title: RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [ChIP-seq]

city: Salt Lake City

first: Timothy

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

summary: ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism, and reveal different mechanisms at two different promoter architectures.

overall_design: Genomic localization of RSC, ISW1a, and SWI/SNF complexes were measured by chromatin immunoprecipitation followed by Illumina paired-end sequencing. Four strains were analyzed, including Rsc8-9xMyc (YBC2882), Sth1-2xFlag (YBC601 p3018), Ioc3-13xMyc (YBC2883), and Snf2-13xMyc (YBC3010). Each sample consists of one chromatin immunoprecipitate and one input chromatin control.

first: Alisha

last: Schlichter

first: Bradley

middle: R

last: Cairns


title: RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [MNase-Seq]

status: Public on Apr 01 2015

middle: J

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Genome-wide nucleosome occupancy maps in RSC and rsc null strains were generated by paired-end sequencing of mononucleosomal DNA. Strains carrying the Sth1 degron allele and either pGal-UBR1 (YBC3386) or ubr1 null (YBC3387) represent RSC null and RSC wildtype, respectively.


title: Enhancer Analysis in Peripheral Nerve: ChIP-seq of H3K27ac in P15 sciatic nerve

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: ChIP-seq of H3K27ac in P15 sciatic nerve was used to identify actively engaged enhancers in Schwann cells, which constitute the majority of nuclei in peripheral nerve.

overall_design: 1 H3K27ac ChIP sample, with respective input

first: Holly

last: Hung

first: Camila

last: Lopez-Anido


title: Transcriptome analysis of alveolar macrophages in asthma

city: Chicago

first: Gye Young

last: Park

state: IL

address: 840 S. Wood St

department: Medicine, Pulmonary

institute: University of Illinois at Chicago

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goal of this study is to investigate the alteration of gene expression pattern of alveolar macrophages by allergen challenge in human asthmatics.
Method: By using subsegmental bronchial provocation with allergen (SBP-AG) protocol, we obtained BAL fluids, before and 48 hours after allergen challenge in the subjects enrolled in the protocol. Alveolar macrophages were purified from the BAL fluids and total RNA was isolated. Next-generation sequencing data were generated by using the Illumina system.
Results: Using an optimized data analysis workflow, we mapped about 75 million sequence reads per sample to the human genome and identified 29,691 transcripts in the macrophage mRNAs. Among them, the change in the expression profiles of 37 transcripts were statistically significant.
Conclusions: It has been well accepted that Th2 cytokine enriched environment transforms the phenotype of macrophages into alternatively activated form. However, the details of a genome-wide gene expression profiles of macrophages were not well investigated. Using RNA-seq technology, we provided comprehensive data of macrophage gene expression profiles in allergic lung inflammation. Our data could offer a framework to study biologic functions of alternatively activated macrophage in chronic inflammatory diseases.

overall_design: mRNA profiles of alveolar macrophages obtained from asthmatics, before and after allergen challenge.

first: Gye

middle: Y

first: Jong

last: Jeong


title: ChIP-seq and RNA-seq analyses identify Wnt and Fgf signaling pathways as Prep1 targets in mouse embryonic stem cells

city: Berlin

first: Hans-Jörg

last: Warnatz

address: Ihnestrasse 63-73

department: Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: The Prep1 (Pknox1) homeodomain transcription factor is essential at multiple stages of embryo development. In the E11.5 embryo trunk, we previously estimated that Prep1 binds about 3,300 genomic sites at a highly specific decameric consensus sequence, mainly governing basal cellular functions. We now show that in embryonic stem (ES) cells Prep1 binding pattern only partly overlaps that of the embryo trunk, with about 2,000 novel sites, highlighting a change of targets between embryonic differentiated v. embryonic stem cells. RNA-seq identifies about 1800 genes down-regulated in Prep1- /- ES cells which belong to gene ontology categories not enriched in the E11.5 Prep1i/i differentiated embryo, including in particular the Wnt and Fgf pathways. Indeed, we find aberrant Wnt and Fgf expression levels in the Prep1-/- ES cells which agrees with a deficient embryoid bodies (EBs) differentiation. Re-establishment of the Prep1 level rescues the phenotype.

overall_design:
[ChIP-Seq] Examination of genome-wide Prep1 binding in mouse ES cells using ChIP-seq and Illumina GAII sequencing.
[RNA-Seq] Examination of gene expression in wild type and Prep1-/- mouse ES cells using RNA-seq and Illumina GAII sequencing.

first: Audrey

last: Laurent

first: Manuela

last: Calabrese

first: Hans

first: Marie

middle: L

last: Yaspo

first: Vsevolod

last: Vsevolod

first: Miguel

last: Torres

first: Francesco

last: Blasi

first: Dmitry

last: Penkov


title: Sox10 Binding Analysis in the Central and Peripheral Nervous System

summary: ChIP-seq of Sox10 in spinal cord and sciatic nerve was performed to determine shared and unique binding sites for Sox10 in oligodendrocytes and Schwann cells, respectively. Sox10 is required for both Schwann cell and oligodendrocyte development. In addition, differentiation of myelinating glia is dependent upon axonal signaling, so these studies were performed in vivo.

