title: The Rhino-Deadlock-Cutoff complex licenses non-canonical transcription of dual-strand piRNA clusters in Drosophila

status: Public on Jun 08 2014

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: Argonaute proteins of the PIWI clade are central to transposon silencing in animal gonads. Their target specificity is defined by 22-30nt PIWI interacting RNAs (piRNAs), which mostly originate from discrete genomic loci termed piRNA clusters. Here we show that the RDC complex composed of Rhino, Deadlock and Cutoff defines dual-strand piRNA clusters genome-wide in Drosophila ovaries. The RDC complex is anchored to H3K9me3-marked chromatin in part via Rhino’s chromo-domain. Depletion of Piwi results in loss of the RDC and small RNAs at euchromatic piRNA source loci, demonstrating a feedback loop between Piwi and genomic piRNA sources. Intriguingly, profiles of RNA Polymerase II occupancy, nascent transcription and steady-state RNA levels reveal that the RDC licenses non-canonical transcription of dual-stranded piRNA clusters. Likely, this process involves 5’end protection of nascent RNAs and subsequent suppression of transcription termination. Together, our data provide a comprehensive model for the regulation and evolution of piRNA clusters.

overall_design: This study aims at indentifying and characterizing genimc sources of piRNA percursour transcripts using genome-wide apporaches such as ChIP-seq, RNA-seq, smallRNA-seq and GRO-seq in adult Drosophila ovaries depleted for several factors implicated in piRNA cluster regulation

first: Grzegorz

last: Sienski

first: Dominik

last: Handler

first: Julius

last: Brennecke


title: Genome-wide analysis of histone modifications in   latently HIV-1 infected T cells

status: Public on Jun 06 2014

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The epigenetic mechanisms established by histone modifications may affect the transcriptional silencing  of HIV-1 and viral latency. A systematic epigenome profiling could be applicable to develop new epigenetic diagnostic markers for detecting HIV-1 latency. In this study, histone modification profiles of HIV-1 latency cell lines were compared with those of uninfected CD4+ T cell line. The HIV-1 latency gave rise to differential histone modification regions. The differential enrichment patterns helped us to define potential effector genes leading to the viral latency.

overall_design: The histone H3K4me3 and H3K9ac profiles were obtained from the HIV-1 latency cell lines (NCHA1, NCHA2, and ACH2) and control CD4+ T cell line (A3.01)

first: Jihwan

last: Park

first: Chae

middle: H

last: Lim

first: Seokjin

last: Ham

first: Sung

middle: S

last: Kim

first: Byeong-Sun

last: Choi


title: Maternal experience with predation risk influences genome-wide embryonic gene expression in threespined sticklebacks (Gasterosteus aculeatus)

status: Public on Jun 07 2014

city: Liege

first: Brett

middle: C

last: Mommer

state: Wallonia

address: Tour Pharmacie (Bat. B36) Quartier Hôpital, Avenue Hippocrate 15

department: GIGA-Neurosciences

country: Belgium

institute: University of Liege

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goal of this study was to compare gene expression in whole embryos to identify transcriptomic changes that result from maternal exposure to predation risk.
Methods: Whole embryo mRNA profiles of 3 day post-fertilizationstickleback embrosof mothers exposed to simulated predation risk and control embryos were generated by RNA-sequencing of pooled embryos using Illumina Hiseq2000. The sequence reads that passed quality filters were aligned to the stickleback reference genome and analyzed at the gene  level (EdgeR) and at the transcript level (Cufflinks/Cuffdiff). Subsets of embryos were also measured for embryo length and eye diameter, and data were analyzed with a general linear model (SPSS).
Results: We mapped ~22 million sequence reads per sample to the stickleback reference genome (BROADS1, Ensembl database version 71.1, Feb 2006) and identified 17440  transcripts with the Tophat workflow. Differential expression analysis using both EdgeR and Cufflinks/Cuffdiff identified 455 transcripts were differentially expressed in embryos of mothers exposed to simulated predation risk as compared to control embryos, with an FDR <0.05 (Cuffdiff) or <0.10 (EdgeR). Gene ontology and pathway analysis (DAVID, IPA) of the differentially expressed gene list revealed enrichment of genes involved in growth, metabolism, neurogenesis, and epigenetics. Embryos of mothers exposed to predation risk had elevated expression of growth and metabolism genes and were also larger than control embryos, suggesting at least some of the genes differentially expressed in this study are involved in the transfer of maternal experience to offspring.
Conclusions: Our results suggest that early stickleback embryos respond to maternal exposure to predation risk via changes in gene expression, and a general acceleration of the developmental program. Further study is needed to elucidate the myriad molecular interactions between genes that are differentially-regulated as a result of maternal exposure to predation risk and to understand their relationships to previously-observed maternal effects in this system.

overall_design: Whole embryo mRNA profiles of 3dpf stickleback embryos of mothers exposed to simulated predation risk [E] and control mothers [C] were generated by barcoded, multiplexed high-throughput RNA-sequencing on Illumina Hiseq-2000.

first: Alison

middle: M

last: Bell


title: RNA-seq analysis of polyhydroxyalkanoate-producing Ralstonia eutropha H16

city: Yokohama

first: Toshiaki

last: Fukui

address: Nagatsuta 4259

department: Department of Bioengineering

country: Japan

institute: Tokyo Institute of Technology

summary:
Ralstonia eutropha H16 is well-known to produce poly(3-hydroxybutyrate) [P(3HB)], a kind of polyhydroxyalkanoates attracted as bio-based biodegradable plastics, efficiently as an energy storage material under unbalanced growth conditions. To obtain further extended knowledge of PHA biosynthesis, this study employed quantitative transcriptome analysis based on deep sequencing of complementary DNA generated from RNA (RNA-seq) for R. eutropha H16.
Total RNAs were extracted from R. eutropha cells in growth, PHA production, and stationary phases on fructose. rRNAs in the preparation were removed by repeated treatments with magnetic beads specific to bacterial rRNAs, and then the 36 bp sequences were determined by using Illumina high-throughput sequencer.
The RNA-seq results supported induction of gene expression for transcription, translation, cell division, peptidoglycan biosynthesis, pilus and flagella assembly, energy conservation, and fatty acid biosynthesis in growth phase, and repression trends for genes involved in central metabolisms in PHA production phase. Interestingly, transcription of genes for Calvin-Benson-Bassham (CBB) cycle and several selected genes for β-oxidation were significantly induced in PHA production phase even when the cells were grown on fructose.

overall_design: mRNA profiles of R. eutropha H16 grown on fructose at different phases were generated by deep sequencing, in duplicate, using Illumina GAIIx.


title: Evollutionally dynamic L1 regulation in embryonic stem cells

status: Public on Jun 09 2014

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

summary: Mobile elements are important evolutionary forces that challenge genomic integrity. Long interspersed element-1 (L1, also known as LINE-1) is the only autonomous transposon still active in the human genome. It displays an unusual pattern of evolution, with at any given time a single active L1 lineage amplifying to thousands of copies before getting replaced by a new lineage likely under pressure of host restriction factors, which act notably by silencing L1 expression during early embryogenesis. Here, we demonstrate that in human embryonic stem cells (hESC) KAP1, the master co-factor of KRAB-containing zinc finger proteins (KRAB-ZFP) previously implicated in the restriction of endogenous retroviruses, represses a discrete subset of L1 lineages predicted to have entered the ancestral genome between 26.8 and 7.6 million years ago. In the mouse, we documented a similar chronologically conditioned pattern, albeit with a much contracted time scale. We could further identify an L1-binding KRAB-ZFP, suggesting that this rapidly evolving protein family is more globally responsible for L1 recognition. KAP1 knockdown in hESC induced the expression of KAP1-bound L1 elements, but their younger, human-specific counterparts (L1Hs) were unaffected. Instead, they were stimulated by depleting DNA methyltransferases, consistent with recent evidence demonstrating that the PIWI-piRNA pathway regulates L1Hs in hESC. Altogether, these data indicate that the early embryonic control of L1 is an evolutionary dynamic process, and support a model whereby newly emerged lineages are first suppressed by DNA methylation-inducing small RNA-based mechanisms, before KAP1-recruiting protein repressors are selected.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: HA-tagged Gm6871 ChIP-seq in mES cells, RNA-seq in control and Gm6871 KD mES cells, KAP1 ChIP-seq in WT mES cells, RNA-seq in  control and DNMTs KD hES cells.

first: Nathaly

last: Castro-Diaz

first: Gabriela

last: Ecco

first: Andrea

last: Coluccio

first: Adamandia

last: Kapopoulou

first: Didier

last: Trono


title: MeDIP sequencing of Ovis aries

city: Shenzhen

first: Min

last: Xie

state: Guangdong

address: 11th Building,Beishan Industrial Zone

department: Science & Technology department

country: China

institute: Beijing Genomics Institute

type: Methylation profiling by high throughput sequencing

summary: We have completed the high quality reference genome for domestic sheep (Oar v3.1).

overall_design: Early-stage Illumina GA sequence platform sequenced less reads in high GC content regions than in other regions. To read through higher GC content regions, we generated 2 Gb MeDIP-seq data for filling gaps in sheep reference genome assembly.

first: Xun

last: Xu

first: Wen

last: Wang


title: The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner [RNA-Seq]

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: UT Southwestern

summary:
In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such as histone H3 lysine 9 (H3K9) methylation. In Arabidopsis thaliana DNA methylation and H3K9 methylation are usually colocated and set up a mutually self reinforcing and stable state. Here, in contrast, we found that SUVR5, a plant Su(var)3-9 homolog with a SET histone methyltransferase domain, mediates H3K9me2 deposition and regulates gene expression in a DNA-methylation-independent manner. SUVR5 binds DNA through its zinc fingers and represses  the expression of a subset of stimulus response genes. This represents a novel mechanism for plants to regulate their chromatin and transcriptional state, which may allow for the adaptability and modulation necessary to rapidly respond to extracellular cues.

