title: Identification of Biologically Relevant Enhancers in Human Erythroid Cells [ChIP-Seq]

summary: Identification of cell-type specific enhancers is important for understanding the regulation of programs controlling cellular development and differentiation. Enhancers are typically marked by the co-transcriptional activator protein p300 or by groups of cell-expressed transcription factors. We hypothesized that a unique set of enhancers regulates gene expression in human erythroid cells, a highly specialized cell type evolved to provide adequate amounts of oxygen throughout the body. Using chromatin immunoprecipitation followed by massively parallel sequencing, genome-wide maps of candidate enhancers were constructed for p300 and four transcription factors, GATA1, NF-E2, KLF1, and SCL, using primary human erythroid cells. These data were combined with gene expression analyses and candidate enhancers identified. Consistent with their predicted function as candidate enhancers, there was statistically significant enrichment of p300 and combinations of co-localizing erythroid transcription factors within 1-50 kb of the TSS of genes highly expressed in erythroid cells. Candidate enhancers were also enriched near genes with known erythroid cell function or erythroid cell phenotypes. Candidate enhancers exhibited only moderate conservation with mouse and minimal conservation with nonplacental vertebrates. Candidate enhancers were mapped to a data set of erythroid-associated, biologically relevant, SNPs from the GWAS catalog of the NHGRI. Fourteen candidate enhancers, representing 10 genetic loci, mapped to sites associated with biologically relevant erythroid traits. Fragments from these loci directed statistically significant expression in reporter gene assays. Identification of enhancers in human erythroid cells will allow a better understanding of erythroid cell development, differentiation, structure, and function, and provide insights into inherited and acquired hematologic disease.

overall_design:
CD34+-selected stem and progenitor cells were expanded for three days in the absence of EPO.  The cells were further cultured in the presence of EPO, and formaldehyde crosslinked chromatin was isolated after cells differentiated into R3/R4 nucleated erythroid cells.  Chromatin Immunoprecipitation followed by sequencing (chIP-seq) was performed using antibodies against GATA1, KLF1, NFE2, TAL1, p300, H3K4me2 and H3K4me3, along with a total input control.
Raw data (fastq, SRA) is missing for the TAL1 chIP-seq dataset

first: Mack

middle: Y

last: Su

last: Steiner

first: Hannah

last: Bogardus

first: Tejaswini

last: Mishra

first: Vincent

middle: P

first: Ross

last: Hardison

first: Patrick

last: Gallagher


title: Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila

status: Public on Jan 29 2013

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

country: USA

institute: National Institutes of Health

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: Chromatin insulators are functionally conserved DNA-protein complexes that are situated throughout the genome and organize independent transcriptional domains.  Previous work implicated RNA as an important cofactor in chromatin insulator activity, although the mechanisms by which RNA affects insulator activity are not yet understood.  Here we identify the exosome, the highly conserved major cellular 3’ to 5’ RNA degradation machinery, as a physical interactor of CP190-dependent chromatin insulator complexes in Drosophila.  High resolution genome-wide profiling of exosome by ChIP-seq in two different embryonic cell lines reveals extensive and specific overlap with the CP190, BEAF-32, and CTCF insulator proteins.  Colocalization occurs mainly at promoters but also well-characterized boundary elements, such as scs, scs’, Mcp, and Fab-8.  Surprisingly, exosome associates primarily with promoters but not gene bodies, arguing against simple cotranscriptional recruitment to RNA substrates.  We find that exosome is recruited to chromatin in a transcription dependent manner, preferentially to highly transcribed genes.  Similar to insulator proteins, exosome is also significantly enriched at divergently transcribed promoters.  Directed ChIP of exosome in cell lines depleted of insulator proteins shows that CTCF is specifically required for exosome association at Mcp and Fab-8 but not other sites, suggesting that alternate mechanisms must also contribute to exosome chromatin recruitment.  Taken together, our results reveal a novel relationship between exosome and chromatin insulators throughout the genome.

overall_design: ChIP-seq of exosome components. RNA-seq after control and exosome subunit knockdown in Drosophila cell lines.

first: Su

middle: J

last: Lim

last: Boyle

first: Madoka

last: Chinen

middle: K

first: Elissa

last: Lei


title: Evolution and Pathogenic Mechanism of Rice Sheath Blight Pathogen

status: Public on Jan 28 2013

city: Chengdu

first: Aiping

last: Zheng

state: Sichuan

address: 555 Dongbei Road, Wenjiang District

country: China

institute: Rice Research Institute of Sichuan Agricultural University

summary: Analysis of RNA expression of Rhizoctonia solani AG1 IA. mRNA-seq of R. solani AG1 IA at 6 timepoints during the plant infection were sequenced. Cufflinks was used for calculating expected fragments per kilobase of transcript per million fragments sequenced (FPKM) values. Expression and regulation were identified. Analysis provides suggestion for discovering novel effectors and understanding pathogen factors.

overall_design: Sequencing mRNA-seq from disease lesions at 10 hour, 18 hour, 24 hour, 32 hour, 48 hour and 72 hour after inoculation to analysis the expression and identify pathogen factors.

first: Runmao

last: Lin

first: Ping

last: Li


title: Identification of in vivo, conserved, FUS RNA binding sites and the impact of FUS on the neuronal transcriptome

status: Public on Jan 25 2013

city: Baltimore

first: Manolis

last: Maragkakis

address: 251 Bayview Blvd

institute: National Institute on Aging

summary: FUS, an RNA binding protein was recently implicated in Amyotrophic Lateral Sclerosis (ALS). ALS is a fatal neurodegenerative disease. We report the identification of  the conserved neuronal RNA targets of FUS and the assessment of the impact of FUS depletion on the neuronal transcriptome. We identified that FUS regulates splicing of conserved intron containing transcripts. FUS retains or excludes the conserved intron by binding to them.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Identification of FUS neuronal targets using normal human brain samples and mouse neurons

first: Tadashi

last: Nakaya

first: Panagiotis

last: Alexiou

first: Alexandra

last: Chang

first: Zissimos

last: Mourelatos


title: Effects of DNA Methylation on Nucleosome Stability

city: West Lafayette

first: Clayton

middle: Kenneth

last: Collings

state: Indiana

address: 915 W. State Street

department: Biological Sciences

institute: Purdue University

summary: Methylation of DNA at CpG dinucleotides represents one of the most important epigenetic mechanisms involved in the control of gene expression in vertebrate cells. In this report, we conducted high-throughput nucleosome reconstitution experiments on 572 KB of human DNA and 668 KB of mouse DNA that was unmethylated or methylated in order to investigate the effects of this epigenetic modification on the positioning and stability of nucleosomes.  The DNA loci from both species contained the genes that encode the serum albumin family, the MYC protein, and the tumor suppressor p53.  The results demonstrated that a small subset of nucleosomes positioned by nucleotide sequence was sensitive to methylation where the modification increased the affinity of these sequences for the histone octamer.  The features that distinguished these nucleosomes from the bulk of the methylation-insensitive nucleosomes were an increase in the frequency of CpG dinucleotides and a unique rotational orientation of CpGs such that their minor grooves tended to face toward the histones in the nucleosome rather than away.  We propose that these features serve to enhance the affinity of methylated DNA for the histone octamer and that this effect could be involved in gene regulatory mechanisms such as silencing.  These methylation-sensitive nucleosomes were preferentially associated with exons as compared to introns while unmethylated CpG islands near transcription start sites became enriched in nucleosomes upon methylation.  The results of this study suggest that the effects of DNA methylation on nucleosome stability in vitro can recapitulate what has been observed in the cell and provide a direct link between DNA methylation and the structure and function of chromatin.

overall_design: For the human data, there were 3 unmethylated nucleosome replicates, 2 methylated nucleosome replicates, an unmethylated MNase control, and an unmethylated sonicated control.  For the mouse data, there were 2 unmethylated nucleosome replicates, 2 methylated nucleosome replicates, an unmethylated MNase control, a methylated MNase control, and an unmethylated sonicated control.

first: John

middle: N

last: Anderson


title: Lamin and Lamin B receptor knockout

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

summary: influence of lamin B rereceptor knockout and lamin A/C knockout on gene expression in cultured myoblast cells and in striated muscle tissue

overall_design: knockout samples are obtained by mating of heterozygous animals. Homozygous KO and wt animals of one litter are compared. Two boilogical replicates of KO samples are processed in parallel. wt samples are used as controls. One wt sample is processed per KO litter. Where appropriate two wt samples are used as biological replicates.

first: Boris

last: Joffe


title: Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes

status: Public on Jan 24 2013

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

type: Non-coding RNA profiling by high throughput sequencing

summary: We provided a full spectrum analysis for E. histolytica AGO2-2 associated 27nt small RNAs. Additionally, comparative analysis of small RNA populations from virulent and non-virulent amebic strains indicates that small RNA populations may regulate virulence genes.

overall_design: AGO2-2 bound small RNAs from E. histolytica strain HM-1:IMSS were immunoprecipitated and sequenced using 454 technology. Three independant sequencing runs were perfomed using the same RNA sample. In addition, size selected small RNAs from E. histolytica strain Rahman were sequenced with the same technology. One sequencing run was performed on this sample.

first: Hanbang

last: Zhang

first: Neil

last: Hall

first: Upinder

last: Singh


title: Chromatin dynamics and genome-wide profiling of repetitive elements during early mammalian embryogenesis.

status: Public on Jan 27 2013

city: ILLKIRCH Cedex

first: Stephanie

last: Le Gras

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary: We have used repetitive elements, including retrotransposons, as model loci to address how and when  heterochromatin forms during development. High throughput RNA-sequencing using a  Nano-CAGE protocol throughout early embryogenesis revealed that the expression of  repetitive elements is abundant in embryonic cells, highly dynamic and stage-specific,  with most repetitive elements becoming repressed before implantation. Furthermore, we  show that Line L1 elements and IAP retrotransposons become reactivated from both  parental genomes in mouse embryos after fertilisation, indicating an open chromatin  configuration at the beginning of development. Our data show that the reprogramming process that follows  fertilisation is accompanied by a robust transcriptional activation of retrotransposons  and suggests that expression of repetitive elements is initially regulated through an  RNA-dependent mechanism in mammals.