overall_design: 2 independent Sox10 ChIP samples each for spinal cord (CNS) and sciatic nerve (PNS), with respective inputs

first: Rajini

last: Srinivasan

first: Guannan

last: Sun

first: Sunduz

last: Keles


title: Regulation of alternative cleavage and polyadenylation by 3’ end processing and splicing factors

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

summary: Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage and polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1, and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly influencing C/P events in 5’ introns and U2 impacting those in efficiently spliced introns. Furthermore, PABPN1 regulates expression of transcripts with pAs near the transcription start site, a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results indicate that the abundance of different C/P factors and splicing factors plays diverse roles in APA, and is relevant to APA regulation in biological conditions.

overall_design: knockdown experiments of 23 C/P factors, 3 splicing factors and U1D in mouse C2C12 myoblast cells

first: Bei

last: You

first: Dinghai

last: Zheng

first: Mainul

last: Hoque

first: Wenting

last: Luo

first: Zhe

last: Ji

first: JiYeon

first: Bin

last: Tian


title: ChIP-seq of Tcfap2c in Neu mammary cancer cells

city: St Louis

first: Tiandao

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: Tumors were harvested from mice carrying the rat activated Neu-oncogene and made into a single cell suspension. ChIP-SEQ was carried out as previously described in Kulak MV, Cyr AR, Woodfield GW, Bogachek M, Spanheimer PM, Li T et al. Transcriptional regulation of the GPX1 gene by TFAP2C and aberrant CpG methylation in human breast cancer. Oncogene 2013; 32: 4043-4051. Tcfap2c and RNA Pol II peaks can be found on their respective tracks.

overall_design: 2 ChIP-Seq data in Neu-oncogene activated mouse.

first: Jung

middle: M

last: Park

first: George

middle: W

last: Woodfield

first: Ronald

last: Weigel


title: In vivo probing of the DNA-binding Architecture by bacterial arginine repressor

city: Daejeon

first: Byung-Kwan

last: Cho

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: Although DNA motifs recognized by the transcription factors (TFs) have been determined, challenges remain in probing in vivo architecture of TF-DNA complexes on a genome-wide scale. Here, we show in vivo architecture of Escherichia coli arginine repressor (ArgR)-DNA complexes using chromatin immunoprecipitation coupled with sequencing (ChIP-exo). The identified 62 ArgR-binding loci were classified into three groups, comprised of single, double, and triple peak-pairs, respectively. Each peak-pair has unique 93 bp-long (±2 bp) ArgR-binding sequence containing two ARG boxes (39 bp) and residual sequence. Moreover, the peak-pairs provided the three ArgR-binding modes defined by the position of the two ARG boxes, indicating that the formation of DNA bending apparently centered between the pair of ARG boxes facilitates the non-specific contacts between ArgR subunits and the residual sequences. Thus, our data postulate the in vivo architecture of ArgR-DNA complexes to understand its transcription regulatory mechanism.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: ChIP-exo profiles of ArgR (+Arginine) and ArgR (-Arginine) were generated by deep sequencing in duplicates using Illumina MiSeq.

first: Suhyung

first: Yoo-Bok

first: Haeji

last: Yum

first: Taek-Jin

last: Kang

first: Sun

middle: C

last: Kim


title: Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary: Upon encounter with antigen, mature B cells undergo complex changes in their physiological state and anatomical localization, and initiate a differentiation process that ultimately produces antibody-secreting cells (ASCs), a major effector population of the immune system. To better characterize this process we have defined the transcriptome of all stages of B cell terminal differentiation by performing a large scale RNA-seq experiment. This analysis provides a molecular signature of ASC populations that highlights the stark transcriptional divide between B cells and plasma cells, and also enables the demarcation ASCs based on location, cell cycle status and maturity. The gene expression changes strongly correlated with cell division history and the acquisition of permissive histone modifications and were clearly evident in the small subset of regulatory genes containing super-enhancers. These findings highlight the core transcriptional program that guides B cell terminal differentiation and the production of antibody, essential processes in the immune response.

overall_design: Transcriptional profiling of ex vivo and in vitro B cell and plasma cell populations in mice using RNA sequencing

first: Yang

last: Liao

first: Simon

middle: N

last: Willis

first: David

last: Tarlinton

first: Nadia

last: Taubenheim

first: Gordon

middle: K

last: Smyth

first: Philip

middle: D

last: Hodgkin

first: Stephen

last: Nutt

first: Lynn

last: Corcoran


title: The Potential Role of Alu Y in the Development of Resistance to SN38 (Irinotecan) or Oxaliplatin in Colorectal Cancer

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

type: Methylation profiling by high throughput sequencing

summary:
Purpose: Irinotecan (SN38) and oxaliplatin are chemotherapeutic agents used in the treatment of colorectal cancer. However, the frequent development of resistance to these drugs represents a considerable challenge in the clinic. Alus as retrotransposons comprise 11% of the human genome. Genomic toxicity induced by carcinogens or drugs can reactivate Alus by altering DNA methylation. Whether or not reactivation of Alus occurs in SN38 and oxaliplatin resistance remains unknown.