Keywords: Expression profiling by high throughput sequencing

overall_design: Investigation of gene expression profiles of suvr5-1, ldl1 ldl2 and suvr5 ldl1 ldl2 mutants. For more information on this study contact Dr. Elena Caro at ecarobernat-at-gmail.com

first: Steve

last: Jacobsen


title: The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner [SELEX]

summary: In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such as histone H3 lysine 9 (H3K9) methylation. In Arabidopsis thaliana DNA methylation and H3K9 methylation are usually colocated and set up a mutually self reinforcing and stable state. Here, in contrast, we found that SUVR5, a plant Su(var)3-9 homolog with a SET histone methyltransferase domain, mediates H3K9me2 deposition and regulates gene expression in a DNA-methylation-independent manner. SUVR5 binds DNA through its zinc fingers and represses  the expression of a subset of stimulus response genes. This represents a novel mechanism for plants to regulate their chromatin and transcriptional state, which may allow for the adaptability and modulation necessary to rapidly respond to extracellular cues.

overall_design: one experiment and one control.

first: Elena

last: Caro


title: Transcriptome sequencing of Ovis aries

summary: We have completed the high quality reference genome for domestic sheep (Oar v3.1) and performed a detailed survey of gene expression across different tissues. RNA-seq data of 7 tissue types from the reference female Texel and  skin tissue from a Gansu alpine fine wool sheep were sequenced.

overall_design: Here is the part of the RNA-seq data sequenced in BGI, including 7 tissue types from the reference female Texel and skin type from a Gansu alpine fine wool sheep.

first: Yaojing

last: Yue


title: High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation [miRNA-Seq]

city: QINGDAO

first: Muyan

last: Chen

address: 5 YUSHAN ROAD

institute: Ocean University of China

type: Non-coding RNA profiling by high throughput sequencing

summary: The regulatory role of miRNA in gene expression is an emerging hot new topic in the control of hypometabolism. Sea cucumber aestivation is a complicated physiological process that includes obvious hypometabolism as evidenced by a decrease in the rates of oxygen consumption and ammonia nitrogen excretion, as well as a serious degeneration of the intestine into a very tiny filament. To determine whether miRNAs play an important regulatory roles in this process, the present study analyzed profiles of miRNA expression in the intestine of sea cucumber (Apostichopus japonicus), using Solexa deep sequencing technology. We identified 309 sea cucumber miRNAs, including 19 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA) after at least 15 days of continuous torpor, were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 42 differentially expressed miRNAs (RPM (reads per million) >10, |FC| (|fold change|) ≥1, FDR<0.01) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-200-3p, miR-2004, miR-2010, miR-22, miR-252a, miR-252a-3p and miR-92 were significantly over-expressed during deep aestivation compared with non-aestivation animals. Preliminary analyses of their putative target genes suggest that these miRNAs could play important roles in global transcriptional depression during aestivation.

overall_design: analyze the global profile of small RNAs in non-aestivation (NA) and deep aestivation (DA) sea cucumbers' intestine using Solexa sequencing technology

first: Kenneth

middle: B

last: Storey


title: Allele-specific expression and eQTL analysis in mouse adipose tissue

status: Public on Jun 05 2014

city: Los Angeles

first: Yehudit

last: Hasin-Brumshtein

state: CA

address: 695 Charles E. Young Drive South

department: David Geffen School of Medicine, Cardiology

institute: UCLA

summary: In this study we use RNAseq to explore allele specific expression (ASE) in adipose tissue of male and female F1 mice, produced from reciprocal crosses of C57BL/6J and DBA/2J strains. Comparison of the identified cis-eQTLs, to local-eQTLs, that were obtained from adipose tissue expression in two previous population based studies in our laboratory, yields poor overlap between the two mapping approaches, while both local-eQTL studies show highly concordant results. Specifically, local-eQTL studies show ~60% overlap between themselves, while only 15-20% of local-eQTLs are identified as cis by ASE, and less than 50% of ASE genes are recovered in local-eQTL studies. Utilizing recently published ENCODE data, we also find that ASE genes show significant bias for SNPs prevalence in DNase I hypersensitive sites that is ASE direction specific. We suggest a new approach to analysis of allele specific expression that is more sensitive and accurate than the commonly used fisher or chi-square statistics. Our analysis indicates that technical differences between the cis and local-eQTL approaches, such as differences in genomic background or sex specificity, account for relatively small fraction of the discrepancy. Therefore, we suggest that the differences between two eQTL mapping approaches may facilitate sorting of SNP-eQTL interactions into true cis and trans, and that a considerable portion of local-eQTL may actually represent trans interactions.

overall_design: 4 samples  - male and female, BxD and DxB adipose of pooled RNA (3 animals per pool) were analyzed with high coverage RNAseq data.

first: Farhad

last: Hormozdiari

first: Lisa

last: Martin

first: Atila

last: van Nas

first: Eleazar

last: Eskin

first: Thomas

middle: A

last: Drake

first: Aldons

middle: J

last: Lusis


title: The transcriptional response to Norrin/Fz4 signaling

city: Baltimore

first: Yulian

last: Zhou

state: MD

address: 725 N. Wolfe Street

institute: JHMI

summary: Using mice with targeted gene mutations, we identify (1) distinct roles for different canonical Wnt signaling components in central nervous system (CNS) vascular development and in the specification of the blood-brain and blood-retina barriers (BBB and BRB) and (2) differential sensitivities of the vasculature in various CNS regions to perturbations in canonical Wnt signaling components. We find nearly equivalent roles for Lrp5 and Lrp6 in brain vascular development and barrier maintenance but a dominant role for Lrp5 in the retinal vasculature, an especially high sensitivity of the BBB in the cerebellum and pons/interpeduncular nuclei to decrements in canonical Wnt signaling, and plasticity in the barrier properties of mature CNS vasculature. Brain and retinal vascular defects caused by loss of Norrin/Frizzled4 signaling can be fully rescued by stabilizing beta-catenin, and loss of beta-catenin’s transcriptional activation domain or expression of a dominant negative Tcf4 recapitulates the vascular development and barrier defects seen with loss of receptor, co-receptor, or ligand, indicating that Norrin/Frizzled4 signaling acts predominantly by beta-catenin-dependent transcriptional regulation. This work strongly supports a model in which identical or nearly identical canonical Wnt signaling mechanisms mediate neural tube and retinal vascularization and maintain the BBB and BRB.

overall_design: Total retina RNA from P10 WT, NdpKO, Ctnnb1flex3/+;Pdgfb-CreER, and NdpKO;Ctnnb1flex3/+;Pdgfb-CreER mice was subjected to RNAseq

first: Jeremy

last: Nathans


title: RRP1B is a Metastasis Modifier that Regulates the Transcriptome through mRNA Splicing

city: Bethesda

first: Nigel

last: Crawford

address: 50 South Drive, Room 5154

institute: Human Genome Research Institute

overall_design: To assess the role of RRP1B in alternative mRNA splicing, we knocked down the expression of Rrp1b in the highly metastatic mouse mammary tumor cell line Mvt-1 using shRNA. Two control and two knockdown stable cell lines were selected for RNA-sequencing.

first: Minnkyong

last: Lee

middle: P

first: Derek

last: Gildea

first: Tyra

middle: G

last: Wolfsberg


title: Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

status: Public on Jun 11 2014

city: New York City

first: Rahul

last: Satija

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Here, we use a microfluidics-based approach to prepare single-cell RNA-Seq libraries from over 1,700 primary mouse dendritic cells (DCs) stimulated with three pathogenic components and examine variation between individual cells exposed to the same stimulus and general strategies that multicellular populations use to establish complex dynamic responses.

overall_design: RNA seq libraries from 1775 single cells and population controls with SMARTer


title: High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation

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

overall_design: Refer to individual Series


title: Reorganization of enhancer patterns in transition from naïve to primed pluripotency

city: Stanford

first: Christa

last: Buecker

state: California

address: 269 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University


title: Reorganization of enhancer patterns in transition from naïve to primed pluripotency (ChIP-seq)

summary: Naïve and primed pluripotency is characterized by distinct signaling requirements, transcriptomes and developmental properties, but both cellular states share key transcriptional regulators, Oct4, Sox2 and Nanog. Here we demonstrate that transition between these two pluripotent states is associated with widespread Oct4 relocalization, mirrored by global rearrangement of enhancer chromatin landscapes. Our genomic and biochemical analyses identified candidate mediators of primed state-specific Oct4 binding, including Otx2 and Zic2/3. Even in the absence of other differentiation cues, premature Otx2 overexpression is sufficient to exit the naïve state, induce transcription of a large subset of primed pluripotency-associated genes and redirect Oct4 to thousands of previously inaccessible sites. However, ability of Otx2 to engage new enhancer regions is determined by its levels, cis-encoded properties of the sites and signaling environment. Our results illuminate regulatory mechanisms underlying pluripotency and suggest that capacity of transcription factors such as Otx2 and Oct4 to function as pioneers is highly context-dependent

overall_design: ChIP-seq analysis was performed to map enhancers and associated transcription factors. We used H3K27ac, H3K4me1 and p300 to call enhancers from 2 different pluripotent cell states: ESC and EpiLC. In addition we performed ChIP-seq for Oct4 and Otx2 from these cell states. All these experiments were carried out in replicates, for the EpiLC state the replicates were performed with and without ActivinA. Additionally we carried out ChIPseq for Otx2 and Oct4 in Otx2ko cell lines in which we integrated an inducible Otx2 gene before and after induction with doxycycline.


title: Reorganization of enhancer patterns in transition from naïve to primed pluripotency (RNA-seq)

overall_design: transcription profile of ESCs and EpiLCs to analzye changes during differentiation and the effect of Otx2 loss and overexpression on the differentiation properties


title: Quantitative transcriptome analysis of a high-GSH producing Saccharomyces cerevisiae and the wild type based on the second generation sequencing.

city: Changshu

first: Jiang

last: Sun

address: No. 99, South Third Ring Road

institute: Changshu Institute of Technology

summary: The mutant Saccharomyces cerevisiae Y518 generated much more intracellular glutathione (GSH) than its counterpart dose. The RNA-seq based global transcriptome analysis was performed for exploring the potential mechanisms. Statistical analysis indicated that 1125 differentially expressed genes (fold-change>=2.0, FDR<=0.001) were up-regulated and 503 were down-regulated. There were 12 genes involved in glutathione metabolism. Of which GSH1, encodes gamma-glutamine cysteine synthetase, the rate-limiting enzyme in GSH biosynthesis process, was up-regulated. And MET17, encodes cysteine synthase A, an enzyme catalyzes the biosynthesis of one of the precursor amino acids L- cysteine, was also up-regulated. Besides, regulator SKN7 and several genes involved in oxidative stress response (GPX2, CTT1, SOD1, TRX2) were up-regulated. Intracellular ROS level of Y518 was also enhanced compared to that of 2-10515. Our results indicate that up-regulations of GSH1 and MET17 might be associated with the increased intracellular GSH content of the mutant, and up-regulated GSH1 may be caused by increased intracellular ROS level.

