title: A Role for Small RNAs in DNA Double-Strand Break Repair

status: Public on Mar 27 2012

first: Yijun

last: Qi

address: #7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute of Biological Sciences

summary: Here we identify a novel class of small RNAs that are ~21-nucleotide in length and are produced from the sequences in the vicinity of DNA double strand break (DSB) sites in Arabidopsis and humans. We named them diRNAs for DSB-induced small RNAs. In Arabidopsis, the biogenesis of diRNAs requires the PI3 kinase ATR, RNA polymerase IV (Pol IV), and Dicer-like proteins. Mutations in these proteins as well as in Pol V cause significant reduction in DSB repair efficiency. diRNAs are recruited by Argonaute 2 (AGO2) to mediate DSB repair. In humans, knocking down Dicer or Ago2 causes a significant reduction in DSB repair. Our findings reveal a novel biological function for small RNAs in the DSB repair pathway. We propose that diRNAs may function as guide molecules for chromatin modifications or recruitment of repair complexes at DSB sites to facilitate repair.

sample_organism:
Arabidopsis thaliana
Homo sapiens

platform_organism:
Arabidopsis thaliana
Homo sapiens

overall_design: 28 samples from Arabidopsis thaliana in various genetic backgrounds and 5 samples from the human cells, small RNA sequencing

first: Wei

last: Wei

first: Zhaoqing

last: Ba

first: Yang

last: Wu


title: Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding [ChIP-Seq and DNAse-Hypersensitivity data]

status: Public on Mar 28 2012

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The t(8;21) translocation fuses the DNA binding domain of the hematopoietic master regulator RUNX1 to the ETO protein. The resultant RUNX1/ETO fusion protein is a leukemia-initiating transcription factor that interferes with RUNX1 function. The result of this interference is a block in differentiation and, finally, the development of acute myeloid leukemia (AML). To obtain insights into RUNX1/ETO-dependant alterations of the epigenetic landscape we measured genome-wide RUNX1- and RUNX1/ETO bound regions in t(8;21) cells and assessed to what extent the effects of RUNX1/ETO on the epigenome depend on its continued expression in established leukemic cells. To this end we determined dynamic alterations of histone acetylation, RNA Polymerase II binding and RUNX1 occupancy in the presence or absence of RUNX1/ETO using a knockdown approach. Combined global assessments of chromatin accessibility and kinetic gene expression data show that RUNX1/ETO controls the expression of important regulators of hematopoietic differentiation and self-renewal. We show that selective removal of RUNX1/ETO leads to a widespread reversal of epigenetic reprogramming and a genome-wide re-distribution of RUNX1 binding, resulting in the inhibition of leukemic proliferation and self-renewal and the induction of differentiation. This demonstrates that RUNX1/ETO represents a pivotal therapeutic target in AML.

overall_design: 14 samples include: RUNX1 Kasumi-1, RUNX1/ETO control, RUNX1/ETO siMM, RUNX1/ETO siRE, RUNX1_non-t(8;21), H3K9Ac_siMM, H3K9Ac_siRE, POLII_siMM and POLII_siRE ChIP-Seq samples, and Kasumi-1, non-t(8;21), t(8;21) paitent#1, t(8;21) paitent#2 and CD34 normal DNasel HS samples.

first: Anetta

last: Ptasinska

middle: A

first: Deepak

last: Mannari

first: Sally

middle: R

last: James

first: Dan

last: Williamson

first: Jenny

last: Dunne

first: Maarten

last: Hoogenkamp

first: Wu

last: Mengchu

first: Matthew

last: Care

first: Hesta

last: McNeill

first: Pierre

last: Cauchy

last: Cullen

first: Reuben

last: Tooze

middle: G

last: Tenen

first: Bryan

last: Young

first: Peter

middle: N

last: Cockerill

first: David

last: Westhead

first: Olaf

last: Heidenreich

first: Constanze

last: Bonifer


title: Deep sequencing the circadian and light-dependent transcriptome of Drosophila brain

city: Philadelphia

first: Michael

last: Hughes

state: PA

address: 421 Curie Bvd, Brb 835

country: USA

institute: UPenn

type: Expression profiling by high throughput sequencing

summary: Eukaryotic circadian clocks include transcriptional/translational feedback loops that drive 24-hour rhythms of transcription.These transcriptional rhythms underlie oscillations of protein abundance, thereby mediating circadian rhythms of behavior, physiology, and metabolism. Numerous studies over the last decade have employed microarrays to profile circadian transcriptional rhythms in various organisms and tissues. Here we use RNA sequencing (RNA-Seq) to profile the circadian transcriptome of *Drosophila melanogaster* brain from wild-type and *period*-null clock-defective animals. We identify several hundred transcripts whose abundance oscillates with 24-hour periods, including a number of non-coding RNAs (ncRNAs) that were not identified in previous microarray studies. Of particular interest are *U snoRNA host genes* (*Uhgs*), a family of cycling ncRNAs that encode the precursors of over 50 box C/D snoRNAs, key regulators of ribosomal biogenesis. Transcriptional profiling at the level of individual exons reveals alternative splice isoforms for many genes whose relative abundances are regulated by either *period* or circadian time, although the effect of circadian time is muted in comparison to that of *period*. Interestingly, *period* loss-of-function significantly alters the frequency of RNA editing at a number of editing sites, suggesting an unexpected link between a key circadian gene and RNA editing. We also identify tens of thousands of novel splicing events beyond those previously annotated by the modENCODE consortium, including several that affect key circadian genes. These studies demonstrate extensive circadian control of ncRNA expression, reveal the extent of clock control of alternative splicing and RNA editing, and provide a novel, genome-wide map of splicing in *Drosophila* brain.

overall_design: RNA-Seq transcriptional profiling of Drosophila brains from wildtype and period loss-of-function (per0) flies with time points taken over two days in constant darkness.  Time points at CT24, 28, 32, 36, 40, 44, 48, 52, 56, 60, 64, and 68. 10-12 brains per time point.

middle: E

first: Gregory

last: Grant

first: Christina

last: Pacquin

first: Jack

last: Qian

last: Nitabach


title: MicroRNA expression profiles in lung cancer tissues versus adjacent lung tissues using next-gen sequencing

status: Public on Mar 31 2012

city: Bronx

first: Miao

last: Shi

state: NY

address: 1301 Morris Park Ave

department: Pulmonary Medicine

institute: Albert Einstein College of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: MicroRNAs (miRNAs) are small noncoding RNAs about 22 nucleotides in length and regulate mRNA expression by binding to 3?UTR of mRNAs and causing translation repression or degradation of mRNAs. Recent studies have revealed that microRNAs play important regulatory roles in carcinogenesis. However, the complement of miRNAs involved in lung carcinogenesis and tumor biology is generally unknown. We used high-throughput sequencing technology to investigate miRNA expression profiles in a study of paired lung non-small cell carcinomas and remote noncancerous lung tissues.
Methods: Total RNA was isolated by Trizol from patient lung tissues, including 1 non-pair of macroscopic lung adenocarcinoma tissue, and 20 pairs of macroscopic lung adenocarcinoma tissues and corresponding paired noncancerous lung tissues from the same patients, 1 non-pair of noncancerous lung tissues of squamous cell carcinoma patient, and 10 pairs of squamous cell carcinoma and corresponding paired noncancerous lung tissues from the same patients. Small RNA library of each total RNA was constructed with Illumina?s Small RNA Sample Prep Kit, followed by high-throughput sequencing. Statistical differences in microRNA expression between groups were analyzed by GenePattern software.
Results: Using 2-fold threshold with FDR<0.05, there were ~90 miRNAs differentiated the lung cancers from nontumor lung tissues, both histologies.  (a) The sets of microRNAs differentiating adenocarcinoma from paired nontumor tissues are largely different from those differentiating squamous tumors. There were 40 upregulated and 23 downregulated microRNAs differentiating adenocarcinoma Tvs.NT .  For squamous cell, the numbers were 19 and 6, respectively.  (b) In common between the two tumor histologies, there were six common upregulated microRNAs (miR-21, 135b, 200a, 494, 708. 1259), and four common down-regulated microRNAs (miR-144, 184, 516a, 1251). (c) Comparing our 22 miRNAs in common with Yanaihara/Harris Cancer Cell 2006 using spotted microarrays, we found similar direction of change in 19/22.  (d) As a group, the top over-expressed miRNA in lung tumors (determined as fold change > 2, and comprising at least .01% of total miRNA) are able to predict mRNAs that are differentially expressed in those same samples (p=4.6x10^-6).
Conclusions: This effort represents one of the more comprehensive surveys of the lung tumor micronome. (i) Tumor microRNA complement differs from far-adjacent lung; (ii) Histologies differ in their overall, and tumor-distinctive microRNA complement; (iii) Statistical correlations of individual microRNA:mRNA (putative) pairing from the same tissue sets are pending.  (iv) Experimental confirmation of microRNA:mRNA targeting, using our microRNA affinity pull down assay is also pending.

overall_design:
Examination of different microRNA expression profiles between lung cancer tissues and adjacent lung tissues.
Our lung tissues were from 32 patients, including 21 adenocarcinoma patient (20 pairs of tumor and non-tumor and 1 non-pair tumor) and 11 squamous cell carcinoma patients (10 pairs of tumor and non-tumor and 1 non-pair non-tumor).

first: Saurabh

last: Gombar

first: Gaby

last: Marquardt

first: Tao

last: Wang

first: Yousin

last: Suh

first: Simon

middle: D

last: Spivack


title: Genome-wide maps of H3K4me2 and DNase I hypersensitivity sites in prostate cancer cell line LNCaP and breast cancer cell line MCF-7.

status: Public on Mar 25 2012

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

country: Canada

institute: UNIVERSITY HEALTH NETWORK

summary: We report the high-throughput profiling of histone modification and DNase I hypersensitivity sites in prostate cancer and breaset cancer cells. We found that while AR binding is associated with nucleosome depletion, ER binding is not. We showed that a quantitative measure of DNase I hypersensitivity changes is a powerful tool in indentifying transcription factor cistromes.

overall_design: Examination of histone modification marked nucleosomes and Dnase I hypersensitivity in prostate cancer and breast cancer cells with and without hormone treatment.

