title: Genetically-driven target tissue over-expression of CD40: A novel mechanism in autoimmune disease

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

summary: The CD40 gene, an important immune regulatory gene, is also expressed and functional on non-myeloid derived cells, many of which are targets for tissue specific autoimmune diseases, including d thyroid follicular cells in Graves’ disease (GD). Whether target tissue CD40 expression plays a role in autoimmune disease etiology has yet to be determined. Here we show for the first time, that target-tissue over-expression of CD40 plays a key role in the etiology of autoimmunity. Using a murine model of GD, we demonstrated that thyroidal CD40 over-expression augmented the production of thyroid specific antibodies, resulting in more severe experimental autoimmune Graves’ disease (EAGD), whereas deletion of thyroidal CD40 suppressed disease. Using transcriptome and immune-pathway analyses we showed that in both EAGD mouse thyroids and human primary thyrocytes, CD40 mediates this effect by activating downstream cytokines and chemokines, most notably IL-6. To translate these findings into therapy, we blocked IL-6 during EAGD induction in the setting of thyroidal CD40 over-expression, and showed decreased levels of TSHR stimulating antibodies and frequency of disease. We conclude that target tissue over-expression of CD40 plays a key role in the etiology of organ specific autoimmune disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CD40 in Thyroid Autoimmunity: 1) Incubation of human thyroid cells with G28.5, a CD40 stimulating antibody, and purification of RNA, conversion to cDNA, measurement of mRNA expression using RNAseq. 2) Removal of thyroid tissues from CD40 over-expressing transgenic mice and wild type mice, purification of RNA, conversion to cDNA measurement of mRNA expression using RNAseq.

first: Amanda

middle: K

last: Huber

first: Fred

middle: D

last: Finkelman

first: Cheuk

middle: W

last: Li

first: Erlinda

last: Concepcion

first: Eric

middle: P

last: Smith

first: Rauf

last: Latif

first: Mehdi

last: Keddache

first: Yaron

last: Tomer


title: Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes

status: Public on Oct 02 2012

city: Columbus

first: Jeffrey

last: Parvin

state: OH

address: 904 Biomedical Research Tower

department: Biomedical Informatics

country: USA

institute: the Ohio State University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary:
We determined the occupancy of SUMO-1 on chromatin in HeLa cells by use of chromatin affinity purification coupled with next generation sequencing
RNA-Seq: The goal is to compare differential gene expression in SUMO-1 depleted cells and control cells (GL2 depleted) to verify the observation in the paper, and to cross-check with RT-PCR results.

overall_design:
18 samples examined in syncrhonized HeLa cells: Cells in G1, early S (S0)/mid (S3)/ late S phase (S6), and mitosis (M), triplicates for each sample. 1 ChIP-SUMO1 sample in S0, and 1 ChIP-IgG control
RNA-Seq: Six cDNA samples containing three pairs of biological replicates (three SUMO-1 depleted samples and three GL2 control samples) were barcoded, pooled together in equal concentration and subjected to sequencing in one lane of Illumina GAII

first: Hui-wen

last: Liu

first: Jie


title: DNMT3B7, an aberrant DNMT3B isoform, suppresses growth, induces differentiation, and alters DNA methylation in human neuroblastoma

status: Public on Oct 05 2012

city: Chicago

first: Kelly

middle: R

last: Ostler

state: IL

address: 900 E. 57th Street

department: Medicine

institute: The University of Chicago

summary: In adult cancers, epigenetic changes and aberrant splicing of the DNMT3B is commonly observed, and the pattern of gene methylation and expression has been shown to be modified by DNMT3B7, a truncated protein of DNMT3B.  Much less is known about the mechanism of epigenetic changes in the pediatric cancer neuroblastoma.  To investigate if aberrant DNMT3B transcripts alter DNA methylation, gene expression and tumor phenotype in neuroblastoma, we measured DNMT3B isoform expression in primary tumors and cell lines. Higher levels of DNMT3B7 were detected in differentiated ganglioneuroblastomas compared to undifferentiated neuroblastomas, suggesting that expression of DNMT3B7 may induce a less clinically aggressive tumor phenotype.  To test this hypothesis, we investigated the effects of forced DNMT3B7 in neuroblastoma cells.  We found that DNMT3B7 expression significantly inhibited neuroblastoma cell proliferation in vitro, and in neuroblastoma xenografts, DNMT3B7 decreased angiogenesis and tumor growth. DNMT3B7-positive cells had higher levels of total genomic methylation, and RNA-sequencing revealed a dramatic decrease in expression of FOS and JUN family members, AP1 complex components.  Consistent with the established antagonistic relationship between AP1 expression and retinoic acid receptor activity, decreased proliferation and increased differentiation was seen in the DNMT3B7-expressing neuroblastoma cells following treatment with all trans retinoic acid (ATRA) compared to controls. Our results demonstrate that high levels of DNMT3B7 modify the epigenome in neuroblastoma cells, induce changes in gene expression, inhibit tumor growth, and increase sensitivity to ATRA.    Further knowledge regarding mechanisms by which DNMT3B7 regulates gene methylation may ultimately lead to the development of therapeutic strategies that reverse the epigenetic aberrations that drive neuroblastoma pathogenesis.

overall_design: DNMT3B7, a truncated DNMT3B isoform, was stably transfected into an N-type neuroblastoma cell line (LA1-55n) using a Tet-off inducible system. DNMT3B7 expressing cells were compared to vector control cells after 21 days of induction.

first: Qiwei

last: Yang

first: Susan

middle: L

last: Cohn

first: Lucy

middle: A

last: Godley


title: S2 WT Repliseq

status: Public on Oct 04 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_5527
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by sequencing replication intermediates that were differentially labeled with BrdU during S-phase progression.  Briefly, cells were pulse labeled with BrdU and sorted into early, middle and late S-phase fractions.  BrdU labeled sequences from each fraction of S-phase were enriched by immunoprecipitation and sequenced on the Illumina platform.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: read length (base pair) ; Cell Line S2-DRSC; read length (base pair)

first: David

last: MacAlpine

first: Yoav

last: Lubelsky

first: Jason

last: Belsky

first: Joseph

last: Prinz


title: Expression data from colorectal cancer patients

city: Rehovot

first: Michal

last: Sheffer

address: Herzel

country: Israel

institute: Weizmann Institute of Science

summary: The study consist of patients who presented at Memorial Sloan-Kettering Cancer Center with a colonic neoplasm between 1992 and 2004. Biological specimens used in this study include primary colon adenocarcinomas, adenomas, metastasis and corresponding normal mucosae.

overall_design: 390 expression arrays

first: Manny

last: Bacolod

first: Or

last: Zuk

first: Sarah

middle: F

last: Giardina

first: Hanna

last: Pincas

first: Francis

last: Barany

first: Philip

middle: B

last: Paty

first: William

last: Gerald

first: Daniel

last: Notterman

first: Eytan

last: Domany


title: Transcriptome sequencing of the halictid, Lasioglossum albipes

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics

country: China

institute: BGI-SHENZHEN

summary:
Deep sequencing of mRNA from the halictid
Part of the Lasioglossum albipes WGS project (BioProject ID: PRJNA174755)

overall_design: Analysis of ploy(A)+ RNA of different specimens:whole body from the halictid (Lasioglossum albipes)

first: Guojie

last: Zhang

first: Cai

last: Li

last: Kocher


title: Human melanoma cells over-express Extracellular Matrix 1 (ECM1) which is regulated in part by TFAP2C

city: Iowa City

first: Thomas

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary: Extracellular Matrix 1(ECM1) expression is increased in multiple tumor cell lines and primary cancers. Activator protein 2C (TFAP2C) is a potent regulator of ECM1 transcription. TFAP2C may contribute to the increased ECM1 expression noted in many cancers. This is the first report identifying the minimal promoter region of the human ECM1 gene and its regulation by TFAP2C

overall_design: Human A375 melanoma cells were assessed for mRNA and protein expression of ECM1. A mininal promoter region for ECM1 transactivation was identified. ECM1 expression was regulated in part by TFAP2C, and in ChIP-Seq experiments, TFAP2C was found to bind directly to the ECM1 gene in A375 melanoma cells and in MCF7 breast cancer cells.

first: Geeta

last: Lal


title: Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

type: Expression profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Paired End CNV S2 DRSC Cells

first: DCC

last: modENCODE

type: Genome variation profiling by high throughput sequencing

summary:
modENCODE_submission_5524
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Analysis of copy number variation across modENCODE Drosophila cell line by high throughput sequencing.  We observe numerous copy number variations for the different cell lines, with each cell line having a distinct ploidy signature.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: deep sequencing analysis. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC

first: David

last: MacAlpine

first: Heather

first: Joseph

last: Prinz


title: Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin [MNase-Seq]

summary: We report that the Schizosaccharomyces pombe CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in nucleosome perturbation across the chromosome, and the production of antisense transcripts in the hrp3∆ cells emphasized the importance of nucleosome architecture for proper transcription

overall_design: Examination of nucleosome positions in wild-type and mutants using the MNase-seq method

first: Shim

last: Young Sam

first: Choi

last: Yoonjung

first: Kang

last: Keunsoo


title: Ncoa3 in mouse embryonic stem cells

city: Singapore

first: Vibhor

last: Kumar

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

country: Singapore

institute: Genome Institute of Singapore


title: A Nuclear Receptor Coactivator is Essential for Esrrb Activity and the Induction and Maintenance of the ES Cell State

summary: Orphan nuclear receptor Esrrb is vital in maintaining ES cells and like Oct4, Sox2 and Nanog is essential for self-renewal and pluripotency. Esrrb functions in somatic cells via LBD/AF-2-dependent coactivator recruitment to target genes. Here we show that in ES cells coactivator recruitment is similarly required and identify Ncoa3 as the Esrrb coactivator needed for activation of its target genes. Ncoa3 is essential for self-renewal and the induction of pluripotency in reprogramming, and genome-wide analysis of Ncoa3 binding reveals extensive overlap with Esrrb and pluripotency factors along with marks of active genes. Mechanistically, we show Ncoa3 is specifically required to bridge RNApol2 to Esrrb. We thus identify a new member of the ES pluripotency network and describe Esrrb and Ncoa3 as key factors linking core pluripotency factors to the general transcription machinery.