Methods: We applied reduced representation bisulfite sequencing (RRBS) to investigate the DNA methylome in SN38- or oxaliplatin-resistant colorectal cancer cell line models. Moreover, we extended the RRBS analysis to tumor tissue from 14 patients with colorectal cancer who either did or did not benefit from capecitabine + oxaliplatin treatment. For the clinical samples, we applied a concept of DNA methylation entropy to estimate the diversity of DNA methylation states of the identified resistance phenotype-associated methylation loci observed in the cell line models.

Results: We identified different loci being characteristic for the different resistant cell lines. Interestingly, 53% of the identified loci were Alu sequences -- especially the Alu Y subfamily. Furthermore, we identified an enrichment of Alu Y sequences that likely results from increased integration of new copies of Alu Y sequence in the drug-resistant cell lines. In the clinical samples, SOX1 and other SOX gene family members were shown to display variable DNA methylation states in their gene regions. The Alu Y sequences showed remarkable variation in DNA methylation states across the clinical samples. Our findings imply a crucial role of Alu Y in colorectal cancer drug resistance. Our study underscores the complexity of colorectal cancer aggravated by mobility of Alu elements and stresses the importance of personalized strategies, using a systematic and dynamic view, for effective cancer therapy.

overall_design: Investigation of the representive methylome of well-established SN38 and Oxaliplatin resistant cell line models and 14 clinical colorectal metastatic samples that have developed resistance to XELOX to review the epigenetic mechnism of the drug resistance.

first: Xue

last: Lin

first: Jan

last: Stenvang

first: Mads

last: Heilskov Rasmussen

first: Shida

last: Zhu

first: Niels

middle: F

last: Jensen

first: Line

middle: S

last: Tarpgaard

first: Guangxia

last: Yang

first: Kirstine

last: Belling

first: Claus

last: Lindbjerg Andersen

first: Lars

last: Bolund

first: Nils

last: Brünner


title: Identification and Characterization of MicroRNAs in Zebrafish Spermatozoa by Illumina Sequencing

city: Guangzhou

first: kun

middle: tong

last: jia

state: Guangdong

address: 135 Xingang Road West Guangzhou, Guangdong,china

country: China

institute: SUN YAT-SEN UNIVERSITY

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are involved in nearly every biological process examined to date. Mounting evidence show that some spermatozoa specific miRNAs play important roles in the regulation of spermatogenesis and germ cells development, but little is known of the exact identity and function of miRNA in sperm cells or their potential involvement in spermatogenesis and germ cells development. Here, we investigated the spermatozoa miRNA profiles using illumina deep sequencing combined with bioinformatic analysis using zebrafish as a model system. Deep sequencing of small RNAs yielded 12 million raw reads from zebrafish spermatozoa. Analysis showed that the noncoding RNA of the spermatozoa included tRNA, rRNA, snRNA, snoRNA and miRNA. By mapping to the zebrafish genome, we identified 400 novel and 204 conserved miRNAs which could be grouped into 104 families, including zebrafish specific families, such as mir-731, mir-724, mir-725, mir-729 and mir-2185. We report the first characterization of the miRNAs profiling in zebrafish spermatozoa. The obtained spermatozoa miRNAs profiling will serve as valuable resources to systematically study spermatogenesis in fish and vertebrate.

overall_design: Examination of small RNA populations in zebrafish spermatozoa

first: Kuntong

last: Jia

first: Peng

first: Jieying

last: Chen

first: Lin

last: Zeng

first: Jing

last: Zhang

first: Meisheng

last: Yi


title: ChIP-seq of E4F1 in primary mouse embryonic fibroblasts (MEFs) and in p53-/-, Ha-RasV12-transformed MEFs

city: Montpellier

first: Claude

last: Sardet

address: 208 rue des Apothicaires

department: Inserm U1194 - Université de Montpellier - Institut Régional du Cancer de Montpellier (ICM)

country: France

institute: Institut de Recherche en Cancérologie de Montpellier (IRCM)

summary: E4F1 is a ubiquitously expressed zinc-finger protein of the Gli-Kruppel family that was first identified, more than 30 years ago, as a cellular target of the adenoviral oncoprotein E1A13S (Ad type V), required for transcriptional regulation of adenoviral genes. In order to decipher E4F1 cellular target genes, we performed chromatin immunoprecipitation of endogenous E4F1 in primary and in p53KO, Ha-RasV12-transformed MEFs. Both input and immunoprecipitated DNA were exhaustively sequenced and mapped on the mouse genome (mm9). Peak detection has been achieved by combining two peak calling algorithms. Intersection of the two E4F1 peak lists on each cell line were considered as E4F1 chromatin bound regions.

overall_design: Genome-wide mapping of E4F1 binding in mouse embryonic fibroblasts.

first: Olivier

last: Kirsh

first: Geneviève

last: Rodier


title: Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation

status: Public on Mar 31 2015

city: Austin

first: Jeffrey

middle: E.