first: Housheng-Hansen

first: Cliff

last: Meyer

first: Myles

last: Brown

first: Xiaole

last: Liu


title: Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

city: Nijmegen

first: Arjen

last: Brinkman

address: NCMLS #274, Geert Grooteplein Zuid 30

department: Molecular Biology

country: Netherlands

institute: Radboud University, Nijmegen Center for Molecular Life Sciences

type: Methylation profiling by high throughput sequencing

summary: Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here we present sequential ChIP-bisulfite-sequencing (ChIP- BS-seq) as an approach to quantitatively assess DNA methylation patterns associated with chromatin modifications or chromatin-associated factors directly. A chromatin- immunoprecipitation (ChIP)-capturing step is used to obtain a restricted representation of the genome occupied by the epigenetic feature of interest, for which a single-base resolution DNA methylation map is then generated. When applied to H3 lysine 27 tri- methylation (H3K27me3), we found that H3K27me3 and DNA methylation are compatible throughout most of the genome, except for CpG islands, where these two marks are mutually exclusive. Further ChIP-BS-seq-based analysis in Dnmt triple- knock-out (TKO) embryonic stem cells revealed that total loss of CpG methylation is associated with alteration of H3K27me3 levels throughout the genome: H3K27me3 in localized peaks is decreased while broad local enrichments (BLOCs) of H3K27me3 are formed. At an even broader scale, these BLOCs correspond to regions of high DNA methylation in wild-type ES cells, suggesting that DNA methylation prevents H3K27me3 deposition locally and at megabase scale. Our strategy provides an unique way of investigating global interdependencies between DNA methylation and other chromatin features.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP (chromatin immunoprecipitation) is followed by bisulfite conversion and deep sequencing to directly assess DNA methylation levels in captured chromatin fragments (ChIP-BS-seq). We used ChIP-BS-seq to study the potential global cross-talk between H3K27me3 and DNA methylation, which are both linked to repression. First, we used capturing of methylated DNA, followed by bisulfite-deep sequencing (MethylCap-BS-seq). Genomic DNA isolated from normal and tumor colon tissues was used for MethylCap-BS-seq as well as for conventional MethylCap-seq experiments. Second, we performed ChIP-BS-seq on H3K27me3, using HCT116 colon carcinoma cells. Third, to further study the relevance of the observations, we generated genome-wide profiles for H3K27me3 and DNA methylation by conventional ChIP-seq and MethylCap-seq, and RNA-seq, respectively. Finally, we performed H3K27me3-ChIP-BS-seq and MethylCap-seq on wild-type mouse ES cells as well as Dnmt-triple-knockout (TKO) mouse ES cells.

first: Arie

middle: B

first: Hongcang

last: Gu

first: Stefanie

middle: J

last: Bartels

first: Yingying

last: Zhang

first: Filomena

last: Matarese

first: Femke

last: Simmer

first: Hendrik

last: Marks

first: Christoph

last: Bock

first: Andreas

last: Gnirke

first: Alexander

last: Meissner

last: Stunnenberg


title: Conserved and Essential Transcription Factors for Cellulase Gene Expression in Ascomycete Fungi.

status: Public on Apr 24 2012

city: Berkeley

first: N

middle: Louise

last: Glass

state: CA

address: 341 Koshland Hall, Univerisity of California

department: Plant and Microbial Biology

institute: UC Berkeley

summary: Transcriptional profiling with next-generation sequencing methods refined our understanding of the N. crassa transcriptional response to cellulose and demonstrated that the newly characterized transcription factors clr-1 and clr-2 were required for the bulk of that response including induction all major cellulase and some major hemicellulase genes.

overall_design:
N. crassa pregrown in Sucrose and transferred to Avicel (cellulose), Sucrose or media with no carbon added.  Biological triplicates used to identify differentially expressed genes in WT.  Single libraries for mutant strains identify which genes show deficient regulation in response to Avicel.

Note: Samples named "cdr1" and "cdr2" correspond to the genes clr-1 and clr-2 respectively.

first: Samuel

middle: T

last: Coradetti

first: James

middle: P

last: Craig

middle: L


title: A protective strategy against hyperinflammatory responses requiring the non-transcriptional actions of GPS2

status: Public on Mar 23 2012

city: Boston

first: Valentina

last: Perissi

state: MA

address: 72 E. Concord St

department: Department of Biochemistry

institute: Boston University School of Medicine

summary: The association between hyper-inflammatory states and numerous diseases is widely recognized, but our understanding of the molecular strategies that have evolved to prevent uncontrolled activation of inflammatory responses remains incomplete. Here, we report a critical, non-transcriptional role of GPS2 as a guardian against hyperstimulation of TNFA-induced gene program. GPS2 cytoplasmic actions are required to specifically modulate RIP1 ubiquitylation and JNK activation by inhibiting TRAF2/Ubc13 enzymatic activity. In vivo relevance of GPS2 anti-inflammatory role is confirmed by inhibition of TNFA target genes in macrophages and by improved insulin signaling in the adipose tissue of aP2-GPS2 transgenic mice. As the non-transcriptional role is complemented by GPS2 functioning as positive and negative cofactor for nuclear receptors, in vivo overexpression also results in elevated circulating level of resistin and development of hepatic steatosis. Together, these studies define GPS2 as a molecular guardian required for precise control of inflammatory responses involved in immunity and homeostasis.

overall_design: RNA-sequencing of polyA selected RNA molecules in 293T cells and ChIP-seq of GPS2, TBL1, and NCOR.

first: Dafne

last: Cardamone

first: Anna

last: Krones

first: Bogdan

last: Tanasa

first: Laura

last: Ricci

first: Kenneth

middle: H

last: Ohgi

first: Christopher

middle: K

first: Michael

last: Rosenfeld


title: High-throughput sequencing of endogenous small RNAs from rat vascular smooth muscle cells with and without Angiotensin II stimulation

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: Angiotensin II (Ang II)-mediated vascular smooth muscle cells (VSMC) dysfunction plays a critical role in cardiovascular diseases. However, the role of microRNAs (miRNAs) in this process is unclear. We used small RNA deep sequencing to profile Ang II-regulated miRNAs in rat VSMC and evaluated their role in VSMC dysfunction. Sequencing results revealed several Ang II-responsive miRNAs and bioinformatics analysis showed that their predicted targets can modulate biological processes relevant to cardiovascular diseases.

overall_design: Examined 4 samples of Rat VSMC. Control (without Ang II treatment) and 3 samples treated with Ang II for 1h, 3h, and 24h. Compared the changes in gene expression in Ang II treated samples relative to control samples.

first: Wen

last: Jin

first: Marpadga

last: Reddy

first: Zhuo

first: Rama

last: Natarajan


title: Integral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function

status: Public on Mar 29 2012

city: La Jolla

first: Ruth

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

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

overall_design: Refer to individual Series

first: Han

last: Cho

first: Ronald

middle: M

last: Evans


title: Time-course HoxB4 ChIP-Seq during HSC development from ES cells

first: Kai

last: Tan

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

summary: Efficient in vitro generation of hematopoietic stem cells (HSCs) from embryonic stem cells (ESCs) holds great promise for cell-based therapies of hematological diseases. To date, HoxB4 remains to be the most effective transcription factor (TF) whose over-expression in ESCs confers long-term repopulating ability to ESC-derived HSCs. Despite its importance, the components and dynamics of the HoxB4 transcriptional regulatory network is poorly understood, hindering efforts to develop a more efficient protocol for in vitro derivation of HSCs. Towards this goal, we performed global gene expression profiling and chromatin immunoprecipitation coupled with deep sequencing (ChIP-Seq) at four stages of the HoxB4-mediated HSC development. Joint analyses of ChIP-Seq and gene expression profiles unveil a number of global features of the HoxB4 regulatory network.

overall_design: Cells from three time points of the developmental processes were collected, including days 6, 16, and 26. Deep sequencing were done for both IP and input DNA from cells from each time point.


title: Essential role of EBF1 in B cell immunity by controlling the generation and function of distinct mature B cell types

status: Public on Mar 20 2012

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

summary: The transcription factor EBF1 is essential for lineage specification in early B cell development. Here we demonstrate by conditional mutagenesis that EBF1 was required for B cell commitment, pro-B cell development and subsequent transition to pre-B cells. Later in B cell development, EBF1 was essential for the generation and maintenance of distinct mature B cell types. Marginal zone and B-1 B cells were lost, whereas follicular and germinal center B cells were reduced in the absence of EBF1. Activation of the B cell receptor resulted in impaired intracellular signaling, proliferation and survival of EBF1-deficient follicular B cells. Immune responses were severely reduced upon Ebf1 inactivation, as germinal centers were formed but not maintained. ChIP- and RNA-sequencing of follicular B cells identified EBF1-activated genes that code for receptors, signal transducers and transcriptional regulators implicated in B cell signaling. Notably, ectopic expression of EBF1 efficiently induced the development of B-1 cells at the expense of conventional B cells. These gain- and loss-of-function analyses uncovered novel important functions of EBF1 in controlling B cell immunity.

overall_design: 29 samples (4 ChIP-seq,16 input, 9 RNA-seq), All ChIP-seq in 2 biological replicates, but EBF1 ChIP-seq Pro-B in 2 technical replicates; All RNA-seq in 2 biological replicates but RNA-seq mature B_FO B_Cd23-Cre Ebf1(fl/–). WT and experimental samples are provided.

first: Bojan

last: Vilagos

first: Martina

last: Minnich

first: Markus

last: Jaritz

first: Elin

last: Axelsson

first: Ivan

last: Bilic

first: Anja

last: Ebert

first: Roger

last: Revilla


title: Transcription factor binding in human embryonic stem cells

status: Public on Mar 17 2012

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Cohesin interacts with Mediator to link the enhancers and core promoters of actively transcribed genes bound by RNA polymerase II.  Activin signaling directs human embryonic stem cells to differentiate into endoderm.   ChIP-seq was performed to determine the gene targets of these factors in human embryonic stem cells.

overall_design: Human ES cells were grown without feeders using mTESR1.  ChIP-seq was performed against RNA Pol2, Cohesin subunits (Smc1 and Smc3) and IgG for cells grown in mTESR1.  Cells were differentiated into endoderm after resting for 24 hours in RMPI-B27 (0hr), and then treating with 50 ng/ml Activin A for two hours (2hr) and 48 hours (48hr).  DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing.

first: Alan

middle: C

last: Mullen

first: Jamie

last: Newman

first: Peter

last: Rahl


title: Mll1 regulates the downstream gene transcription activated by TNFa

city: Wuhan

first: Min

last: Wu

state: Hubei

address: Room 5005, College of Life Sciences, Wuhan University

department: College of Life Science

country: China

institute: Wuhan University

summary: Genes of mixed lineage leukemia family regulate transcription via methylating histone H3K4. we studied the role of MLL1 in innate immunity and found it selectively regulates the activation of NF-kB downstream genes mediated by TNFa.

overall_design: Mll1+/+ and Mll1-/- MEF cells were treated for 4 hr with 10ng/ml TNFa or control solution respectively. The same treatment were performed three times independently and the harvested cells of same treatment were mixed together and submitted for high throughput sequencing.