overall_design: ChIP experiments were carried out with chromatin prepared from E14 cells as previously described (Stock et al., 2007), using 8-10 ug primary antibody for NcoA3 and 600 ug pre-cleared chromatin per IP. Antibody for NcoA3 was from  Santacruz (sc-9119) .

first: Michelle

last: Percharde

first: Jia

last: Hui


title: Functional characterization of the RNA chaperone Hfq in opportunistic human pathogen Stenotrophomonas maltophilia

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary: Stenotrophomonas maltophilia is an important opportunistic pathogen affecting primarily hospitalized and immuno-compromised hosts. We constructed an hfq deletion mutant (Delta-hfq) of S. maltophilia, and compared the behaviour of wild-type and Delta-hfq S. maltophilia cells in a variety of assays. Differential RNA sequencing analysis (dRNA-seq) of RNA isolated from S. maltophilia wild-type and Delta-hfq strains showed that Hfq regulates expression of genes encoding flagellar and fimbrial components, transmembrane proteins, as well as enzymes involved in different metabolic pathways. Moreover, we analysed expression of several sRNAs identified by dRNA-seq in wild-type. The accumulation of two sRNAs was strongly reduced in the absence of Hfq.

overall_design: TEX (terminator exonuclease) treated and untreated libraries of the wild type and the Delta-hfq mutant were sequenced and compared

first: Emanuela

last: Roscetto

first: Tiziana

last: Angrisano

first: Valerio

last: Costa

first: Mariassunta

last: Casalino

middle: U

first: Cynthia

middle: M

last: Sharma

first: Pier

last: Di Nocera

first: Eliana

last: De Gregorio


title: YAP mediates crosstalk between the Hippo and PI3K-TOR pathway by suppressing PTEN via miR-29

status: Public on Oct 01 2012

city: La Jolla

first: Karen

last: Tumaneng

state: CA

address: 2880 Torrey Pines Scenic Drive

institute: UCSD-SCRM

type: Non-coding RNA profiling by high throughput sequencing

summary: We aimed to identify microRNAs that are regulated by YAP in human mammary epithelial cells.

overall_design: We utilized deep sequencing technology to identify microRNAs that are induced by YAP overexpression and repressed by YAP knockdown.

first: Kun-Liang

last: Guan


title: Comparative profiling of human fetal and adult erythropoiesis

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital


title: Transcriptome sequencing and comparative expression profiling analysis of Saccharina japonica under blue light

city: Qingdao

first: Yun

middle: Yan

last: Deng

address: Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: Saccharina japonica is one of the most important marine economic crops worldwide. Blue light usually plays a significant role in the lives of Saccharina that may be beneficial to the culture system. Here we applied high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of Saccharina japonica with blue light and dark exposure respectively. Comparative analysis of gene expression was conducted to understand the underlying molecular mechanisms. RNA-seq analysis yielded 70,497 non-redundant unigenes. 25,924 unigenes of them had good comparability with known gene sequences in existing species. Based on the values of RPKM, 11,660 differentially expressed unigenes were detected in expression profiles between blue light and dark exposed samples. Our results provide clues to potential genes identification in the species and lay the foundation for future functional genomics study.

overall_design: mRNA expression of Saccharina japonica with 2 different treatment (sample exposed to Dark condition, and sample exposed to blue light respectively)  was determined by method of RNA-Seq

first: Yunyan

first: Xiuliang

last: Wang

first: Jianting

last: Yao

first: Hui

last: Guo

first: Delin

last: Duan


title: Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation

city: Irvine

first: Yongsheng

last: Shi

address: B228 Med Sci I

department: Microbiology and Molecular Genetics

institute: University of California, Irvine

summary: We mapped CstF64-RNA interactions at the transcriptome level and studied CstF64-mediated regulation of global mRNA alternative polyadenylation by using iCLIP-seq and direct RNA sequencing analyses.

overall_design: CstF64 iCLIP-seq in HeLa cells;  direct RNA sequencing (DRS) of control HeLa cells, CstF64-RNAi cells and CstF64&CstF64tau-RNAi cells

first: Chengguo

first: Jacob

last: Biesinger

first: Ji

last: Wan

first: Lingjie

last: Weng

first: Yi

last: Xing

first: Xiaohui

last: Xie


title: DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington

status: Public on Oct 03 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This track is produced as part of the mouse ENCODE Project. This track shows DNaseI sensitivity measured genome-wide in mouse tissues and cell lines using the Digital DNaseI methodology (see below), and DNaseI hypersensitive sites. DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promotors, locus control regions and novel elements. For each experiment (tissue/cell type) this track shows DNaseI sensitivity as a continuous function using sequencing tag density (Signal), and discrete loci of DNaseI sensitive zones (HotSpots) and hypersensitive sites (Peaks).

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

overall_design: Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell/mouse). Fresh tissues were harvested from mice and the nuclei prepared according to the tissue appropriate protocol (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell/mouse). Digital DNaseI was performed by DNaseI digestion of intact nuclei, isolating DNaseI 'double-hit' fragments as described in Sabo et al. (2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Illumina IIx (and Illumina HiSeq by early 2011) platform (36 bp reads). Uniquely mapping high-quality reads were mapped to the genome using the bowtie aligner. DNaseI sensitivity is directly reflected in raw tag density, which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). DNaseI sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). 1.0% false discovery rate thresholds (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm (I-max).

first: Richard

last: Sandstrom


title: Genome-wide map of lysine specific demethylase 1 (LSD1) in mouse embryonic stem cells.

city: New York

first: Venugopalan

last: Nair

address: 1 Gustave L. Levy Place

department: Neurology

summary: We report the identification of LSD1 binding genomic regions in mouse embryonic stem cells (ESC) by high throughput sequencing. By obtaining over 10 million 36 bp reads of sequence from each chromatin immunoprecipitated DNA, we generated genome-wide maps for LSD1 and histone H3 dimethylated on lysine 4 (H3K4me2), the substrate for LSD1 in mouse ESCs. Our results showed an extensive overlap between the LSD1 and H3K4me2 genomic regions and a correlation between the genomic levels of LSD1/H3K4me2 and gene expression, including many highly expressed ESC genes. LSD1 is recruited to the chromatin of cells in the G1/S/G2 phases and is displaced from the chromatin of M phase cells, suggesting that LSD1 or H3K4me2 alternatively occupies LSD1 genomic regions during cell cycle progression. LSD1 knockdown by RNA interference or its displacement from the chromatin by anti-neoplastic agents caused an increase in the levels of a subset of LSD1 target genes. Taken together, these results suggest that cell-cycle dependent association and dissociation of LSD1 with chromatin mediates short-time scale gene expression changes during ES cell cycle progression.

overall_design: Examination of LSD1 and lysine 4 dimethylated  histone H3 (H3K4me2) binding genomic regions in embryonic stem cells. Input genomic DNA and DNA immunoprecipitaed with control IgG was included as controls.

first: Yongchao

last: Ge


title: Comparative transcriptome analyses of deltmethrin resistant and suscpetible Anopheles gambiae mosquitoes

first: Mariangela

last: Bonizzoni

state: California

address: Hewitt Hall, Rm 3501B

institute: Univ of California Irvine

summary: we report the RNA-seq based analyses of the transcriptional changes in the Anopheles gambiae mosquitoes from East Africa classified as deltamethrin-resistant or -suscpetible accordign the WHO test

overall_design: comparison of the transcriptome of Anopheles gambiae mosquitoes with phenotypically resistant or suscpetible to deltamethrin

first: William

last: Dunn

first: Guiyun

last: Yan


title: Transcriptome wide analysis of  classically  and alternatively activated macrophages

city: Bonn

first: Andrea

last: Nino Castro

state: NRW

address: Carl Troll str. 31

institute: Life and Medical Sciences institute

summary:
Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived human M1- and M2-like macrophage profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to establish a high resolution transcriptome of human macrophages.
Total RNA was isolated from classically and aternative activated human macrophages.mRNA profiles were generated by deep sequencing og M1 and M2 macrophages from 3 donors using Illumina HiSeqSQ. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Casava1.8 and TopHat followed by Cufflinks. qRT–PCR validation was performed using LightCycler and SYBR Green assays.

first: Michael

last: Mallmann

first: Marc

last: Beyer

first: Joachim

last: Schultze


title: Hfq-coIP overgrowth

first: Konrad

last: Förstner

summary: The small RNAs associated with protein Hfq constitute one of the largest classes of post-transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free-standing genes. Here, deep sequencing of Hfq-bound transcripts from multiple stages of growth of Salmonella Typhimurium revealed a plethora of new small RNA species from within mRNA loci, including DapZ which overlaps with the 3’ region of the biosynthetic gene, dapB. Synthesis of the DapZ small RNA is independent of DapB protein synthesis, and controlled by HilD, the master regulator of Salmonella invasion genes. DapZ carries a short G/U-rich domain similar to that of the globally acting GcvB small RNA, and uses GcvB-like seed pairing to repress translation of the major ABC transporters, DppA and OppA. This exemplifies double functional output from an mRNA locus by the production of both a protein and an Hfq-dependent trans-acting RNA. Our atlas of Hfq targets suggests that the 3’ regions of mRNA genes constitute a rich reservoir to feed the Hfq network with new regulatory small RNAs.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Hfq-associated RNAs were systemically analyzed in Salmonella at 7 different growth stages in standard labortory condition (LB)

first: Yanjie

last: Chao

first: Kai

last: Papenfort

last: Reinhardt

first: Cynthia

last: Sharma

first: Jörg

last: Vogel


title: Genome wide DNA methylation analysis of leukemia and reprogrammed leukemia cells