overall_design: Genome Wide profiling of CAGE transcripts using Nano-CAGE and RNAseq in oocytes and 3 different stages of mouse pre-implantation development

first: Anas

last: Fadloun

first: Maria

last: Torres Padilla


title: Extensive changes in DNA methylation are associated with expression of mutant huntingtin [RRBS]

city: Cambridge

first: Christopher

last: Ng

state: Massachusetts

address: 77 Massachusetts Ave.

institute: Massachusetts Institute of Technology

type: Methylation profiling by high throughput sequencing

summary: The earliest stages of Huntington’s disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin protein (HTT).  To explore the hypothesis DNA methylation may be altered in cells expressing mutated HTT, we use reduced-representation bisulfite sequencing (RRBS) to map sites of DNA methylation in cells carrying either wild-type or mutant HTT.  We find that a large fraction of the genes that change in expression in the presence of mutant huntingtin demonstrate significant changes in DNA methylation.  Regions with low CpG content, which have previously been shown to undergo methylation changes in response to neuronal activity, are disproportionately affected.  Based on the sequence of regions that change in methylation, we identify AP-1 and SOX2 as transcriptional regulators associated with DNA methylation changes, and we confirm these hypotheses using genome-wide chromatin immunoprecipitation (ChIP-Seq).  Our findings suggest new mechanisms for the effects of polyglutamine-expanded HTT.  These results also raise important questions about the potential effects of changes in DNA methylation on neurogenesis and at later stages, cognitive decline in Huntington’s patients.

overall_design: RRBS in STHdhQ7/Q7 and STHdhQ111/Q111 cells

middle: W

first: Ernest

last: Fraenkel


title: Extensive changes in DNA methylation are associated with expression of mutant huntingtin [mRNA-seq]

overall_design: mRNA-seq in STHdhQ7/Q7 and STHdhQ111/Q111 cells


title: Expression data from 0.15M and 0.7M-fed wild-type and ChREBP mutant, third instar Drosophila larval fat bodies (FBs)

city: Saint Louis

first: Thomas

middle: John

last: Baranski

state: MO

address: 660 S. Euclid Ave. Box 8127

institute: Washington University School of Medicine

summary: Chronic high sugar feeding induces obesity, hyperglycemia, and insulin resistance in flies and mammals. These phenotypes are controlled by the fat body, a liver- and adipose- like tissue in Drosophila flies. To gain insight into the mechanisms underlying the connection between diet and insulin sensitivity, we used Illumina RNA-seq to profile gene expression in fat bodies isolated from chronically high sugar fed, wandering (post-prandial) third instar wild type larvae w(L3). These data were compared to control-fed wild-type wL3 fat bodies as well as those expressing transgenic interfering RNA (i) targeting CG18362 (Mio/dChREBP) in the fat body on both diets.

overall_design: Female VDRC w1118, cgGAL4, UAS-Dcr2 or UAS-ChREBPi(52606), cgGAL4, UAS-Dcr2 wandering third instar larvae were fed control (0.15M) or high (0.7M) sucrose and fat bodies isolated for RNA extraction.

first: Michael

middle: R

last: Brent

first: Laura

last: Musselman


title: Extensive changes in DNA methylation are associated with expression of mutant huntingtin [MeDIP-seq]

overall_design: MeDIP-seq in STHdhQ7/Q7 and STHdhQ111/Q111 cells


title: Identification of in vivo, conserved, TAF15 RNA binding sites and the impact of TAF15 on the neuronal transcriptome

first: Manolis

last: Maragkakis

summary: TAF15, an RNA binding protein was recently implicated in Amyotrophic Lateral Sclerosis (ALS). ALS is a fatal neurodegenerative disease. We report the identification of  the conserved neuronal RNA targets of TAF15 and the assessment of the impact of TAF15 depletion on the neuronal transcriptome. Our study uncovers regulation of splicing of sets of neuronal RNAs encoding proteins with essential roles in synaptic activities including glutamergic receptors such as zeta-1 subunit of the glutamate N-methyl-D-aspartate (NMDA) receptor (Grin1).

overall_design: Identification of TAF15 neuronal targets using normal human brain samples and mouse neurons.  Mouse background: E14Tg2a.4 wildtype cells derived from 129P2/OlaHsd.

first: Fadia

last: Ibrahim

first: Panagiotis

last: Alexiou

first: Margaret

middle: A

last: Maronski

first: Marc

last: Dichter

first: Zissimos

last: Mourelatos


title: Deep sequencing reveals abundant non-canonical onco-retroviral microRNAs in B-cell leukemia/lymphoma

city: Bruxelles

first: Nicolas

last: Rosewick

address: 121 Boulevard de Waterloolaan

department: Insitut Jules Bordet

country: Belgium

institute: Université Libre de Bruxelles

summary: Viral tumor models have significantly contributed to our understanding of oncogenic mechanisms. How transforming delta-retroviruses induce malignancy however remains poorly understood, especially as viral mRNA/protein are tightly silenced in tumors. Here, using deep sequencing of broad windows of small RNA sizes in the Bovine Leukemia Virus ovine model of leukemia/lymphoma, we provide evidence of the production of non-canonical Pol III-transcribed viral microRNAs in leukemic B-cells in the complete absence of Pol II 5' LTR-driven transcriptional activity. Processed from a cluster of five independent self-sufficient transcriptional units located in a proviral region dispensable for in vivo infectivity, BLV microRNAs represent ~ 40 % of all microRNAs in both experimental and natural malignancy. They are conserved across tumors and associate with Argonautes, consistent with a critical function in silencing of important cellular and/or viral targets. BLV microRNAs are strongly expressed at pre-leukemic stages and remain at high levels in malignant cells despite the absence of structural and regulatory gene expression, suggesting a key role in tumor onset and progression.

overall_design: Identification of small RNA populations in BLV-induced leukemia

first: Keith

last: Durkin

first: Mélanie

last: Momont

first: Haruko

last: Takeda

first: Florian

last: Caiment

first: Yvette

last: Cleuter

first: Céline

last: Vernin

first: Franck

last: Mortreux

first: Eric

last: Wattel

first: Arsène

last: Burny

first: Michel

last: Georges

first: Anne

last: Van den Broeke


title: Identification and Analysis of Red Sea Mangrove (Avicennia marina) microRNAs by High-Throughput Sequencing and their Association with Stress Responses

status: Public on Jan 23 2013

city: Thuwal

first: Pugalenthi

last: Ganesan

address: Ibn AlHaythamm Bldg

department: Division of Biological and Environmental Sciences and Engineering

country: Saudi Arabia

institute: king abdullah university of science and technology

summary: we used high-throughput Illumina Genome Analyzer IIx (GAIIx) technology to sequence the small RNA transcriptomes of the mangrove species, Avicennia marina. Based on sequence similarity or the secondary structure of precursors, we have identified 193 conserved miRNAs and 26 novel miRNAs in the small RNA transcriptome of Avicennia marina.

overall_design: 1 sample

first: Basel

last: Khraiwesh

first: Ganesan

last: Pugalenthi

first: Nina

middle: V

last: Fedoroff


title: Analysis of TF binding sites and histone modification in IRF8-induced monocyte differentiation

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

summary:
Chromatins were prepared from myeloid progenitor cell line Tot2 cells transduced with retrovirus for control MSCV or MSCV-IRF8. Chromatin immunoprecipitation (ChIP) was carried out by using anti-IRF8 antibody, anti-PU.1 antibody or anti-histone H3K4me1 antibody.
ChIP-Seq peaks were identified using the FindPeaks tool in the HOMER package or SICER with input DNA tags as background distribution.
Potential IRF8-direct target genes were identified based on ChIP-Seq and the alteration of expression by IRF8-induction.

overall_design: Examination of 2 transcription factor occupancy and 1 histone modifications in myeloid progenitor cells and monocyte-like cells differetiated by IRF8 expression

first: Akira

last: Nishiyama


title: Quality evaluation of Methyl Binding Domain based kits for enrichment DNA-methylation sequencing

city: Ghent

first: Tim

last: De Meyer

address: Coupure Links 653

department: Dept. of Mathematical Modelling, Statistics and Bioinformatics

institute: Ghent University

summary: Purpose: to compare different Methyl Binding Domain (MBD) based kits for DNA-methylation sequencing using Reduced Representation Bisulfite Sequencing (RRBS) data for validation, and to determine whether data quality can also be derived from inherent sequence data characteristics

overall_design: MBD-seq using 5 different kits (MethylCap, MethylCollector, MethylCollector Ultra, MethylMiner, MethylMagnet) was applied on 3 commonly used cell lines (DU145, HCT15, PC3), for which also RRBS data were generated.


title: Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

status: Public on Jan 22 2013

city: Oxford

first: David

last: Sims

address: Parks Road

department: MRC Functional Genomics Unit

country: United Kingdom

institute: University of Oxford

summary: Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation. In lower vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates.  Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution.

sample_organism:
Danio rerio
Xenopus tropicalis
Gallus gallus
Ornithorhynchus anatinus
Homo sapiens
Mus musculus
Anolis carolinensis

overall_design: Bio-CAP was used to identify non-methylated regions of the genome in seven diverse vertebrates (human, mouse, platypus, chicken, lizard, frog and zebrafish) across a number of tissues.

first: Hannah

last: Long

first: Chris

last: Ponting

first: Robert

last: Klose


city: Copenhagen

first: Johannes

middle: Eichler

last: Waage

address: Ole Maaløesvej 5

department: Biotech Research and Innovation Center

country: Denmark

institute: University Of Copenhagen

summary: Temporal mapping of C/EBPα and –β binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries.

overall_design: Timeseries ChIP-seq of transcription factors C/EBPα and –β, and Pol II in time points 0, 3, 8, 16, 24, 36, 48, 168 hours after partial hepatectomy. Additionally, an IgG mock to 0h was sequenced, as well as the transcription factor Egr1.

first: Janus

middle: S

last: Jakobsen

middle: E

first: Nicolas

last: Rapin

first: Hanne

middle: C

last: Bisgaard

first: Fin

last: Larsen

first: Bo

middle: T

last: Porse


title: Deep Sequencing identifies regulated small RNAs in Dugesia japonica

city: Shenzhen

first: Maoshan

last: Chen

state: Guangdong

address: F2, Building 11, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics Center

institute: Beijing Genomics Institute

summary: We applied Illumina sequencing to identify microRNAs (miRNAs) and piwi-interacting small RNAs (piRNAs) in Dugesia japonica. Dugesia were cut up after seven day’s starvation. DJ1 is the whole Dugesia body, DJ2 is the head part, DJ3 is the tail part, DJ4 is the left part and DJ5 is the right part. Total RNA was extracted by Trizol, and preserved in ethanol, stored at -80°C until further use.