first: Xiang

last: Wang

first: Kun

last: Zhu

first: Yifang

last: Liao

first: An-Yuan

last: Guo

first: Lianyun

last: Li


title: ChIP-seq of chromatin modifications and factors associated with transcriptionally active regions of the genome in mES cells

middle: A

summary: Post-translational modification of histones are coupled to transcription where certain modifications are indicative of an active or inactive region of the genome.  Additionally, protein complexes can regulate the placement of nucleosomes across the genome and this influences the ability of DNA-binding proteins to interact with regions of the genome.  The datasets presented here are ChIP-seq datasets for chromatin modifications associated with active or poised genes (H2Bub, H3K9,K14Ac and H3K4me3).  Brg1 is a subunit of the SWI/SNF chromatin remodeling complex.

overall_design: An antibody specific to the chromatin modification or indicated factor was used to enrich for DNA fragments in murine embryonic stem cells. DNA was purified and prepared for Illumina/Solexa sequencing following their standard protocol.

first: Lee

last: Lawton

first: Warren

last: Whyte

first: Steve

last: Bilodeau


title: Gene expression profiling and ChIP-Seq study of HoxB4-mediated HSC development from ES cells

first: Kai

last: Tan


title: Functional Specialization of the Small Interfering RNA Pathway in Response to Virus Infection

status: Public on Mar 16 2012

city: Evanston

last: Carthew

state: IL

address: 633 Clark Street

institute: Northwestern University

summary: In Drosophila, the siRNA pathway is initiated when exogenous or endogenous double stranded RNA (dsRNA) is processed into siRNAs by Dicer-2 (Dcr-2) and a dsRNA-binding protein (dsRBP) cofactor called Loquacious (Loqs). The siRNAs are then loaded onto Argonaute-2 (Ago2) protein by the action of Dcr-2 with another dsRBP cofactor called R2D2. Loaded Ago2 executes the destruction of target RNAs that have sequence complementarity to the siRNA. Dcr-2, R2D2, and Ago2 have also been shown to be required for innate antiviral defense in Drosophila. However, the biogenesis of virus-derived siRNAs (vsiRNAs) and their targets in virus-infected cells remain unclear. Here, we analyzed the antiviral response in Drosophila by monitoring the replication of different RNA viruses and deep sequencing of small RNAs in infected animals. We show that vsiRNAs are generated by Dcr-2 processing of dsRNA formed during viral genome replication and transcription. These vsiRNAs then directly target viral transcripts but not genomes, to inhibit viral replication. The biogenesis of vsiRNAs was virtually independent of Loqs and R2D2. R2D2, however, was essential for sorting and loading of vsiRNAs onto Ago2 and effective silencing of viral RNA expression. Loqs was completely dispensable for silencing of viruses in contrast to its role in silencing of endogenous targets. Our results suggest the existence of a specific siRNA pathway triggered by viral infection independent of conserved dsRBP cofactors and separate from the endogenous pathway. Inhibition of virus replication resulting from direct injection of viral RNA into Drosophila embryos was also not dependent on Loqs, suggesting the distinction of the two pathways is not related to the mode of entry but recognition of intrinsic features of viral RNA or its mode of replication. We speculate that this unique framework might be necessary for a prompt and efficient antiviral response

overall_design: We analyzed the small RNA reponse to viral infection by deep sequencing of small RNA libraries from wild type and RNAi mutant adult flies infected with Sindbis birus and Vesicular Stomatatis virus.

first: Joao

last: Marques

middle: W


title: Recurrent amplifications of the histone methyltransferase SETDB1 in melanoma

summary: The most common mutation in human melanoma, BRAF(V600E), activates the serine/threonine kinase BRAF and causes excessive activity in the mitogen-activated protein kinase pathway. BRAF(V600E) mutations are also present in benign melanocytic naevi, highlighting the importance of additional genetic alterations in the genesis of malignant tumours. Such changes include recurrent copy number variations that result in the amplification of oncogenes. For certain amplifications, the large number of genes in the interval has precluded an understanding of the cooperating oncogenic events. Here we have used a zebrafish melanoma model to test genes in a recurrently amplified region of chromosome 1 for the ability to cooperate with BRAF(V600E) and accelerate melanoma. SETDB1, an enzyme that methylates histone H3 on lysine 9 (H3K9), was found to accelerate melanoma formation significantly in zebrafish. Chromatin immunoprecipitation coupled with massively parallel DNA sequencing and gene expression analyses uncovered genes, including HOX genes, that are transcriptionally dysregulated in response to increased levels of SETDB1. Our studies establish SETDB1 as an oncogene in melanoma and underscore the role of chromatin factors in regulating tumorigenesis.

overall_design: DNA was enriched from short-term cultures of cells and chromatin immunoprecipitations (ChIPs) were analyzed by Solexa sequencing. ChIPs were performed using an antibody against SetDB1 in WM853.2. Whole cell extracts are provided for WM262, WM451Lu and WM853.2 cells.


title: The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis and atopic dermatitis

city: Seoul

first: Sin-Gi

last: Park

address: 19, Sadang-ro, Dongjak-Gu

department: Department of Bioinformatics & Life science

country: South Korea

institute: Soongsil univ.

summary:
Psoriasis and atopic dermatitis (AD) are characterized by polarized CD4+ T cell responses. During the polarization of naïve CD4+ T cells, DNA methylation plays an important role in the regulation of gene transcription. In this study, we profiled the genome-wide DNA methylation status of naïve CD4+ T cells in patients with psoriasis or AD and healthy controls using a ChIP-seq method. As a result, twenty-six regions in the genome ranging in size from 10 to 70 kb were markedly hypomethylated in patients with psoriasis. These regions were mostly pericentromeric on 10 different chromosomes and overlapped with various strong epigenomic signals, such as histone modifications and transcription factor binding sites, that were observed in the ENCODE project. Gene-centric analysis indicated that the promoter regions of 124 genes on the X chromosome had dramatically elevated methylation levels in patients with psoriasis as compared to those from healthy controls (> 4-fold). Moreover, immune-related genes on the X chromosome had higher hypermethylation than other genes (P < 0.05). These findings imply that methylation changes in naïve CD4+ T cells may affect CD4+ T cell polarization, especially in the pathogenesis of psoriasis.

Keywords: Psoriasis, Atopic dermatitis, DNA methylation, naïve CD4+ T cells

overall_design:
Sample submission examines DNA methylation from human naive CD4+ T cells in patients with psoriasis and atopic dermatitis.

Note: Raw data available only for Sample GSM871288.

first: Ji

last: Han

first: Sin

middle: G

first: Jae

last: Bae

first: Jung

last: Choi

last: Lyu

first: Sung

first: Hei

middle: S

last: Kim

first: Young

first: Sang

first: Tae

middle: Y


title: Genome-wide map of HBO1  in cancer derived human cell line

status: Public on Mar 15 2012

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary: We used ChIP-seq technology in order to map chromatin binding sites of the HBO1 MYST complex in the RKO cell line. We obtained a significant enrichment of the HBO1 signal right after TSS regions of genes and also In the proximal promoter region, with no signal on TSS. This enrichment also correlates with gene expression level.

overall_design: HBO1 signal in RKO cell line.

first: Nikita

last: Avvakumov

first: Marie-Eve

last: Lalonde

first: Nehmé

last: Saksouk

first: Anne-Julie

last: Landry

first: Yannick

last: Doyon

first: Christelle

last: Cayrou

first: Geneviève

last: Robitaille

first: Darren

last: Richard

first: Xiang-Jiao

last: Yang

first: Tatiana

last: Kutateladze

first: Jacques

last: Côté


title: Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

first: Justin

last: Cotney

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

summary: The regulatory elements that direct tissue-specific gene expression in the developing mammalian embryo remain largely unknown. Although chromatin profiling has proven to be a powerful method for mapping regulatory sequences in cultured cells, chromatin states characteristic of active developmental enhancers have not been directly identified in embryonic tissues. Here we use whole transcriptome analysis coupled with genome-wide profiling of H3K27ac and H3K27me3 to map chromatin states and enhancers in mouse embryonic forelimb and hindlimb. We show that gene expression differences between forelimb and hindlimb, and between limb and other embryonic cell types, are correlated with tissue-specific H3K27ac signatures at promoters and distal sites. Using H3K27ac profiles, we identified 28,377 putative enhancers, many of which are likely to be limb-specific based on strong enrichment near genes highly expressed in the limb and comparisons with tissue-specific p300 sites and known enhancers. We describe a chromatin state signature associated with active developmental enhancers, defined by high levels of H3K27ac marking, nucleosome displacement, hypersensitivity to sonication, and strong depletion of H3K27me3. We also find that developmental enhancers exhibit components of this signature, including hypersensitivity, H3K27ac enrichment and H3K27me3 depletion, at lower levels in tissues in which they are not active. Our results establish histone modification profiling as a tool for developmental enhancer discovery, and suggest that enhancers maintain an open chromatin state in multiple embryonic tissues independent of their activity level.

overall_design: Examination of genome wide H3K27ac and H3K27me3 histone modifications and gene expression in early mouse embryonic limb tissue.

first: James

last: Noonan


title: Integral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function [ChIP_seq]

first: Ruth

last: Yu

summary: The circadian clock acts at the genomic level to coordinate internal behavioral and physiologic rhythms via the CLOCK-BMAL transcriptional heterodimer.  Although the nuclear receptors REV-ERBα and β have been proposed to contribute to clock function, their precise roles and importance remain unresolved.  To establish their regulatory potential we generated comparative cistromes of both Rev-erb isoforms, which revealed shared recognition at over ~50% of their total sites and extensive overlap with the master clock regulator Bmal.  While Rev-erbα has been shown to directly regulate Bmal expression, the cistromic analysis reveals a more profound connection between Bmal and Rev-erbα and β regulatory circuits than previously suspected. Genes within the intersection of the Bmal and Rev-erb cistromes are highly enriched for both clock and metabolic functions. As predicted by the cistromic analysis, dual depletion of Rev-erbα/β function by creating double-knockout mice (DKOs) profoundly disrupted circadian expression of core clock and lipid homeostatic genes. As a result, DKOs show strikingly altered circadian wheel-running behavior and deregulated lipid metabolism.  These data reveal an integral role of Rev-erbα/β in clock function as well as provide a cistromic basis for the integration of circadian rhythm and metabolism.

overall_design: Identification of Reverb alpha and Reverb beta binding sites in mouse liver at ZT8

first: Han

last: Cho

first: Ronald

last: Evans


title: Ribosome profiling of early zebrafish embryos -- miRNA-mediated regulation during embryogenesis causes translational repression before mRNA decay

city: New Haven

first: Antonio

middle: J.