last: Barrick

state: TX

address: 2500 Speedway, Stop A4800

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components, including RNA and proteins at deep genomic coverage, as well as lipid modifications and flux through central metabolism. Our study focuses on the physiological response of E. coli to starvation, not on the genetic adaptation of E. coli to utilize alternative nutrients. In our analysis, we have taken advantage of the temporal correlations within and among RNA and protein abundances to identify systematic trends in gene regulation. Specifically, we have developed a general computational strategy for classifying expression-profile time courses into distinct categories in an unbiased manner. We have also developed, from dynamic models of gene expression, a framework to characterize protein degradation patterns based on the observed temporal relationships between mRNA and protein abundances. By comparing and contrasting our transcriptomic and proteomic data, we have identified several broad physiological trends in the E. coli starvation response. Strikingly, mRNAs are widely down-regulated in response to glucose starvation, presumably as a strategy for reducing new protein synthesis. By contrast, protein abundances display more varied responses. The abundances of many proteins involved in energy-intensive processes mirror the corresponding mRNA profiles while proteins involved in nutrient metabolism remain abundant even though their corresponding mRNAs are down-regulated.

overall_design: Time course of E. coli growth and starvation in glucose-limited minimal medium

middle: E


title: Laser capture microdissection followed by next-generation sequencing identifies disease-related microRNAs in psoriatic skin that mirror the systemic psoriatic miRNome

city: New York

first: Miguel

last: Brown

state: New York

address: 1230 York Ave Box 186

institute: The Rockefeller University

summary: Psoriasis is a systemic disease with cutaneous manifestations. MicroRNAs (miRNAs) are non-coding RNA molecules that are differentially expressed in psoriatic skin, however; only few miRNAs have been localized to specific cells or regions of psoriatic lesions. We used laser capture microdissection (LCM) and next-generation sequencing to study the specific miRNA expression profiles in the epidermis (Epi) and dermal inflammatory aggregates (RD/ICs) of psoriatic skin. We identified 24 deregulated miRNAs in the Epi and 37 deregulated miRNAs in the RD/ICs of lesional psoriatic skin compared with non-lesional psoriatic skin (FCH>2, FDR<0.05). Interestingly, 9 of the 37 miRNAs, including miR-193b and miR-223 that have recently been described as deregulated in circulating peripheral blood mononuclear cells (PBMCs) from patients with psoriasis. Using flow cytometry and qRT-PCR, miR-193b and miR-223 were found to be expressed in Th17 cells. In conclusion, we demonstrate that LCM combined with small RNA sequencing provides a robust strategy to explore the global miRNA expression in the epidermal and dermal compartments of psoriatic skin. Furthermore, our results indicate that the altered local miRNA changes seen in the RD/ICs is reflected in the circulating immune cells, altogether emphasizing that miRNAs may contribute to a systemic component in the pathogenesis of psoriasis.

overall_design: Examination of the global miRNA expression in epidermis (Epi) and dermis (RD/ICs) of paired (non-lesional vs. lesional) psoriatic skin using a combination of laser-capture microdissection and barcoded small RNA sequencing

first: Marianne

middle: B

last: Løvendorf

first: Hiroshi

last: Mitsui

first: John

last: Zibert

first: Mads

middle: A

last: Røpke

first: Markus

last: Hafner

first: Beatrice

last: Dyring-Andersen

first: Charlotte

last: Bonefeld

first: James

middle: G

last: Krueger

first: Lone

last: Skov


title: Mecp2: an unexpected regulator of macrophage gene expression and function [ChIP-Seq]

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Mutations in methyl-CpG-binding protein 2 (MeCP2), a major epigenetic regulator, are the predominant cause of Rett syndrome. We previously found that Mecp2-null microglia are deficient in phagocytic ability, and that engraftment of wild-type monocytes into the brain of Mecp2-deficient mice attenuates pathology. We have observed that Mecp2 deficiency is associated with increased levels of histone acetylation at the cis-regulatory regions of the Mecp2-regulated genes in macrophages. We hypothesized that Mecp2 recruits protein complexes containing histone deacetylases (HDACs) to repress the expression of its target genes. Our ChIP-Seq studies in bone-marrow derived macrophages revealed that Mecp2 co-localizes with Ncor2/Hdac3 protein complex at cis-regulatory regions of the target genes. These results suggest a role for Mecp2 in the recruitment and regulation of Ncor2/Hdac3 repressosome that plays a critical role in the regulation of inflammatory responses in macrophages.

overall_design: Examination of NCOR2 and HDAC3 genome-wide location in bone-marrow derived macrophages.

first: V

last: Litvak


title: Mycobacterial infection induces a specific human innate immune response

last: Blischak

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: The innate immune system provides the first response to pathogen infection and orchestrates the activation of the adaptive immune system. Though a large component of the innate immune response is common to all infections, pathogen-specific innate immune responses have been documented as well. The innate immune response is thought to be especially critical for fighting infection with Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB). While TB can be a deadly disease, only 5-10% of individuals infected with MTB develop active disease, and this inter-individual variation is, at least partly, heritable. Studies of inter-individual variation in the innate immune response to MTB infection may therefore shed light on the genetic basis for variation in susceptibility to TB. Yet, to date, we still do not know which properties of the innate immune response are specific to MTB infection and which represent a general response to pathogen infection. To begin addressing this gap, we infected macrophages with eight different bacterial pathogens, including different MTB strains and related mycobacteria, and studied the transcriptional response to infection. We found that although the gene expression changes were largely consistent across the bacterial infection treatments, we were able to identify a novel subset of genes whose regulation was affected specifically by infection with mycobacteria. Genetic variants that are associated with regulatory differences in these genes should be considered candidate loci for explaining inter-individual susceptibility TB.

overall_design:
RNA-seq of monocyte-derived macrophages isolated from 6 healthy European males at 4, 18, and 48 hours post-infection with the following 8 bacteria:  Mycobacterium tuberculosis (MTB) H37Rv, Mycobacterium tuberculosis GC1237, MTB GC1237, bacillus Calmette-Guérin (BCG), Mycobacterium smegmatis, Yersinia pseudotuberculosis, Salmonella typhimurium, and Staphylococcus epidermidis. table-s1.txt is a tab-delimited text file that contains the batch-corrected log2 counts per million for each of the 156 samples, as well as the Ensembl gene ID and gene name.