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

type: Methylation profiling by high throughput sequencing


title: Histone H3K9 and H3K14 acetylation mark active enhancers and promoters together with bivalent promoters in mouse embryonic stem cells

city: Strasbourg

first: Krishanpal

last: Karmodiya

email: krish@igbmc.fr, laszlo@igbmc.fr

address: 1 rue Laurent Fries / BP 10142

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

summary: Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Here we have investigated the genome-wide occurrence of two histone marks, acetylation of histone H3K9 and K14 (H3K9ac and H3K14ac), in mouse ES cells. We demonstrate genome-wide that H3K9ac and H3K14ac show very high correlation.

overall_design: Examination of H3K9ac and H3K14ac in mES cells

first: Laszlo

last: Tora


title: Evolution of mammalian miRNA genes

city: Lausanne

first: Henrik

last: Kaessmann

address: Génopode

department: Center For Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species that represent all main mammalian lineages and birds (the evolutionary outgroup), with the aim to unravel the evolution of mammalian miRNAs. Our analyses reveal an overall expansion of miRNA repertoires in mammals, with three-fold accelerated birth rates of miRNA families in placentals and marsupials, facilitated by the de novo emergence of miRNAs in host gene introns. Generally, our analyses suggest a high rate of miRNA family turnover in mammals, with many newly emerged miRNA families being lost soon after their formation. Selectively preserved mammalian miRNA families gradually evolved higher expression levels as well as altered mature sequences and target gene repertoires, and were apparently mainly recruited to exert regulatory functions in nervous tissues. However, miRNAs that originated on the X chromosome evolved high expression levels and potentially diverse functions during spermatogenesis, including meiosis, through selectively driven duplication-divergence processes. Overall, our study thus provides detailed insights into the birth and evolution of mammalian miRNA genes and the associated selective forces.

sample_organism:
Gallus gallus
Ornithorhynchus anatinus
Didelphis virginiana
Macaca mulatta
Homo sapiens
Mus musculus
Monodelphis domestica

overall_design: 30 main samples from five adult tissues (brain, cerebellum, heart, kidney and testis) collected in six species (human, macaque, mouse, opossum, platypus and chicken) + 5 biological replicates + 3 samples from spermatogenic cells in adult mouse testis  (Sertoli cells, spermatocytes and spermatids)

first: Julien

last: Meunier

first: Frédéric

last: Lemoine

first: Magali

last: Soumillon

first: Angélica

last: Liechti

first: Manuela

last: Weier

first: Katerina

last: Guschanski

first: Haiyang

last: Hu

first: Philipp

last: Khaitovich


title: Gene Expression Changes in a Tumor Xenograft by a Py-Im Polyamide

city: PASADENA

first: Jevgenij

middle: A.

last: Raskatov

address: 1200 EAST CALIFORNIA BOULEVARD

department: CCE

institute: CalTech

summary: Gene regulation by DNA binding small molecules could have important therapeutic applications. This study reports the investigation of a DNA-binding pyrrole-imidazole polyamide targeted to bind the DNA sequence 5’-WGGWWW-3’ with reference to its potency in a subcutaneous xenograft tumor model. The molecule is capable of trafficking to the tumor site following subcutaneous injection and modulates transcription of select genes in vivo. A FITC-labeled analogue of this polyamide can be detected in tumor-derived cells by confocal microscopy. RNA deep sequencing (RNA-seq) of tumor tissue allowed the identification of further affected genes, a representative panel of which were interrogated by qRT-PCR and correlated with cell culture expression levels.

overall_design: Xenografts. Grafting with A549-luc-C8. Experiments were performed in female SCID-beige mice (Charles River) between 8 and 12 weeks of age. Cells were injected into the left flank area of the animals as suspensions of 25 x 106 mL-1 in RPMI, 200 µL per injection. Treatment and tumor proliferation monitoring. Mice were treated following the schedule delineated in treatment protocol. Tumor proliferation was monitored using the XENOGEN imaging device. The animals were anesthetized with 2 5 % isoflurane and subsequently transferred to the imaging chamber, whereupon the isoflurane levels were reduced to 1-2.5 %. The floor of the imager was heated to +37 ºC to avoid hypothermia. Breathing frequency was monitored and not allowed to drop below 1 s-1, adjusting the isoflurane levels accordingly at all times. Endpoint criteria and euthanasia. Animal endpoint criteria encompassed weight loss of over 15 %, restriction of motor function by the engrafted tumor, dehydration of over 10 % and moribund behavior. Where appropriate, the animals were euthanized by asphyxiation in a CO2 chamber. Tumor tissue harvest. Animals were resected and tumors excised using standard forceps, scissors and surgical blades. The tumors were combined into one sample per condition and mechanically sheared in TRIZOL, employing a specialized device (tissue tearer, model 985370). Total RNA workup was performed following the standard TRIZOL procedure, followed by a DNAse digest.

first: J

first: N

middle: G

last: Nickols

first: A

middle: E

last: Hargrove

first: G

last: Marinov

first: B

last: Wold

first: P

last: Dervan


title: Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (RNA-Seq)

status: Public on Sep 30 2012

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: FUS/TLS and TDP-43 are RNA/DNA-binding proteins integrally involved in amyotrophic lateral sclerosis (ALS) and frontal temporal dementia. FUS/TLS is shown to bind RNAs from >5,500 genes in mouse and human brain, primarily through a GUGGU binding motif. A characteristic sawtooth-like binding pattern is identified, supporting co-transcriptional deposition of FUS/TLS. Depletion of FUS/TLS from the adult nervous system is shown to alter levels or splicing of >970 mRNAs, most of which are distinct from the RNAs whose maturation is dependent on TDP-43. Nonetheless, only 55 RNAs are reduced upon depletion of either TDP-43 or FUS/TLS from mouse brain and human neurons differentiated from pluripotent stem cells, including mRNAs transcribed from genes with exceptionally long introns and that encode proteins essential for neuronal integrity. A subset of these is significantly lowered in FUS/TLSR521G and TDP-43G298S mutant fibroblasts and in TDP-43 aggregate-containing motor neurons in sporadic ALS, evidence pointing to a common loss-of-function pathway as one component underlying motor neuron death from misregulation of TDP-43 or FUS/TLS.

overall_design: RNA-Seq of Fus/Tls in 8 week mouse brain

first: Don

last: Cleveland


title: Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (CLIP-Seq)

overall_design: CLIP of Fus/Tls in 8 week mouse brain and adult human brain


title: Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human brain

city: Atlanta

first: Tao

last: Wang

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary: 5-hydroxymethylcytosine (5-hmC) is a  newly discovered  modified form of cytosine that has been suspected to  be an important epigenetic modification  in  neurodevelopment. While  DNA  methylation dynamics  have already been implicated during  neurodevelopment, little is known about hydroxymethylation in this process. Here we report DNA hydroxymethylation dynamics during  cerebellum development in  the  human brain.  Overall, we find a positive correlation  between 5-hmC levels and cerebellum development. Genome-wide profiling reveals that 5-hmC is highly enriched  on specific gene regions, including  exons and especially the  untranslated regions (UTRs), but it is depleted on introns and intergenic regions. Furthermore, we have identified fetus-specific and adult-specific differentially hydroxymethylated regions (DhMRs), most of which overlap with genes and  CpG island shores. Surprisingly, during development DhMRs are highly enriched in genes encoding mRNAs that can be regulated by fragile X mental retardation protein (FMRP), some of which are disrupted in autism, as well as in many known autism genes. Our results suggest that 5-hmC-mediated epigenetic regulation  may  broadly impact the development of  the  human brain, and  its dysregulation could  contribute to the molecular pathogenesis of neurodevelopmental disorders.

overall_design: We generated comprehensive genome-wide profiles of 5hmC in human cerebellum.


title: Analysis of conjugation-specific 26-32nt siRNAs of Tetrahymena thermophila

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

institute: Institute of Human Genetics, CNRS

summary: Distinct classes of small RNAs are often selectively sorted to different Argonaute proteins. Various properties of small RNAs, such as length, terminal nucleotide, thermodynamic asymmetry and duplex mismatches, can impact sorting in different RNA silencing pathways in diverse eukaryotes. The developmentally regulated ~26-32 nt siRNAs, which are involved in programmed DNA elimination in Tetrahymena, show a strong bias for uracil at the 5' end. In this study, we analyzed loaded and unloaded populations of ~26-32 nt siRNAs by deep RNA sequencing. We show that the production process is the main determinant of size, whereas the 5' uracil bias is attributed not only to the process of loading siRNAs into the Argonaute protein Twi1p but also significantly to the initial processing of the siRNAs. We also show that both the loaded and the unloaded ~26-32 nt siRNAs have a strong bias for adenine as the 3rd base from the 3' terminus, suggesting that most of these siRNAs are direct Dicer products and little post-processing amplification of this class of siRNAs occurs. Further, we demonstrate that the siRNA-loading process in vivo can be deduced from the fraction of siRNAs with uracil as the first base. These findings provide biochemical bases for the attributes of ~26-32 nt siRNAs, which should help improve our understanding of their production and turnover in vivo.