last: Giraldez

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: MicroRNAs regulate gene expression through deadenylation, repression and mRNA decay. However, the contribution of each mechanism in non-steady-state situations remains unclear.  We monitored the impact of miR-430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR-430. Our results indicate that miR-430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation, and disrupting deadenylation using an internal poly(A) tail did not block target repression. Finally, we observe that ribosome density along the length of the target mRNA remains constant, suggesting that translational repression occurs by reducing the initiation rate rather than reducing elongation or causing ribosomal drop-off. In summary, our results show that miR-430 regulates translation initiation before inducing mRNA decay.

overall_design: Time course parallel ribosome profiling and input mRNA quantification in wildtype and MZdicer mutant embryos

first: Ariel

last: Bazzini

first: Miler

last: Lee


title: Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding

first: Salam

middle: Adli

last: Assi

address: IBR

institute: University of Birmingham

summary:
The t(8;21) translocation fuses the DNA binding domain of the hematopoietic master regulator RUNX1 to the ETO protein. The resultant RUNX1/ETO fusion protein is a leukemia-initiating transcription factor that interferes with RUNX1 function. The result of this interference is a block in differentiation and, finally, the development of acute myeloid leukemia (AML). To obtain insights into RUNX1/ETO-dependant alterations of the epigenetic landscape we measured genome-wide RUNX1- and RUNX1/ETO bound regions in t(8;21) cells and assessed to what extent the effects of RUNX1/ETO on the epigenome depend on its continued expression in established leukemic cells. To this end we determined dynamic alterations of histone acetylation, RNA Polymerase II binding and RUNX1 occupancy in the presence or absence of RUNX1/ETO using a knockdown approach. Combined global assessments of chromatin accessibility and kinetic gene expression data show that RUNX1/ETO controls the expression of important regulators of hematopoietic differentiation and self-renewal. We show that selective removal of RUNX1/ETO leads to a widespread reversal of epigenetic reprogramming and a genome-wide re-distribution of RUNX1 binding, resulting in the inhibition of leukemic proliferation and self-renewal and the induction of differentiation. This demonstrates that RUNX1/ETO represents a pivotal therapeutic target in AML.

This SuperSeries is composed of the SubSeries listed below.

first: Anetta

last: Ptasinska

first: Deepak

last: Mannari

first: Sally

last: James

first: Dan

last: Williamson

first: Jenny

last: Dunne

first: Maarten

last: Hoogenkamp

first: Wu

last: Mengchu

first: Matthew

last: Care

first: Hesta

last: McNeill

first: Pierre

last: Cauchy

last: Cullen

first: Reuben

last: Tooze

last: Tenen

first: Bryan

last: Young

first: Peter

middle: N

last: Cockerill

first: David

last: Westhead

first: Olaf

last: Heidenreich

first: Constanze

last: Bonifer


title: Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis

city: Atlanta

first: Tim

last: Read

address: 615 Michael Street, Suite 301

institute: Emory University

summary: Although genome-wide transcriptional analysis has been used for many years to study bacterial gene expression, many aspects of the bacterial transcriptome remain undefined.  A prominent example is antisense transcription, which has been observed in a number of bacteria, though the function of antisense transcripts, and their distribution across the bacterial genome, is still unclear.  Single-stranded RNA-seq results revealed a widespread and non-random pattern of antisense transcription covering more than two-thirds of the B. anthracis genome.  Our analysis revealed a variety of antisense structural patterns, suggesting multiple mechanisms of antisense transcription.  The data revealed several instances of sense and antisense expression changes in different growth conditions, suggesting that antisense transcription may play a role in the ways in which B. anthracis responds to its environment.  Significantly, genome-wide antisense expression occurred at consistently higher levels on the lagging strand, while the leading strand showed very little antisense activity. Intrasample gene expression comparisons revealed a gene dosage effect in all growth conditions, where genes farthest from the origin showed the lowest overall range of expression for both sense and antisense directed transcription.  Additionally, transcription from both strands was verified using a novel strand-specific assay. The variety of structural patterns we observed in antisense transcription suggests multiple mechanisms for this phenomenon, indicating that some antisense transcription may play a role in regulating the expression of key genes, while some may be due to chromosome replication dynamics and transcriptional noise.

overall_design: Four different growth conditions (cold challenge, ethanol challenge, osmotic challenge, control) with four replicates of one read on the bottom strand.

first: Karla

middle: D

last: Passalaqca

first: Nicholas

last: Bergman

first: Timothy


title: Ezh2 and H3K27me3 in cardiomyocytes

first: Michael

last: Hsing

address: 300 Longwood Ave.

department: Cardiology

institute: Children's Hospital Boston


title: Personal Omics Profiling Reveals Dynamic Molecular Phenotypes and Actionable Medical Risks

city: Stanford

first: Hogune

last: Im

address: 300 Pasteur Dr. Alway M308

institute: Stanford

summary: We have determined the whole genome sequence of an individual at high accuracy and performed an integrated analysis of omics profiles over a 1.5 year period that included healthy and two virally infected states. Omics profiling of transcriptomes, proteomes, cytokines, metabolomes and autoantibodyomes from blood components have revealed extensive, dynamic and broad changes in diverse molecular components and biological pathways that occurred during healthy and disease states. Many changes were associated with allele- and edit-specific expression at the RNA and protein levels, which may contribute to personalized responses. Importantly, genomic information was also used to predict medical risks, including Type II Diabetes (T2D), whose onset was observed during the course of our study using standard clinical tests and molecular profiles, and whose disease progression was monitored and subsequently partially managed. Our study demonstrates that longitudinal personal omics profiling can relate genomic information to global functional omics activity for physiological and medical interpretation of healthy and disease states.

overall_design:
Examination of blood component in 20 different time points over 1.5 years which includes 2 disease state and 18 healty state

Related exome studies at:
SRX083314
SRX083313
SRX083312
SRX083311

first: Rui

last: Chen

first: George

middle: I

last: Mias

first: Jennifer

last: Li-Pook-Than

first: Hugo

last: Lam

first: Lihua

last: Jiang

first: Rong

first: Elana

last: Miriami

first: Konrad

last: Karczewski

first: Manoj

last: Hariharan

first: Frederick

last: Dewey

first: Shin

last: Lin

first: Lukas

last: Habegger

middle: J

last: Clark

first: Sugnthi

last: Balasubramanian

first: Yong

last: Cheng

first: Maeve

last: O'Huallachain

first: Joel

last: Dudley

first: Sara

last: Hillemenyer

first: Rajini

last: Haraksingh

first: Donald

last: Sharon

first: Ghia

last: Euskirchen

first: Phil

last: Lacroute

first: Keith

last: Bettinger

first: Scott

last: Seki

first: Marco

last: Garcia

first: Michelle

last: Whirl-Carrillo

first: Mercedes

last: Gallardo

first: Maria

last: Blasco

last: Greenberg

first: Phyllis

last: Snyder

first: Teri

middle: E

last: Klein

first: Russ

middle: B

last: Altman

first: Atul

last: Butte

first: Euan

last: Ashley

first: Kari

last: Nadeau

first: Mark

last: Gerstein

first: Hua

last: Tang


title: A unique role of Cohesin-SA1 in gene regulation and development

city: Madrid

first: Silvia

last: Remeseiro

state: Madrid

address: Calle Melchor Fernandez Almagro 3

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

first: Ana

last: Cuadrado

first: Gonzalo

last: Gomez-Lopez

first: David

last: Pisano

last: Losada


title: Small RNAs in H9 embryonic stem cells

status: Public on Mar 21 2012

city: San Francisco

first: Yun

last: Choi

address: 513 Parnassus Ave.

department: Diabetes Center

institute: UCSF

summary: Non-templated 3'-end oligouridylation of RNA occurs in many species, including humans. Unlike the familiar phenomenon of polyadenylation, non-templated addition of uridines to RNA is poorly characterized in higher eukaryotes. Recent studies have reported non-templated 3'-end oligouridylation of small RNAs and mRNAs. Oligouridylation is involved in many aspects of microRNA biology from biogenesis to turnover of the mature species and it may also mark long mRNAs for degradation by promoting decapping of the protective 5'-cap structure. To determine the prevalence of oligouridylation in higher eukaryotes, we used next-generation sequencing technology to deeply examine the population of small RNAs in human cells. Our data revealed widespread non-templated nucleotide addition to the 3'-ends of many classes of RNA, with short stretches of uridine being the most frequently added nucleotide.

overall_design: Strand-specific RNA-Seq and paired-end sequencing was used to directly analyze the 3'-ends of small RNAs to identify post-transcriptional RNA processing.

first: Michael

middle: T

last: McManus


title: Integrated analysis of omics profiles

first: Hogune

last: Im

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


title: Profiling of small RNA populations in tricellular pollen of rice

city: Chengdu

first: Sheng-hua

last: Wang

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

summary: To investigate the potential function of miRNAs during male gametogenesis in rice, 13-40 nt RNA were extrected from tricellular pollen (TCP) for high-throughput sequencing. We identified 104 unique miRNAs from TCP library, 57 of which are novel derived from 39 pre-miRNAs.

overall_design: This subseries contain one small RNA sequencing data in tricellular pollen (TCP) stage.

last: Peng

first: Jun

last: Chun

first: Tao-bo

last: Ai

first: Yong-ao

last: Tong


title: MicroRNA Profiles and Their Control of Male Gametophyte Development in Rice

summary:
Plant microRNAs (miRNAs) act as negative regulators of gene expression by slicing target transcripts or inhibiting the translation, and a number of miRNAs play important roles in development. In order to investigate the potential function of miRNAs during male gametogenesis in rice, we obtained both gene and small RNA expression profiles by combining Affymetrix microarray and high-throughput sequencing technologies. In genome-scale, we compared arrays and sRNA-Seq datasets in different stages/organs of rice by applying computational and statistical approaches.

Subsequently, we identified 13363 expressed genes and 104 expressed unique miRNAs in pollen, thus, we constructed an interaction network of miRNA-target basing on two datasets. By employing enrichment analysis, we found miRNA-regulated targets involved in both up and down pathways, but predominantly in down pathways including 30 GO biological processes and 34 KEGG pathways. Our findings indicated that miRNAs plays a broad regulatory role during male gametophyte development in rice.