overall_design: Saccharomyces cerevisiae mRNA profiles of 24-h wild type 2-10515 and mutant Y518 were generated by deep sequencing using Illumina HiSeqTM 2000

first: Qi

last: Bin

first: Zhu

last: Yibo

first: Wang

last: Limei

first: Sun

last: Jiang


title: Transcriptomic profiling reveals new aspects of progestin signaling in breast cancer

city: Ioannina

first: Angeliki

last: Magklara

address: University Campus

department: Medicine

country: Greece

institute: University of Ioannina

summary: We have identified differentially PR-regulated genes in T47D cells and mapped PR-binding sites by using next generation sequencing

overall_design: RNA-seq  and ChIP-seq in progestin treated cells


title: Hypoxia transcriptome sequencing of blind mole rat (BMR, Spalax galili) and rat (Rattus norvegicus)

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: Deep sequencing of mRNA from Spalax galili and Rattus norvegicus

sample_organism:
Rattus norvegicus
Nannospalax galili

platform_organism:
Rattus norvegicus
Nannospalax galili

overall_design: Total RNAs were isolated from the brain of female BMRs under various oxygen concentrations (3%, 6%, 10%, 14%, and 21%) for 6 hours. We also got RNAs from the brain of rats under 6%, 10%, 14%, and 21% oxygen conditions.

first: Xiaodong

last: Fang

first: Eviatar

last: Nevo

first: Lijuan

last: Han

first: Leonid

last: Brodsky


title: Infinium Monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis) RRBS-seq

city: Singapore

first: Joanna

last: Holbrook

address: 30 Medical Drive

country: Singapore

institute: SICS

summary:
Infinium 450K is a hybridization array designed for the human genome, but the relative conservation between the macaque and human genomes makes its use in macaques feasible.
We used the Infinium450K array to assay twelve Cynomolgus macaque muscle biopsies and compared it to Reduced Representation Bisulphite Sequencing (RRBS) data generated on the same samples.

overall_design: Muscle biopsies were performed on eleven adult male cynomologus macaques


title: RNA clamping by Vasa assembles a piRNA Amplifier complex on transposon transcripts

status: Public on Jun 04 2014

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: Germline-specific Piwi-interacting RNAs (piRNAs) protect the genome against selfish  genetic elements and are essential for fertility in animals. piRNAs targeting active  transposons are amplified by a feed-forward loop known as the Ping-pong cycle, which  links endonucleolytic slicing of target RNAs by Piwi proteins to biogenesis of new  piRNAs. However, the biochemical framework for this pathway remains elusive. Here,  we describe the identification of a transient Amplifier complex mediating the biogenesis  of secondary piRNAs in insect cells. This complex is nucleated by the RNA helicase  Vasa and contains the two Piwi proteins participating in the Ping-pong loop, the Tudor  protein Qin/Kumo and antisense piRNA guides. These components assemble on the  surface of Vasa's helicase domain, which functions as an RNA clamp to anchor  Amplifier onto transposon transcripts. We show that ATP-dependent RNP remodelling  by Vasa facilitates the transfer of 5'-sliced piRNA precursors between the Ping-pong  partners, and failure to achieve this results in Drosophila female sterility.

overall_design: Immunoprecipitated small RNA were purified from untransfected or transfected Bmn4 cells for preparation of high-throughput sequencing libraries.

first: Jordi

last: Xiol

first: Pietro

last: Spinelli

first: Maike

last: Laussmann

first: David

last: Homolka

first: Zhaolin

last: Yang

first: Elisa

last: Cora

first: Yohann

last: Couté

first: Simon

last: Conn

first: Jan

last: Kadlec

first: Ravi

last: Sachidanandam

first: Marko

last: Kaksonen

first: Stephen

last: Cusack

first: Anne

last: Ephrussi


title: Comparison of nucleosome occupancy and chromatin states between normal and cancer cell lines

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

summary: Background: Epigenetic modification is a hallmark of cancer cells achieved through altered patterns of DNA methylation, histone modifications and nucleosome positions. These events have only been described in detail at gene promoters.  Results: Here, we integrate multiple epigenome-wide maps to evaluate the scope of global epigenetic reprogramming in cancer cells at enhancers and insulators. Using high-resolution simultaneous mapping of global DNA methylation and nucleosome positions within individual DNA strands (NOMe-Seq), we observe a reorganization of the DNA methylome coupled with simultaneous modulation of nucleosome depleted regions (NDRs) at distal regulatory elements in cancer cells. We show that while NDRs are preferentially found at enhancers in normal breast and prostate epithelial cells, there are fewer NDRs coupled with increased DNA methylation detected at enhancersin cancer cells. Our data suggests that the acquisition of a nucleosome is key to DNA hypermethylation susceptibility and contributes to epigenetic silencing of enhancers in cancer, which can notably occur without loss of H3K4me1. Further we observe that NDRs are not necessary for peripheral phasing of adjacent nucleosomes, contrary to the common dogma, and show that nucleosomes remain organized and phased, even in the absence of a NDR as an anchor. Finally we observe the potential for transcription factors (TF) to organize NDRs genome-wide; all TF-binding sites are strongly hypomethylated and some show extensive peripheral nucleosome phasing. Conclusion: Together our findings suggest that, in addition to epigenetic alterations to promoter regions in cancer, there is substantial disruption to the distal regulatory architecture that provides an additional layer of epigenetic plasticity in malignancy.

overall_design: NOMe-seq, ChIP-seq for 5 marks and input control for breast normal (HMEC), breast cancer (MCF7), prostate normal (PrEC) and prostate cancer (PC3) cell lines

middle: L

first: Phillippa

last: Taberlay


title: Infinium Monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis)

first: Joanna

last: Holbrook

type: Methylation profiling by genome tiling array

platform_organism:
Macaca fascicularis
Homo sapiens


title: Epigenomic comparison of distinct pluripotent stem cell states reveals a new class of enhancers with roles throughout mammalian development (ChIP-seq)

city: Clev

first: Paul

middle: J.

last: Tesar

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University School of Medicine

summary: Naïve mouse embryonic stem cells (mESCs) and primed epiblast stem cells (mEpiSCs) represent successive snapshots of pluripotency during embryogenesis. Using transcriptomic and epigenomic mapping, we show that a small fraction of transcripts are differentially expressed between mESCs and mEpiSCs and these genes show expected changes in chromatin at their promoters and enhancers. Unexpectedly, the cis-regulatory circuitry of genes that are expressed at identical levels between these cell states also differs dramatically. In mESCs, these genes are associated with dominant proximal enhancers and dormant distal enhancers, which we term seed enhancers. In mEpiSCs, the naïve-dominant enhancers are lost, and the seed enhancers take up primary transcriptional control. Seed enhancers have increased sequence conservation and show preferential usage in downstream somatic tissues, often expanding into super enhancers. We propose that seed enhancers ensure proper enhancer utilization and transcriptional fidelity as mammalian cells transition from naïve pluripotency to a somatic regulatory program.

overall_design: ChIP sequencing of histone modifications in mouse epiblast stem cells

first: Daniel

last: Factor


title: Epigenomic comparison of distinct pluripotent stem cell states reveals a new class of enhancers with roles throughout mammalian development (DNase-seq)

overall_design: DNase sequencing of histone modifications in mouse epiblast stem cells


title: Epigenomic comparison of distinct pluripotent stem cell states reveals a new class of enhancers with roles throughout mammalian development


title: Epigenomic comparison of distinct pluripotent stem cell states reveals a new class of enhancers with roles throughout mammalian development (RNA-seq)

overall_design: RNA sequencing in quadruplicate of mouse embryonic stem cells and epiblast stem cells


title: Chemical potentiator of copper-accumulation and -toxicity: Probing iron- regulons of Saccharomyces cerevisiae

city: Durham

first: Nigel

last: Robinson

address: South Road

department: Department of Chemistry, School of Biological and Biomedical Sciences

country: United Kingdom

institute: Durham University

summary: RNA-seq was used to assess mRNA transcript abundance in wild type and fra2Δ S. cerevisiae (BY4741) cells treated with 2-(6-benzyl-2-pyridyl)quinazoline (BPQ) and CuSO4. BPQ potentiates copper toxicity and in yeast, in common with other organisms, a major cause of copper toxicity is damage of iron-sulphur clusters. Iron sensing within yeast relies on mitochondrial iron-sulphur cluster biosynthesis and therefore treatment with BPQ and copper can be used to mimic iron deficiency. Fra2 is known to be a key component of the iron sensing mechanism; however, this mechanism can operate, to an extent, independently of Fra2. BPQ (+CuSO4) treatment was used with the aim of probing the regulation of the iron regulon of S. cerevisiae and the role of Fra2 in the suppression of the low iron response. This study has uncovered nine new Cth2 target-transcripts, plus a new Aft1 target-gene and paralogous non-target. Fra2 dominates basal repression of the iron regulon in iron-replete cultures, however, Fra2-independent control of the iron regulon is also observed with CTH2 appearing to be atypically Fra2-dependent. Transcripts from untreated and CuSO4 treated cells were included as controls.

overall_design: Three independent biological replicates were analysed for each condition (BPQ and CuSO4 treated wild type and fra2Δ cells, CuSO4 treated wild type and fra2Δ cells and untreated wild type and fra2Δ cells)

first: Andrew

middle: W

last: Foster

first: Samantha

last: Dainty

first: Andy

last: Corran


title: MOF-associated complexes have overlapping and unique roles in regulating pluripotency in embryonic stem cells and during differentiation [ChIP-seq]

city: Illkirch

first: Sarina

last: Ravens

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

summary: The histone acetyltransferase (HAT) Mof is essential for mouse embryonic stem cells (mESC) pluripotency and early development. Mof is the enzymatic subunit of two different HAT complexes, MSL (Male-Specific Lethal) and NSL (Non-specific lethal). The individual contribution of MSL and NSL complexes to transcription regulation in mESCs is not well understood. Our genome-wide analysis of MSL and NSL localization show that i) MSL and NSL bind to specific and common sets of expressed genes, ii) NSL binds at promoters, iii) while MSL binds in gene bodies. Knockdown of Msl1 leads to a global loss of histone H4K16ac indicating that MSL is the main HAT acetylating H4K16 in mESCs. MSL was enriched at many mESC-specific genes, but also at bivalent domains. Thus, NSL and MSL HAT complexes differentially regulate specific sets of expressed genes in mESCs. Furthermore, MSL is essential for the regulation of key mESC-specific and bivalent developmental genes.