overall_design:
5 samples examined：DJ1,DJ2,DJ3,DJ4,DJ5.
SRA study (not submitted by GEO): SRP017693

first: Zhenbiao

last: Xu

first: Zhonggan

last: Ren


title: Extensive changes in DNA methylation are associated with expression of mutant huntingtin

first: Christopher

last: Ng

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

overall_design: Refer to individual Series


title: NKX2-1 occupancy in human lung adenocarcinoma cell lines

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To better understand how genomic alterations of NKX2-1 drive tumorigenesis, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma, and analyzed DNA binding sites of NKX2-1 by genome-wide chromatin immunoprecipitation from NKX2-1-amplified human lung adenocarcinoma cell lines.  Combining these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1, in addition to consensus binding motifs including a nuclear hormone receptor signature and a Forkhead box motif in NKX2-1-bound sequences.  RNA interference analysis of NKX2-1-amplified cells compared to non-amplified cells demonstrated that LMO3 mediates cell proliferation downstream of NKX2-1; cistromic analysis that NKX2-1 may cooperate with FOXA1.  Our findings provide new insight into the transcriptional regulatory network of NKX2-1 and suggest that LMO3 is a transducer of lineage specific cell survival of NKX2-1-amplified lung adenocarcinomas.

overall_design: NKX2-1 ChIP-seq from three lung adenocarcinoma cell lines with amplification of NKX2-1


title: In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures [ChIP-Seq]

city: Singapore

first: Vibhor

last: Kumar

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

country: Singapore

institute: Genome Institute of Singapore

summary: The limited number of in vivo germ cells poses an impediment to genome-wide studies. Here, we applied a small-scale ChIP-Seq method on purified mouse fetal germ cells to generate genome-wide maps of four histone modifications (H3K4me3, H3K27me3, H3K27ac and H2BK20ac), facilitating the identification of active and repressed cis-regulatory elements in germ cells in vivo. Comparison of active chromatin state between somatic, embryonic stem cells (ESC) and germ cells revealed promoters and enhancers needed for stem cell maintenance and germ cell development. The nuclear receptor Nr5a2 motif is enriched at a subset of cis-regulatory regions and we confirm its role in germ cell differentiation. Interestingly, germ cells have comparatively more H3K27me3-marked sites that are absent in ESC and other somatic cell types. These repressed regions are enriched for retrotransposons and MHC genes and this indicates that these loci are specifically silenced in germ cells. Together, our study provides the first genome-wide histone modification maps of in vivo germ cells and revealed the molecular chromatin signatures unique to germ cells.

overall_design: Germ cells were FACS-purified from gonadal single cell suspension based on Pou5f1-GFP expression. ChIP-seq of Histone modification was done for two timepoints in this study: E11.5 (male/female), E13.5 (male). For E13.5 timepoint, two biological replicates were analyzed. In order to validate small scale ChIP-seq method limited number of ES cells were used to check consistency of ChIP-seq data.

first: Jia-Hui

first: Huck-Hui


title: The transposable element composition of human lincRNAs reveals a role for HERVH elements to promote stem cell specific expression of lincRNAs

first: David

last: Kelley

state: MA

address: 7 Divinity Ave.

institute: Harvard University

summary: Numerous studies over the past decade have elucidated a substantial set of long intergenic noncoding RNAs (lincRNAs). It has since become clear that lincRNAs constitute an important layer of genome regulation across a wide spectrum of species. Yet, the factors governing their evolution and origins remain relatively unexplored. One possible factor that may have shaped lincRNA biology are transposable elements (TEs). Here we set out to comprehensively characterize the TE content of lincRNAs relative to genomic averages and protein coding transcripts. Our analysis of the TE composition across 9241 human lincRNAs revealed that, in sharp contrast to protein coding genes, a striking majority (83%) of lincRNAs contain a TE, and TEs comprise 42% of lincRNA transcript sequences. LincRNA TE composition varies significantly from genomic averages, being depleted of LI and Alu elements and enriched for a broad class of endogenous retroviruses (ERVs). Furthermore, specific TE families occur in biased positions and orientations within lincRNAs, particularly at their transcription start sites, suggesting a role in the origin of those lincRNAs. Finally, we find that TEs can drive gene expression regulation of lincRNAs—we observed a dramatic correlation between lincRNAs containing HERVH elements and almost exclusive expression in pluripotent cells. Conversely, those lincRNAs that are devoid of TEs are more highly expressed in testis. Collectively, TEs pervade lincRNAs and have shaped lincRNA evolution and function via bestowing tissue-specific expression from donated transcriptional regulatory signals.

overall_design: We extracted profiled the transcriptome expression polyadenylated mRNA-Seq.  We then used these to reconstruct the transcriptome using de-novo assemblers and identify long non coding RNAs and their expression.

first: John

middle: L

last: Rinn


title: TDP-43 Neurotoxicity in late D. melanogaster pupae

city: St Lucia

first: Marina

last: Naval Sanchez

address: Carmody Road 306

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

summary: The aim of this study is to understand the mechanisms of TDP-43 neurotoxicity. Here, we perform a RNA-Seq analysis in  TDP-43 gain-of-fucntion (GOF) , TDP-43 loss-of-function and wild-type late pupae heads (73-90 hours APF) and perform TDP-43 GOF vs wild type and TDP-43 LOF vs wild-type differential expression analysis to show that both mechanisms presents defects in ecdysone receptor (ECR)-dependeint transcriptional program switching, and strongly deregulate expression from the neuronal microtubule associated protien Map205.

overall_design: RNA-seq was performed in two wild-type D.melanogaster biological replicates (Canton S, w1118 ), four biological replicates for TDP-43 (LOF) with two distinct genotypes (dTDP-43Δ142/Df(2R)106,dTDP-43Δ23/Δ142 ) and two TDP-43 GOF biological replicates (act5c>dTDP-43 ).

first: Bart

last: Dermaut


title: Next-generation sequencing facilitates quantitative analysis of wild type and Bmp4f/f;Wnt1Cre tooth mesenchyme transcriptomes

city: Cincinnati

first: Shihai

last: Jia

state: Ohio

address: 3333 Burnet Ave

department: Division of Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Previous studies have suggested that Bmp4 is a key Msx1-dependent mesenchymal odontogenic signal for driving tooth morphogenesis through the bud-to-cap transition. Whereas the bud stage tooth developmental arrest in Msx1-/- mutant mice was accompanied by reduction in mesenchymal Bmp4 mRNA expression, we show that depleting functional Bmp4 mRNAs in the tooth mesenchyme, through neural crest-specific gene inactivation in Bmp4f/f;Wnt1Cre mice, caused mandibular molar developmental arrest at the bud stage but allowed maxillary molars and incisors to develop to mineralized teeth. We show that the Wnt inhibitors Dkk2 and Wif1 were much more abundantly expressed in the mandibular than maxillary molar mesenchyme in wildtype embryos and that Dkk2 expression was significantly unregulated in the tooth mesenchyme in Bmp4f/f;Wnt1Cre embryos. In addition, expression of Osr2, which encodes a zinc finger protein that antagonizes Msx1-mediated activation of odontogenic mesenchyme, is significantly upregulated in the molar mesenchyme in Bmp4f/f;Wnt1Cre embryos. Msx1 heterozygosity enhanced maxillary molar developmental defects whereas Osr2 heterozygosity rescued mandibular first molar morphogenesis in Bmp4f/f;Wnt1Cre mice. Moreover, in contrast to complete lack of supernumerary tooth initiation in Msx1-/-Osr2-/- mutant mice, Osr2-/-Bmp4f/f;Wnt1Cre compound mutant mice exhibit formation and subsequent arrest of supernumerary tooth germs that correlated with down regulation of Msx1 expression in the tooth mesenchyme. Taken together, our data indicate that, while reduction in mesenchymal Bmp4 expression alone could not account for the tooth bud arrest phenotype in Msx1-/- mutant mice, Bmp4 signaling synergizes with Msx1 and antagonizes Osr2 to activate mesenchymal odontogenic activity to drive tooth morphogenesis and sequential tooth formation.

overall_design: E13.5 mouse embryos tooth germs were microdissected by laser capture microdissection (LCM), and the mandibular molar and maxillary molar were separated. 3 pairs of control and mutant samples were pooled for the RNA extraction.

first: Rulang

last: Jiang


title: Distribution of Drosophila insulator proteins during interphase and mitosis

status: Public on Jan 21 2013

city: Atlanta

first: Elizabeth

last: Sung

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

summary: Here we compare the distribution of insulator proteins during interphase and mitosis.  We performed ChIP-seq analysis on purified populations of interphase and mitotic Kc cells, using antibodies against CP190, dCTCF, BEAF, and Su(Hw).

overall_design: Examination of 4 different insulator proteins during interphase and mitosis

first: Victor

middle: G

last: Corces


title: Dnmt3a protects active chromosome domains against cancer-associated hypomethylation

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

summary: The results of the study uncover conserved features of cancer methylomes and provide a mechanistic explanation for the tumor-promoting effects of Dnmt3a mutations.

overall_design: Whole genome methylation analysis of Mus musculus. Five samples were analyzed, one control sample containing normal healthy lung tissue, two samples containing big (WTB) or small (WTS) Dnmt3a WT tumors, two samples containing big (KOB) or small (KOS) Dnmt3a knock-out tumors

first: F

last: Lyko

first: R

last: Jaenisch


title: Activation of the chromatin-remodeling factor Smarca4/Brg1 cooperates with Olig2 to establish oligodendrocyte identity and control CNS myelination [ChIP-seq]

status: Public on Jan 20 2013

city: Chengdu

first: Yang

last: Yu

state: Si Chuan

address: Ren Min Nan road

institute: Si Chuan University

summary: We investigate the role of Brg1 and Olig2 during oligodendrocyte differentiation by combining gene conditional knockout and next generation sequencing technology. We generate genome-wide maps of RNA polymerase II (RPolII), Brg1 (Smarca4), Olig2 and histone modifications in primary rat oligodendrocyte precursor cells (iOLs), differentiating oligodendrocytes and mature oligodendrocytes.We found that Brg1 is intensely regulated by RPolII at the initiation of oligodedrocyte differentiation. The genomic distribution of Brg1 in differentiating oligodendrocytes is pre-directed by Olig2 in iOLs. The dynamic interaction of Brg1 and chromatin is correlate with the distinct stages of gene expression during maturation. Finally, we show that Brg1 and Olig2 localization predict critical genes controling CNS myeliantion. Our study represents the first detailed analysis of genomic landscape during the oligodendrocyte development and provides a framework for further understanding of molecular mechanisms underlying oligodendrocyte lineage progression.