BCG = bacillus Calmette-Guérin
GC =  Mycobacterium tuberculosis GC1237
Rv = Mycobacterium tuberculosis (MTB) H37Rv
Rv+ = heat-inactivated MTB H37Rv
Salm = Salmonella typhimurium
Smeg = Mycobacterium smegmatis
Staph = Staphylococcus epidermidis
Yers = Yersinia pseudotuberculosis

first: Ludovic

last: Tailleux

first: Amy

last: Mitrano

first: Luis

last: Barreiro

first: Yoav

last: Gilad


title: SKIP Confers Salt Tolerance through Controlling Gene Alternative Splicing in Arabidopsis

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

summary: A better understanding of the mechanisms for plant in response to abiotic stresses is key for the improvement of plant to resistant to the stresses. Much has been known for the regulation of gene expression in response to salt stress at transcriptional level, however, little is known at posttranscriptional level for this response. Recently, we identified that SKIP is a component of spliceosome and is necessary for the regulation of alternative splicing and mRNA maturation of clock genes. In this study, we observed that skip-1 is hypersensitive to salt stress. SKIP is necessary for the alternative splicing and mRNA maturation of several salt tolerance genes, e.g. NHX1, CBL1, P5CS1, RCI2A, and PAT10. Genome-wide analysis reveals that SKIP mediates the alternative splicing of many genes under salt stress condition, most of the new alternative splicing events in skip-1 is intron retention, which leads to the premature termination codon in their mRNA. SKIP also controls the alternative splicing by modulating the recognition or cleavage of 5' and 3' splice donor and acceptor sites under salt stress condition. Therefore, this study addresses a fundamental question on how the mRNA splicing machinery contributes to salt response at a posttranscriptional level.

overall_design: Totally six samples, two treatments and two genotypes, and each have two replicats.

first: Jinli

last: Feng

first: Zhaoxu

first: Ligeng

last: Ma


title: Tri-methylation of lysine 36 on H3 restricts gene expression variation during aging and impacts lifespan

city: Ithaca

first: Mintie

last: Pu

address: Biotechnology Building 341

department: Molecular Biology and Genetics

institute: Cornell University

summary: Functional data indicate that specific histone modification enzymes can be key to longevity in Caenorhabditis elegans, but epigenetic mechanisms of lifespan regulation are not well understood.  In this study, we profiled the genome-wide pattern of tri-methylation of lysine 36 on histone 3 (H3K36me3) in the somatic cells of young and old C. elegans. We revealed a new role of H3K36me3 in maintaining gene expression stability through aging with important consequence on longevity. We found that genes with dramatic expression change during aging are marked with low or even undetectable levels of H3K36me3 in their gene-bodies, irrespective of their corresponding mRNA abundance. Importantly, inactivation of the methyltransferase met-1 resulted in a decrease in global H3K36me3 marks, an increase in mRNA expression change with age, and a shortened lifespan, suggesting a causative role of the H3K36me3 marking in modulating age-dependent gene expression stability and longevity.

overall_design:
We performed genome-wide mapping of histone H3 and H3K36me3 in young (D2A) and old (D12A) C.elegans somatic cells by ChIP-seq in glp-1(e2141).
mRNA-seq was performed in young (D2A) and old (D12A) glp-1(e2141) somatic cells to identify mRNA expression change during aging from D2A to D12A.

first: Siu Sylvia

last: Lee


title: MicroRNA sequencing of mouse soleus muscle

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

summary: MicroRNA sequencing using Ion Torrent Proton platform

overall_design: Single run of a pool of m.soleus from 5 male mice

first: Thomas

last: Boettger

first: Judith

last: Schweisgut


title: Mecp2: an unexpected regulator of macrophage gene expression and function

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

overall_design: Refer to individual Series


title: Restricted Feeding Reveals Maternal Entrainment of Weak Circadian Oscillators in Fetal Mouse Livers

city: Shenzhen

first: Gaille

last: Joo

address: Beishan Industrial Zone, Yantian District

institute: BGI

summary: Although circadian clocks oscillate in most cells, it has been difficult to detect canonical expression of clock genes in fetal rodent tissues, including the fetal liver. The oscillation status of fetal clocks and the maternal influence on these clocks have not yet been conclusively defined. Here we report that, when the mother mice are under restricted feeding, the expression rhythms of several clock genes can be detected in fetal mouse livers. Those rhythms, although of low amplitude, reversed their profiles under opposite feeding cycles, suggesting maternal entrainment of the weak fetal liver clocks. However, Bmal1 could show biphasic expression in the fetal livers. The expression of some metabolic genes (e.g. Insig1) also showed biphasic daily changes in fetal livers, possibly as a result of interactions between the unique in utero milieu and the fetal liver clocks. Regular rhythms of clock gene expression were detected in dissociated fetal hepatocytes in culture. Differential expression of metabolic genes were found between fetal and adult livers, suggesting that metabolic features affected clock amplitude. Genome-wide differences in DNA methylation were also found between adult and fetal livers. Some of those epigenetic changes were likely critical for the developmental changes in clock amplitudes.