overall_design: Genome-wide comparions of Msl1 and Nsl1 binding in mESCs

first: Marjorie

last: Fournier

first: Tao

last: Ye

first: Matthieu

last: Stierle

first: Doulaye

last: Dembele

first: Virginie

last: Chavant

first: Laszlo

last: Tora


title: Paternal RNA contributions in the C. elegans zygote

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Development of the early embryo is thought to be mainly driven by maternal gene products and post-transcriptional gene regulation. Here, we used metabolic labeling to show that RNA can be transferred by sperm into the embryo. To identify genes with paternal expression in the embryo, we performed crosses of males and females from divergent C. elegans strains. RNA sequencing of mRNAs and small RNAs in the 1-cell hybrid embryo revealed that about two hundred paternal mRNAs are reproducibly expressed in the embryo, and that about half of assayed endogenous siRNAs and piRNAs are also of paternal origin. Together, our results suggest an unexplored paternal contribution to early development.

overall_design: To reveal the identity of paternal RNA molecules, we performed a cross of males and females from two divergent C. elegans strains because we reasoned that sequencing of embryonic RNA and SNP analysis should then identify and quantify maternal and paternal transcripts. These sequencing experiments were carried out in purified hybrid 1-cell embryos and comprised small RNAs and mRNAs. For comparison we sequenced mRNAs and small RNAs from the parental strains: paternal (Hawaiian males, CB4856) and maternal (fem-1(hc17ts)/TX189(OMA-1::GFP). For the annotation of strain specific mutations (SNPs) we sequenced mRNA and small RNAs extracted from whole worms. All experiments were performed in at least two independent biological replicates.

first: Marlon

last: Stoeckius

first: Nikolaus

last: Rajewsky


title: Characterization of the human cumulus cell transcriptome during final follicular maturation and ovulation

city: Ramat Gan

first: Gil

last: Yerushalmi

address: 2 Sheba rd.

department: Obstetrics and Gynecology

country: Israel

institute: Sheba Medical Center

summary:
Purpose:  The goal of this study was to identify differentially expressed genes and pathways between the cumulus of compact/unstimulated cumulus-oocyte-complex  (COC) and the cumulus of expanded/stimulated COC.
Methods: mRNA profiles of  Compact/unstimulated cumulus cells (CCs) from germinal vesicle (GV) COC obtained from two patients undergoing unstimulated IVM procedure and  expanded/stimulated CCs from metaphase 2 (MII) COC obtained from three patients undergoing IVF/ICSI were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were mapped to the human genome (hg19) using Tophat software. Differential expression analysis was done using DESeq bioconductor package. qRT–PCR validation was performed using SYBR Green assays.
Results: A total of 40-80 million sequence reads per sample were mapped to the human genome (hg19). A total of 1746 differentially expressed genes between compact and expanded CCs with fold change > 2, and adjusted p value < 0.05 were identified. Gene ontology analysis of differentially expressed genes revealed a number of cellular processes regulated during the periovulatory interval including cellular movement, inflammatory response, immune cell trafficking, tissue development, lipid metabolism,  tissue morphology, DNA replication and cell cycle.  A total of 116 of the differentially expressed genes were annotated as long non-coding RNAs, 10 of them coded from introns of genes known to be involved in granulosa cell processes suggesting that unique non coding RNA transcripts may contribute to the regulation of cumulus expansion and oocyte maturation. Results were validated using qRT-PCR.
Conclusions: Using global transcriptome sequencing we identified new important genes and non coding RNAs involved in COC maturation and cumulus expansion, which may contribute to improve the process of in vitro maturation of immature oocytes utilized in IVM cycles

first: Mali

last: Salmon-Divon

first: Ariel

last: Hourvitz


title: Role of the Snf2-Related Protein required to maintain repression1 (RMR1) in Heterosis

city: Columbus

first: Joy-El

middle: Renee Barbour

last: Talbot

address: 574 Aronoff Lab, 318 W 12th Ave

department: Molecular and Cell Biology & Molecular Genetics

institute: University of California - Berkeley & The Ohio State University

summary:
Combining dissimilar parents often leads to increased vigor in the hybrid offspring.  “Heterosis” describes both this behavior and its underlying Mendelian and non-Mendelian interactions [1], although its molecular basis remains largely unknown.  Recent comparisons of small RNA (sRNA) profiles from parents and their heterotic progeny identified correlations between interparental 24-nucleotide (24-nt) RNA variation and non-additive 24-nt RNA changes in the resulting hybrid [2,3].  24-nt RNAs guide de novo cytosine methylation, and several proteins are required for their biogenesis, including a Snf2-like ATPase: required to maintain repression1 (RMR1) [4].  We found height variation between heterotic hybrids +/- RMR1 activity, implicating a role for RMR1 in heterosis.  Based on the published correlations mentioned above [2,3], we hypothesized that RMR1-loss reduces parental sRNAs, altering their relative ratios and changing the sRNA profiles in the resulting hybrid from those of a standard hybrid (from +RMR1 parents).  To probe this hypothesis, we profiled sRNAs from parents and hybrids +/- RMR1 function, limiting the parental diversity to only portions of chromosomes 6 and 9.  Our analysis will address how RMR1 loss changes hybrid sRNAs in the presence and absence of underlying genetic variation and help to determine how this loss results in different phenotypic outcomes from heterotic crosses.

1. Shull (1948) Genetics
2. Groszmann et al (2011) PNAS
3. Barber et al (2012) PNAS
4. Hale et al (2007) PLoS Biology

overall_design: We used an interchange chromosome (T6-9 043-1) introgressed into B73 (~95% B73) to create a local region of genetic diversity when crossed as a female parent to 100% B73 individual.  Small RNAs from immature cobs were sequenced from both of these parents and their resulting hybrid (2 samples each).  Additionally, a similar cross where the T6-9 containing female parent lacked RMR1 activity (rmr1-1 / rmr1-1) was used to generate a counterpart hybrid whose small RNAs were also profiled (2 samples) from immature cobs.  Finally, small RNAs from 2 immature cobs of an unrelated rmr1 heterozygote (again highly introgressed into B73) were sequenced as well.

middle: R

first: Irene

middle: T

last: Liao

first: Jay

last: Hollick


title: Next generation sequencing of small RNAs isolated from exosomes in human semen

city: Seattle

first: Sangsoon

last: Woo

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Preparation of exosomes isolated from semen contain a substantial amount of RNA, mostly from 20 to 100 nucleotides in length. We sequenced separately 20-40 and 40-100 nucleotide fractions of  RNA from exosomes isolated from semenal fluid from six healthy donors. We found various classes of small non-coding RNA, including mature microRNA and piwi-RNA,  as well as abundant Y RNAs and tRNAs present in both full length and fragmented forms. Specific RNAs were consistently present in all donors. For example, fifteen (of ~2,600 known) microRNAs constituted over 80% of mature microRNA in SE. Additionally, tRNA fragments were strongly enriched for 5’-ends of 18-19 or 30-34 nucleotides in length.

overall_design: Size-fractionated small RNA profiles from exosomes isolated from the seminal fluid of six healthy donors

first: Florian

last: Hladik

first: Lucia

middle: N

last: Vojtech


title: TET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells [DREAM]

city: Houston

first: CHUNLEI

last: JIN

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: We report that full length TET1 (TET1-FL) overexpression fails to induce global DNA demethylation in HEK293T cells. The preferential binding of TET1-FL to hypomethylated CpG islands (CGIs) through its CXXC domain leads to its inhibited 5-hydroxymethylcytosine (5hmC) production as methylation level increases. TET1-FL-induced 5hmC accumulates at CGI edges, while TET1 knockdown induces methylation spreading from methylated edges into hypomethylated CGIs. However, TET1 can regulate gene transcription independent of its dioxygenase catalytic function. Thus, our results identify TET1 as a maintenance DNA demethylase that does not purposely decrease methylation levels, but specifically maintains the DNA hypomethylation state of CGIs in adult cells.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the DNA methylation profiles of HEK293T cells overexpressing mTET1-CD, TET1-CD, mTET1-FL, or TET1-FL. In this approach, genomic DNA is sequentially cut at CCCGGG sites with the methylation sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5’CCGG overhangs), creating different end sequences that represent methylation status of the CCCGGG sites. These end sequences are analyzed by next generation sequencing, and thereafter the methylation status at individual CCCGGG sites across the genome can be determined.

first: Chunlei

last: Jin

first: Yue

last: Lu

first: Jaroslav

last: Jelinek

first: Shoudan

last: Liang

first: Marocs

last: Estecio

first: Michelle

last: Barton

first: Jean-Pierre

last: Issa


title: TET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells

overall_design: Refer to individual Series


title: TET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells [MeDIP-Seq]

overall_design: hMeDIP-seq analysis of genomic 5-hydroxymethylcytosine in HEK293T cells overexpressing mTET1-CD, TET1-CD, mTET1-FL, or TET1-FL

first: Marcos


title: Genome-wide localization of Trf2 and TBP in Drosophila embryos

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

summary: Here we use ChIP-seq in Drosophila embryos to determine the genome-wide binding pattern of TBP and Trf2 using two different antibodies for each factor.

overall_design: ChIP-seq using anti-Trf2 and anti-TBP antibodies in Drosophila embryos

first: Yuan

last: Wang

first: Kai

last: Chen

first: Jeff

last: Johnston

first: James

last: Kadonaga

first: Sascha

last: Duttke

first: George

last: Kassavetis


title: Acinetobacter oleivorans DR1 : Cell treated Kanamycin 4 µg/ml in nutrient media

status: Public on Jun 03 2014

city: Seoul

first: Aram

last: Heo

address: Anam Campus, Anam-dong 5-ga, Seongbuk-gu

department: Environmental Science and Ecological Engineering

institute: Korea university

summary: Transcriptional profiling of A. oleivorans DR1  treated Kanamycin 4µg/ml for 15min  .

overall_design: To identify effect of kanamycin in A. oleivornas DR1, the cells were grown to exponential phase (OD600 ~0.4) and treated kanamycin 4µg/ml for 15 min.