overall_design: Genomic distribution of Brg1, Olig2, RPolII and three different histone modifications in three oligodendrocyte developemtal stages were examined using primary cells by ChIP-sequencing. Spinal cord mRNA profiles of 14-day old control and Brg1c/c;Olig1-Cre mice were generated by RNA-sequencing.

first: Qing

last: Lu

first: Ying

last: Chen


title: Differential gene expression and exon usage in bone marrow from RARS patients with SF3B1 somatic mutations compared to healthy patients.

status: Public on Jan 18 2013

city: Cleveland

last: Barnard

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic Foundation

summary: SF3B1, splicing factor 3b subunit 1 is a component of the RNA splicing machinery and it has been found to be highly mutated in refractory anemia with ring sideroblasts (RARS) and RARS associated with thrombocytosis (RARS-T). The aim of this study is to investigate the RNA splicing patterns in bone marrow from patients with SF3B1 somatic mutations compared to normal physiologic splicing. We compared the RNA splicing pattern as exon usage, differential gene expression, and pathway analysis with normal splicing

overall_design: mRNA profiles, as measured by RNA-Seq, in bone marrow derived mononuclear cells from 2 RARS patients with SF3B1 somatic mutations were compared to the mRNA profile of a normal donor.

first: Ramon

last: Tiu

first: Valeria

last: Visconte


title: PRDM14 Ensures Naïve Pluripotency through Dual Regulation of Signaling and Epigenetic Pathways in Mouse Embryonic Stem Cells

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Mouse embryonic stem cells (mESCs) fluctuate between a naïve inner cell mass (ICM)-like state and a primed epiblast-like state of pluripotency in serum, but are harnessed exclusively in a distinctive, naïve state of pluripotency that more faithfully captures the ICM state (the ground state) with inhibitors for mitogen-activated protein kinase (MAPK) and glycogen synthase kinase 3 pathways (2i). Understanding the mechanism ensuring the naïve states of pluripotency will be critical to realizing the full potential of ESCs. We show here that PRDM14, a PR domain-containing transcriptional regulator, ensures naïve pluripotency by a dual mechanism: Antagonizing fibroblast growth factor receptor (FGFR) signaling that is activated paradoxically by the core transcriptional circuitry for pluripotency and directs a primed state, and repressing de novo DNA methyltransferases that create a primed epiblast-like epigenome. PRDM14 exerts these functions by recruiting polycomb repressive complex 2 (PRC2) specifically to key targets and repressing their expression.

overall_design: ChIP-seq of PRDM14 and that of H3K27me3 and SUZ12 on Prdm14 wildtype and knockout ES cells

first: Masashi

last: Yamaji

first: Jun

last: Ueda

first: Katsuhiko

last: Hayashi

first: Hiroshi

last: Ohta

first: Kazuki

last: Kurimoto

first: Ryuichiro

last: Nakato

first: Yasuhiro

last: Yamada

last: Shirahige

first: Mitinori

last: Saitou


title: Centromere-Like Regions in Budding Yeast

city: New Haven

first: Raymond

last: Auerbach

state: CT

address: 266 Whitney Ave

institute: Yale University

summary: Accurate chromosome segregation requires centromeres (CENs), the chromosomal sites where kinetochores form, to bridge DNA and attach to microtubules.  In contrast to most eukaryotes, Saccharomyces cerevisiae possesses sequence-defined point centromeres.  Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) of four kinetochore components reveals regions of overlapping, extra-centromeric protein localization upon overproduction of the centromeric histone, Cse4 (CENP-A or CenH3). These identified sequences enhance proper plasmid and chromosome segregation, and are termed Centromere-like Regions (CLRs).  CLRs form in close proximity to S. cerevisiae CENs and share characteristics typical of point and regional centromeres.  CLR sequences are conserved among related budding yeasts, suggesting a role in vivo.  These studies provide new insights into the origin and evolution of centromeres.

overall_design: ChIP-Seq analysis of the kinetochore components Cse4, Mif2, Ndc10 and Ndc80 in budding yeast strains (Saccharomyces cerevisiae) with normal and elevated levels of Cse4

first: Philippe

last: Lefrancois

first: Christopher

middle: M

last: Yellman

first: G

last: Roeder

first: Michael

last: Snyder


title: Next-Generation Transcriptome Sequencing (RNA-Seq) of Human Endobronchial Biopsies: Asthma vs Controls

city: Amsterdam

first: Ching Yong

last: Yick

address: Meibergdreef 9

department: Respiratory Medicine

country: Netherlands

institute: Academic Medical Center

summary:
Rationale: The cellular and molecular pathways in asthma are highly complex. Increased understanding can be obtained by unbiased transcriptomic analysis (RNA-Seq).
Hypothesis and Aims: We hypothesized that the transcriptomic profile of whole human endobronchial biopsies differs between patients with asthma and controls. First, we investigated the feasibility to obtain RNA from whole endobronchial biopsies suitable for RNA-Seq. Second, we examined the difference in transcriptomic profiles between asthma and controls.
Methods: This cross-sectional study compared 4 steroid-free atopic asthma patients and 5 healthy non-atopic controls.  RNA of ASM from 4 endobronchial biopsies per subject was isolated and sequenced (GS FLX+, 454/Roche). Ingenuity Pathway Analysis was used to identify gene networks. Comparison of the numbers of reads per gene in asthma and controls was based on the Poisson distribution. At the current sample size the estimated false discovery rate was 4%.
Results: Yield of isolated RNA was 900-9,300ng. We identified 10,167 and 11,006 unique genes for asthma and controls, respectively. Forty-six genes were differentially expressed between asthma and controls, including pendrin, periostin, and BCL2. Ten gene networks involved in cellular morphology, movement, and development had an IPA network score ≥2.
Conclusion:RNA isolated from whole human endobronchial biopsies is suitable for RNA-Seq, showing different transcriptomic profiles between asthma and controls. Novel and confirmative genes were found to be linked to asthma. These results indicate that biological processes in the airways of asthma patients are differently regulated compared to healthy controls, which may be relevant for the pathogenesis and treatment of the disease.

overall_design: This cross-sectional transcriptomics study consisted of 2 visits. At visit 1, atopic asthma patients (n=4), and healthy non-atopic controls (n=5) were screened for eligibility to participate according to the in- and exclusion criteria. Spirometry and a methacholine bronchoprovocation test were performed. At visit 2, FEV1 reversibility was measured and 4 endobronchial biopsies per subject were collected during a bronchoscopy. Total RNA from whole endobronchial biopsies was collected. cDNA was prepared using the Ovation RNA-Seq System (NuGEN). RNA-Seq was performed using the GS FLX+ instrument (454/Roche). Sequence reads were mapped against the human genome (hg19; UCSC). Comparison of the numbers of reads per gene between asthma and healthy controls was based on the Poisson distribution.

first: Ching

middle: Y


title: A novel proteomic approach reveals GREB1 as an Estrogen Receptor co-factor

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Methods for identifying protein-protein interactions have mostly been limited to tagged exogenous expression approaches. We now establish a rapid, robust and comprehensive method for finding interacting proteins using endogenous proteins from limited cell numbers. We apply this approach called ‘Rapid IP-Mass Spectrometry of Endogenous proteins (RIME)’ to identify ER, FoxA1 and E2F4 interacting proteins in breast cancer cells. From small numbers of starting cells, we find a comprehensive collection of known ER, FoxA1 and E2F4 targets, plus a number of novel unexpected interactors. One of the most ER (and FoxA1) associated interactors is GREB1, an estrogen induced gene with almost no known function. We apply RIME, in parallel with ER ChIP-seq, to identify ER protein interactors and ER binding events from solid tumor xenografts, resulting in the validation of the ER-GREB1 interactions. Furthermore, we establish a method for identifying endogenous interacting proteins from solid primary breast cancer samples, whih we apply to validate ER interactions with GREB1 and additional co-factors. Mechanistically, we show that GREB1 is recruited with ER to the chromatin where it functions as an essential estrogen-mediated regulatory factor required for effective ER transcriptional activity. Our novel approach enables, for the first time, the ability for discovery and validation of protein-protein interactions in whole tissue and solid tumors, revealing significant insight into ER regulatory factors.

overall_design: Examination of ERGREB1 and E2F4 genomic binding patterns in cell line and xenograft tumour models

first: Hisham

last: Mohammed

first: Jason

last: Carroll

first: Suraj

last: Menon


title: Activation of the chromatin-remodeling factor Smarca4/Brg1 cooperates with Olig2 to establish oligodendrocyte identity and control CNS myelination

first: Yang

last: Yu

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Direct Conversion of Fibroblasts to Neurons by Reprogramming PTB-Regulated microRNA Circuits

status: Public on Jan 17 2013

city: La Jolla, San Diego

first: Jie

last: Huang

address: 9500 Gilman Drive, Room 231

department: Department of Cellular and Molecular Medicine

institute: UC San Diego

summary: The induction of pluripotency or trans-differentiation of one cell type to another  can be accomplished with cell lineage-specific transcription factors. Here we report that  repression of a single RNA binding protein PTB, which occurs during normal brain  development via the action of miR-124, is sufficient to induce trans-differentiation of  fibroblasts into functional neurons. Besides its traditional role in regulated splicing, we  show that PTB has a previously undocumented function in the regulation of microRNA  functions, suppressing or enhancing microRNA targeting by competitive binding on  target mRNA or altering local RNA secondary structure. A key event during neuronal  induction is the relief of PTB-mediated blockage of microRNA action on multiple  components of the REST complex, thereby de-repressing a large array of neuronal genes,  including miR-124 and multiple neuronal-specific transcription factors, in non-neuronal  cells. This converts a negative feedback loop to a positive one to elicit cellular  reprogramming to the neuronal lineage.