overall_design: Examination of siRNA populations in wild-type and TWI1 KO Tetrahymena cells

first: Henriette

last: Kurth


title: Global gene expression analysis of Dot1l-deficient and control intestinal villus cells in mouse

status: Public on Oct 19 2012

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Methylation of H3K79 is associated with chromatin at expressed genes, though it is unclear if this histone modification is required for transcription of all genes. Recent studies suggest that Wnt-responsive genes depend particularly on H3K79 methylation, which is catalyzed by the methyltransferase DOT1L. Human leukemias carrying MLL gene rearrangements show DOT1L-mediated H3K79 methylation and aberrant expression of leukemogenic genes. DOT1L inhibitors reverse these effects but their clinical use is potentially limited by toxicity in Wnt-dependent tissues such as intestinal epithelium. Genome-wide positioning of the H3K79me2 mark in Lgr5+ mouse intestinal stem cells and mature intestinal villus epithelium correlated with mRNA expression levels but not with Wnt-responsive genes per se. Selective Dot1l disruption in Lgr5+ stem cells or in all intestinal epithelial cells eliminated H3K79me2 from the respective compartments, allowing genetic evaluation of DOT1L requirements. Absence of methylated H3K79 did not impair health, intestinal homeostasis or expression of Wnt target genes in crypt epithelium for up to 4 months, despite increased crypt cell apoptosis. Global transcript profiles in Dot1l-null cells were barely altered. Thus, H3K79 methylation is not essential for transcription of Wnt-responsive or other intestinal genes and intestinal toxicity is not imperative when DOT1L is rendered inactive in vivo.

overall_design: Examination of differential gene expression between Dot1l control (Dot1 f/f) and Dot1l mutant (Villin-Cre, Dot1l f/f) villus cells.

first: Li

last: Ho

first: Scott

last: Armstrong

first: Ramesh

last: Shivdasani


title: Genome wide DNA methylation analysis of leukemia and reprogrammed leukemia cells (sequencing)

first: Touati

last: Benoukraf

summary: We analyzed the methylation pattern of a well characterized leukemia cell line, named K562. Furthermore, we decided to investigate how the malignant epiegenome change during the reprogramming process

overall_design: We used RRBS analysis to investigate the methylation pattern in leukemia and reprogrammed leukemia (LiPS).We show that the erasure of the epigenetic aberrancies have functional consequences on leukemia phenotype

first: Giovanni

last: Amabile

first: Annalisa

last: Di Ruscio

first: Alexander

last: Ebralidze

first: Sarawut

last: Wongphayak


title: BRCA1 functions independently of homologous recombination in DNA interstrand crosslink repair

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

institute: University of Pennsylvania

summary: Brca1 is required for DNA repair by homologous recombination (HR) and normal embryonic development. Here we report that deletion of the DNA damage responsefactor 53BP1 overcomes embryonic lethality in Brca1-nullizygous mice, and rescues HR deficiency, as measured by hypersensitivity to PARP (polyADPribose polymerase) inhibition. However, Brca1,53BP1 double-deficient cells are hypersensitive to DNA interstrand crosslinks (ICLs), indicating that BRCA1 has an additional role in DNA cross-link repair that is distinct from HR. Disruption of the non-homologous end-joining (NHEJ) factor, Ku, promotes DNA repair in Brca1-deficient cells; however deletion of either Ku or 53BP1 exacerbates genomic instability in cells lacking FANCD2, a mediator of the Fanconi Anemia pathway for ICL repair. Brca1 therefore has two separate roles in ICL repair, whereas FANCD2 provides a key activity that can not be bypassed by ablation of 53BP1 or Ku.

overall_design: B cells were stimulated to undergo class switch recombination in vitro. Chromatin from B cells was harvested 72 hours post-stimulation and used for RPA ChIP to study the extent of resection of DNA DSBs.

first: Samuel

last: Bunting

first: Elsa

last: Callen

first: Marina

last: Kozak

first: Jung-Min

last: Kim

first: Nancy

last: Wong

first: Andres

middle: J

last: Lopez-Contreras

first: Thomas

last: Ludwig

first: Richard

last: Baer

first: Amy

last: Malhowski

first: Hua-Tang

last: Chen

first: Oscar

last: Fernandez-Capetillo

first: Alan

last: D'Andrea

first: Andre

last: Nussenzweig


title: Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification [ChIP-Seq]

status: Public on Sep 28 2012

first: Aaron

last: Arvey

institute: Memorial Sloan-Kettering Cancer Center

summary: Regulatory T (Treg) cells, whose identity and function are defined by the transcription factor Foxp3, are indispensable for immune homeostasis.  It is unclear whether Foxp3 exerts its Treg lineage specification function through active modification of the chromatin landscape and establishment of new enhancers or by exploiting a pre-existing enhancer landscape.  Analysis of the chromatin accessibility of Foxp3-bound enhancers in Treg and Foxp3-negative T cells showed that Foxp3 was bound overwhelmingly to pre-accessible enhancers occupied by its cofactors in precursor cells or a structurally related predecessor. Furthermore, the bulk of Foxp3-bound Treg cell enhancers lacking in Foxp3- CD4+ cells became accessible upon T cell receptor activation prior to Foxp3 expression with only a small subset associated with several functionally important genes being exclusively Treg cell-specific.  Thus, in a late cellular differentiation process Foxp3 defines Treg cell functionality in an “opportunistic” manner by largely exploiting the preformed enhancer network instead of establishing a new enhancer landscape.

overall_design: Four transcription factors (Foxp3, Ets1, Elf1, and Cbfb) were immunoprecipated while crosslinked to chromatin.  These experiments were then combined with DNase-seq data (being uploaded separately as part of ENCODE project) to find that Foxp3 binds exclusively to open chromatin.  Data was also leveraged from Foxo1 ChIP-seq performed in GSE40657 and confirmed by Runx/Cbfb ChIP-seq performed in GSE33653.

last: Samstein

last: Rudensky


title: Functional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant: Small RNA immunoprecipitation

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary: The Arabidopsis ARGONAUTE (AGO) protein AGO1 associates with microRNA (miRNA) and specific classes of short-interfering RNA (siRNA). AGO1-small RNA complexes recognize target RNA transcripts through base-pairing interactions and inhibit translation of target RNAs through endonucleolytic cleavage (slicing) or non-degradative mechanisms. The PIWI domain of AGO1 contains a metal-coordinating triad [Asp-Asp-His] (DDH) that is required for slicer activity. Here, we compared the activities of wild type (DDH) and slicer active-site defective (DAH) forms of AGO1 by sequencing small RNA and target transcript RNAs that co-immunoprecipitated with hemagglutinin (HA)-tagged AGO1 proteins. We found that the population of miRNA that associated with both AGO1-DDH and AGO1-DAH proteins largely overlapped, suggesting that cleavage activity does not affect miRNA maturation. In contrast, slicer-defective AGO1-miRNA complexes associated with target RNA more effectively than did wild type AGO1-miRNA. These data indicate that slicer-defective AGO proteins can be used as an approach to capture AGO-small RNA-target RNA ternary complexes more efficiently for genome-wide analyses.

overall_design: AGO1-DDH (wild type) AGO1-DAH (slicer mutant) proteins were immunoprecipitated (N-terminal 3xHA) from Arabidopsis (Columbia) flower (stages 1-12) lysate. Immunoprecipitations were also done from control plants transformed with vector only. Small RNA from immunoprecipitate fractions of vector, AGO1-DDH and AGO1-DAH were sequenced.

first: Alberto

last: Carbonell

first: Noah

last: Fahlgren

first: Hernan

last: Garcia-Ruiz

first: Kerrigan

last: Gilbert

first: Taiowa

last: Montgomery

first: Tammy

last: Nguyen

first: Josh

middle: T

last: Cuperus


title: Functional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant: Transcript immunoprecipitation

overall_design: AGO1-DDH (wild type) AGO1-DAH (slicer mutant) proteins were immunoprecipitated (N-terminal 3xHA) from Arabidopsis (Columbia) flower (stages 1-12) lysate. Immunoprecipitate fractions were treated with nuclease P1 before cleanup to trim free RNA ends, and therefore enrich samples in AGO1 target sites. All samples were treated with Ribominus (Life Technologies) to reduce ribosomal RNA abundance. Transcript fragments from two replicates of AGO1-DDH and AGO1-DAH immunoprecipitates were sequenced. Ribominus-treated total RNA (input controls) was also sequenced for each replicate.


title: Differential methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis

city: Changchun

first: Mingyuan

last: Liu

state: Jilin

address: 5333 Xian Road

department: Institute of Zoonosis

institute: Jilin University

summary: We present the first study to confirm the existence of  DNA  methylation  in  the  parasitic  nematode  Trichinella  spiralis,  and  we characterize  the  methylomes  of  the  three  life-cycle  stages  of  this  food-borne infectious human pathogen. We observe a drastic increase in DNA methylation during the  transition  from  the  new  born  to  mature  stage,  and  we  further  identify parasitism-related  genes  that  show  changes  in  DNA  methylation  status  between  life cycle stages. We also evaluated differential gene expression among  the three life stages using  Illumina HiSeq 2000 RNA-seq technology.

overall_design: Examination of DNA methylation status and gene expression status in three life stages (Adult, muscle larvae, newborn larvae) of Trchinella Spiralis using MethylC-seq.