This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Oryza sativa
Oryza sativa Indica Group

overall_design: Refer to individual Series.


title: ChIP-seq of Ezh2 and H3K27me3 in E12.5 heart apex

last: Hsing

summary: Ezh2 and H3K27me3 binding sites in E12.5 heart apex

overall_design: PRC2 binding sites in wild type cardiomyocytes

first: He

last: Aibin

first: Pu

last: William


title: Polycomb-like 3 is a PRC2 component that supports embryonic stem cell self-renewal

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

summary: Polycomb repressive complex 2 (PRC2) trimethylates lysine 27 of histone H3 (H3K27me3), which regulates gene expression and controls diverse biological transitions in development, embryonic stem cell (ESC) differentiation, and cancer.  Here we show that Polycomb-like 3 (Pcl3) is a component of PRC2 that promotes H3K27 trimethylation in ESCs.  Chromatin immunoprecipitation and sequencing (ChIP-seq) revealed that Pcl3 co-localizes and recruits Suz12 to CpG islands.  Depletion of Pcl3 decreased Suz12 binding at over 60% of PRC2 targets, including many bivalent genes.  Pcl3 promotes ESC self-renewal as knockdown of Pcl3 increased spontaneous differentiation.  However, Pcl3 does not affect ESC pluripotency as teratomas derived from Pcl3-depleted ESCs were able to form all three germ layers.  Mutation of conserved residues within the Pcl3 TUDOR domain, a domain that recognizes methylated histones, compromises H3K27me3, suggesting that the TUDOR domain of Pcl3 is crucial for function.  Thus, Pcl3 is a component of PRC2 critical for histone methylation and PRC2 recruitment.

overall_design: We reverted a Suz12 gene trap (Suz12Gt/+) allele generated in a mouse ESC line to produce an allele that re-expresses Suz12 but that contains a loxP targeting site (Suz12Rev/+). Using a modified Floxin shuttle vector, we inserted an exon encoding amino acids 277-741 of Suz12 fused to a carboxy-terminal 6xHis-3xFlag TAP tag.  The resultant allele (Suz12Suz12TAP/+) expresses the full-length TAP-tagged Suz12 from the endogenous locus. We then reduced Pcl3 expression by siRNA or shRNA. Finally, we performed ChIP-Seq using the Flag tag of Suz12Suz12TAP/+ cells expressing either Pcl3 or control shRNA.  To perform Pcl3 ChIP-seq, we created ESC clones expressing Pcl3-shRNAs and a TAP-tagged Pcl3 not recognized by the Pcl3-shRNAs.

first: Julie

last: Hunkapiller

first: Yin

last: Shen

first: Aaron

last: Diaz

first: Gerard

last: Cagney

last: McCleary

first: Miguel

last: Ramalho-Santos

first: Nevan

last: Krogan

first: Bing

last: Ren

first: Jeremy

middle: F

last: Reiter


title: A unique role of Cohesin-SA1 in gene regulation and development [ChIP-Seq]

first: Silvia

last: Remeseiro

summary: Vertebrates have two cohesin complexes that consist of Smc1, Smc3, Rad21/Scc1 and either SA1 or SA2, but their functional specificity is unclear. Mouse embryos lacking SA1 show developmental delay and die before birth. Comparison of the genome wide distribution of cohesin in wild-type and SA1-null cells reveals that SA1 is largely responsible for cohesin accumulation at promoters and at sites bound by the insulator protein CTCF. As a consequence, ablation of SA1 alters transcription of genes involved in biological processes related to Cornelia de Lange syndrome (CdLS), a genetic disorder linked to dysfunction of cohesin. We show that the presence of cohesin-SA1 at the promoter of myc and of protocadherin genes positively regulates their expression, a task that cannot be assumed by cohesin-SA2. Cohesin binding pattern along some gene clusters is also affected by the lack of SA1, leading to dysregulation of the genes within. We hypothesize that impaired cohesin-SA1 function in gene expression underlies the molecular etiology of CdLS.

overall_design: Examination of genome wide distribution of cohesin subunits in wildtype and SA1-null cells

first: Ana

last: Cuadrado

first: Gonzalo

last: Gomez-Lopez

first: David

last: Pisano

last: Losada


title: RNA-seq analysis of Tetrahymena thermophila

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

summary: We present a comprehensive transcriptome of ciliate T. thermophila using the Illumina RNA-seq platform. The data was generated from the six mRNA samples of growth, starvation and conjugation of Tetrahymena. Despite an AT rich genome, there are about 124.6 million reads mapped to T. thermophila genome. Using these mapped reads, we have significantly improved the previous genome annotation and investigated the gene expression. Besides, our result also provided a comprehensive understanding of the alternative splicing in T. thermophila, and suggested the existence of the regulated unproductive splicing and translation (RUST) in the single-celled eukaryote.

overall_design: RNA-seq for six samples of Tetrahymena growth, starvation and conjugation.


title: Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia

status: Public on Mar 14 2012

city: New York

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

overall_design: Refer to individual Series


title: Core transcriptional regulatory circuit controlled by the tal1 complex in human t-cell acute lymphoblastic leukemia (Subseries)

first: Richard

last: Young

summary: The oncogenic transcription factor TAL1/SCL is aberrantly overexpressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing the importance of the TAL1-regulated transcriptional program in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, GATA3, ETS1 and RUNX1 in T-ALL cells. We find that TAL1 forms an interconnected auto-regulatory loop with its partners, which contributes to the sustained upregulation of its direct target genes. Importantly, we also find the MYB oncogenic transcription factor is directly activated by the TAL1 complex and positively regulates many of the same target genes, thus forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program.

overall_design:
Human T-ALL cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total TAL1 (Santa Cruz SC-12984), TCF12/HEB (Santa Cruz SC-357),TCF3/E2A (Santa Cruz SC-349X), LMO1 (Santa Cruz SC-10494), LMO2 (R&D Systems AF2726),  GATA3 (Santa Cruz SC-22206) and RUNX1 (Santa Cruz SC-8563). This represents the ChIP-seq portion of this dataset.
Human Jurkat cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total TAL1 (Santa Cruz SC-12984), TCF12/HEB (Santa Cruz SC-357),TCF3/E2A (Santa Cruz SC-349X), LMO1 (Santa Cruz SC-10494), GATA3 (Santa Cruz SC-22206) and RUNX1 (Santa Cruz SC-8563). This represents the ChIP-seq portion of this dataset.

first: Lee

last: Lawton


title: MicroRNA profiling of murine T lymphopoiesis

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

summary: Here we describe microRNA profiling of a single differentiation pathway from the stem cell through to terminally differentated mature cells.

overall_design: Populations corresponding to distinct stages in T lymphocyte development, from the hematopoietic stem cell-enriched Lin-Sca+Kit+ population through to mature CD4+ and CD8+ T cells were FACS-sorted to purity from the bone marrow and thymus of C57BL/6 mice. Total RNA was extract from each population from which microRNA sequencing libraries were constructed.

middle: M


title: Transcription-associated Loading of Condensin II on Chromosome Arms in Embryonic Stem Cells (nocodazole ChIP-Seq)

middle: A

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Vertebrate condensin I and II molecules are loaded onto the genome to mediate essential changes in chromosome condensation during mitosis, but it is not clear how the two forms of condensin become distributed on chromosomes.  We report here that condensin II, the form of condensin present in the nucleus throughout the cell cycle, is loaded at transcriptionally active promoters, migrates through these genes in a transcription-dependent fashion and accumulates in transcription termination regions during interphase.  During mitosis, condensin I is recruited to actively transcribed genes and replaces condensin II.  We conclude that the two forms of condensin are loaded at different times during the cell division cycle at the promoters of actively transcribed genes.

overall_design: ChIP-Seq data for Condensin II in v6.5 ESCs treated or not with nocodazole

first: Steve

last: Bilodeau

first: Jill

last: Dowen


title: RNA mapping of Drosha deficient cells

summary: Here we show the microRNA genes can been very large and displaying many summarizing structural characteristics

overall_design: MicroRNA biogenesis was ablated in CD4+ and CD8+ by deleted Rnasen gene (encoding Drosha). Poly A RNAs were extracted and analyzed by ultra high throughput sequencing


title: RNA mapping of Drosha deficient cells, chromatin maps of mature T cells, and miRNA profiling of lymphopoiesis


title: Genome wide mapping of gH2AX in quiescent and irradiation-induced senescent human fibroblasts

status: Public on Mar 13 2012

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

country: Italy

institute: Università vita e Salute Ospedale San Raffaele

summary: We observe preferential accumulation of gH2AX at chromosome ends upon irradiation

overall_design: comparison of quiescent vs senescent human fibroblasts

first: Fabrizio

last: Fagagna

first: Marzia

last: Fumagalli

first: Francesca

last: Rossiello

first: Davide

last: Cittaro


title: Genome-wide profiling of small RNAs in Arabidopsis seedlings under salt and cold stresses

status: Public on Mar 12 2012

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

summary: To identify novel miRNA and NAT-siRNAs that are associated with salt and cold stresses in Arabidopsis, we generated small RNA sequences from Arabidopsis plants under salt and cold stress treatments.

overall_design: Sequencing of small RNAs in Arabidopsis under salt, and cold stress conditions.

first: Blanca

last: Barrera-Figueroa

first: Viswanathan

last: Chinnusamy

first: Yunchao

last: Kan

first: Weixiong

last: Zhang

first: Hailing

last: Jin

first: Jian-kang

last: Zhu


title: Epigenetic dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: Studies on the epigenetic regulation of gene expression during germ cell development are still at the beginning stage. In the present study, we used our highly specific 5hmC-labeling and enrichment technique coupled with DNA deep-sequencing to profile the global 5hmC distribution in 8 serial stages of male germ cells during spermatogenesis, as well as in the the Sertoli cells (SE) which are the only somatic cell type inside seminiferous tubules. We analyzed the genomic distribution and dynamic changes of 5hmC during spermatogenesis. Moreover, to dissect the functional significance of 5hmC modifications for transcriptional regulation of gene expression, we also performed RNA-Seq transcriptome analysis in all of the 8 corresponding stages of male germ cells and found that 5hmC is positively correlated with gene expression.

overall_design:
RNA-seq: Examination of the transcriptomes during mouse spermatogenesis.
5hmC-seq: Identification of 5hmC enriched genmoic regions in mouse germ cell.

first: Wen

last: Lu

first: Fuchou

last: Tang

first: Shangying

last: Liao

first: Haiyun

last: Gan


title: Small RNA sequencing of melanoma samples to deduce microRNA expression profiles

city: Farmington

first: Sam

last: Dadras

address: Cell and Genome Science Building, 400 Farmington Ave.

department: Genetics and Cell Biology

institute: UCONN Health Center

summary: We report results on microRNA profiles revealing the distribution of "isomirs" of microRNA in a cancerous state. Deep sequencing was conducted at Stanford University and data analysis was conducted at the University of Connecticut Health Center.