overall_design: Examination of PTB regulated  AGO2/microRNA targeting in Hela cells by CLIP-seq (two biological replicates) , paired-end RNA-seq (control and PTB knockdown) and 3’end stability RNA-seq  (control and PTB knockdown)

first: Yuanchao

last: Xue

first: Kunfu

last: Ouyang

first: Yu

last: Zhou

first: Hong

first: Gang

last: Wang

first: Qijia

last: Wu

first: Chaoliang

last: Wei

first: Yanzhen

last: Bi

first: Li

last: Jiang

first: Zhiqiang

last: Cai

first: Hui

last: Sun

first: Kang

last: Zhang

first: Yi

first: Ju

last: Chen

first: Xiang-Dong

last: Fu


title: Extensive changes in DNA methylation are associated with expression of mutant huntingtin [ChIP-seq]

first: Christopher

last: Ng

address: 77 Massachusetts Ave.

institute: Massachusetts Institute of Technology

summary: The earliest stages of Huntington’s disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin protein (HTT).  To explore the hypothesis DNA methylation may be altered in cells expressing mutated HTT, we use reduced-representation bisulfite sequencing (RRBS) to map sites of DNA methylation in cells carrying either wild-type or mutant HTT.  We find that a large fraction of the genes that change in expression in the presence of mutant huntingtin demonstrate significant changes in DNA methylation.  Regions with low CpG content, which have previously been shown to undergo methylation changes in response to neuronal activity, are disproportionately affected.  Based on the sequence of regions that change in methylation, we identify AP-1 and SOX2 as transcriptional regulators associated with DNA methylation changes, and we confirm these hypotheses using genome-wide chromatin immunoprecipitation (ChIP-Seq).  Our findings suggest new mechanisms for the effects of polyglutamine-expanded HTT.  These results also raise important questions about the potential effects of changes in DNA methylation on neurogenesis and at later stages, cognitive decline in Huntington’s patients.

overall_design: ChIP-seq for FRA-2, JUND, and SOX2 in STHdhQ7/Q7 and STHdhQ111/Q111 cells

first: Ernest

last: Fraenkel


title: CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression

city: San Francisco

first: Nevan

last: Krogan

address: 1700 4th Street

department: Cellular & Molecular Pharmacology

institute: University of California, San Francisco

first: Paul

middle: D

last: Hartley

middle: J


title: In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures

first: Vibhor

last: Kumar


title: Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary:
Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA-DNA interactions between the mitochondrial and nuclear genomes (Mito-nDNA) in Saccharomyces cerevisiae cells grown under three different metabolic conditions. The interactions that form between mitochondrial and nuclear loci are dependent on the metabolic state of the yeast. Moreover, the frequency of specific mitochondrial - nuclear interactions (i.e. COX1-MSY1 and Q0182-RSM7) showed significant reductions in the absence of mitochondrial encoded reverse transcriptase machinery. Furthermore, these reductions correlated with increases in the transcript levels of the nuclear loci (MSY1 and RSM7). We propose that these interactions represent an inter-organelle DNA mediated communication system and that reverse transcription of mitochondrial RNA plays a role in this process.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Genome-wide quantitative enhancer activity maps identified by STARR-seq

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: Genomic enhancers are important regulators of gene expression, but their identification is a challenge and methods depend on indirect measures of activity. We developed a method termed STARR-seq to directly and quantitatively assess enhancer activity for millions of candidates from arbitrary sources of DNA, enabling screens across entire genomes. When applied to the Drosophila genome, STARR-seq identifies thousands of cell type-specific enhancers across a broad continuum of strengths, linking differential gene expression to differences in enhancer activity and creating a genome-wide quantitative enhancer map. This map reveals the highly complex regulation of transcription, with several independent enhancers for both developmental regulators and ubiquitously expressed genes. STARR-seq can be used to identify and quantitate enhancer activity in other eukaryotes, including human.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: STARR-seq was performed in S2 and OSC cells with paired-end sequencing in two replicates and respective inputs. DHS-seq was done with single-end sequencing in two replicates for S2 and OSC cells. RNA-seq was performed with a strand-specific protocol using single-end sequencing in two replicates within S2 and OSC cells. STARR-seq was also performed in HeLa cells with single-end sequencing with a respective input.

first: Cosmas

last: Arnold

first: Christoph

last: Stelzer

first: Lukasz

last: Boryn

first: Martina

last: Rath

first: Alexander

last: Stark


title: Human subcutaneous adipose tissue gene expression (SOS Sib-pair study, offspring cohort)

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary:
Obesity has considerable effects on morbidity and mortality, and the prevalence of obesity has been increasing rapidly worldwide during the past two decades. Even if obesity affects the entire individual, adipose tissue plays a central role in the development of obesity. Expression profiling of adipose tissue may give insights into the mechanisms contributing to obesity and obesity-related disorders.

The Swedish Obese Subjects (SOS) Sib-Pair Study consists of 154 nuclear families with BMI-discordant sib pairs (BMI difference more than 10 kg/m2) resulting in a study population consisting of 732 subjects. The full SOS Sib-Pair study offspring cohort consists of 425 subjects. Microarray expression analysis in subcutaneous adipose tissue was performed in 375 subjects (262 women and 113 men) of the SOS Sib-Pair offspring cohort.

overall_design: Microarray expression analysis in subcutaneous adipose tissue was performed in women (n=262) and men (n=113) of the SOS Sib-Pair offspring cohort.

first: Peter

last: Jacobson

first: Margareta

last: Jernås

first: Johanna

last: Andersson-Assarsson

first: Per-Arne

last: Svensson

first: Lars

last: Sjöström

first: Lena

last: Carlsson


title: Inter- and intra- chromosomal interactions change on a global scale according to the metabolic regime employed by Saccharomyces cerevisiae

summary: Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA-DNA interactions between the mitochondrial and nuclear genomes (Mito-nDNA) in Saccharomyces cerevisiae cells grown under three different metabolic conditions. The interactions that form between mitochondrial and nuclear loci are dependent on the metabolic state of the yeast. Moreover, the frequency of specific mitochondrial - nuclear interactions (i.e. COX1-MSY1 and Q0182-RSM7) showed significant reductions in the absence of mitochondrial encoded reverse transcriptase machinery. Furthermore, these reductions correlated with increases in the transcript levels of the nuclear loci (MSY1 and RSM7). We propose that these interactions represent an inter-organelle DNA mediated communication system and that reverse transcription of mitochondrial RNA plays a role in this process.

overall_design: Genome Conformation Capture (GCC) has been performed on exponentially growing Saccharomyces cerevisiae cultures in glycerol lactate or galactose media. Paired end sequencing on an Illumina Genome Analyser was performed before the sequences were analysed by the propieatry software Topography 1.19. Inter- and intra- chromosomal interactions were mapped onto the S. cerevisiae S288 genome scaffold.

first: C

last: Rodley

first: J


title: ChIP-seq study of inheritence of Myc in Drosophila

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

summary: Myc is an important oncogene. It is considered as a transcription factor, but the function of Myc in normal or cancer cells have not been fully understood. In addition, Myc plays a role in cell proliferation and differentiation. It is also important for cell identity and stay on chromatin throughout the cell cycle. However, the inheritance of Myc is still a mystery. Here we study the function and inheritance of Myc in D. melanogaster by mapping the binding sites of Myc during interphase and mitosis using ChIP-seq.

overall_design: DNA sample of ChIP for Myc are collected from Kc cells in interphase or mitosis. Input sequences from previous study in the same cell type (GSM762848, GSM762849) are used as control.

first: Victor

last: Corces


title: Transcriptomic analysis of cellulolytic fungus Penicillium decumbens strains in response to different carbon sources

city: Qingdao

first: Guodong

last: Liu

state: Shandong

address: Binhai Road 72

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: Digital gene expression profiling (DGE) was used to compare the responses of Penicillium decumbens strains to different carbon sources including glucose, cellulose and cellulose-wheat bran. In both wild-type strain 114-2 and cellulase hyperproducing mutant JU-A10-T, transcription of lignocellulolytic enzymes were significantly up-regulated in the presense of cellulose. Relative to 114-2, coordinated up-regulation of lignocellulolytic enzymes and down-regulation of amylases and proteases were observed in JU-A10-T, especially in the cellulose-wheat bran medium. The expression of the principal β-glucosidase BGLI gene was not elevated in JU-A10-T, like the cellulases and hemicellulases, suggesting a different regulatory mechanism for this enzyme. Functional analysis of genes up-regulated in JU-A10-T relative to 114-2 also showed enrichment of proteins involved in amino acid synthesis, protein synthesis, and post-translational modification, compatible with the higher level of production of secreted proteins in JU-A10-T.

overall_design: Examination of differential gene expressions by Penicillium decumbens strains 114-2 and JU-A10-T grown in three different media.

first: Mei

last: Chen

first: Kai

last: Zheng

first: Yinbo

last: Qu


title: CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression [ChIP-seq]

first: Nevan

last: Krogan

summary:
The HIV-1 accessory protein Vif hijacks a cellular
Cullin-RING ubiquitin ligase, CRL5, to promote
degradation of the APOBEC3 (A3) family of restriction factors. Recently, the cellular transcription
cofactor CBFb was shown to form a complex with
CRL5-Vif and to be essential for A3 degradation
and viral infectivity. We now demonstrate that
CBFb is required for assembling a well-ordered
CRL5-Vif complex by inhibiting Vif oligomerization
and by activating CRL5-Vif via direct interaction.
The CRL5-Vif-CBFb holoenzyme forms a welldeﬁned heterohexamer, indicating that Vif simultaneously hijacks CRL5 and CBFb. Heterodimers of
CBFb and RUNX transcription factors contribute
toward the regulation of genes, including those with
immune system functions. We show that binding of
Vif to CBFb is mutually exclusive with RUNX heterodimerization and impacts the expression of genes
whose regulatory domains are associated with
RUNX1. Our results provide a mechanism by which
a pathogen with limited coding capacity uses one
factor to hijack multiple host pathways.