first: Fei

last: Gao


title: Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification

state: NY

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

overall_design: Refer to individual Series


title: c-Myc is a universal amplifier of gene expression

status: Public on Sep 27 2012

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

first: Zuqin

last: Nie

first: Gang

last: Wei

first: Kairong

last: Cui

first: Arito

last: Yamane

first: Wolfgang

last: Resch

first: Ruoning

last: Wang

first: Douglas

middle: R

last: Green

first: Lino

last: Tessarollo

first: Rafael

last: Casellas

first: Keji

last: Zhao

first: David

last: Levens


title: Functional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant

first: James

last: Carrington

first: Alberto

last: Carbonell

first: Noah

last: Fahlgren

first: Hernan

last: Garcia-Ruiz

first: Kerrigan

last: Gilbert

first: Taiowa

last: Montgomery


title: c-Myc is a universal amplifier of gene expression [ChIP-Seq]

first: Gangqing

last: Hu

summary: The c-Myc HLH-bZIP protein has been implicated in physiological or pathological growth, proliferation, apoptosis, metabolism and differentiation at the cellular, tissue or organismal levels via regulation of numerous target genes. In part due to the incomplete inventory and functional accounting of Myc’s targets, no principle unifies Myc action. To relate the dynamics of Myc-binding with target expression and function in a system where Myc-levels are temporally and physiologically regulated, the transcriptomes and the genome-wide distributions of Myc, RNA polymerase II and chromatin modifications were compared during lymphocyte activation and in ES cells. A remarkably simple rule emerged from this quantitative analysis: Myc is not an on-off switch, but is a non-linear amplifier of expression, acting universally at active genes, except for immediate early genes that are strongly induced before Myc. This rule of Myc action explains the vast majority of Myc biology observed in literature.

overall_design: Quiescent B-cells (B0) were treated with lipopolysaccharide (LPS) for 4 hrs (B4), and resting T-cells (T0) were activated with conA for 4 hrs (T4) and for 14 hrs (T14). Following treatments, RNA was harvested and chromatin was prepared at these time points. The chromatin was immunoprecipitated using anti-EGFP antibodies and analyzed by ChIP-seq.

first: Zuqin

last: Nie


title: Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.

status: Public on Sep 26 2012

city: Princeton

first: John

middle: Russell

last: Bracht

state: NJ

address: Washington Rd. Guyot Hall rm 323

institute: Princeton University

summary: We report the existence of both methylcytosine and hydroxymethylcytosine in the genomic DNA of the ciliate Oxytricha trifallax during its genome rearrangement process. These modifications are dynamically added, de novo, to sequences targeted for elimination and are not present after the rearrangement process (in vegetative cells). We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine.

overall_design: We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine, and used an IgG control for nonspecific immunoprecpitation. Immunoprecipitation was performed on both vegetative (negative control) and 46h cells (with methylation). The data were normalized to RPKM, then the number of vegetative reads was subtracted from the number of 46h reads, giving excess reads at 46h, which we denote as the methylation/hydroxymethylation "signal". Those data are reported in the tab-deliminated data files included with this dataset.

middle: H

last: Perlman

first: Laura

last: Landweber


title: Transcriptional state during endodermal differentiation

status: Public on Sep 25 2012

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: ChIP-seq was performed to determine the transcriptional activity of genes during endodermal differentiation

overall_design: RNA pol II occupancy and histone marks of elongation and gene repression were analyzed during early endodermal differentiation

first: Alan

last: Mullen


title: hDot1L and RNAPII-5p in NCCIT cells.

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

summary: We generated high-throughput sequencing (ChIP-seq) data for genome wide occupancy of hDot1L and RNAPII-5p in human embryonic carcinoma cell.

overall_design: Performing ChIP-seq for hDot1L and RNAPII-5p in NCCIT cell lines (embryonic carcinoma cell lines in human).

first: Seung-Kyoon

last: Kim

first: Mirang

first: Dongsup

first: Daeyoup

last: Lee


title: cMyc and Max ChIP-seq analysis in small cell lung carcinoma cells

summary: cMyc and Max ChIP-seq analysis in a high MYC expressing small cell lung carcinoma cell line (H2171) and a low MYC expressing small cell lung carcinoma cell line (H128).

overall_design: H2171 cells (expressing high levels of cMyc protein) and H128 cells (expressing low levels of cMyc protein) were used to analyze how cMyc overexpression influences its genome-wide occupancy.

first: Rahl

last: Peter


title: Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [single-end MNase-seq]

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Biology

institute: University of North Carolina at Chapel Hill

summary: Experiments performed over the past three decades have shown that nucleosomes are transcriptional repressors. In Saccharomyces cerevisiae, depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds genes. The mechanism of de-repression is hypothesized to be rooted directly in chromatin changes. To test this, we reproduced classical H4 depletion experiments by conditional repression of all histone H3 transcription, which depletes the supply of nucleosomes in vivo. RNA-seq results were consistent with the earlier studies, but much more sensitive, revealing nearly 2500 de-repressed genes. Changes in chromatin organization were determined by MNase-seq. Nucleosomes that were preferentially retained occurred in regions of high DNA-encoded nucleosome affinity, and were marked with H3K36me2, which is linked to transcription elongation. Nucleosomes harboring acetyl marks or that contained the variant histone H2A.z were preferentially lost. Genes that were de-repressed lost or rearranged nucleosomes at their promoter, but not in the gene body. Therefore, a combination of DNA-encoded nucleosome stability and nucleosome composition dictates which nucleosomes will be lost under conditions of limiting histone protein. This, in turn, governs which genes will experience a loss of regulatory fidelity.

overall_design: MNase-seq experiments consist of three wildtype (1 single-end and 2 paired-end) and four mutant (DCB200.1/H3 shutoff; 2 single-end, 2 paired-end) replicates. Each replicate contains two timepoints reflecting chromatin immediately after ("O hours") and 3 hours after transition to media containing dextrose. RNA-seq data includes three replicates from wildtype or H3 depleted cells after 3 hours in media containing dextrose.

first: Andrea

last: Gossett


title: Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [RNA_seq]


title: Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs

city: La Jolla

first: Gene

last: Yeo


title: Transcriptome-wide Analysis of Exosome Targets in the Budding Yeast Saccharomyces cerevisiae

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

summary:
Purpose: The exosome plays major roles in RNA processing and surveillance but the in vivo target range and substrate acquisition mechanisms remain unclear. We applied an in vivo cross-linking technique coupled with deep sequencing (CRAC) that captures transcriptome-wide interactions between individual yeast exosome subunits and their targets in a living cell.
Methods: We apply CRAC to HTP-tagged proteins (HTP: His6 - TEV cleavage site - two copies of the z-domain of Protein A): Two nucleases (Rrp44, Rrp6) and two structural subunits (Rrp41, Csl4) of the yeast exosome. At least two independent experiments were performed in each case and analyzed separately. We performed CRAC on wild-type (WT) Rrp44 and two catalytic mutants, rrp44-endo (D91N, E120Q, D171N, D198N) and rrp44-exo (D551N). We further developed CRAC using cleavable proteins (split-CRAC) to compare endonuclease and exonuclease targets of Rrp44. Plasmids designed for split-CRAC contain a PreScission protease cleavage site (PP) inserted between aa 241 and 242 in the RRP44 ORF to allow in vitro cleavage of purified protein, and a His6 tag to select the respective cleaved fragment.
Results: Analysis of wild-type Rrp44 and catalytic mutants showed that both the CUT and SUT classes of noncoding RNA, snoRNAs and, most prominently, pre-tRNAs and other Pol III transcripts are targeted for oligoadenylation and exosome degradation. Unspliced pre-mRNAs were also identified as targets for Rrp44 and Rrp6. CRAC performed using cleavable proteins (split-CRAC) revealed that Rrp44 endonuclease and exonuclease activities cooperate on most substrates. Mapping oligoadenylated reads suggests that the endonuclease activity may release stalled exosome substrates. Rrp6 was preferentially associated with structured targets, which frequently did not associate with the core exosome. This indicates that substrates can follow multiple pathways to the nucleases.
Conclusion: Our study represents the first transcriptome-wide map of substrates for the yeast exosome nuclease complex.

overall_design: Identification of targets for individual exosome subunits in wild-type and mutant yeast cells.

first: Claudia

last: Schneider

first: Wiebke

last: Wlotzka

first: Alex

last: Tuck

first: David

last: Tollervey


title: Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues (ChIP-Seq and MeDIP-Seq)

status: Public on Sep 24 2012

city: Rehovot

first: Gilad

last: Landan

address: 234 Herzl Street

institute: Weizmann Institute of Science

summary: DNA methylation has been comprehensively profiled in normal and cancer cells, but the dynamics that form, maintain and reprogram differentially methylated regions remain enigmatic. We show that methylation patterns within populations of cells from individual somatic tissues are heterogeneous and polymorphic. Using in vitro evolution of immortalized fibroblasts for over 300 generations, we track the dynamics of polymorphic methylation at regions developing significant differential methylation on average. The data indicate that changes in population-averaged methylation occur through a stochastic process that generates a stream of local and uncorrelated methylation aberrations. Despite the stochastic nature of the process, nearly deterministic epigenetic remodeling emerges on average at loci that lose or gain resistance to methylation accumulation. Changes in the susceptibility to methylation accumulation are correlated with changes in histone modifications and CTCF occupancy.  Characterizing epigenomic polymorphism within cell populations is therefore critical for understanding methylation dynamics in normal and cancer cells.

overall_design: Genomewide sequencing data is included herein: H3K27me3 profiled throughout the microevolutionary timecourse using ChIP-seq, DNA methylation profiled through the timecourse using MeDIP-seq, and H3K4me3 and CTCF profiled in late and early timepoints using ChIP-seq. Deep Bisulfite sequencing amplicon data and results can be obtained at: http://compgenomics.weizmann.ac.il/tanay/?page_id=99 .


status: Public on Sep 22 2012

first: Pengfei

last: Yu

address: 9500 Gilman Drive MC 0419

department: Bioengineering

institute: University of California San Diego

summary: Genome-wide maps of cytosine methylation, cytosine hydroxylmethylation and small non coding RNAs in mouse ES cells and upon guided differentiation to mesoendoderm cells. Mouse embryonic stem cells (E14) were guided differentiated into mesoendoderm lineages by activin-A induction. cells in three time points (day0, day4 and day6) were collected. The genome-wide studies on three cell types were summerized as following: cytosine methylation data were generated using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq); DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. Biotechnol. 2011, 29, 68-72). E14 Day0 data for MRE-seq and MeDIP-seq are released first in previous publication and included in prior series GSE36114

overall_design: ChIP-seq, 5-hmC-seq, MeDIP-Seq, MRE-Seq, ncRNA-Seq, and RNA-seq on activin-induced differentiating ES cells at 3 time points.