overall_design: The whole genome methylation status of two samples (Fetal and Adult) were analysed by reduced representational bisulfite sequencing (RRBS)

first: Xiaodong

last: Li

first: Jialou

last: Zhu


title: Transcriptome response of Salmonella enterica subsp. enterica serovar Typhimurium N-15 and Bifidobacterium thermophilum RBL67  in co-culture

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

summary: Bifidobacterium thermophilum RBL67 (RBL67), a human fecal isolate and promising probiotic candidate, showed antagonistic and protective effects against Salmonella and Listeria in vitro. However, the underlying mechanisms fostering these health-related effects remain unknown. Therefor the transcriptome response of RBL67 and Salmonella enterica subsp. enterica serovar Typhimurium N-15 (N-15) in co-culture compared to the response in their respective mono-cultures. RNA was extracted from culture samples taken after 4 (N-15) or 5 h (RBL67) and RNAseq was performed on an Illumina HiSeq 2000 sequencer. Three biological replciates were performed resulting in 12 data sets: 3 RBL67 mono culture, 3 N15 mono-culture, 3 RBL67 co-culture, 3 N15 co-culture. Our study provided first insights into probiotic-pathogen interaction on transcriptional level and suggests a mechanism for how probiotic organisms can protect the host from infections.

first: Sabine

last: Tanner

first: Christophe

last: Chassard

last: Lacroix

first: Eugenia

last: Rigozzi

middle: J


title: Impact of bariatric surgery on RNA-seq gene expression profiles of adipose tissue in humans

city: Paris

first: Laurence

last: Tiret

address: 91 Bd de l'Hôpital

institute: INSERM

summary: Bariatric surgery is the most effective therapy of severe human obesity. It is associated with improvements in metabolic and non metabolic co-morbidities which are thought to be mediated by a decrease of adipose tissue inflammation. However, the molecular mechanisms behind these beneficial effects are poorly understood. We analyzed expression profiles in subcutaneous adipose tissue from 22 obese women before and 3 months after surgery using the RNA-seq technology. Of 15,972 detected genes, 1214 were differentially expressed after surgery. Upregulated genes were mostly involved in the basal cellular machinery. Downregulated genes were enriched in metabolic functions of adipose tissue. At baseline, we identified 26 modules of coexpressed genes. The four most stable modules reflected the innate and adaptive immune responses of adipose tissue, including a general signature of innate immune cells, an adaptive immune response elicited by T lymphocytes, a neutrophil-mediated inflammatory signature and an interferon-signaling pathway, respectively. After surgery, a few crucial molecules involved in chemotaxis and activation of immune cells were disconnected from their respective networks. These molecules may represent therapeutic targets against adipose inflammation.

overall_design: mRNA sequencing of subcutaneous adipose tissue (SAT) samples from 22 obese women before and 3 months after bariatric surgery

first: Claire

last: Perret

first: François

last: Mathieu

first: Vinh

last: Truong

first: Hervé

last: Durand

first: Ewa

last: Ninio

first: Christine

last: Poitou

first: Karine

last: Clément

first: Rohia

last: Alili

first: Nadjim

last: Chelghoum

first: Adriana

last: Torcivia


title: The Chromatin Remodelers RSC and ISW1 Display Functional and Chromatin-based Promoter Antagonism

city: Salt Lake City

first: Timothy

last: Parnell

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

type: Genome binding/occupancy profiling by genome tiling array

type: Expression profiling by genome tiling array


title: Mecp2: an unexpected regulator of macrophage gene expression and function [RNA-Seq]

first: Stephen

last: Turner

summary: Mutations in methyl-CpG-binding protein 2 (MeCP2), a major epigenetic regulator, are the predominant cause of Rett syndrome, an X-linked neurodevelopmental disorder. We previously found that Mecp2-null microglia are functionally impaired, and that engraftment of wild-type monocytes into the brain of Mecp2-deficient mice attenuates pathology. In this study we show that Mecp2 is expressed in macrophage and monocyte populations throughout the body, and is indispensable for their transcriptional regulation in multiple contexts. We demonstrate that Mecp2-null mice progressively lose or are chronically deficient in several macrophage populations and resident monocytes. Postnatal re-expression of Mecp2 driven by a tamoxifen-inducible CX3CR1 promoter significantly increased the lifespan of otherwise Mecp2-null mice, suggesting that epigenetic regulation of macrophage function by Mecp2 significantly contributes to pathology. RNA-Seq of acutely isolated microglia and peritoneal macrophages (to our knowledge, the first cell-specific RNA-Seq analysis comparing Mecp2-null and wild type cells of any kind) revealed significantly increased transcription of glucocorticoid- and hypoxia-signaling genes in Mecp2-null cells compared to that in their wild-type counterparts, suggesting that Mecp2 functions as a repressor of these pathways. Furthermore, in-vitro and in vivo validation studies demonstrated that the absence of Mecp2 is associated with cell-intrinsic dysfunction of signaling underlying inflammatory activation, suggesting that Mecp2 is important for regulation of specific macrophage gene-expression programs in response to stimuli and stressors. Our findings demonstrate a fundamental role for Mecp2 in the regulation of macrophage functions, which may provide a link to pathologies in Rett syndrome across multiple organs.