overall_design: Identification of RUNX1 binding sites in the Jurkat cell line

first: Paul

last: Hartley


title: The Saccharomyces cerevisiae genome is highly connected by inter- and intra- chromosomal interactions

first: Justin

last: O'Sullivan

overall_design: Genome Conformation Capture (GCC) has been performed on exponentially growing Saccharomyces cerevisiae cultures in glucose containing media. Paired end sequencing on an Illumina Genome Analyser was performed before the sequences were analysed by the propieatry software Topography 1.19. Inter- and intra- chromosomal interactions were mapped onto the S. cerevisiae S288 genome scaffold.


title: Stalled spliceosomes are a signal for RNAi-mediated genome defense

first: Phillip

middle: Anthony

last: Dumesic

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

summary: Using the yeast Cryptococcus neoformans, we describe a mechanism by which transposons are initially targeted for RNAi-mediated genome defense. We show that intron-containing mRNA precursors template siRNA synthesis. We identify a Spliceosome-Coupled And Nuclear RNAi (SCANR) complex required for siRNA synthesis and demonstrate that it physically associates with the spliceosome. We find that RNAi target transcripts are distinguished by suboptimal introns and abnormally high occupancy on spliceosomes. Functional investigations demonstrate that the stalling of mRNA precursors on spliceosomes is required for siRNA accumulation. Lariat debranching enzyme is also necessary for siRNA production, suggesting a requirement for processing of stalled splicing intermediates. We propose that recognition of mRNA precursors by the SCANR complex is in kinetic competition with splicing, thereby promoting siRNA production from transposon transcripts stalled on spliceosomes. Disparity in the strength of gene expression signals encoded by transposons versus genes offers an avenue for the evolution of genome defense.

overall_design: Small RNA profile of wild-type Cryptococcus neoformans was determined by deep sequencing using the Illumina SBS platform

first: Prashanthi

last: Natarajan

first: Changbin

first: Ines

last: Drinnenberg

first: Benjamin

last: Schiller

first: James

last: Thompson

last: Moresco

first: John

last: Yates III

first: David

middle: P

last: Bartel

first: Hiten

last: Madhani


title: Regional Differences in gene expression and promoter usage in aged human brains

status: Public on Jan 15 2013

first: Luba

last: Pardo

address: de Boelelaan

department: Clinical Genetics

institute: VU Medical Center

summary: Cap analysis of gene expression (CAGE) and massive parallel sequencing were used to profile the promoterome of aged human brains from five regions, namely: caudate, frontal cortex, hippocampus, putamen and temporal cortex.

overall_design: 25 RNA  libraries from post-mortem brain tissue (five caudate, five frontal, 5 hippocampus, 5 putamen, five temporal RNA libraries from seven individuals) were processed using CAGE protocol and CAGE tags derived from the 25 libraries were sequenced with Illumina.

first: Peter

last: Heutink

first: Piero

last: Carninci


title: Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (FAIRE-seq)

first: Iros

last: Barozzi

address: Borschkegasse 8a

institute: Medical University Vienna

summary: According to current models, transcription factors (TFs) activated by extracellular stimuli operate in the context of a pre-established enhancer repertoire induced and maintained by lineage-specific TFs. Here, we uncovered the existence of latent enhancers, defined as regions of the genome that in terminally differentiated cells are poorly accessible and lack the histone marks characteristic of enhancers, but readily acquire these features in response to extracellular cues. Stimulation of resting macrophages caused simultaneous binding of stimulus-activated TFs and lineage-determining TFs to these regions, enabling deposition of enhancer-specific features. Once unveiled, these enhancers did not return to a latent state even when stimulation ceased; instead, they persisted and mediated a faster and stronger response upon restimulation. We suggest that stimulus-specific expansion of the available cis-regulatory repertoire provides an epigenomic memory of the exposure to environmental agents.

overall_design: Formaldehyde-Assisted Isolation Of Regulatory Elements (FAIRE) followed by multiparallel sequencing was performed in untreated murine bone marrow-derived macrophages.

first: Renato

last: Ostuni

first: Viviana

last: Piccolo

first: Sara

last: Polletti

first: Serena

last: Ghisletti

first: Gioacchino

last: Natoli


title: Erf chromatin binding-sites in E13.5 mouse embryo fibroblasts

city: Oxford

first: Stephen

last: Taylor

address: Headington

institute: CBRG

summary: We show that reduced dosage of ERF, which encodes an inhibitory ETS transcription factor directly bound by ERK1/2 , causes complex craniosynostosis (premature fusion of the cranial sutures) in humans and mice. Features of this newly recognized clinical disorder include multiple suture synostosis, craniofacial dysmorphism, Chiari malformation and language delay. Mice with functional Erf reduced to ~30% of normal exhibit postnatal multisuture synostosis; by contrast, embryonic calvarial development appears mildly delayed. Using chromatin immunoprecipitation in mouse embryonic fibroblasts and high-throughput sequencing, we find that ERF binds preferentially to distal regulatory elements containing RUNX or AP1 motifs. This work identifies ERF as a novel regulator of osteogenic stimulation by RAS-ERK signaling, potentially by competing with activating ETS factors in multifactor transcriptional complexes.

overall_design: Examination of Erf binding site in E13.5 mouse embryo fibroblasts, growing in the presence or absence of serum for 4 hours

first: Andrew

last: Wilkie

first: George

last: Mavrothalasitis

last: Twigg


title: Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression

status: Public on Jan 16 2013

city: Stanford

middle: Acuña

last: Combs

address: Gilbert Rm 309, 371 Serra Mall

institute: Stanford University

summary: We sequenced mRNA from transverse slices of embryos at the blastoderm stage to determine genome-wide patterns of gene expression.

overall_design: mRNA from transverse sections of single D. melanogaster embryos was sequenced

first: Michael

middle: B

last: Eisen


title: Importance of Polη for damage-induced cohesion reveals differential regulation of cohesion establishment at the break site and genome-wide

city: Tokyo

first: Yuki

last: KATOU

address: 1-1-1 Yayoi,Bunkyo-ku

institute: Research assistant

summary: Correct chromosome segregation requires that sister chromatids are held together by the protein complex cohesin, from S phase until anaphase. This S phase established cohesion is, together with DSB recruitment of cohesin and formation of damage induced (DI) cohesion, also important for repair of DSBs. Eco1 is a common essential factor for S phase and DI-cohesion. The fission yeast Eco1ortholog, Eso1, is important both for S phase cohesion and for bypass of UV induced lesions, and is expressed as a fusion protein with Polη. The cohesion function has been attributed solely to Eso1 and the lesion bypass function to the Polη part of the protein. As we found the interaction between the two proteins intriguing we decided to look for a functional connection also in budding yeast. Indeed, despite being dispensable for S phase cohesion, budding yeast Polη is required for formation of DI genome-wide cohesion. However, Polη deficient cells are DSB repair competent, revealing differential regulation of DI-cohesion at the break and genome-wide. This finding challenges the importance of DI genome-wide cohesion for DSB repair, and based on our findings we suggest that S phase cohesion is not sufficient for correct chromosome segregation in the presence of DNA damage.

overall_design: Whole Genome binding of G2 expressed Scc1 in the presence and absence of Rad30.

first: Emma

last: Lindgren

first: Elin

last: Enervald


title: Genome-wide identification of Ikaros binding sites in primary pre-B cells

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary: Ikaros DNA binding proteins are important regulators of haematopoiesis and genetic deletion of Ikaros results in severe developmental disturbances, including delayed thymocyte differentiation and an early and complete block in B cell development. Although Ikaros ChIP-seq data are available for mouse thymocytes and human haematopoietic progenitors, it has not been achieved in B cell progenitors. The goal of this study was to identify Ikaros binding sites in pre-B cells to define Ikaros target genes which could explain the essential role of Ikaros proteins in B cell differentiation.

overall_design: We carried out chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) with antibodies to the C-terminus of endogenous Ikaros in primary pre-B cells isolated from mouse fetal livers.

first: Isabel

last: Ferreirós Vidal

first: Anna

last: Terry

first: Matthias

last: Merkenschlager


title: Activation of the chromatin-remodeling factor Smarca4/Brg1 cooperates with Olig2 to establish oligodendrocyte identity and control CNS myelination [RNA-seq]

city: Chengdu

first: Yang

last: Yu

address: Ren Min Nan road

institute: Si Chuan University

summary: Spinal cord mRNA profiles of 14-day-old control (Brg1c/+;Olig1-Cre) and Smarca4/Brg1 conditional knockout (Brg1c/c;Olig1-Cre) mice were generated by RNA-seq. Differential expressed genes are identified using Cuffdiff and validated with qPCR.

overall_design: Spinal cord mRNA profiles of 14-day old control and Brg1c/c;Olig1-Cre mice were generated by RNA-sequencing.

first: Qing

middle: R

last: Lu

first: Ying

last: Chen


title: Transcriptome sequencing of Chinese tree shrew, Tupaia belangeri chinensis

status: Public on Jan 14 2013

city: shenzhen

first: zhiyong

last: huang

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

institute: BGI-Shenzhen, Shenzhen 518083, China

summary: Deep sequencing of mRNA from Chinese tree shrew; Chinese tree shrew (Tupaia belangeri chinensis) is placed in Order Scandentia and embraces many unique features for a good experimental animal model. Currently, there are many attempts to employ tree shrew to establish model for a variety of human disorders such as social stress, myopia, HCV and HBV infection, and hepatocellular carcinoma .We present here a publicly available annotated genome sequence for Chinese tree shrew. Phylogenomic analysis of tree shrew and other mammalians highly supported its close affinity to primates. Characterization of key factors and signaling pathways of the nervous and immune systems in tree shrews showed that this animal had common and unique features, and had essential genetic basis for being a promising model for biomedical researches.

overall_design: Analysis of ploy(A)+ RNA of different specimens:kidney, pancreas, heart, liver, brain, testis and ovary form Chinese tree shrew

first: Yu

last: Fan

first: Zhiyong

last: Huang

first: Guojie

last: Zhang

first: Yonggang

last: yao


title: Nurr1 maintains fiber integrity and nuclear-encoded mitochondrial gene expression in dopamine neurons