first: Shu

last: Xiao

first: Wei

last: Huang

first: Xiaoyun

last: Xin

first: Chunxiao

last: Song

first: Darina

last: McDee

first: Tetsuya

last: Tanaka

first: Ting

last: Wang

first: Chuan

last: He

first: Sheng

last: Zhong


title: Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [Paired-end Mnase-seq]

first: Jason

last: Lieb

first: Andrea

last: Gossett


title: Tag-seq profiling in eye-antennal and wing imaginal discs of D. melanogaster, D. yakuba and D. virilis

status: Public on Sep 21 2012

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

summary: The aim of this study is to identify a set of eye-specific genes across Drosophila species. Species are used as replicates to remove biological noise and identify a core set of conserved eye-developmental genes. We analyze this conserved core using the motif discovery tool i-cisTarget, and identify master regulators of retinal determination, including the Zinc Finger transcription factor Glass.

sample_organism:
Drosophila melanogaster
Drosophila virilis
Drosophila yakuba

overall_design: Six samples were analyzed by Illumina Digital Gene Expression (DGE) using the NlaIII restriction enzyme, namely two different tissues (eye-antennal discs and wing discs) for each of the three species under study.


title: RNA-seq in wild-type and glass mutant eye-antennal discs in Drosophila melanogaster

summary: The aim of this data set is to perform a differential expression analysis between wild type eye-antennal imaginal disc and discs that are homozygous glass mutant gl[60j]. This data set is used to validate Glass target gene predictions identified by i-cisTarget on a set of conserved eye-specific genes.

overall_design: RNA-seq was performed in eye-antennal imaginal discs of two D.melanogaster wild-type strains (Canton S and strain RAL-208 (Jordan et al. 2007, Ayroles et al. 2009)), representing two biological replicates; and in glass mutant (gl[60j]) discs for two technical replicates.


title: Molecular profiling of activated neurons by phosphorylated ribosome capture

status: Public on Sep 20 2012

city: New York

first: Zachary

last: Knight

address: 1230 York Ave

institute: Rockefeller University


title: Genome-wide expression analysis of dikaryotic colonies of Schizophyllum commune under various conditions: wild-type, delta-wc2, delta-wc2 hsp3(pr)-wc2

city: Utrecht

last: Wösten

address: Padualaan 8

country: Netherlands

institute: Utrecht University

summary: The blue light receptor WC-2 was shown to be involved in mushroom development in the basidiomycete Schizophyllum commune. When the gene encoding WC-2 was deleted, no mushrooms formed and colony morphology was radial. This phenotype was similar to the wild-type colony grown in the dark. This phenotype could be complemented by transforming the wc-2 deletion strain with a construct encompassing the wc-2 coding sequence under the control of the heat inducible promoter hsp3. A daily heat shock of 1 hour at 42 degrees Celsius resulted in mushroom development and an asymmetrical colony. In this study we performed a genome-wide expression analysis on dikaryons of wild-type (not heat shocked), delta-wc2 (heat shocked or not heat shocked) and the complemented strain delta-wc2 hsp3-wc2 (heat shocked or not heat shocked).

overall_design: A total of five samples were analyzed. One wild-type (not heat shocked), delta-wc2 (heat shocked or not heat shocked) and the complemented strain delta-wc2 hsp3-wc2 (heat shocked or not heat shocked).

first: Robin

last: Ohm

first: Luis

last: Lugones

first: Han


title: Tag-seq in eye-antennal and wing imaginal discs of D.melanogaster, D.yakuba, and D.virilis; RNA-seq in wild-type and glass mutant D.melanogaster eye-antennal imaginal discs.

summary:
In this study we use Tag-sequencing in eye-antennal and wing imaginal discs across Drosophila species to determine a set of conserved eye-specific developmental genes. Next, we perform motif discovery analysis using the tool i-cisTarget, to depict the core gene developmental network underlying compound eye photoreceptor. The Glass position weight matrix appears as the most highly overrepresented motif, thus positioning Glass as a master regulator in compound eye photoreceptor development. Differential gene expression analysis by RNA-seq in D.melanogaster wild-type eye-antennal versus glass mutant [gl 60j] shows that the majority of our predicted Glass targets show strong downregulation in the glass mutant.

This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Drosophila melanogaster
Drosophila virilis
Drosophila yakuba

overall_design: Refer to individual Series.


title: Translational regulation of Anopheles gambiae mRNAs in the midgut during Plasmodium falciparum infection

city: Blacksburg

first: Jinsong

last: Zhu

state: VA

address: 313 Engel Hall

department: Biochemistry

institute: Virginia Tech

summary: Malaria is caused by Plasmodium parasites, which are transmitted via the bites of infected Anopheline mosquitoes. Midgut invasion is a major bottleneck for Plasmodium development inside the mosquito vectors as a rapidly responding immune system recognizes ookinetes and recruits killing factors from the midgut and surrounding tissues, dramatically reducing the population of invading ookinetes before they can successfully traverse the midgut epithelium. Understanding molecular details of the parasite-vector interactions requires precise measurement of nascent protein synthesis in the mosquito during Plasmodium infection. Current expression profiling primarily monitors alterations in steady-state levels of mRNA, but does not address the equally critical issue of whether the proteins encoded by the mRNAs are actually synthesized. In this study, we used sucrose density gradient centrifugation to isolate actively translating Anopheles gambiae mRNAs based upon their association with polyribosomes (polysomes). The proportion of individual gene transcripts associated with polysomes, which is determined by RNA deep sequencing, reflects mRNA translational status. This approach led to identification of 1017 mosquito transcripts that were primarily regulated at the translational level after ingestion of Plasmodium falciparum-infected blood. Caspar, a negative regulator of the NF-kappaB transcription factor Rel2, appears to be substantially activated at the translational levels during Plasmodium infection. In addition, transcripts of Dcr1, Dcr2 and Drosha, which are involved in small RNA biosynthesis, exhibited enhanced associations with polysomes after P. falciparum challenge. This observation suggests that mosquito microRNAs may play an important role in reactions against Plasmodium invasion. We analyzed both total cellular mRNAs and mRNAs that are associated with polysomes to simultaneously monitor transcriptomes and nascent protein synthesis in the mosquito. This approach provides more accurate information regarding the rate of protein synthesis, and identifies some mosquito factors that might have gone unrecognized because expression of these proteins is regulated mainly at the translational level rather than at the transcriptional level after mosquitoes ingest a Plasmodium-infected blood meal.

overall_design: Midguts from female Anopheles gambiae mosquitoes were dissected at around 24 h after ingestion of P. falciparum-infected blood. Mosquitoes fed on uninfected blood were used as control. A portion of the midguts were used for isolation of total cellular RNA. Extracts of the remaining midguts were fractionated over sucrose density gradients, and fifteen fractions were collected from the top of each gradient. Non-polysomal fractions, as well as polysomal fractions were combined, respectively, to obtain two RNA pools per gradient for three independent experiments. The first, last and the sample between non-polysomal and polysomal, were all discarded to ensure pure pools from each set. A fourth experiment was conducted where the polysomal and non-polysomal samples were not pooled, to be used later for qRT-PCR. The mRNA levels of individual mosquito genes in polysome (PS) fractions, nonpolysome (NP) fractions and unfractionated steady-state (total) RNA were determined using high throughput RNA deep sequencing. Each RNA pool generated 2.1-9.8 million raw read .  Signal intensities of transcripts from each PS pool were compared to those of transcripts from a matching NP pool. To quantify the translational status of individual mRNA species, we define the relative PS loading [PL=P/(P+NP)] as the extent of mRNA association with polysomes. PL values were compared between the mosquitoes fed on P. falciparum-infected or -uninfected blood.

first: Edward

last: Mead

first: Meng

last: Li

first: Zhijian

last: Tu


title: Molecular profiling of activated neurons by phosphorylated ribosome capture [RNA-Seq]

summary: We report that phosphorylated ribosomes can be immunoprecipitated from mouse brain homogenates, resulting in enrichment of transcripts expressed in activated neurons.

overall_design: Mice were either injected with a concentrated salt solution or vehicle, hypothalami dissected, and phosphorylated ribosomes immunoprecipitated. RNA was sequenced from the input and IP for each condition (4 samples total).

first: Jeffrey

last: Friedman


title: The Neuregulin 1-HER axis as a key mediator of hyperglycemic memory effects in breast cancer

status: Public on Sep 19 2012

city: Dallas

first: Thomas

middle: Nathan

last: Person

state: Texas

address: 5323 Harry Hines Blvd

department: Clinical Sciences

institute: UT Southwestern

summary: Poor outcomes in diabetic patients are observed across a range of human tumors, suggesting that cancer cells develop unique characteristics under diabetic conditions. Cancer cells exposed to hyperglycemic insults acquire permanent aggressive traits of tumor growth, even after a return to euglycemic conditions. Comparative genome-wide mapping of hyperglycemia-specific open chromatin regions and concomitant mRNA expression profiling revealed that neuregulin-1 gene, an established endogenous ligand for the HER3 receptor, is activated through a putative distal enhancer. Our findings highlight the targeted inhibition of NRG1-HER3 pathways as a potential target for the treatment breast cancer patients with associated diabetes

overall_design: Chromatin was extracted from hyperglycemic (HyG) and euglycemic (Control) cancer cells; FAIRE DNA and input DNA from each sample were used to generate libraries for single end sequencing on the the SOLiD 4 HQ system

first: Jiyoung

last: Park

first: Venetia

last: Sarode

first: David

last: Euhus

first: Ralf

last: Kittler

first: Philipp

last: Scherer


title: Genome-wide analysis of the SNAPc complex [ChIP-Seq]