overall_design: Small RNA profiling to deduce differential microRNA expression levels along various stages of melanoma. Deep sequencing was performed on formalin-fixed paraffin-embedded (FFPE) archived tissue samples, fresh frozen samples from melanomas, and cell lines.

first: Jim

last: Kozubek

first: Elizabeth

last: Fleming


title: A whole transcriptome approach to investigate the genes involved in permethrin resistance in the Southern house mosquito, Culex quinquefasciatus

city: Auburn

first: Nannan

state: AL

address: 301 Funchess Hall

department: Entomology

institute: Auburn University

summary: Illumina HiSeq 2000 was conducted on the mRNA fraction of fourth instar Cx. quinquefasciatus from a highly permethrin resistant strain (HAmCqG8) and its parental low resistance strain (HAmCqG0). After aligning reads to the Johannesburg genome using the GTF annotations file from Ensembl Metazoa, we found that 367 genes were upregulated in the high resistant strain and 3982 were downregulated. The upregulated genes were associated with cytochrome P450s and proteases while the downregulated genes were mostly found in the “no annotation” category for the Structural Classification of Proteins classifications for Cx. quinquefasciatus. This study identified the upregulated genes in the highly resistant HAmCqG8 strain that may be involved in resistance to permethrin.

overall_design: RNA Seq profiling of the mRNA of fourth instar HAmCqG0 and HAmCqG8 Cx. quinquefasciatus (whole insect pooled samples)

first: Lee


title: Genome-wide profiling of small RNAs in rice under abiotic stresses

first: Renyi

summary: To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in rice, we generated small RNA sequences from inflorescences from rice under control and under dought, salt, and cold stress treatments. Over 30 million reads were generated.

overall_design: sequencing of small RNAs in rice under control, drought, salt, and cold stress conditions.


title: Genome-wide maps of H3K4me3 and H3K27me3 in HY(Hwayong) and chd1(chr729) rice.

status: Public on Mar 10 2012

city: paris

first: yongfeng

last: hu

address: univercite paris-sud Bat 630

country: France

institute: IBP

summary: We report the application of CHIP-seq technology for high-throughput profiling of histone modifications in HY(Hwayong) and chd1(chr729). By obtaining about 12 million reads of sequence from chromatin immunoprecipitated DNA, we generated genome-wide H3K4me3 and H3k27me3 maps of HY(Hwayong) and chd1(chr729). We find that lysine 4 and lysine 27 trimethylation marked genes effectively losed in chd1 compared to HY.

overall_design: Examination of two histone modifications in two rice species.

first: Dengnian

first: Daoxiu

last: Zhou


title: Genome-wide profiling of small RNAs in Arabidopsis under abiotic stresses

last: Liu

summary: To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in Arabidopsis, we generated small RNA sequences from adult Arabidopsis plants under control and under dought, salt, and cold stress treatments. Over 23 million reads were generated.

overall_design: Sequencing of small RNAs in Arabidopsis under control, drought, salt, and cold stress conditions.

first: Blanca

first: Weixiong


title: ATRX-mediated chromatin association of histone variant macroH2A1 regulates alpha globin gene expression

status: Public on Mar 08 2012

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: The histone variant macroH2A generally associates with transcriptionally inert chromatin, however the factors that regulate its chromatin incorporation remain elusive. Here, we identify the SWI/SNF helicase, ATRX, as a novel macroH2A interacting protein. Unlike its role in assisting H3.3 chromatin deposition, ATRX acts as a negative regulator of macroH2A’s chromatin association. In human erythroleukemic cells deficient for ATRX, ChIP-sequencing studies reveal that macroH2A accumulates at the HBA gene cluster on the subtelomere of chromosome 16, coinciding with the loss of α globin expression. Collectively, our results implicate deregulation of macroH2A’s distribution as a contributing factor to the α thalassemia phenotype of ATRX syndrome.

overall_design: Mononucleosomes from K562 cells bearing integrated lentiviral shRNA constructs targeting either luciferase (shluc) or ATRX (sh92) were isolated and ChIP'd with mH2A1 antibody. DNA from shluc Input and the two mH2A1 ChIPs were isolated and sequenced on Illumina's Hiseq.

first: Kajan

last: Ratnakumar

first: Dan

last: Hasson


title: Genome-wide assay of Vezf1 and RNA Polymerase II binding

status: Public on Mar 09 2012

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

summary: The protein Vezf1 plays multiple roles important for embryonic development. In Vezf1-/- mouse embryonic stem (MES) cells our earlier data showed widespread changes in gene expression profiles, including decreased expression of the full length active isoform of Dnmt3b methyltransferase and concomitant genome wide reduction in DNA methylation.  Here we show that, in HeLaS3 cells, there is a strong genome-wide correlation between Vezf1 binding and peaks of elongating Ser2-P Pol ll, reflecting Vezf1 dependent slowing of elongation. In Wt MES cells the elongating form of RNA polymerase II accumulates near Vezf1 binding sites within the dnmt3b gene and at several other Vezf1 sites, and this accumulation is significantly reduced at these sites in Vezf1-/- MES cells.  Depending upon genomic location, Vezf1 mediated Pol II pausing can have different regulatory roles in transcription and splicing.   We find examples of genes in which Vezf1 binding sites are located near cassette exons, and in which loss of Vezf1 leads to a change in the relative abundance of alternatively spliced messages. We further show that Vezf1 interacts with Mrg15/Mrgbp, a protein that recognizes H3K36 tri-methylation, consistent with the role of histone modifications at alternatively spliced sites.

overall_design: Comparison of Vezf1 and RNA Pol II binding in mouse and human cells.

first: Humaira

last: Gowher

first: Gary

last: Felsenfeld


title: Rev-erb(alpha) and (beta) Coordinately Protect the Circadian Clock and Normal Metabolic Function

city: RTP

first: Logan

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: We report the genomic regions enriched for Rev-erb(beta) binding in WT mouse liver, in addition to the false positive regions enriched by ChIP for Rev-erb(alpha) in Rev-erb(alpha) KO liver. In conjunction with previously published data for Rev-erb(alpha) in GSE26345 (GSM647029, GSM647033, and GSM647034), we report the common and subtype specific cistromes for Rev-erb using a quantitative analysis method.

overall_design: Rev-erb(beta) ChIP-seq in liver from WT mice at 5AM/ZT22 and 5PM/ZT10, and Rev-erb(alpha) ChIP-seq in liver from Rev-erb(alpha) KO mice at 5PM/ZT10.

first: Anne

last: Bugge

last: Feng

first: Erika

last: Briggs

first: Shannon

last: Mullican

first: Fenfen

last: Wang

first: Jennifer

last: Jager

first: Mitchell

last: Lazar


title: Genome-wide maps of chromatin state in NCCIT cells

status: Public on Mar 07 2012

city: Daejeon

first: Inkyung

last: Jung

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

department: Biological Sciences

institute: KAIST

summary: H2B mono-ubiquitylation is required for multiple methylations of both H3K4 and H3K79 and has been implicated in gene expression from yeast to human. However, molecular crosstalk between H2BUb1 and other modifications, especially H3K4 and H3K79 methylations, remains unclear in vertebrates. To understand the functional role of H2BUb1, genome-wide histone modification patterns were measured in human cells. This study proposes dual roles of H2BUb1 that are both H3 methylation dependent and independent. First, H2BUb1 is a 5'-enriched active transcription mark and is co-occupied with H3K79 methylations in actively transcribed regions. Importantly, this study found a unique role of H2BUb1 in chromatin architecture independent of histone H3 methylations. H2BUb1 is well positioned in exon-intron boundaries of highly expressed exons and is specifically enriched in 5'-biased exons. Furthermore, H2BUb1 demonstrates increased occupancy in skipped exons compared to flanking exons for the human and mouse genome. Our findings suggest that a potentiating mechanism links H2BUb1 to both H3K79 methylations in actively transcribed regions and the exon-intron structure of highly expressed exons through the regulation of nucleosome dynamics during transcription elongation.

overall_design: We generated high-throughput sequencing (ChIP-seq) data for genome-wide occupancy of H2BUb1, nucleosome, H3K4me3, H3K36me3, H379me1/2/3, H3Ac, and mRNA in human embryonic carcinoma cells. We performed ChIP-seq for seven different histone modifications, MNase-seq, mRNA-seq (two replications), and inputDNA-seq in NCCIT cell lines (human embryonic carcinoma cell lines). We also performed mRNA-seq for RNF20-siRNA transfected NCCIT cells, where H2BUb1 signals decreased.

first: Seung-Kyoon

last: Kim

first: Dongsup

first: Daeyoup

last: Lee


title: Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana

status: Public on Mar 05 2012

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: Nucleosomes package eukaryotic DNA and are composed of four different histone proteins, H3, H4, H2A and H2B. Histone H3 has two main variants, H3.1 and H3.3, which show different genomic localization patterns in animals. We profiled H3.1 and H3.3 variants in the genome of the plant Arabidopsis thaliana and show that the localization of these variants shows broad similarity in plants and animals, in addition to some unique features. H3.1 was enriched in silent areas of the genome including regions containing the repressive chromatin modifications H3 lysine 27 methylation, H3 lysine 9 methylation, and DNA methylation. In contrast, H3.3 was enriched in actively transcribed genes, especially peaking at the 3’ end of genes, and correlated with histone modifications associated with gene activation such as histone H3 lysine 4 methylation, and H2B ubiquitylation, as well as by RNA Pol II occupancy. Surprisingly, both H3.1 and H3.3 were enriched on defined origins of replication, as was overall nucleosome density, suggesting a novel characteristic of plant origins. Our results are broadly consistent with the hypothesis that H3.1 acts as the canonical histone that is incorporated during DNA replication, whereas H3.3 acts as the replacement histone that can be incorporated outside of S-phase during chromatin disrupting processes like transcription.

overall_design:
ChIP-seq - 4 samples: 2 experiment and 2 controls
RNA-seq - 1 sample

first: H


title: Genome-wide transcription factor binding and chromatin methylation marks in the G1ME megakaryocytic progenitor model cell line

city: Chicago

first: Louis

middle: C

last: Dore

address: 303 E Superior St., Lurie Bldg 5-250D

department: Feinberg School of Medicine

institute: Northwestern University

summary: There are many examples of transcription factor families whose members control gene expression profiles of diverse cell types. However, the mechanism by which closely related factors occupy distinct regulatory elements and impart lineage specificity is largely undefined. Here we demonstrate on a genome wide scale that the hematopoietic GATA factors GATA-1 and GATA-2 bind overlapping sets of genes, often at distinct sites, as a means to differentially regulate target gene expression and to regulate the balance between proliferation and differentiation. We also reveal that the GATA switch, which entails a chromatin occupancy exchange between GATA2 and GATA1 in the course of differentiation, operates on more than a third of GATA1 bound genes. The switch is equally likely to lead to transcriptional activation or repression and, in general, GATA1 and GATA2 act oppositely on switch target genes. In addition, we reveal that genomic regions co-occupied by GATA2 and the ETS factor ETS1 are strongly enriched for regions marked by H3K4me3 and occupied by Pol II. Finally, by comparing GATA1 occupancy in erythroid cells and megakaryocytes, we find that the presence of ETS factor motifs is a major discriminator of megakaryocyte versus red cell specification.