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

summary: Nurr1 (Nr4a2, nuclear receptor subfamily 4 group A member 2) is needed for the development of ventral midbrain dopaminergic neurons, and has been associated with Parkinson's disease. We used mice where the Nurr1 gene is ablated by tamoxifen treatment selectively in dopaminergic neurons. As a control, we used tamoxifen-treated mice where Nurr1 is not ablated. By laser microdissection of neurons selected by their TH1 (Th1l, TH1-like homolog) gene expression, we selected dopaminergic neurons for RNA extraction and high-throughput mRNA sequencing, in order to identify genes regulated by Nurr1. We found the main functional category of Nurr1-regulated genes are the nuclear-encoded mitochondrial genes.

overall_design:
Dopaminergic neurons with or without Nurr1 knocked out.
TH-positive neurons were laser capture microdissected from cryostat coronal sections of the midbrain.

first: Banafsheh

last: Kadkhodaei

first: Thomas

last: Perlmann


title: Ikaros target genes in the mouse pre-B cell line B3

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

overall_design: Refer to individual Series


title: Genome-wide identification of Ikaros binding sites in pre-B cells

overall_design: We carried out chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) with antibodies to the C-terminus of endogenous Ikaros in B3 cells and with anti-haemagglutinin (HA) in B3 cells transduced with epitope-tagged HA-Ikaros.


title: Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq

city: East Lansing

first: Chad

middle: E.

last: Niederhuth

state: M

address: 612 Wilson Road

department: Plant Biology

institute: Michigan State University

summary: The receptor-like protein kinases encoded by HAESA (HAE) and HAESA-LIKE 2 (HSL2) are essential for floral organ abscission in Arabidopsis thaliana and the double hae hsl2 mutant fails to abscise. Expression of HAE and HSL2 is specific to Abscission Zone (AZ) cells and is higher in stage 15 flowers than in earlier developmental stages. By stage 16 floral organs have begun to abscise, suggesting that HAE HSL2 are most active in stage 15 flowers. Samples were enriched for AZ RNA by isolating RNA from flower receptacles, the region from the base of the flower to slightly above the base of attachment of the sepals, petals, and stamen. RNA-seq was then used to analyze and compare the transcriptomes of wild type and hae-3 hsl2-3 mutants. 2034 genes were differentially expressed with a False Discovery Rate adjusted p < 0.05, of which 349 genes 2 fold or greater change. Of these 349, 277 were lower in the mutant and 72 were higher. Differentially expressed genes with lower expression were enriched for hydrolytic enzymes, cell-wall modifying enzymes, and defense related genes. This suggests that HAE HSL2 signaling regulates gene expression of enzymes necessary for abscission.

overall_design: 6 samples were sequenced, 3 biological replicates of Col-0 wild type and 3 biological replicates of the hae-3 hsl2-3 double mutant. Samples were barcoded and all 6 samples multiplexed and sequenced on 3 lanes, each lane on a separate flow cell, of an Illumina HiSeq 2000.

first: Rahul

last: Patharkar

first: John

last: Walker


title: Effects of cocaine and withdrawal on the mouse nucleus accumbens transcriptome.

status: Public on Jan 10 2013

city: Farmington

first: Jodi

last: Eipper-Mains

address: 263 Farmington Ave.

department: Genetics & Developmental Biology

institute: University of Connecticut Health Center

summary: Genetic association studies, pharmacological investigations and analysis of mice-lacking individual genes have made it clear that Cocaine administration and Withdrawal have a profound impact on multiple neurotransmitter systems. The GABAergic medium spiny neurons of the nucleus accumbens (NAc) exhibit changes in the expression of genes encoding receptors for glutamate and in the signaling pathways triggered by dopamine binding to G-protein-coupled dopamine receptors. Deep sequence analysis provides a sensitive, quantitative and global analysis of the effects of Cocaine on the NAc transcriptome. RNA prepared from the NAc of adult male mice receiving daily injections of Saline or Cocaine, or Cocaine followed by a period of Withdrawal, was used for high-throughput sequence analysis. Changes were validated by quantitative polymerase chain reaction or Western blot. On the basis of pathway analysis, a preponderance of the genes affected by Cocaine and Withdrawal was involved in the cadherin, heterotrimeric G-protein and Wnt signaling pathways. Distinct subsets of cadherins and protocadherins exhibited a sustained increase or decrease in expression. Sustained down-regulation of several heterotrimeric G-protein β- and γ-subunits was observed. In addition to altered expression of receptors for small molecule neurotransmitters, neuropeptides and endocannabinoids, changes in the expression of plasma membrane transporters and vesicular neurotransmitter transporters were also observed. The effects of chronic Cocaine and Withdrawal on the expression of genes essential to cholinergic, glutamatergic, GABAergic, peptidergic and endocannabinoid signaling are as profound as their effects on dopaminergic transmission. Simultaneous targeting of multiple Withdrawal-specific changes in gene expression may facilitate development of new therapeutic approaches that are better able to prevent relapse.

overall_design: High-throughput sequence analysis of RNA prepared from the nucleus accumbens of adult male mice receiving daily injections of Saline or Cocaine, or Cocaine followed by a period of Withdrawal. Nucleus accumbens libraries were sequenced in nine lanes (three technical replicates per sample) on an Illumina GAIIx using a 37-cycle paired-end sequencing protocol. Replicates were analyzed for intra-sample disparity and read data from all three lanes were then merged into one composite data file per sample; intra-sample coefficient of determination, R2 ≥ 0.98. The composite file was used for subsequent analyses.

first: Drew

last: Kiraly

first: Michael

middle: O

last: Duff

last: Horowitz

first: C

last: McManus

first: Betty

middle: A

last: Eipper

first: Brenton

last: Graveley

first: Richard

last: Mains


title: Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell of origin model for prostate cancer heterogeneity

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary: We used RNA-seq to compare the expression profiles of mouse prostate tumors originated from epithelial basal cells to those originated from luminal cells. We next generated expression signatures for both basal and luminal origin tumors by comparison of tumor samples to their respective controls. By comparing luminal to basal signatures we identified a prognostic molecular signature for prostate cancer patient survival.

overall_design: Pten was deleted in prostate basal or luminal cells to induce tumor formation and tumor expression profiles were analyzed by RNA-seq.

first: Zhu

last: Wang

first: Sarah

middle: K

last: Bergren

first: Cory

last: Abate-Shen

first: R

last: Cardiff

first: Andrea

last: Califano

last: Shen


title: Saccharomyces cerevisiae 3' poly(A) site mapping

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented efficiency by using an on-cluster dark T-fill procedure on the Illumina sequencing platform. Our method outperforms former protocols in quality and throughput, and reveals new insights into polyadenylation in Saccharomyces cerevisiae.

overall_design: Experimental benchmark of five different protocols (3tfill, bpmI, internal, rnaseq and yoon) for genome-wide identification of polyadenylation sites in Saccharomyces cerevisiae and transcript quantification. RNA was extracted from WT cells grown in glucose (ypd) or galactose (ypgal) as carbon source. The same RNA was used for 3 independent library constructions (technical replicates, rep).

first: Stefan

last: Wilkening

first: Vicent

last: Pelechano

middle: I

first: Manu

last: Tekkedil

first: Simon

last: Anders

first: Vladimir

last: Benes

first: Lars

last: Steinmetz


title: Three acyltransferases and a nitrogen responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

summary: Three acyltransferases, DGAT1, DGTT1, and PDAT1, are induced by nitrogen starvation and are likely to have a role in TAG accumulation based on their patterns of expression. Each gene also shows increased mRNA abundance in other TAG-accumulating conditions (-S, -P, -Zn, -Fe). Insertional mutants, pdat1-1 and pdat1-2, accumulate 25% less TAG compared to the parent strain, D66+, which demonstrates the relevance of the trans-acylation pathway in Chlamydomonas. The biochemical functions of DGTT1 and PDAT1 were validated by rescue of oleic acid sensitivity and restoration of TAG accumulation in a yeast strain lacking all acyltransferase activity.  Time course analysis suggest than an SBP domain transcription factor protein, whose mRNA increases precede that of other genes like DGAT1, is a candidate regulator of the N-deficiency response. An insertional mutant, nrr1-1, accumulates only 50% of the TAG compared to the parental strain in N-starvation conditions and is unaffected by other nutrient stresses, suggesting the operation of multiple signaling pathways leading to stress-induced TAG accumulation.

overall_design: Sampling of Chlamydomonas 2137 cultivated in TAP, N-Free TAP or TAP with varying amounts of N.

first: N

last: Boyle

first: M

last: Page

first: B

last: Liu

first: I

last: Blaby

first: D

last: Casero

first: J

last: Kropat

first: S

last: Cokus

first: A

last: HongHermesdorf

last: Shaw

last: Karpowicz

last: Johnson

last: Grossman

first: C

last: Benning

last: Pellegrini

middle: S


title: 5'-Serial Analysis of Gene Expression of the transcriptomes of Coprinopsis cinerea during fruiting body initiation

city: Shatin

first: CHI KEUNG

last: CHENG

address: Rm 386, Science Center South Block

department: Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Large scale assessment of the transcriptomes of the vegetative mycelium and primordium will facilitate the generation of a more comprehensive picture of the fruiting process in basidiomycetes. We coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes (URGs) among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis  cinerea during fruiting body development. We evaluated the expression of >3,000 genes in the two respective growth stages and demonstrated that almost one-third of these genes were preferentially expressed in either stage, which implicated a significant transcriptomic switch during fruiting body initiation. We annotated >34,000 and >45,000 transcription start sites (TSSs) in the transcriptomes of Myc and S1-Pri respectively. We identified a wealth of potential URGs related to early fruiting events, although their functions and roles are not exactly known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea.

overall_design: 5'-SAGE analysis of the transcriptomes of vegetative mycelium and primordium of C. cinerea by 454 GS20 high-throughput pyrosequencer

first: Chi

last: Cheng

first: Chun

middle: H

last: Au

first: Patricia

last: Pukkila

first: Jason

middle: E

last: Stajich

first: Sarah

last: Wilke

first: Miriam

last: Zolan

first: Hoi

last: Kwan


title: Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza Sativa L.)