first: Woojun

last: Park


title: LIN-42, the Caenorhabditis elegans PERIOD homolog, negatively regulates microRNA transcription

city: Cold Spring Harbor

first: Roberto

last: Perales

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: We performed ChIP-seq analysis of LIN-42 from extracts obtained from staged late L4 hermaphrodites. We found 413 high confidence peaks that are predominately found at promoter regions and transcription start sites of mRNA and microRNA genes.

overall_design: ChIP assays using a functional GFP tagged transgene of LIN-42 using an anti-GFP antibody, as well as using an antibody raised agans the endogenous LIN-42 protein.

first: Christopher

last: Hammell


title: Acinetobacter oleivorans DR1 : Cell treated Ampicillin 100 µg/ml in nutrient media

summary: Transcriptional profiling of A. oleivorans DR1  treated Ampicillin 100 µg/ml for 15min  .

overall_design: To identify effect of ampicillin in A. oleivornas DR1, the cells were grown to exponential phase (OD600 ~0.4) and treated  ampicillin 100 µg/ml for 15 min.


title: MOF-associated complexes ensure stem cell identity and Xist repression

city: New York

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

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


title: Taf7l Modulates Brown Adipose Tissue Formation

city: Berkeley

first: Haiying

last: Zhou

address: 188 Li Ka Shing Center

department: MCB

institute: HHMI/UCB

summary: Brown adipose tissue (BAT) plays an essential role in metabolic homeostasis by dissipating energy via thermogenesis through uncoupling protein 1 (Ucp1). Previously, we reported that the TATA-binding protein Associated Factor 7L (Taf7l) is an important regulator of white adipose tissue (WAT) differentiation. Here, we show that Taf7l also serves as a molecular switch between brown fat and muscle lineages in vivo and in vitro. In adipose tissue, Taf7l containing TFIID complexes associate with PPAR to mediate DNA looping between distal enhancers and core promoter elements. Our findings suggest that presence of the tissue-specific Taf7l subunit in TFIID functions to promote long-range chromatin interactions during BAT lineage specification.

overall_design: mRNA-seq expression profiling wild type and Taf7l knockout interscapular brown adipose tissue (BAT)

first: Bo

last: Wan

first: Ivan

last: Grubisic

first: Tommy

last: Kaplan

first: Robert

last: Tjian


title: RNA-Seq using two populations reveals genes and alleles controlling wood traits and growth in Eucalyptus nitens

city: Acton

first: Saravanan

last: Thavamanikumar

state: ACT

address: Clunies Ross Street

institute: CSIRO

summary:
Purpose: Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY.
Methods: We analyzed samples from the extremes of the distribution of KPY in two Eucalyptus nitens trials which also differed in growth to identify genes having differential expression between high and low KPY samples. We used reference-guided transcriptome mapping to study gene expression.
Results: Several genes showed differential expression between low and high KPY samples. Gene ontology (GO) enrichment tests revealed up-regulation of stress-related gene categories and down-regulation of gene categories related to wood formation and growth in low KPY samples. More than 110,000 single nucleotide polymorphisms (SNPs) were detected in both the trials and 2103 of these showed differential allelic expression. Allelic expression of 30% of these variants was correlated with total gene expression. To identify the genes showing patterns of positive selection among the genes expressed in the cambial tissue we compared Ka/Ks ratios. The Ka/Ks ratios compare the rate of nonsynonymous substitutions (Ka) to synonymous substitutions (Ks) which can help identifying genes under selection. By comparing the two trials we observed in total 196 genes which had Ka/Ks ratios of more than 1.5 in both the trials strongly suggesting that these genes are under positive selection. A total of six GO categories were enriched in both trials for genes showing signatures of positive selection . All six categories include genes involved in apoptosis, cell death and defense responses.
Conclusions: By conducting RNA-Seq analysis in two trials we identified a number of candidate genes and alleles whose expression is correlated with KPY and growth traits in E. nitens. Most of the down-regulated genes in low KPY samples are cell wall-related genes, suggesting that the identified candidate genes are biologically relevant. A number of potential functional polymorphisms were also identified that showed DAE. We detected positive selection signatures in numerous genes that are consistent with the results from RNA-Seq study in E. camaldulensis. The genes and alleles identified in this study form a valuable resource for association and genomic selection studies.

overall_design: Xylem mRNA profiles of Eucalyptus nitens from low and high KPY samples were generated by deep sequencing, in two trials, using Illumina HiSeq.

first: Bala

last: Thumma


title: High-throughput SuperSAGE for transcript profiling in berry tissues of Vitis vinifera L. under different light regimes

city: Higashi-Hiroshima

first: Kazuya

last: Koyama

state: Hiroshima

address: 3-7-1, Kagamiyama

department: Fundamental Reesearch Division

institute: National Research Institute of Brewing

summary: SuperSAGE is a method of digital gene expression profiling that allows isolation of 26bp tag fragments from expressed transcripts. Because its tag size is larger than that of conventional SAGE, SuperSAGE allowed a secure tag-to-gene annotation using BLAST search against grape genome databases.Transcript profiles in nine samples of grape berry tissues under different light conditions were obtained by SuperSAGE analysis and used for screening the genes which have co-ordinated transcript profiles with the change in the flavonoid composition in the samples analyzed. Candidate genes related to flavonoid biosynthesis and regulation were identified.

overall_design: Nine different grape samples, i.e., flowers, grape berries of Cabernet Sauvignon at 2, 7, 9 weeks after flowering (WAF), berry skins at 17 days after flowering (DAF) shaded after flowering, and berry skins at 17DAF shaded from flowering to 14DAF and then light exposed, were analyzed.

first: Hideo

last: Matsumura


title: SPIB and BATF provide alternate determinants of IRF4 occupancy in Diffuse Large B-cell Lymphoma linked to disease heterogeneity

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

summary: ChIP-seq data for the transcription factors (TFs) IRF4, PU.1 and SPIB from the cell lines OCI-LY3, OCI-LY10 and H929, and BATF from the cell lines OCI-Ly3 and OCI-Ly10. In addition ChIP-seq for the TFs IRF4, PU.1 and SPIB from the cell line OCI-LY3 following transfections of scramble/SPIB-siRNA.

first: Mario

last: Cocco

first: Reuben

last: Tooze


title: Functional characterization of a new grapevine MYB transcription factor and regulation of proanthocyanidin biosynthesis in grapes

sample_organism:
Arabidopsis thaliana
Vitis vinifera

platform_organism:
Arabidopsis thaliana
Vitis vinifera


title: Cell-type restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing

city: Chicago

first: Chonghui

last: Cheng

state: IL

address: 303 E Superior Street, Robert H. Lurie Comprehensive Cancer Center 5-119

department: Hematology/Oncology Division, Feinberg School of Medicine

institute: Northwestern University

summary: Tumor metastasis remains the major cause of cancer-related death, but its molecular basis is still not well understood. Here we uncovered a splicing-mediated pathway that is essential for breast cancer metastasis. We show that the RNA-binding protein hnRNPM promotes breast cancer metastasis by activating the switch of alternative splicing that occurs during epithelial-mesenchymal transition (EMT). Genome-wide deep sequencing analysis suggests that hnRNPM potentiates TGFb signaling and identifies CD44 as a key downstream target of hnRNPM. hnRNPM ablation prevents TGFb-induced EMT and inhibits breast cancer metastasis in mice, whereas enforced expression of the specific CD44s splice isoform overrides the loss of hnRNPM and permits EMT and metastasis. Mechanistically, we demonstrate that the ubiquitously expressed hnRNPM acts in a mesenchymal-specific manner to precisely control CD44 splice isoform switching during EMT. This restricted cell-type activity of hnRNPM is achieved by competition with ESRP1, an epithelial-splicing regulator that binds to the same cis-regulatory RNA elements and is repressed during EMT. Importantly, hnRNPM is associated with aggressive breast cancer and correlates with increased CD44s in patient specimens. These findings demonstrate a novel molecular mechanism through which tumor metastasis is endowed by the hnRNPM-mediated splicing program.

overall_design: RNAseq for control, hnRNPM siRNA treated lung metastatic LM2 clonal line, derived from the mesenchymal MDA-MB-231 cells

first: Xiao

last: Xinshu

first: Cheng

last: Chonghui


title: ChIP-seq of MOF, MSL and NSL complex members in mouse ES cells and neuronal progenitors

summary: We assessed the genome-wide binding of the histone acetylase MOF and members of its two associated complexes, the male-specific lethal and the non-specific lethal complex (MSL, NSL). We generated ChIP-seq profiles for MOF, MSL1, MSL2, KANSL3, and MCRS1 from mouse embryonic stem cells and neuronal progenitor cells.  By using two replicates per sample and stringent filtering criteria, we identify five basic groups of genome regions where the proteins show either mutual or exclusive binding. We find that the NSL complex members (KANSL3, MCRS1) target the TSSs of broadly expressed genes with housekeeping functions in both cell types. MOF and particularly the MSL complex target a subset of these NSL-complex-targets, too. In addition, we find several thousand TSS-distal binding sites, particularly in ESCs, where KANSL3, MSL2 and MCRS1 show strong enrichments for annotated ESC enhancers. The vast majority of the binding to these ESC distal regulatory elements is lost in NPCs. Finally, we identify mostly intronic and intergenic regions with predominant MSL2 enrichments without the presence of its known interactors. These binding sites do not overlap with ESC marks of active chromatin (e.g. DNase hypersensitivity sites), but the they increase in number upon differentiation and we detect a strong signature of the (CAGA)n motif. Our study provides the first comprehensive analysis of MOF in the context of its two complexes in the mouse and reveals shared as well as distinct and dynamic functions for gene regulation and pluripotency.

overall_design: ChIP-seq of MOF and members of its associated complexes (MSL complex: MSL1, MSL2; NSL complex: KANSL3, MCRS1) in male mouse embryonic stem cells and  neuronal progenitor cells derived from them.

first: Tomasz

last: Chelmicki

last: Turley

first: Khanam

last: Tasneem

first: Tugce

last: Aktas

first: Fidel

last: Ramirez

first: Anne-Valerie

last: Gendrel

first: Edith

last: Heard

first: Thomas

last: Manke

first: Asifa

last: Akhtar


title: Identification of genes regulated by Rcor1 in CD71+, TER119- erythroid progenitors using mRNA-seq analysis

city: Portland

first: Huilan

last: Yao

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: OHSU

summary: Transcription cofactor Rcor1 has been linked biochemically both to neurogenesis and hematopoiesis. Here we studied the function of Rcor1 in vivo and showed it is essential to erythropoeisis during embryonic development. Rcor1 mutant proerythroblasts, unlike normal cells, can form myeloid colonies in vitro. To investigate the underlying molecular mechanisms for block of erythropoiesis and increased myeloid potential, we used RNA-seq to reveal the differentially expressed genes from erythroid progenitors due to depletion of Rcor1.

