistance. We also show that NCL is commonly overexpressed in human breast tumors, and its expression correlates with that of NCL-dependent miRNAs. Finally, this study indicates that NCL-binding guanosine-rich aptamers affect the levels of NCL-dependent miRNAs and their target genes, reducing breast cancer cell aggressiveness, both in vitro and in vivo. These findings illuminate a path to novel therapeutic approaches based on NCL-targeting aptamers for the modulation of miRNA expression in the treatment of breast cancer.

overall_design: Identification of NCL regulated miRNAs by using miRNA high-throughput sequencing of HeLa cells stably expressing double-strand (ds) interfering RNA against NCL or scrambled sequences (sh-NCL or sh-Scr).

first: Flavia

last: Pichiorri

first: Dario

last: Palmieri

first: Luciana

last: De Luca

first: Jessica

last: Consiglio

first: Jia

last: You

first: Alberto

last: Rocci

first: Tiffany

last: Talabere

first: Claudia

last: Piovan

first: Alessandro

last: Lagana

first: Jingwen

last: Guan

first: Pierluigi

last: Gasparini

first: Veronica

last: Balatti

first: Vincenzo

last: Coppola

first: Craig

middle: C

last: Hofmeister

first: Guido

last: Marcucci

first: John

last: Byrd

first: Stefano

last: Volinia

first: Charles

last: Shapiro

last: Freitas

first: Carlo

last: Croce


title: The role of Ldb1 in hemangioblast development: genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis (sequencing)

first: Supat

last: Thongjuea

summary: The first site exhibiting hematopoietic activity in mammalian development is the yolk sac blood island, which originates from the hemangioblast. Here we performed differentiation assays, as well as genome-wide molecular and functional studies in BL-CFCs to gain insight into the function of the essential Ldb1 factor in early primitive hematopoietic development. We show that the previously reported lack of yolk sac hematopoiesis and vascular development in Ldb1-/- mouse result from a decreased number of hemangioblasts and a block in their ability to differentiate into erythroid and endothelial progenitor cells. Transcriptome analysis and correlation with the genome wide binding pattern of Ldb1 in hemangioblasts revealed a number of direct target genes and pathways misregulated in the absence of Ldb1. The regulation of essential developmental factors by Ldb1 defines it as an upstream transcriptional regulator of hematopoietic/endothelial development. We show the complex interplay that exists between transcription factors and signaling pathways during the very early stages of hematopoietic/endothelial development and the specific signalling occurring in hemangioblasts in contrast to more advanced hematopoietic developmental stages. Finally, by revealing novel genes and pathways, not previously associated with early development, our study provides novel candidate targets to manipulate the differentiation of hematopoietic and/or endothelial cells.

overall_design:
Examination of endogenous Ldb1 genome-wide binding sites comparsion between ChIP and Control on Flk1+ BL-CFCs
RNA was isolated from Ldb1+/+ and Ldb1-/- Flk1+ cells with the QIAGEN RNeasy Mini Kit and integrity was checked on the Agilent 2100 Bioanalyzer. RNA sequencing was performed on Illumina HiSeq 2000 platform according to the manufacturer instructions.

first: Athina

last: Mylona

first: Charlotte

last: Andrieu-Soler

first: Andrea

last: Martella

first: Eric

last: Soler

first: Rudd

last: Jorna

first: Jun

last: Hou

first: Christel

last: Kockx

first: Wilfred

last: van Ijcken

first: Boris

last: Lenhard

first: Frank

last: Grosveld


title: Genome-wide binding of Yki and GAF in embryos and wing imaginal discs

city: Chicago

first: Kevin

middle: P.

last: White

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

department: Institute for Genomics and Systems Biology

institute: University of Chicago


title: Genome-wide binding of Yki and GAF in embryos and wing imaginal discs [RNA-Seq]

summary: The Hippo pathway regulates metazoan growth, acting through the transcriptional co-activators Yorkie (in Drosophila) and Yap and Taz (in vertebrates). Much attention has been focused on upstream regulators of Yorkie and its homologues. In contrast, the mechanisms by which they actually promote transcription have remained poorly understood. Genome-wide chromatin binding experiments support extensive functional overlap between Yorkie and GAF. Chromatin binding identifies thousands of Yorkie sites, the majority of which are associated with elevated transcription, based on genome-wide analysis of mRNA and histone H3K4Me3 modification. Our studies establish a molecular basis for transcriptional activation by Yorkie and implicate it as a global regulator of transcriptional activity in Drosophila.

overall_design: This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This dataset was generated in collaboration with Ken Irvine at HHMI/Rutgers University and Richard S. Mann at Columbia University.  It contains RNA-seq data for larval wing imaginal discs.

first: Matthew

last: Slattery

first: Hyangyee

last: Oh

first: Lijia

last: Ma

first: Alex

last: Crofts

first: Jason

last: Grundstad

first: Richard

last: Mann

first: Kenneth

last: Irvine


title: NFIB: A Governor of Epithelial-Melanocyte Stem Cell Behaviour in a Shared Niche

first: Chiung-Ying

last: Chang

address: 1230 York Avenue

institute: Rockefeller University

summary: To identify direct NFIB target genes in HFSCs, we performed chromatin immunoprecipitation and deep sequencing (ChIP-seq) analysis using FACS-isolated HFSCs.

overall_design: Two independent NFIB ChIP-seq experiments were conducted.

first: Elaine

last: Fuchs