status: Public on Jan 09 2013

city: Guangzhou

first: Lujun

last: Yu

state: Guandong

address: xingangxilu 135

institute: Sun Yat-sen University

summary: Arsenic (As) is a carcinogenic metalloid that is a contaminant widely polluting rice paddy soils around the world. In order to gain better insight into molecular mechanism of rice exposed to As(III) stress, we used next-generation sequencing technology to acquire global transcriptome alteration and miRNA regulation in rice upon As(III) treatments.   Our results suggest time course and As(III)-dosing treatments were devised. Cluster analyses show that root and shoot samples were differentially grouped. For roots, sub-clusters were more distinct in the dosage course whereas for shoots they were most recognizable for the time course treatments.   Other than the significantly regulated gene expression in the heavy metal-responsive sulfur and glutathione metabolism pathways, the expression of genes related to heavy metal transportation, jasmonate biosynthesis and signaling pathways, lipid metabolism and gene transcription were sharply regulated, indicating that rice allocates energy and resources from growth to stress response under As(III) stress. In addition to the detection of previously identified stress-related miRNAs, we further discovered 36 new As(III)-responsive miRNAs.  These results expand our understanding of As(III) stress mechanism to the As(III)-responsive mRNA and miRNA transcriptomes, which provide a foundation for subsequent functional research.

overall_design: 10 mRNA samples examined   10 miRNA samples examined

first: Lu-jun

first: Ying-feng

last: Luo

first: Bin

last: Liao

first: Li-juan

last: Xie

first: Liang

last: Chen

first: Shi

last: Xiao

first: Li-jin

last: Tian

first: Song-nian

last: Hu

first: Wen-sheng

last: Shu


title: Circadian cycling of genome-wide histone methylation

status: Public on Jan 08 2013

city: Cambridge

first: Akhilesh

middle: Basi

last: Reddy

address: Hills Road

department: Institute of Metabolic Science

institute: University of Cambridge

summary: Daily (circadian) clocks are essential for regulating and coordinating physiology in mammals. Modulation of local chromatin structure has been shown for only a small number of genes, principally thought to be directly modulated by Clock-mediated histone acetylation. Here we show that genome-wide changes of active and suppressive histone marks control global chromatin architecture over the day and night.

overall_design: Examination of mouse liver tissue at 4 time-points around the clock in "free-running", continuous conditions (constant darkness, temperature and food available ad libitum).

first: Daniel

last: Turner


title: Cell of origin determines clinically relevant subtypes of MLL-rearranged AML

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

summary: MLL-fusion proteins can induce acute myeloid leukemias (AML) from either hematopoietic stem cells (HSC) or granulocyte macrophage progenitors (GMP), but it remains unclear if the cell of origin influences the biology of the resultant leukemia. MLL-AF9 transduced single HSC or GMP could be continuously replated, but HSC-derived clones were more likely than GMP-derived clones to initiate AML in mice. Leukemia stem cells derived from either HSC or GMP had a similar immunophenotype consistent with a maturing myeloid cell (LGMP). Gene expression analyses demonstrated that LGMP inherited gene expression programs from the cell of origin including high-level Evi-1 expression in HSC derived LGMP. The gene expression signature of LGMP derived from HSC was enriched in poor prognosis human MLL-rearranged AML in three independent data sets. Moreover, global 5’-mC levels were elevated in HSC-derived leukemias as compared to GMP-derived leukemias. This mirrored a difference seen in 5-mC between MLL-rearranged human leukemias that are either EVI1-positive or EVI1-negative. Finally, HSC derived leukemias were more resistant to chemotherapy than GMP-derived leukemias. These data demonstrate that the cell of origin influences the gene expression profile, the epigenetic state, and the drug response in AML, and that these differences can account for clinical heterogeneity within a molecularly defined group of leukemias.

overall_design: Differential DNA methylation between of LSC isolated from murine HSC and GMP derived AMLs

first: Andrei

last: Krivstov

first: Scott

last: Armstrong

first: Ari

last: Melnick


title: Transcriptomics studies in Eugenia uniflora

status: Public on Jan 07 2013

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

first: Frank

last: Guzman

first: Ana

last: Körbes

first: Rogério


title: Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells

first: Dario

last: Beraldi

address: Robinson Way

institute: Cambridge Research Institute


title: Genome-wide mapping of FOXM1 binding reveals co-binding with oestrogen receptor alpha in breast cancer cells (ChIP-seq)

summary: The forkhead transcription factor FOXM1 is a key regulator of the cell cycle and is overexpressed in cancer. Increased levels of FOXM1 are associated with both poor prognosis and oestrogen receptor (ERalpha) status in primary breast cancer. In this study, we map FOXM1 binding genome wide in both ERalpha-positive (MCF-7) and -negative (MDA-MB-231) breast cancer cells. We identify a common set of FOXM1 binding events at cell cycle-regulating genes, but in addition, in MCF-7 cells we find a high level of concordance with ERalpha-binding regions. FOXM1 binding at these co-binding sites is dependent on ERalpha binding, as depletion of ER protein levels reduced FOXM1 binding. FOXM1 interacts directly with both ERalpha co-activator CARM1 and is required for H3 arginine methylation at the ERalpha complex. Inhibition of FOXM1 activity with the ligand thiostrepton resulted in decreased FOXM1 binding at cca. 1400 sites genome wide and reduced expression of genes correlated with poor prognosis in ERalpha-positive tumour samples. These data demonstrate a novel role for the forkhead protein FOXM1 as an ERalpha cofactor and provide insight into the role of FOXM1 in ERalpha-positive breast cancer.

overall_design: The FOXM1-binding sites were mapped by ChIP-Seq in MCF-7 and MDA-MB-231 cells. Cells were treated either with thiostrepton, a FOXM1 inhibitor, or with DMSO (as control). Four replicates were performed in MCF7 cells and two replicates in MDA-MB-231 cells.

first: Deborah

last: Sanders

first: Caryn

last: Ross-Innes

first: Jason

last: Carroll

first: Shankar

last: Balsubramanian


title: Identification of miRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis [mRNA-seq]

summary: miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance without previous studies about its gene expression and regulation. To date, there is not miRNAs reported in species of Myrtaceae. A small RNA library was constructed to identify miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library and the data obtained was analysed using bioinformatics tools. From 14,489,131 clean reads, we obtained 1,852,722 small RNAs representing 45 known miRNA families that have been identified in other plant species. Further analysis using contigs assembled from Illumina mRNA sequencing of leaves from the same individual allowed the prediction of secondary structures of 25 known and 17 novel miRNAs. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. This study provide the first large scale identification of miRNAs and their potential targets of a species from Myrtaceae without previous genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights the miRNAs species-specific.

overall_design: mRNA profiles in 1 leaf library of Eugenia uniflora by deep sequencing (Illumina HiSeq2000)


title: In vivo nucleosome occupancy in yeast (MNase-seq)

status: Public on Jan 06 2013

city: Daejeon, Seoul

first: kwoneel

last: kim

address: Gwahangno, Yuseong gu

country: South Korea

institute: KAIST

summary: Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. Regulatory DNA elements are made accessible by nucleosome-depeleted states. Thus, nucleosome remodelling and modification should be intimately coupled with open chromatin formation and regulation. However, our knowledge of nucleosome regulation is largely limited to promoter regions, which comprise only a subset of all regulatory loci in the genome. In order to examine nucleosome patterns in open chromatin regions, we performed micrococcal nuclease (MNase) sequencing for a laboratory strain of yeast.

overall_design: Nucleosome occupancy profiled by Micrococcal nuclease (MNase) digestion

first: Sanjanaa

last: Nagarajan

first: Kwoneel

last: Kim

first: Jung-Kyoon

last: Choi


title: Polycomb Group proteins are retained at specific sites on chromatin in mitosis

status: Public on Jan 04 2013

first: Nicole

last: Follmer

address: 16 Divinity Avenue

country: USA

institute: Harvard University

summary: Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionation, we find PcG proteins associated with mitotic chromosomes in Drosophila S2 cells.  Genome-wide sequencing of chromatin immunoprecipitations (ChIP-SEQ) from mitotic cells indicates that Posterior Sex Combs (PSC) and Polyhomeotic (PH) are not present at well-characterized PcG targets including Hox genes in mitosis, but do remain at 11% of their interphase sites.  26% of interphase PSC sites overlap with recently described chromatin domain borders (Sexton et al., 2012), which are genomic regions characterized by low levels of long range contacts.  PSC and PH are preferentially retained at these sites in mitosis, including borders flanking both Hox gene clusters. We hypothesize that disruption of long range chromatin contacts in mitosis contributes to PcG protein release from most sites, while persistent binding at sites with minimal long range contacts may nucleate re-establishment of PcG binding and chromosome organization after mitosis.

overall_design: Drosophila S2 cells were colchicine-treated and stained with anti-H3S10p antibody and FACS sorted to give mitotic samples.  In parallel asynchronous Drosophila S2 cell cultures were stained for anti-H3 antibody and FACS sorted to give control samples.  Chromatin from each of these sorted populations was immunoprecipitated using biotinylated antibodies against PSC.  Two replicates of these samples are included.  A stable Drosophila S2 cell line expressing biotin-tagged PH was also FACS sorted as above to give mitotic and control samples, and streptavidin-coated beads were used to pulldown biotinlyated PH.  Inputs are included for each sample.

first: Ajazul

last: Wani

middle: J

last: Francis


title: Dual Functions of TAF7L in Adipocyte Differentiation

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

summary: The diverse transcriptional mechanisms governing cellular differentiation and development of mammalian tissue remains poorly understood. Here we report that TAF7L, a paralogue of TFIID subunit TAF7, is enriched in adipocytes and mouse white fat tissue (WAT). Depletion of TAF7L reduced adipocyte-specific gene expression and compromised adipocyte differentiation as well as WAT development. Ectopic expression of TAF7L in myoblasts reprograms these muscle precursors into adipocytes upon induction. Genome-wide mRNA-seq expression profiling and ChIP-seq binding studies confirmed that TAF7L is required for activating adipocyte-specific genes via a dual mechanism wherein it interacts with PPARγ at enhancers and TBP/Pol II at core promoters. In vitro binding studies confirmed that TAF7L forms complexes with both TBP and PPARγ. These findings suggest that TAF7L plays an integral role in adipocyte gene expression by targeting enhancers as a cofactor for PPARγ and promoters as a component of the core transcriptional machinery.

overall_design: Genome-wide mapping of TAF7L and additional factors, and mRNA-seq expression profiling prior to and following mouse adipocyte differentiation.

first: Haiying

last: Zhou

first: Yan

last: Li

first: Ivan

last: Grubisic

first: Zhengjian

last: Zhang

first: P

last: Wang

first: Michael

last: Eisen

first: Robert

last: Tjian