overall_design: RNA were extracted from FACS sorted CD71+,TER119- erythroid progenitors from control (Rcor1+/+ and Rcor1+/-) or Mutant (Rcor1-/- ) E13.5 fetal liver. Each library was made by pooling RNA from several fetal livers. Two biological replicates were made for either control or mutant condition.

first: Mandel

last: Gail


title: Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (K9 KO Methyl-Seq)

city: Zurich

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

institute: Uiversity Hospital Zurich

summary: During mammalian development DNA methylation patterns need to be reset in primordial germ cells (PGC) and preimplantation embryos. However, many retro-transposons and imprinted genes are resistant to such global epigenetic reprogramming via hitherto undefined mechanisms. Here, we report that some of these sequences are immune to widespread erasure of DNA methylation in the mouse embryonic stem cells (mESCs) lacking de novo DNA methyltransferases. Persistence of DNA methylation at these loci in mESCs depends on the histone H3K9 methyltransferase Setdb1, as deletion of Setdb1 results in reduction of H3K9me3 and DNA methylation levels concomitant with an increase in 5-hydroxymethylation (5hmC). In addition, depletion of H3K9 methyltransferase G9a leads to genome-wide reduction of DNA methylation but to a lesser extent at the above sequences. Taken together, these data reveal that Setdb1 ensures the fidelity of DNA methylation at specific loci in mESCs, which may reflect mechanisms functioning in vivo during key developmental stages.

overall_design: Examination of genome-wide DNA methylation status in 3 cell types.

first: Danny

last: Leung

first: Tingting

last: Du

first: Wei

last: Xie

first: Ah

middle: Y

last: Lee

first: Preeti

last: Goyal

first: Yujing

last: Li

first: Keith

middle: E

last: Szulwach

first: Peng

last: Jin

last: Lorincz

first: Bing

last: Ren


title: TET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells [RNA-seq]

first: CHUNLEI

last: JIN

overall_design: Genome-wdie profiling of gene expression in HEK293T cells following overexpression of wild type or catalytically mutant TET1-FL or TET1-CD

first: Chunlei

first: Yue

last: Lu

first: Jaroslav

last: Jelinek

first: Shoudan

last: Liang

first: Marcos

last: Estecio

first: Michelle

last: Barton

first: Jean-Pierre

last: Issa


title: Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (K9 KO ChIP-Seq)

first: Ulrich

last: Wagner

overall_design: Examination of H3K9me3 histone modifications in 2 cell types.

first: Danny

last: Leung

first: Matthew


title: Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO ChIP-Seq)

first: Tingting

last: Du

first: Wei

last: Xie

first: Ah


title: Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO RNA-Seq)

overall_design: Examination of gene expression in 2 cell types by RNA-seq.

last: Lee

first: Preeti

last: Goyal

first: Yujing

first: Keith


title: Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases


title: Histone variant H3.3 is an essential maternal factor for oocyte reprogramming

status: Public on Jun 02 2014

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

summary: Mature oocyte cytoplasm can reprogram somatic cell nuclei to the pluripotent state through a series of sequential events including protein exchange between the donor nucleus and ooplasm, chromatin remodeling, and pluripotency gene reactivation. Maternal factors that are responsible for this reprogramming process remain largely unidentified. Here, we demonstrate that knockdown of histone variant H3.3 in mouse oocytes results in compromised reprogramming and down-regulation of key pluripotency genes; and this compromised reprogramming both for developmental potentials and transcription of pluripotency genes can be rescued by injecting exogenous H3.3 mRNA, but not H3.2 mRNA into oocytes in somatic cell nuclear transfer (SCNT) embryos. We show that maternal H3.3, and not H3.3 in the donor nucleus, is essential for successful reprogramming of somatic cell nucleus into the pluripotent state. Furthermore, H3.3 is involved in this reprogramming process by remodeling the donor nuclear chromatin through replacement of donor nucleus-derived H3 with de novo synthesized maternal H3.3 protein. Our study shows that H3.3 is a crucial maternal factor for oocyte reprogramming and provides a practical model to directly dissect the oocyte for its reprogramming capacity.

overall_design: Transcriptome sequencing of 4-cell NT embryos, Luciferase 4-cell SCNT embryos, 4-cell NT embryos_H3.3KD, 4-cell NT embryos_H3.3KD+H3.3mRNA, H3.3 KD + H3.2 mRNA SCNT embryos

first: Duanchen

last: Wen

first: Laura

last: Banaszynski

first: C

middle: D

last: Allis

first: Shahin

last: Rafii


title: Cooperativity and Equilibrium with FOXA1 Define Androgen Receptor Transcriptional Program

first: Hong-Jian

last: Jin

state: IL - Illinois

address: 303 E Superior St

overall_design: Refer to individual Series


title: The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

institute: University of Bern


title: The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis [ChIP-Seq]

summary: The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in phoP lead to compromised production of pathogen-specific cell wall components and attenuation both ex vivo and in vivo. Using antibodies against the native protein in ChIP-seq experiments (chromatin immunoprecipitation followed by high-throughput sequencing) we demonstrated that PhoP binds to at least 35 loci on the M. tuberculosis genome. The PhoP regulon comprises several transcriptional regulators as well as genes for polyketide synthases and PE/PPE proteins. Integration of ChIP-seq results with high-resolution transcriptomic analysis (RNA-seq) revealed that PhoP controls 30 genes directly, whilst regulatory cascades are responsible for signal amplification and downstream effects. The most prominent site of PhoP regulation was located in the intergenic region between rv2395 and PE_PGRS41, where the mcr7 gene codes for a small non-coding RNA (ncRNA). Northern blot experiments confirmed the absence of Mcr7 in the M. tuberculosis phoP mutant as well as low-level expression of the ncRNA in M. tuberculosis complex members other than M. tuberculosis. By means of genetic and proteomic analyses we demonstrated that Mcr7 modulates translation of the tatC mRNA thereby impacting the activity of the Twin Arginine Translocation (Tat) protein secretion apparatus. As a result, secretion of the immunodominant Ag85 complex and the beta-lactamase BlaC is affected, among others. Mcr7, the first ncRNA of M. tuberculosis whose function has been established, therefore represents a missing link between the PhoPR two-component system and the downstream functions necessary for successful infection of the host.

overall_design: ChiP-Seq: M. tuberculosis H37Rv (GC1237) cultures grown in vitro to exponential phase. Two wild type samples plus one isogenic phoP mutant as control

first: Luis

last: Solans

first: Jesús

last: Gonzalo-Asensio

first: Claudia

last: Sala

first: Christophe

last: Guilhot

first: Jacques

last: Rougemont

first: Carlos

last: Martín

first: Stewart

last: Cole


title: FoxA1 inhibits androgen receptor expression and suppresses prostate cancer metastasis [LNCaP, ChIP-seq]

summary: FoxA1 has been shown critical for prostate development and prostate-specific gene expression regulation. In addition to its well-established role as an AR pioneering factor,several studies have recently revealed significant AR binding events in prostate cancer cells with FoxA1 knockdown. Furthermore, the role of FoxA1 itself in prostate cancer has not been carefully examined.  Thus, it is important to understand the role of FoxA1 in prostate cancer and how it interacts with AR signaling. To address these questions, we generated LNCaP cells with stable FoxA1 knockdown.  We performed AR/FoxA1 ChIP-seq and microarray analysis of these cells.

overall_design: ChIP_Seq examination of AR and FoxA1 binding sites in LNCaP shCtrl and shFoxA1 cells

first: Hongjian

first: Jindan

last: Yu


title: Interactions of ARF6 with PIF4, BZR1, and RGA integrate auxin signaling with environmental and other hormonal signals in Arabidopsis [RNA-Seq]

city: Stanford

first: Eunkyoo

last: Oh

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution

summary: Auxin is a major plant hormone for both development and environmental adaptation. Auxin responses are context dependent and highly modulated by light, temperature, the circadian clock, brassinosteroid, and gibberellin, but the underlying mechanisms remain unclear. Here, we show that auxin signaling integrates with other signals through direct interactions of AUXIN RESPONSE FACTOR6 (ARF6) with PHYTOCHROME INTERACTING FACTOR4 (PIF4), the brassinosteroid-signaling transcription factor BZR1, and the gibberellin-signaling repressor RGA.  ChIP-Seq and RNA-Seq experiments show that ARF6, PIF4, and BZR1 bind to largely overlapping targets in the genome and synergistically activate gene expression. In vitro and in vivo assays show that ARF6-promoter binding is enhanced by PIF4 and BZR1 but blocked by RGA. Furthermore, a tripartite HLH/bHLH module feedback regulates PIF activity and thus modulates auxin sensitivity according to additional developmental and environmental cues. Our results demonstrate a central growth-regulation transcriptional network that coordinates hormonal, environmental, and developmental control of cell elongation and plant growth.

overall_design: Seedlings (Col-0 and iaa3) were grown on medium containing 2 µM propiconazole (PPZ) in the dark for 5 days and treated with mock or 100 nM BL for 4 hr before harvesting for total RNA extraction.

first: Zhiyong

last: Wang


title: Genomic Determinants of Gene Regulation by 1,25-Dihydroxyvitamin D3 During Osteoblast-Lineage Cell Differentiation [ChIP-Seq]

city: Madison

first: Mark

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

summary: The biological effects of 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) on osteoblast differentiation and function differ significantly depending upon the cellular state of maturation.  To explore this phenomenon mechanistically, we examined the impact of 1,25(OH)2D3 on the transcriptomes of both pre-osteoblastic (POBs) and differentiated osteoblastic (OBs) MC3T3-E1 cells, and assessed localization of the vitamin D receptor (VDR) at sites of action on a genome-scale using ChIP-seq analysis. We observed that the 1,25(OH)2D3-induced transcriptomes of POBs and OBs were quantitatively and qualitatively different, supporting not only the altered biology observed but the potential for a change in VDR interaction at the genome as well.  This idea was confirmed through discovery that VDR cistromes in POBs and OBs were also strikingly different.  Depletion of VDR binding sites in OBs, due in part to reduced VDR expression, was the likely cause of the loss of VDR-target gene interaction. Continued novel regulation by 1,25(OH)2D3, however, suggested that factors in addition to the VDR might also be involved.  Accordingly, we show that transcriptomic modifications are also accompanied by changes in genome binding of the master osteoblast regulator RUNX2 and the chromatin remodeler C/EBPβ.  Importantly, genome occupancy was also highlighted by the presence of epigenetic enhancer signatures which were selectively changed in response to both differentiation and 1,25(OH)2D3. The impact of VDR, RUNX2, and C/EBPβ on osteoblast differentiation is exemplified by their actions at the Runx2 and Sp7 gene loci.  We conclude that each of these mechanisms may contribute to the diverse actions of 1,25(OH)2D3 on differentiating osteoblasts.