overall_design: We used Illumina ChIP-Seq to examine binding of GATA1, GATA2, and ETS1 transcription factors as well as the genomic locations of two histone methylation marks, H3K4me3 and H3K27me3. Except H3K4me3 (1 sample), all data were generated from at least 2 biological replicates of immunoprecipitations from megakaryocyte progenitor cells, G1ME. Input DNA was prepared and sequenced along with each immunoprecipitation and used as a control dataset for binding site identification.

first: Timothy

last: Chlon

first: Christopher

last: Brown

middle: P

last: White

first: John

last: Crispino


title: RNA-Seq analysis of quorum sensing-dependent genes in Burkholderia glumae BGR1

city: Seoul

first: Ingyu

last: Hwang

address: Kwanak Gu Daehak Dong

department: Agricultural Biotechnology

institute: Seoul National University

summary: Burkholderia glumae causes rice grain rot and sheath rot by producing toxoflavin, whose expression is regulated by quorum sensing (QS). The QS systems of the bacterium rely on N-octanoyl homoserine lactone, synthesized by TofI and its cognate receptor TofR, to activate toxoflavin biosynthesis genes and an IclR-type transcriptional regulator gene, qsmR. To understand genome-wide transcriptional profiling of QS signaling, we employed RNA-Seq of the wild type Burkholderia glumae BGR1 and two QS-defective mutants, BGS2 (BGR1 tofI::Ω) and BGS9 (BGR1 qsmR::Ω), with two different types of culture conditions including 6hr liquid culture (before onset QS) and 10hr liquid culture (after onset QS).

overall_design: 3 samples examined: Burkholderia glumae BGR1 wild type, and two QS-defective mutants, BGS2 (BGR1 tofI::Ω) and BGS9 (BGR1 qsmR::Ω). Two conditions: cultured in LB media for 6hrs or 10hrs.

first: Seo

last: Young-Su

first: Lim

last: Jae Yun

first: Hwang

last: Ingyu


title: Comparison of systematic sequencing errors using spike-in standards

status: Public on Mar 03 2012

city: Gaithersburg

first: Justin

last: Zook

state: Maryland

address: 100 Bureau Dr., MS8313

department: Biochemical Science Division

institute: National Institute of Standards and Technology

summary: While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants.  These SSEs can cause base quality scores to underestimate the probability of error at certain genomic positions, resulting in false positive variant calls, particularly in mixtures such as samples with RNA editing, tumors, circulating tumor cells, bacteria, mitochondrial heteroplasmy, or pooled DNA.  Most algorithms proposed for correction of SSEs require a training data set, which is typically either from a part of the data set being “recalibrated” (Genome Analysis ToolKit, or GATK) or from a separate data set with special characteristics (SysCall).  Here, we combine the advantages of these approaches by adding synthetic RNA spike-in standards to human RNA, and use GATK to recalibrate base quality scores with reads mapped to the spike-in standards. Compared to conventional GATK recalibration that uses reads mapped to the genome, spike-ins improve the accuracy of Illumina base quality scores by a mean of 5 units, and by as much as 13 units  at CpG sites.  In addition, since reads mapping to the genome are not used for recalibration, our method allows run-specific recalibration even for the many species without a comprehensive and accurate SNP database.  We also use GATK with the spike-in standards to demonstrate that the Illumina RNA sequencing runs overestimate quality scores for AC, CC, GC, GG, and TC dinucleotides, while SOLiD has less dinucleotide SSEs but more SSEs for certain cycles.  We conclude that using these DNA and RNA spike-in standards with GATK improves base quality score recalibration.

overall_design: Four human RNA samples with equimolar ERCC spike-in standards were sequenced on Illumina.  Two human brain/liver/muscle RNA mixtures with dynamic range of ERCC spike-in standards were sequenced on SOLiD.

first: Marc

last: Salit

first: Shurjo

last: Sen

last: McDaniel


title: Chromatin maps of mature T cells

first: Mark

last: Chong

summary: We report the chromatin maps of CD4+ and CD8+ T cells

overall_design: Examination of 2 different histone modifications different T cell populations


title: Whole-genome study reveals distinct mechanisms used by p53 to regulate activated and repressed genes in embryonic stem cells

first: Jing

last: Huang

institute: National Cancer Institute

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

overall_design: Refer to individual Series


title: Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia [ChIP-Seq]

first: Hans-Ulrich

last: Klein

state: NY

institute: Columbia University Medical Center

summary: All-trans-retinoic acid (ATRA) has been successfully used in therapy of acute promyelocytic leukemia (APL), a cytogenetically distinct subtype of acute myeloid leukemia (AML) but the response of non-APL AML cases to ATRA-based treatment has been poor. Here we show that, via epigenetic reprogramming, inhibitors of LSD1/KDM1 demethylase including tranylcypromine (TCP) unlocked the ATRA-driven therapeutic response in non-APL AML. LSD1 inhibition did not lead to an increase in genome-wide H3 lysine4 dimethylation (H3K4me2) but did increase H3K4me2 and expression of myeloid differentiation-associated genes. Importantly, treatment with ATRA plus TCP dramatically diminished engraftment of primary human AML cells in vivo in NOD.SCID mice, suggesting that ATRA in combination with TCP may target leukemia-initiating cells. Furthermore, initiation of ATRA plus TCP co-treatment 15 days post-engraftment of human AML cells in NOD.SCID gamma mice also revealed the ATRA plus TCP drug combination to have a potent anti-leukemic effect, which was superior to treatment with either drug alone. These data identify LSD1 as a therapeutic target and strongly suggest that it may contribute to AML pathogenesis by inhibiting the normal pro-differentiative function of ATRA, paving the way for novel combinatorial therapies of AML.

overall_design: ChIP-seq was used to study the effects of ATRA, TCP and ATRA/TCP treatment on H3K4 dimethylation. In addition to the three treatment samples, two reference samples were processed: (i) An untreated sample using the same anti-H3K4me2 antibody and an untreated sample using IgG. These five sequencing experiments were conducted using HL-60 cells and TEX cells, leading to 10 ChIP-seq samples in total.

first: Tino

last: Schenk

first: Weihsu

last: Chen

first: Stefanie

last: Göllner

first: Louise

last: Howell

first: Liqing

last: Jin

first: Katja

last: Hebestreit

first: Andreea

last: Popescu

first: Alan

last: Burnett

first: Ken

last: Mills

first: Robert

last: Casero Jr

first: Laurence

last: Marton

first: Patrick

last: Woster

last: Minden

first: Martin

last: Dugas

first: Jean

last: Wang

last: Dick

first: Carsten

last: Müller-Tidow

first: Kevin

last: Petrie

first: Arthur

last: Zelent


title: ChIP-seq analysis of H3K4Me3- and H3K27Me3-marked chromatin in mesenchymal stem cells (MSCs), osteoblasts derived from MSCs and the osteosarcoma cell line U2OS

status: Public on Mar 02 2012

city: BALTIMORE

first: hari

last: easwaran

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

summary: Many DNA-hypermethylated cancer genes are occupied by the polycomb (PcG) repressor complex in embryonic stem cells (ESCs). Their prevalence in the full spectrum of cancers, the exact context of chromatin involved, and their status in adult cell renewal systems are unknown. Using a genome-wide analysis, we demonstrate that approximately 75% of hypermethylated genes are marked by PcG in the context of bivalent chromatin in both ESC and adult stem/progenitor cells. A large number of these genes are key developmental regulators and a subset, which we call the "DNA hypermethylation module", comprise a portion of the PcG target genes that are downregulated in cancer. Genes with bivalent chromatin have a low, poised gene transcription state that has been shown to maintain stemness and self-renewal in normal stem cells. However, when DNA-hypermethylated in tumors, we find these genes are further repressed. We also show that the methylation status of these genes can cluster important subtypes of colon and breast cancers. By evaluating the subsets of genes that are methylated in different cancers with consideration of their chromatin status in ESCs, we provide evidence that DNA-hypermethylation preferentially targets the subset of PcG genes that are developmental regulators, and this may contribute to the stem-like state of cancer.  Additionally, the capacity for global methylation profiling to cluster tumors by phenotype may have important implications for further refining tumor behavior patterns that may ultimately aid therapeutic interventions.

overall_design:
The goal was to analyze the chromatin in MSCs, osteoblasts and U2OS cells of genes that are methylated in the osteosarcoma cell line U2OS.

Cell culture: MSCs derived from adult  bone marrow were cultured and differentiated to osteoblasts as described by Jaiswal et al., 1997 (J Cell Biochem 64, 295-312). U2OS cells were cultured in McCoy's 5A medium supplemented with 10% FBS.

ChIP-seq: Cells were crosslinked in 3.7% formaldehyde, lysed and sonicated to obtain chromatin fragments in the range of 200 to 600 base pairs. Sonicated chromatin was incubated with primary antibody, H3K4Me3 (Millipore, 07-473) or H3K27Me3 (kind gift from Thomas Jenuwein/ Nicholas Shukeir), overnight at 4°C, followed by capturing primary antibodies by adding ProteinA/G magnetic beads (DynaBeads) and incubating at room temperature for 3-4 hrs. Captured chromatin was washed in low- and high-salt buffers, as well as TE. Chromatin fragments were subjected to simultaneous elution, de-crosslinking and Proteinase-K treatment at 65°C in elution buffer followed by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.

Sequencing and alignment: Purified DNA was used to prepare the sequencing library and sequenced on Applied Biosystems SOLiD (V3). Sequencing reads were aligned to hg18 (NCBI 36) using Bioscope 1.2.1. The software guarantees finding all alignments between the first 25 base pairs of the read (seed) and the reference sequence with up to 2 mismatches. Each match is extended to the full length of the read, scoring 1 point for matching and -2 points for mismatching bases. The read is trimmed to the length with the highest score. If there is only one alignment or if an alignment scores significantly higher than the others for the same read, it is considered unique and reported.