overall_design: Mecp2-null microglia and resident peritoneal macrophages from 10-12 week old mice were acutely isolated via AutoMACS, total RNA collected, and analyzed via RNA-Seq to compare for transcriptional differences in microglia and macrophages in the absence of Mecp2.

first: James

last: Cronk

first: Noel

last: Derecki

first: Jonathan

last: Kipnis


title: Global regulation of neuronal transcriptome by miR-9/tristetraprolin circuitry

city: Bridgewater

first: Wencheng

last: Li

institute: PTC Therapeutics

summary: Nervous system (NS) development relies on coherent up-regulation of extensive sets of genes in a precise spatiotemporal manner. How such transcriptome-wide effects are orchestrated at the molecular level remains an open question. Here we show that 3’-untranslated regions (3’UTRs) of multiple neuronal transcripts contain A/U-rich cis-elements (AREs) recognized by tristetraprolin (TTP/Zfp36), an RNA-binding protein previously reported to destabilize mRNAs encoding predominantly cytokines, growth factors and proto-oncogenes. We further demonstrate that the efficiency of ARE-dependent mRNA degradation declines during neural differentiation due to a decrease in the TTP protein expression mediated by the NS-enriched microRNA miR-9. Our experiments with transgenenic cell lines suggest that TTP down-regulation is essential for proper neuronal differentiation. Moreover, inactivation of TTP in neuroblastoma cells or mouse embryonic fibroblasts induces major changes in their transcriptomes accompanied by significantly elevated expression of NS-specific genes. We conclude that the newly identified miR-9/TTP circuitry limits unscheduled accumulation of neuronal mRNAs in non-neuronal cells and ensures coordinated up-regulation of these transcripts in neurons.

overall_design: 3'READS of undifferentiated and 3.5-day differentiated P19 cells

first: Mainul

last: Hoque

first: Weijun

last: Dai

first: Eugene

middle: V

last: Makeyev

first: Bin

last: Tian


title: Genome-wide H3K4me3 analysis in Angus cattle with divergent tenderness

city: College Park

first: Jose

middle: Adrian

last: Carrillo

state: MD

address: 1413 Animal Sciences Center

department: Department of Animal and Avian Sciences

institute: University of Maryland

summary: Tenderness is one of the most important properties of meat quality, which is influenced by genetic and environmental factors. As an intensively studied epigenetic marker, histone methylation, occurring on arginine and lysine residues, has pivotal regulatory functions on gene expression. To examine whether histone methylation involves in beef tenderness variation, we analyzed the transcriptome and H3K4me3 enrichment profiles of muscle strips obtained from the longissimus dorsi (LD) of Angus steers previously classify to the tender or tough group. We first plotted a global bovine H3K4me3 map on chromosomes and called peak-enriched regions and genes. We found that majorities of H3K4me3 on genes were occupying the first intron and intergenic regions and its maps displayed similar patterns in tender and tough groups, with high H3K4me3 enrichment surrounding the transcription start site (TSS). We also explored the relationship of H3K4me3 and gene expression. The results showed that H3K4me3 enrichment is highly positively correlated with gene expression across the whole genome. Cluster analysis results confirmed the relationship of H3K4me3 enrichment and gene expression. By using a pathway-based approach in genes with H3K4me3 enrichment in promoter regions from the tender cluster, we revealed that those genes involved in the development of different tissues–connective tissue, skeletal and muscular system and functional tissues–; while in tough group those genes engaged in cell death, lipid metabolism and  small molecule biochemistry. The results from this study provide a deep insight into understanding of the mechanisms of epigenetic regulations in meat quality and beef tenderness.

overall_design: Nineteen purebred Angus steers were obtained from the Wye Farm. At approximately 12 months of age, the animals were serially harvested. Immediately after harvest, samples of longissimus dorsi (LD) from the right side of the carcass were obtained and placed in RNAlater solution at -80°C. The carcass were stored at 4°C for a total of 14 days. After this period, steaks were obtained from the LD at the level of the 12th intercostal space and then frozen. For measurement of the WBSF, steaks were thawed at room temperature to an internal temperature of 4°C. Then, the steaks were cooked to a core temperature of 70°C using a George Foreman Lean Mean Fat Grilling Machine. The cooked steaks were then cooled down to room temperature. Using a sharp cylinder, especially designed for muscle, six cores (1.27 cm in diameter) were sampled parallel to the muscle fiber orientation. The Warner-Bratzler shear forces (WBSF) of the cores were obtained. The average WBSF of the six cores was calculated and used as the WBSF for the samples. From these 19 steers, 4 with the lowest WBSF values (6.77±0.56 kg) were identified as tender and 5 samples with the largest WBSF values (19.93±0.39 kg) labeled as tough. Then both groups underwent further analysis..