overall_design: 4 transcription factors and 5 histone modifications were examined in undifferentiated MC3T3-E1 cells as well as post 15 day osteogenic differentiation MC3T3-E1 cells, which were treated for 3 hours prior to ChIP assay with ethanol vehicle or with 10-7M 1,25(OH)2D3. For the vehicle matched samples for RUNX2, CEBP beta and histones, please refer to study GSE41955.  The samples were completed in biological replicate and examined separately.

first: Nancy

last: Benkusky

first: J

last: Pike


title: FoxA1 inhibits androgen receptor expression and suppresses prostate cancer metastasis [DU145, ChIP-seq]

summary: FoxA1 has been shown critical for prostate development and prostate-specific gene expression regulation. In addition to its well-established role as an AR pioneering factor,several studies have recently revealed significant AR binding events in prostate cancer cells with FoxA1 knockdown. Furthermore, the role of FoxA1 itself in prostate cancer has not been carefully examined.  Thus, it is important to understand the role of FoxA1 in prostate cancer and how it interacts with AR signaling.

overall_design: ChIP-Seq examination of AR and FoxA1 binding sites, FAIRE-seq detection of open chromatin genomic regions in DU145 AR +/- FOXA1 cells


title: Small-RNA expression in normal and malignant mature B cells

status: Public on Jun 01 2014

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: Small-RNA profiles were generated for normal mature germinal center (GC) B cells and GC-derived lymphomas.

overall_design: Normal and tumor samples are derived from different donors.

first: Katia

last: Basso

first: Antony

last: Holmes


title: Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

country: Netherlands

institute: Erasmus MC


title: Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO Methyl-Seq)

first: Ulrich

last: Wagner

overall_design: Examination of genome-wide DNA methylation status in 2 cell types.

first: Danny

last: Leung

first: Tingting

last: Du

first: Wei

last: Xie

first: Ah

last: Lee

first: Preeti

last: Goyal

first: Yujing

last: Li

first: Keith

last: Szulwach

first: Peng

last: Jin

first: Matthew

last: Lorincz

first: Bing

last: Ren


title: Evolution and genetic architecture of chromatin accessibility and function in yeast

city: Worcester

first: Caitlin

middle: F

last: Connelly

state: MA

address: 364 Plantation Street, LRB

department: Biochemistry & Molecular Pharmacology

institute: University of Massachusetts Medical School

summary: Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects.  Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign.

sample_organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

overall_design: There are 20 samples in total. These consist of 10 FAIRE-seq samples, specifically 6 haploid samples, S. cerevisiae strain UWOPS05_217_3 replicates 1 and 2, S. cerevisiae strain DBVPG1373 replicates 1 and 2, and S. paradoxus strain CBS432 replicates 1 and 2.  There are also 4 diploid hybrid samples, hybrid between S. cerevisiae strain UWOPS05_217_3 and S. paradoxus strain CBS432 replicates 1 and 2, and the hybrid between S. cerevisiae strain DBVPG1373 and S. paradoxus strain CBS432 replicates 1 and 2.  There are also RNA-seq samples for each of these 10 samples.

first: Jon

last: Wakefield

first: Joshua

middle: M

last: Akey


title: Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines (ChIP-seq data).

summary:
Background: Germ Cell Cancers (GCC), originating from Primordial Germ Cells /gonocytes, are the most common cancer in young men, subdivided in seminoma (SE) and non-seminoma (NS, stem cell component: embryonal carcinoma (EC)). Somatic mutations are rarely found in GCC. It has been proposed that disruption of the epigenetic constitution, either primarily or secondary (e.g. environmental influences), is involved in cancer, and specifically in GCC.
Results: This study aims at identifying epigenetic footprints of SE and EC cell lines in genome-wide profiles by studying the interaction between gene expression, DNA CpG methylation and histone modifications, and their function in GCC and related disruption of germ cell maturation. Two well characterized GCC-derived cell lines were compared, one representative for SE (TCam-2) and the other for EC (NCCIT). Data was acquired using the Illumina HumanHT-12-v4 (gene expression) and HumanMethylation450 BeadChip (methylation) microarrays as well as ChIP sequencing (activating histone modifications (H3K4me3, H3K27ac)). The data show that known germ cell markers are not only present and differentiating between SE and NS at the expression level, but also in the epigenetic landscape.
Conclusion: The overall similarity between TCam-2 / NCCIT supports an erased embryonic gem cell arrested in early gonadal development as common origin. Subtle difference in the (integrated) epigenetic and expression profiles indicated TCam-2 to exhibit a more germ cell like profile (enrichment Androgen regulation) while NCCIT proved more pluripotent. The results provide insight into an integrated analysis of the functional genome in GCC cell lines.

overall_design: Two wildtype germ cell cancer (type II germ cell tumor) cell lines were analyzed. TCam-2 (representative for the seminomatous subtype of germ cell cancer) , [1, 2]) and NCCIT (representative of the non-seminomatous (embryonal carcinoma) subtype of germ cell cancer, [3]). Of each cell line two biological replicates were included. Genomic positions reported are based on the GRch37/hg19 assembly.  1. Mizuno, Y., et al., [Establishment and characterization of a new human testicular germ cell tumor cell line (TCam-2)]. Nihon Hinyokika Gakkai Zasshi, 1993. 84(7): p. 1211-8.  2. de Jong, J., et al., Further characterization of the first seminoma cell line TCam-2. Genes Chromosomes Cancer, 2008. 47(3): p. 185-96.  3. Teshima, S., et al., Four new human germ cell tumor cell lines. Lab Invest, 1988. 59(3): p. 328-36.

first: Yvonne

last: van der Zwan

middle: A

first: Fernando

middle: J

last: Rossello

first: Amanda

last: Notini

first: Suzan

last: de Boer

first: D

last: Watkins

first: Ad

last: Gillis

first: Lambert

middle: C

last: Dorssers

first: Stefan

last: White

first: Leendert

middle: H

last: Looijenga


title: Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome [ChIP-Seq]

city: Los Angeles

first: Jared

last: Peace

state: CA - California

address: 1050 Childs Way RRI 203

department: Molecular and Computational Biology

institute: University of Southern California

summary: Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins.  Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase.  This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors.  Rif1 has recently been identified as a genome-wide regulator of replication timing in fission yeast and in mammalian cells.  However, previous studies in budding yeast have suggested that Rif1’s role in controlling replication timing may be limited to subtelomeric domains and derives from its established role in telomere length regulation.  We have analyzed replication timing by analyzing BrdU incorporation genome-wide, and report that Rif1 regulates the timing of late/dormant replication origins throughout the S. cerevisiae genome.  Analysis of pfa4∆ cells, which are defective in palmitoylation and membrane association of Rif1, suggests that replication timing regulation by Rif1 is independent of its role in localizing telomeres to the nuclear periphery.  Intra-S checkpoint signaling is intact in rif1∆ cells, and checkpoint-defective mec1∆ cells do not comparably deregulate replication timing, together indicating that Rif1 regulates replication timing through a mechanism independent of this checkpoint.  Our results indicate that the Rif1 mechanism regulates origin timing irrespective of proximity to a chromosome end, and suggest instead that telomere sequences merely provide abundant binding sites for proteins that recruit Rif1.  Still, the abundance of Rif1 binding in telomeric domains may facilitate Rif1-mediated repression of non-telomeric origins that are more distal from centromeres.

overall_design: 4 samples BrdU-IP-seq in HU, 2 strains with 2-replicates each (strains:WT and rif1 delta)

first: Anna

last: Ter-Zakarian

first: Oscar

last: Aparicio


title: Transcriptional gene silencing by Arabidopsis Microrchidia homologues involves the formation of heteromers

city: Seattle

first: Christopher

middle: Joel

last: Hale

address: 1959 NE Pacific St., HSC H-458

institute: University of Washington

summary: Epigenetic gene silencing is of central importance to maintain genome integrity and is mediated by an elaborate interplay between DNA methylation, histone posttranslational modifications and chromatin remodeling complexes. DNA methylation and repressive histone marks usually correlate with transcriptionally silent heterochromatin, however there are exceptions to this interdependence. In Arabidopsis, mutation of MORPHEUS MOLECULE 1 (MOM1) causes transcriptional derepression of heterochromatin independently of changes in DNA methylation. More recently, two Arabidopsis homologs of mouse Microrchidia (MORC) have also been implicated in gene silencing and heterochromatin condensation without altering genome-wide DNA methylation patterns. In this study, we show that AtMORC6 physically interacts with AtMORC1 and with its close homologue AtMORC2 in two mutually exclusive protein complexes. RNA-seq analysis of high-order mutants indicates that AtMORC1 and AtMORC2 act redundantly to repress a common set of loci. We also examined the genetic interactions between AtMORC6 and MOM1 pathways. Although AtMORC6 and MOM1 control the silencing of a very similar set of genomic loci, we observed synergistic transcriptional regulation in the mom1/atmorc6 double mutant, suggesting that these epigenetic regulators act mainly by independent silencing mechanisms.

overall_design: RNA-seq libraries were prepared for two suites of mutants to allow direct comparisons between mutants within each set. The two sets consisted of the following samples: Set_1) A wildtype (Col) control, the morc1 mutant, the morc2 mutant, the morc1 morc2 double mutant, the morc6 mutant, and the morc1 morc2 morc6 triple mutant ; Set_2) A wildtpe (Col) control, the morc6 mutant, the mom1 mutant, and the mom1 morc6 double mutant. For each sample, two biological replicates were performed (denoted "bio_replicate_1" or "bio_replicate_2"). Whole genome bisulifte libraries were sequenced from material grown in parallel.