Peak identification: Aligned reads were analyzed using Model-based Analysis of ChIP-Seq (MACS) to detect regions enriched for the histone marks (called peaks) with default settings. Input was used as background for peak identification.

first: Hariharan

last: Easwaran

first: Stephen

last: Baylin


title: Degradation of cellular miR-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo.

status: Public on Mar 01 2012

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: Cytomegaloviruses express large amounts of viral miRNAs during lytic infection, yet, they only modestly alter the cellular miRNA profile. The most prominent alteration upon lytic murine cytomegalovirus (MCMV) infection is the rapid degradation of the cellular miR-27a and miR-27b. Here, we report that this regulation is mediated by the <1.7 kb spliced and highly abundant MCMV m169 transcript. Specificity to miR-27a/b is mediated by a single, apparently optimized, miRNA binding site located in its 3'-UTR. This site is easily and efficiently retargeted to other cellular and viral miRNAs by target site replacement. Expression of the 3'-UTR of m169 by an adenoviral vector was sufficient to mediate its function, indicating that no other viral factors are essential in this process. Degradation of miR-27a/b was found to be accompanied by 3'-tailing and -trimming. Despite its dramatic effect on miRNA stability, we found this interaction to be mutual, indicating potential regulation of m169 by miR-27a/b. Most interestingly, three mutant viruses no longer able to target miR-27a/b, either due to miRNA target site disruption or target site replacement, showed significant attenuation in multiple organs as early as 4 days post infection, indicating that degradation of miR-27a/b is important for efficient MCMV replication in vivo.

overall_design: Small RNA sequencing from total RNA or Ago2 associated small RNAs extracted from mock- or MCMV-infected NIH-3T3 cells

first: Lisa

last: Marcinowski

first: Mélanie

last: Tanguy

first: Astrid

last: Krmpotic

first: Bernd

last: Rädle

first: Vanda

last: Lisnić

first: Lee

last: Tuddenham

first: Béatrice

last: Chane-Woon-Ming

first: Zsolt

last: Ruzsics

first: Florian

last: Erhard

first: Corinna

last: Benkartek

first: Marina

last: Babic

first: Ralf

last: Zimmer

first: Joanne

last: Trgovcich

first: Ulrich

last: Koszinowski

first: Stipan

last: Jonjic

first: Lars

last: Dölken


title: Dynamic loss of H2B ubiquitylation without corresponding changes in H3K4 tri-methylation during myogenic differentiation

status: Public on Mar 06 2012

city: New York

first: Brian

last: Dynlacht

address: 550 1st avenue

institute: NYU Langone Medical Center

summary: Ubiquitylation of H2B on lysine 120 (H2Bub) is associated with active transcriptional elongation. H2Bub has been implicated in histone cross-talk and is generally regarded to be a prerequisite for H3K4 and H3K79 tri-methylation in both yeast and mammalian cells. We performed a genome-wide analysis of epigenetic marks during muscle differentiation, and, strikingly, we observed a near-complete loss of H2Bub in the differentiated state. We examined the basis for global loss of this mark and found that the H2B ubiquitin E3 ligase, RNF20, was depleted from chromatin in differentiated myotubes, indicating that recruitment of this protein to genes substantially decreases upon differentiation. Remarkably, during the course of myogenic differentiation, we observed retention and acquisition of H3K4 tri-methylation on a large number of genes in the absence of detectable H2Bub. The Set1 H3K4 trimethylase complex was efficiently recruited to a subset of genes in myotubes in the absence of detectable H2Bub, accounting in part for H3K4 tri-methylation in myotubes. Our studies suggest that H3K4me3 deposition in the absence of detectable H2Bub in myotubes is mediated via Set1 and, perhaps, MLL complexes, whose recruitment does not require H2Bub. Thus, muscle cells represent a novel setting in which to explore mechanisms that regulate histone cross-talk.

overall_design: Mapping of H2Bub in growing myoblasts (MB) and fully differentiated myotubes (MT).

first: Vasupradha

last: Vethantham

first: Yan

last: Yang

first: Christopher

last: Bowman

first: Patrik

last: Asp

first: Jeong-Heon

last: Lee

first: David

middle: G

last: Skalnik


title: Bisulfite Sequencing Reveals that Aspergillus flavus Holds A Hollow in DNA Methylation

city: Guangzhou

first: Zhumei

last: He

address: 135 Xingangxi Street

institute: Sun Yat-sen University

summary: Aspergillus flavus first gained scientific attention for its production of aflatoxin, the most potent naturally occurring toxin and hepatocarcinogenic secondary metabolite. For several decades, The DNA methylation status of A. flavus remains to be controversial. We first applied bisulfite sequencing, the gold standard at present, in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Our results reveal that the DNA methylation level of this fungus turns out to be negligible, comparable to the unmethylated lambda DNA we set as the false positive control of our bisulfite experiments. When comparing the DNA methyltransferase homolog of A. flauvs with that from several selected hypermethylated speices, we find that the DNA methyltransferase homolog of A.flavus as well as the other Aspergillus members groups closely with the RID from Neurospora crassa and Masc1 from Ascobolus immerses, which has been reported as DMT-incapable, but it diverges distantly from the other capable DNA methyltransferases. We observe significant depletion of repeat components within the A. flavus, which may possibly explain the lack of DNA methylation in this fungus. What's more, the RIP-index of the repeat of A. flavus turns out to be higher than the fungi without RID-like enzyme, suggesting this asexual fungus may possibly possess RIP process during the obscure sexual-stage which is very evanescent and may potentially related to DNA methylation.   This work contributes to our understanding on the DNA methylation status of A. flavus. Also, it reinforces our views on the DNA methylation in fungal species. What's more, our strategy of applying bisulfite sequencing to DNA methylation detection on species with low DNA methylation may serve as a reference for later scientific investigations on other hypomethylated species.

overall_design: Two replicates were subjected to bisulfite conversion independently, unmethylated lambda DNA as a false positive control is added to both replicates.


title: Deep-sequencing influences the results obtained in small-RNA sequencing

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: This study presents a comparison of small RNA sequencing libraries generated from the same cell lines but using different sequencing platforms and protocols. The samples were analyzed and compared at the level of miRNAs expression and as a population of small RNAs derived from repetitive elements. Despite a good correlation between sequencing platforms, there are qualitative and quantitative variations in the results depending on the protocol used.

overall_design: 10 samples were examined: 6 from the ES E14 XY cell type: 1 454, 2 SOLiD from 2 technological versions, and 3 SOLEXA from 3 different protocols, and 4 samples from ES PGK XX cells: 1 454 and 1 SOLEXA sample, and 2 SOLiD samples from 2 technological versions.

first: Joern

last: Toedling

first: Constance

last: Ciaudo

first: Laurent

last: Farinelli

first: Olivier

last: Voinnet

first: Edith

last: Heard

first: Emmanuel

last: Barillot


title: E. coli strain E24377A

city: Baltimore

first: Jason

last: Sahl

address: 801 West Baltimore St.

department: School of Medicine

institute: University of Maryland

platform_organism:
Escherichia coli
Shigella
Escherichia coli O139:H28 str. E24377A


title: Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response (sequencing)

first: Terry

last: Fang

address: 1230 York Ave

institute: Rockefeller University

summary: Effective anti-viral immunity depends on the ability of infected cells or cells triggered with virus-derived nucleic acids to produce type I interferon (IFN), which activates transcription of numerous antiviral genes. However, disproportionately strong or chronic IFN expression is a common cause of inflammatory and autoimmune diseases. Here we describe an epigenetic mechanism that determines cell-type specific differences in IFN and IFN-stimulated gene expression in response to exogenous signals. We identify di-methylation of histone H3 at lysine 9 (H3K9me2) as a suppressor of IFN and IFN-inducible antiviral gene expression. We show that levels of H3K9me2 at IFN and IFN stimulated genes (ISG) correlate inversely with the scope and amplitude of IFN and ISG expression in fibroblasts and dendritic cells. Accordingly, genetic ablation or pharmacological inactivation of lysine methyltransferase G9a, which is essential for the generation of H3K9me2, resulted in phenotypic conversion of fibroblasts into highly potent IFN-producing cells and rendered these cells resistant to pathogenic RNA viruses. In summary, our studies implicate H3K9me2 and enzymes controlling its abundance as key regulators of innate antiviral immunity.

overall_design: Examination of epigenetic modifications in WT and G9a deficient MEFs and splenic DCs

first: Alexander

last: Tarakhovsky


title: Global transcriptomics of enterotoxigenic E. coli strain E24377A

summary: ETEC is an important human pathogen.  Although the mechanism of diarrhea is known in ETEC, the regulatory networks are less understood.  This study was conducted to understand the global expression of ETEC isolate E24377A under different growth and environmental conditions.

overall_design: ETEC E24377A was grown in LB or LB+bile salts (3% w/v).   For each condition, three biological replicates were combined into a single sample.

last: Rasko


title: Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response


title: Genome-wide analysis revealed a crosstalk between p53 and the pluripotent gene networks in mouse embryonic stem cells (ChIP-Seq)

first: Jing

last: Huang

summary:
Study of the function of p53 in regulating gene expression in mouse embryonic stem cells.
It is critical for embryonic stem cells to maintain their genomic stability. The guardian of the genome, p53, plays important roles in maintaining the genomic integrity of ES cells through regulating the differentiation of ES cells. However, the underlying mechanism of this differentiation is still unclear. We plan to use the integrative genome-wide approach, combining ChIP-seq and gene expression microarray, to explore the mechanisms.

overall_design: Total six samples: two inputs (untreated and treated with adriamycin) and four ChIP samples (p53_untreated, p53_adr8h, p53S18P_untreated, p53S18P_adr8h). The two inputs will serve as controls for identifying the binding sites.


title: Analysis of small RNA population in Arabidopsis drb2 and drb4 mutants

city: Perpignan

first: Jean-Marc

last: Deragon

address: 58 avenue Paul Alduy

department: Biology

institute: Université de Perpignan, CNRS

summary: We have compared populations of small (21 to 24-nt) RNAs from Arabidopsis immature flowers of WT, drb2 and drb4 mutants and found that DRB2 and DRB4 are needed for the proper biogenesis of polymerase IV-dependent siRNAs

overall_design: Examination of small RNA populations from three backgournd: Col0 (WT), drb2 and drb4 mutants

first: Cristian

last: Chaparro


title: Transcriptome-wide analysis of small RNA expression in early zebrafish development

city: Boston

first: Chunyao

last: Wei

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

summary: During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity, expression levels, and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small non-coding RNAs that play important roles in gene regulation during early embryonic development.  Here, we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs, the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the 5' and 3' ends of miRNAs with a large number of extra nucleotides added in a non-template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development, far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis.

overall_design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through-put sequencing

first: Leonidas

last: Salichos