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary: The small nuclear RNA (snRNA)-activating protein complex (SNAPc) is a basal transcription factor that mediates the transcriptional activation of snRNAs. Here, we describe the genome-wide occupancy of the SNAPC1 and SNAPC4 subunits of SNAPc. While the SNAPC4 occupancy was in accord with the role for SNAPc in snRNA transcription, SNAPC1 displayed a broader genomic profile mirroring that of RNA polymerase II at highly active protein-coding genes. Our functional analysis revealed a role for SNAPc1 in regulation of both basal and activator-induced transcription of protein-coding genes. These studies expand the role for SNAPC1 beyond its regulation of snRNA transcription.

overall_design: Comparison of the genome wide profiles of different SNAPc subunits and RNAPII in human cells

first: Ramin

last: Shiekhattar


title: DPN and Tamoxifen treatments of parathyroid adenoma cells

city: Solna

first: Mikael

last: Huss

address: Tomtebodav. 23A

country: Sweden

institute: Science for Life Laboratory Stockholm

summary: Stimulation of estrogen receptor beta in PHPT, genetic changes after 24 and 48h of treatments vs. Control

overall_design: Treatment of parathyroid adenomas (4 patients, 4 adenomas) with DPN 24h (4 samples), DPN 48h (4 samples), OHT 24h (4 samples), OHT 48h (4 samples), control 24h (3 samples), control 48h (4 samples). Omission of 1 sample based on low RNA quality.

first: Felix

last: Haglund

first: Ran

last: Ma

first: Luqman

last: Sulaiman

first: Ming

last: Lu

first: Inga-Lena

last: Nilsson

first: Anders

last: Höög

first: C

last: Juhlin

first: Johan

last: Hartman

first: Catharina

last: Larsson


title: smRNA under high osmotic stress

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: To identifiy osmotic stress responsive smRNAs, we used a deep-sequencing technique to profile small RNA populations in leaf and root tissues of plants under high osmotic stress and control conditions.

overall_design: We treated 30day-old plants with high osmotic stress and sampled leaves and roots from the same plant with 3 biologial replicates. Then, 3 replicates were pooled and total RNA was extracted and prepared for smRNA deep sequencing. After normalization and annotation, we selected potential osmotic stress responsive smRNAs.

first: Natsuko

last: Kinoshita

first: Hiroyuki

last: Kasahara

first: Jun

last: Liu

first: Cameron

last: MacPherson

first: Yasunori

last: Machida

first: Yuji

last: Kamiya

first: Matthew

last: Hannah

first: Nam-Hai

last: Chua


title: DNaseI Digital Genomic Footprinting from ENCODE/University of Washington [Mouse]

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).
This track, produced as part of the mouse ENCODE Project, contains deep sequencing DNase data that will be used to identify sites where regulatory factors bind to the genome (footprints).
Footprinting is a technique used to define the DNA sequences that interact with and bind DNA-binding proteins, such as transcription factors, zinc-finger proteins, hormone-receptor complexes, and other chromatin-modulating factors like CTCF. The technique depends upon the strength and tight nature of protein-DNA interactions. In their native chromatin state, DNA sequences that interact directly with DNA-binding proteins are relatively protected from DNA degrading endonucleases, while the exposed/unbound portions are readily degraded by such endonucleases. A massively parallel next-generation sequencing technique to define the DNase hypersensitive sites in the genome was adopted. The DNase samples were sequenced using next-generation sequencing machines to significantly higher depths of 300-fold or greater. This produces a base-pair level resolution of the DNase susceptibility maps of the native chromatin state. These base-pair resolution maps represent and are dependent upon the nature and the specificity of interaction of the DNA with the regulatory/modulatory proteins binding at specific loci in the genome; thus they represent the native chromatin state of the genome under investigation. The deep sequencing approach has been used to define the footprint landscape of the genome by identifying DNA motifs that interact with known or novel DNA binding proteins.

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell/mouse). Digital DNaseI was performed by DNaseI digestion of intact nuclei, followed by isolating DNaseI "double-hit" fragments (Sabo et al., 2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Solexa platform (27 bp reads). High-quality reads were mapped to the NCBI37/mm9 mouse genome using Bowtie 0.12.5; only unique mappings were kept. DNaseI sensitivity is directly reflected in raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). DNaseI hypersensitive zones (HotSpots) were identified using the HotSpot algorithm (Sabo et al., 2004). False discovery rate thresholds of 1.0% (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36-mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within 1.0% (FDR 0.01) hypersensitive zones using a peak-finding algorithm. Only DNase Solexa libraries from unique cell types producing the highest quality data, as defined by Percent Tags in Hotspots (PTIH ~40%), were designated for deep sequencing to a depth of over 200 million tags.
Results were validated by conventional DNaseI hypersensitivity assays using end-labeling/Southern blotting methods.

first: Richard

last: Sandstrom


title: Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome

first: Jason

last: Lieb

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

overall_design: Refer to individual Series

first: Andrea

last: Gossett


title: Identification of a FOXO3/IRF7 circuit that limits inflammatory sequelae of antiviral responses (ChIP-Seq)

city: Seattle

first: Ayush

last: Raman

state: WA

address: 401 Terry Avenue North

department: Computational Dept.

institute: Institute for Systems Biology

summary: We predict that a member of the forkhead family of transcription factors, FOXO3, is a negative regulator of a subset of antiviral genes. This prediction was validated using macrophages isolated from Foxo3-null mice. Genome-wide location analysis combined with gene deletion studies identified the Irf7 gene as a critical target of FOXO3. FOXO3 was identified as a negative regulator of Irf7 transcription. Our data suggest that the FOXO3-IRF7 regulatory circuit represents a novel mechanism for establishing the requisite set points in the interferon pathway.

overall_design: C57BL/6 mice were obtained from Jackson Laboratories. Foxo3-/- mice in the FVB background were obtained from MMRRC and were backcrossed to C57BL/6 mice at least 5 times to generate congenic mice. C57BL/6 Foxo3+/- heterozygotes were intercrossed to generate Foxo3-/- mice. Mice were maintained at the animal facility of the Institute for Systems Biology and used at 8–12 weeks of age. All animals were housed and handled according to the approved protocols of University of Washington and Institute for Systems Biology's Institutional Animal Care and Use Committees.

first: Vladimir

last: Litvak


title: In vitro and in vivo monitoring of valproic acid effects on gene expression signatures in adult acute myeloid leukemia

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

summary:
PURPOSE: Inhibitors of histone deacetylases (HDACIs) like valproic acid (VPA) display activity in murine leukemia models, and induce tumor-selective cytoxicity against blasts from patients with acute myeloid leukemia (AML). However, despite of the existing knowledge of the potential function of HDACIs, there remain many unsolved questions especially regarding the factors that determine whether a cancer cell undergoes cell cycle arrest, differentiation, or death in response to HDACIs. Furthermore, there is still limited data on HDACIs effects in vivo, as well as HDACIs function in combination with standard induction chemotherapy, as most studies evaluated HDACIs as single agent in vitro. Thus, our first goal was to determine a VPA response signature in different myeloid leukemia cell lines in vitro, followed by an in vivo analysis of VPA effects in blasts from adult de novo AML patients entered within two randomized multicenter treatment trials of the German-Austrian AML Study Group.
PATIENTS AND METHODS: To define a VPA in vitro response signature we profiled gene expression in myeloid leukemia cell lines (HL60, NB4, HEL, and K-562) following 48 hours of VPA treatment by using DNA Microarray technology. Next, we evaluated the VPA effects on gene expression in AML samples collected within the AMLSG 07-04 trial for younger (age<60yrs) and within the AMLSG 06-04 trial for older adults (age>60yrs), in which patients are randomized to receive standard induction chemotherapy (idarubicine, cytarabine, and etoposide = ICE) with or without concomitant VPA. We profiled gene expression in diagnostic AML blasts and following 48 hours of treatment with ICE or ICE/VPA.

overall_design: cDNA microarrays from the Stanford Functional Genomics Facility were used to perform mRNA transcript profiling of 4 leukemia cell lines treated with 1mM VPA for 48 hours in comparison to untreated cell lines, and to perform mRNA transcript profiling of freshly-frozen, from matched acute myeloid leukemia peripheral blood specimens collected from 14 AML patients at diagnosis and following 48 hours of treatment with either chemotherapy +/- VPA.

first: Lars

last: Bullinger


title: Identification of a FOXO3/IRF7 circuit that limits inflammatory sequelae of antiviral responses


title: Identification of Transcription Factor EOR-1::POL-2 Binding Regions in L3

status: Public on Sep 18 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3160
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene ama-1; Strain OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Identification of Transcription Factor EGL-5::POL-2 Binding Regions in L3

summary:
modENCODE_submission_3162
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene ama-1; Strain OP54(official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim ); temp (temperature) 20 degree celsius


title: A validated regulatory network for Th17 cell specification

institute: Solvuu

summary: Th17 cells have critical roles in mucosal defense and are major contributors to inflammatory disease. Their differentiation requires the nuclear hormone receptor RORγt working with multiple other essential transcription factors (TFs). We have used an iterative systems approach, combining genome-wide TF occupancy, expression profiling of TF mutants, and expression time series to delineate the Th17 global transcriptional regulatory network. We find that cooperatively-bound BATF and IRF4 contribute to initial chromatin accessibility, and with STAT3 initiate a transcriptional program that is then globally tuned by the lineage-specifying TF RORγt, which plays a focal deterministic role at key loci. Integration of multiple datasets allowed inference of an accurate predictive model that we computationally and experimentally validated, identifying multiple new Th17 regulators, including Fosl2, a key determinant of cellular plasticity. This interconnected network can be used to investigate new therapeutic approaches to manipulate Th17 functions in the setting of inflammatory disease.