title: Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome

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


title: Native Elongating Transcript sequencing (NET-seq) in wild-type and three members of the CAF-I complex

city: Boston

first: Steve

last: Buratowski

address: 240 Longwood Ave

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: We performed a fluorescent reporter based screen to identify factors determining transcriptional directionality from bidirectional promoters that give rise to a coding and a non-coding transcript. Promoters like these are most frequent in many organisms and non-coding transcription from this origin represents a large fraction of total long non-coding transcripts. We applied NET-seq to compare nascent transcription in yeast wild-type and mutations in the three members of the CAF-I complex. This technique avoids the technical issue of co-transcriptional RNA degradation and is a powerful approach to address questions concerning non-coding transcription. We find divergent non-coding transcription to be elevated in CAF-I mutants.

overall_design: One condition, yeast grown in YPD media to mid-log phase. 8 NET-seq libraries are deposited, 2 biological repeats of the wild-type and two biological repeast each of the CAF-I complex member mutants (CAC1, CAC2, CAC3).

first: Sebastian

last: Marquardt

first: Renan

last: Escalante-Chong

first: Nam

last: Pho

first: Jue

last: Wang

first: L

middle: S

last: Churchman

first: Michael

last: Springer

first: Stephen


title: The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis [RNA-Seq]

first: Andrej

last: Benjak

overall_design: RNA-Seq: M. tuberculosis H37Rv (GC1237) cultures grown in vitro to exponential phase. One wild type sample plus one isogenic phoP mutant sample

first: Luis

last: Solans

first: Jesús

last: Gonzalo-Asensio

first: Claudia

last: Sala

first: Swapna

last: Uplekar

first: Jacques

last: Rougemont

first: Christophe

last: Guilhot

first: Carlos

last: Martín

first: Stewart

last: Cole


title: Coordinating Expression of RNA Binding Proteins with Their mRNA Targets

city: Tianjin

first: Huifeng

last: Jiang

address: #32XiQiDao Tianjin airport economic park

institute: Tianjin Institute of Industrial Biotechnology

summary: Post-transcriptional regulation by RNA binding proteins (RBPs) plays prominent roles in a variety of biological processes. In this study, by analyzing the global regulatory relationship between RBPs and their target mRNAs in yeast, we discovered that most RBP genes are co-regulated with their target genes, but the RBPs tend to dampen expression variation among their target mRNAs. We further examined a well-studied RBP gene, PUF3, and found that the protein decreases the variation of its target mRNAs by differentially affecting their decay. Our results provided new insights into the functional importance of RBPs in coordinating their target genes expression.

overall_design: Both the PUF3 deletion strain and wild type BY4742 (MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0) strain were cultured overnight in YPD media. 0.01 OD cells were transferred into fresh YPEG media until 1.0 OD. Total RNA was extracted by the standard Trizol protocol. mRNA was then purified using oligo-dT DynaBeads. cDNA sequencing library was constructed according to the protocol described by Wang et al. After sequencing, the reads were also mapped into S. cerevisiae genome by SOAP2 with no more than two mismatches. RPKM was used to represent the expression level of each gene.

first: Lin

last: Xu

first: Zhe

first: Jack

last: Keene

first: Zhenglong

last: Gu


title: eRNA: A graphic user interface-based tool for RNA sequencing data analysis [microRNA-Seq]

city: Milwaukee

first: Liang

state: Wisconsin

address: 8701 Watertown Plank Rd.

institute: Medical College of Wisconsin

summary: we performed RNA sequencing analysis using 7 human plasma samples and evaluated efficiency and accuracy of eRNA on miRNA-seq data analysis.

overall_design: We sequenced microRNAs from the 7 human tissue samples with replicates (A1/A8, B2/B9, C3/C10, D4/D11, E5/E12, F6/F13, G7/G14) using NEBNext Multiplex Small RNA library Prep Set from New England Biolab (NEB). After that, we identified miRNAs in these plasma samples against known human matured miRNAs.

first: Tiezheng

last: Yuan

first: Xiaoyi

last: Huang


title: eRNA: A graphic user interface-based tool for RNA sequencing data analysis

last: Wang


title: eRNA: A graphic user interface-based tool for RNA sequencing data analysis [mRNA-Seq]

summary: we performed RNA sequencing analysis using 10 tissue samples from human prostate and evaluated efficiency and accuracy of eRNA on mRNA-seq data analysis.

overall_design: We sequenced mRNAs from the 10 human tissue samples. After that, we identified mRNAs in these samples against known human genes.


title: Histone H3 Acetylation and microRNA(s) Regulate Inflammatory response in Mastitis Mice, induced by Staphylococcus aureus Infection

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur P.O.

department: Molecular Biology & Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

overall_design: Refer to individual Series


title: Tyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

summary: In mammals, the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II consists of 52 conserved heptapeptide repeats containing the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA maturation. Here we describe Tyr1 phosphorylation (Tyr1P) as a hallmark of initiating Pol II in mammalian cells, in contrast to what was described in yeast. Tyr1P is predominantly found in antisense orientation at promoters but is also specifically enriched at active enhancers. Mutation of Tyr1 to phenylalanine (Y1F) prevents the formation of the hyper-phosphorylated Pol IIO form, induces degradation of Pol II to the Pol IIB form and results in a lethal phenotype. Our results suggest that Tyr1P has evolved specialized and essential functions in higher eukaryotes associated with antisense promoter and enhancer transcription, and Pol II stability.

overall_design: This study was performed in a human Raji cell line. It contains ChIP-seq data for H3K36me3 (two replicates), H3K4me1 (two replicates), H3K4me3 (two replicates), Pol II (three replicates), Ser2P (two replicates), Ser5P (two replicates), Ser7P (two replicates), Tyr1P 3D12 (two replicates) and Tyr1P 8G5 (one replicate).  MNase-experiment for nucleosomes was performed in paired-end sequencing on one replicate, 4 replicates for the input genomic DNA was used and one replicate was generated for the short strand specific RNA experiment.

first: Nicolas

last: Descostes

first: Martin

last: Heidemann

first: Lionel

last: Spinelli

first: Roland

last: Schüller

first: Muhammad

last: Maqbool

first: Romain

last: Fenouil

first: Frederic

last: Koch

first: Charlene

last: Innocenti

first: Marta

last: Gut

first: Ivo

first: Dirk

last: Eick

first: Jean-Christophe

last: Andrau


title: Automated high-throughput chromatin immunoprecipitation

first: Georgi

middle: Kolev

last: Marinov

state: California

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

department: Genetics

institute: STANFORD UNIVERSITY

summary: The submitted files contain ChIP-seq data for the p300 transcriptional coactivator in GM12878 cells and for the NRSF transcription factor in GM12878 and Jurkat cells generated using a fully automated robotic chromatin immunoprecipitation protocol. Cells were fixed using 1% formaldehyde (NRSF samples) or 1% formaldehyde at 37C (p300 samples).

overall_design: Characterization of monoclonal anti-p300 antibodies and of NRSF binding in GM12878 and Jurkat cells using automated high-throughput chromatin immunoprecipitation

middle: K

first: Barabra

last: Wold


title: Histone H3 Acetylation and microRNA(s) Regulate Inflammatory response in Mastitis Mice, induced by Staphylococcus aureus Infection [smallRNA-Seq]

summary: Bacterial infection in the mammary gland parenchyma induces local inflammation that can lead to a multietiological complex disease called mastitis. Globally Staphylococcus aureus is the single largest mastitis pathogen and the infection can ultimately result in either subclinical or chronic and sometimes lifelong infection. In the present report we have addressed the differential inflammatory response in the mice mammary tissue during intramammary infection  and the altered epigenetic context induced by two closely related strains of S. aureus. Immunohistochemical and immunoblot analysis showed strain specific hyperacetylation at histone H3K9 and H3K14 residues. Real-time PCR and genome-wide gene expression studied showed expression of a set of proinflammatory genes and cytokines in a temporal manner. Remarkably, over expression of the genes significantly correlated with the promoter specific acetylation in these residues. Furthermore, we have identified several differentially expressed known miRNAs and 4 novel miRNAs in the S. aureus infected mice mammary tissue by small RNA sequencing. By employing these gene expression data, an attempt has been made to delineate the gene regulatory networks in the strain specific inflammatory response. Apparently, one of the isolates of S. aureus activated the NFkB signaling leading to drastic inflammatory response and induction of immune surveillance, which could lead to rapid clearance of the pathogen. The other strain repressed most of the inflammatory response, which might help in its sustenance in the host tissue. Taken together, our studies shed substantial lights to understand the mechanisms of strain specific differential inflammatory response to S. aureus infection during mastitis.

overall_design: One control and two samples infected with two different strains of S. aureus

first: Rahul

last: Modak

first: Susweta

last: Das Mitra

first: Bibek

middle: R

last: Shome


title: Autophagy regulator DRAM1 functions downstream of MYD88 in defense against tuberculosis

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

institute: Institute of Biology, Leiden University


title: Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (K9 KO 5hmC-capture-seq)

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

institute: Uiversity Hospital Zurich

summary: During mammalian development DNA methylation patterns need to be reset in primordial germ cells (PGC) and preimplantation embryos. However, many retro-transposons and imprinted genes are resistant to such global epigenetic reprogramming via hitherto undefined mechanisms. Here, we report that some of these sequences are immune to widespread erasure of DNA methylation in the mouse embryonic stem cells (mESCs) lacking de novo DNA methyltransferases. Persistence of DNA methylation at these loci in mESCs depends on the histone H3K9 methyltransferase Setdb1, as deletion of Setdb1 results in reduction of H3K9me3 and DNA methylation levels concomitant with an increase in 5-hydroxymethylation (5hmC). In addition, depletion of H3K9 methyltransferase G9a leads to genome-wide reduction of DNA methylation but to a lesser extent at the above sequences. Taken together, these data reveal that Setdb1 ensures the fidelity of DNA methylation at specific loci in mESCs, which may reflect mechanisms functioning in vivo during key developmental stages.

overall_design: Examination of genome-wide DNA hydroxy-methylation status in 3 cell types.

first: Danny

last: Leung

first: Tingting

last: Du

first: Wei

last: Xie

first: Ah

middle: Y

last: Lee

first: Preeti

last: Goyal

first: Yujing

last: Li

first: Keith

last: Szulwach

first: Peng

last: Jin

first: Matthew

last: Lorincz

first: Bing

last: Ren