overall_design: 143 RNA-seq, 83 ChIP-seq, 65 ChIP-seq controls, and 16 FAIRE-seq

first: Maria

last: Ciofani

first: Aviv

last: Madar

first: Carolina

last: Galan

first: Maclean

last: Sellars

first: Kieran

last: Mace

first: Florencia

last: Pauli

first: Wendy

last: Huang

first: Christopher

middle: N

last: Parkurst

first: Michael

last: Muratet

first: Kim

last: Newberry

first: Sarah

last: Meadows

first: Alex

last: Greenfield

first: Yi

last: Yang

first: Preti

last: Jain

first: Francis

middle: K

last: Kirigin

first: Carmen

last: Birchmerier

first: Erwin

middle: F

last: Wagner

first: Kenneth

last: Murphy

first: Richard

last: Myers

last: Bonneau

first: Dan

last: Littman


title: Genome-wide mapping of human DNA-replication origins: levels of transcription at Orc1 sites regulate origin selection and replication timing

city: Milano

first: Lucilla

last: Luzi

address: Via Adamello 16

country: Italy

institute: IFOM FIRC Institute for Molecular Oncology Foundation

summary: We report the genome-wide mapping of Orc1 binding-sites in mammals and their validation as active DNA-replication origins (ORIs). Orc1 sites are universally associated with transcription start sites (TSSs) of coding or non-coding RNAs. Transcription levels at the Orc1 sites directly correlate with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (≥1 RNA copy/cell), replicating in early S and mapping to the TSSs of coding RNAs, and those associated with low transcription levels (<1 RNA copy/cell), replicating throughout the entire S and mapping to TSSs of non-coding RNAs. These findings are compatible with a scenario whereby TSS expression-levels influence the efficiency of Orc1 recruitment at G1 and the probability of firing during S.

overall_design: Identification of Orc1 binding sites in human cells

first: Gaetano

middle: I

last: Dellino

first: Davide

last: Cittaro

first: Rossana

last: Piccioni

first: Stefania

last: Banfi

first: Simona

last: Segalla

first: Matteo

last: Cesaroni

first: Mauro

last: Giacca

first: Pier

last: Pelicci


title: BATF-JUN is critical for IRF4-mediated transcription in T cells

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Interferon regulatory factor 4 (IRF4) is an IRF family transcription factor with critical roles in lymphoid development and in regulating the immune response. IRF4 binds DNA weakly owing to a carboxy-terminal auto-inhibitory domain, but cooperative binding with factors such as PU.1 or SPIB in B cells increases binding affinity, allowing IRF4 to regulate genes containing ETS–IRF composite elements (EICEs; 5'-GGAAnnGAAA-3'). Here we show that in mouse CD4+ T cells, where PU.1/SPIB expression is low, and in B cells, where PU.1 is well expressed, IRF4 unexpectedly can cooperate with activator protein-1 (AP1) complexes to bind to AP1–IRF4 composite (5'-TGAnTCA/GAAA-3') motifs that we denote as AP1–IRF composite elements (AICEs). Moreover, BATF–JUN family protein complexes cooperate with IRF4 in binding to AICEs in pre-activated CD4+ T cells stimulated with IL-21 and in TH17 differentiated cells. Importantly, BATF binding was diminished in Irf4-/- T cells and IRF4 binding was diminished in Batf-/- T cells, consistent with functional cooperation between these factors. Moreover, we show that AP1 and IRF complexes cooperatively promote transcription of the Il10 gene, which is expressed in TH17 cells and potently regulated by IL-21. These findings reveal that IRF4 can signal via complexes containing ETS or AP1 motifs depending on the cellular context, thus indicating new approaches for modulating IRF4-dependent transcription.

overall_design: Genome-wide transcription factors mapping and binding of IRF4, BATF, IRF8, STAT3, JUN etc in WT, Irf4-/- and Batf-/- mice in different cell types (B cells, CD4+ T cells and TH17 cells) cultured with or without IL-21 was conducted. RNA-Seq is conducted in mouse B cells, CD4+ T cells, TH1/TH2/TH9/TH17/Treg.

first: Rosanne

last: Spolski

first: Wei

last: Liao

first: Lu

last: Wang

first: Theresa

middle: L

middle: M

first: Warren

last: Leonard


title: Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

first: Gilad

last: Landan

institute: Weizmann Institute of Science


title: Identification of the hemogenic endothelial progenitor and its direct precursor in human pluripotent stem cell differentiation cultures

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

institute: University of Wisconsin

summary: Hemogenic endothelium (HE) is the source of HSCs in the developing embryo. In this study we have identified the hemogenic endothelial progenitors and their precursors originating from differentiated H1 cells on OP9 stromal cells.

overall_design: RNA-seq of  hemogenic endothelial progenitors and their precursors originating from differentiated H1 cells on OP9 stromal cells.

first: Kyung-Dal

last: Choi

first: Maxim

last: Vodyanik

first: Padma

middle: P

last: Togarrati

first: Kran

last: Suknuntha

first: Akhilesh

last: Kumar

first: Fnu

last: Samarjeet

first: Mitchell

last: Probasco

first: Shulan

last: Tian

first: Ron

last: Stewart

first: James

last: Thomson


title: Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

summary: DNA methylation at the 5-position of cytosine (5-mC) is a key epigenetic mark critical for varius biological and pathological processes. 5-mC can be converted to 5-hydroxymethylcytosine (5-hmC) by the Ten-Eleven Translocation (TET) family of DNA hydroxylases. Here we report that "loss of 5-hmC" is an epigenetic hallmark of melanoma with diagonostic and prognostic implications. Genome-wide mapping of 5-hmC in nevi and melanomas for the first time revealed loss of 5-hmC landscape in the melanoma epigenome. Downregulation of Isocitrate Dehydrogenase 2 (IDH2) and TET family enzymes proved to be one of the mechanisms underlying the loss of 5-hmC during melanoma development, and rebuilding the 5-hmC landscape in the melanoma epigenome by reintroducing active TET2 or IDH2 suppressed melanoma growth and increased tumor-free survival. Thus, our study establishes that "loss of 5-hmC" is a new epigenetic hallmark of melanoma and links IDH and TET family enzymes-mediated 5-hmC putative tumor suppressor pathway to the suppression of melanoma progression.

overall_design: Determine the genome-wide distribution of 5mC and 5hmC in benign nevus tissue, melanoma tissue, A2058 MOCK cells (overexpressing empty vector), A2058 TET2 cells (overexpressing wild type human TET), and A2058 TET2M cells (overexpressing mutant human TET).

first: Yujiang

last: Shi

first: Yufei

last: Xu


title: High-fat or ethinyl-estradiol intake during pregnancy increases mammary cancer risk in several generations of offspring

city: Arlington

first: Ye

department: ECE

summary: Maternal exposures during pregnancy influence the risk of many chronic adult-onset diseases in the offspring. We investigated whether feeding pregnant rats a high fat (HF) or ethinyl-estradiol (EE2)-supplemented diet affects carcinogen-induced mammary cancer risk in daughters, granddaughters and great-granddaughters. Here we show that mammary tumorigenesis is higher in daughters and granddaughters of HF rat dams and in daughters, granddaughters and great-granddaughters of EE2 rat dams. Outcross experiments indicate that increased mammary cancer risk is transmitted to HF granddaughters equally through the female or male germlines, but it is only transmitted to EE2 granddaughters through the female germline. The effects of maternal EE2 exposure on offspring's mammary cancer risk are associated with alternations in the DNA methylation machinery and methylation patterns in mammary tissue of all three EE2 generations. We conclude that dietary and estrogenic exposures in pregnancy increase breast cancer risk in multiple generations of offspring, possibly through non-genetic means

overall_design: We examined the whole genome methylation status of both control and EE2-supplemented diet rats in three consecutive generations

first: Sonia

last: de Assis

first: Anni

last: Warri

first: M

last: Cruz

first: Olusola

last: Laja

first: Bai

last: Zhang

first: Yue

last: Wang

first: Tim

last: Huang

first: Leena

last: Hilakivi-Clarke


title: Oncofusion protein AML1-ETO targets ERG factor binding sites in AML

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: ERG has been identified as an essential factor for the function and maintenance of adult hematopoietic stem cells and high ERG expression is a negative prognostic marker for treatment outcome in AML. The molecular function of ERG and its interplay with other factors is however largely unknown. Here we demonstrate that ERG has cell type specific distributions in normal CD34+ myeloid progenitors and in AML cells and identify ERG as a potential pioneering protein for binding of oncofusion protein complexes. In addition, we identify H3 acetylation as the epigenetic mark preferentially associated with ERG binding. This intimate connection between ERG binding and H3 acetylation implies that one of the molecular strategies of the oncofusion proteins PML-RARa and AML1-ETO could involve the targeting of histone deacetylase activities to ETS factor bound hematopoietic regulatory sites.

overall_design: Examination of AML1-ETO, RUNX1, CBFb, HEB, FLI1 and ERG binding sites (ChIP-seq) in leukemic and normal hematopoietic cells, association with chromatin modifications and expression (RNA-seq) analysis of an AML1-ETO expressing cell line (SKNO-1)

first: Henk

middle: G

first: Joost

last: Martens

first: Amit

last: Mandoli

first: Femke

last: Simmer

first: Lucia

last: Altucci

first: Edo

last: Vellenga

first: Bart-Jan

last: Wierenga