first: Chunping

last: Zhao

first: José

first: Linsen

last: Zan

first: Michael

last: Updike

first: Keji

first: Fei

last: Zhan

first: Jiuzhou

last: Song


title: Specific molecular signatures underlie response to decitabine in CMML [ERRBS]

city: Miami

first: Maria

last: Figueroa

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

summary: Myelodysplastic syndromes and chronic myelomonocytic leukemia (CMML) are characterized by mutations in epigenetic modifiers and aberrant DNA methylation. DNA methyltransferase inhibitors (DMTis) are used to treat these disorders, but response is highly variable with few means to predict which patients will benefit. To develop a molecular means of predicting response at diagnosis, we examined baseline differences in mutations, DNA methylation, and gene expression in 40 CMML patients responsive and resistant to decitabine (DAC). While somatic mutations did not differentiate responders and non-responders, we were able to identify for the first time 158 differentially methylated regions (DMRs) at baseline between responders and non-responders using next-generation sequencing. These DMRs were primarily localized to non-promoter regions and overlapped with distal regulatory enhancers. Using the methylation profiles, we developed an epigenetic classifier that accurately predicted DAC response at the time of diagnosis. We also found 53 differentially expressed genes between responders and non-responders. Genes up-regulated in responders were enriched in the cell cycle, potentially contributing to effective DAC incorporation. Two chemokines overexpressed in non-responders -- CXCL4 and CXCL7 -- were able to block the effect of DAC on normal CD34+ and primary CMML cells in vitro, suggesting their up-regulation contributes to primary DAC resistance.

overall_design: DNA methylation profiling in bone marrow mononuclear cells (BM MNC) from 39 CMML patients (19 decitabine responders vs. 20 non-responders).

first: Kristen

last: Meldi

first: Tingting

last: Qin

first: Valeria

last: Santini


title: Specific molecular signatures underlie response to decitabine in CMML


title: The transcription factor E4F1 coordinates CHK1-dependent checkpoint and mitochondrial functions

first: Claude

last: Sardet


title: Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant

city: Jena

first: Fabian

last: Horn

address: Beutenbergstr. 11a

department: Systems Biology / Bioinformatics

institute: Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI)

summary: Following antifungal treatment, Candida albicans, and other human pathogenic fungi can undergo microevolution, which leads to the emergence of drug resistance. However, the capacity for microevolutionary adaptation of fungi goes beyond the development of drug resistance. Here we used an experimental microevolution approach to show that one of the central pathogenicity mechanisms of C. albicans, the yeast-to-hyphae transition, can be subject to experimental evolution. The C. albicans cph1Δ/efg1Δ mutant is non-filamentous, as central signalling pathways linking environmental cues to hypha formation are disrupted. We subjected this mutant to constant selection pressure in the hostile environment of the macrophage phagosome. In a comparatively short time-frame, the mutant evolved the ability to escape macrophages by filamentation. To investigate the transcriptional response underlying the yeast-to-filament transition in the evolved strain, we applied RNA-Seq technology. Furthermore, RNA-Seq data were used to identify SNPs, which are specific for the evolved strain.

overall_design: For both strains, the cph1Δ/efg1Δ mutant and the Evo-strain, two conditions, one promotes yeast growth the other filamentous growth, were investigated. For each condition three biological replicates were analysed.

first: Anja

last: Lüttich

first: Jörg

last: Linde

first: Sascha

last: Brunke


title: β-catenin regulates primitive streak induction through collaborative interactions with SMAD2/3 and OCT4

city: Copenhagen N

first: Karen

last: Schachter

address: Blegdamsvej 3B, building 6.4.24

department: The Danish Stem Cell Center (DanStem)

institute: University of Copenhagen

summary: Canonical Wnt and Nodal signaling are both required for induction of the primitive streak (PS), which guides organization of the early embryo. The Wnt effector β-catenin is thought to function in these early lineage specification decisions via transcriptional activation of Nodal signaling. Here, we demonstrate a broader role for β-catenin in PS formation by analyzing its genome-wide binding in a human embryonic stem cell model of PS induction. β-catenin occupies regulatory regions in numerous PS and neural crest genes, and direct interactions between β-catenin and the Nodal effectors SMAD2/3 are required at these regions for PS gene activation. Furthermore, OCT4 binding in proximity to these sites is likewise required for PS induction, suggesting a collaborative interaction between β-catenin and OCT4. Induction of neural crest genes by β-catenin is repressed by SMAD2/3, ensuring proper lineage specification. This study provides mechanistic insight into how Wnt signaling controls early cell lineage decisions.

overall_design: Examination of β-catenin binding in hESC incubated in media control (RPMI), media containing CHIR or CHIR+SB for 6h and analyzed by ChIP-sequencing

first: Nina

last: Funa

first: Mads

last: Lerdrup

first: Jenny

last: Ekberg

first: Katja

last: Hess

first: Nikolaj

last: Dietrich

first: Christian

last: Honore

first: Klaus

last: Hansen

first: Henrik

last: Semb


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and pro1 mutant Transcriptomes

city: shanghai

first: Gang

last: Wang

state: Shanghai

address: No. 333 of Nanchen Road

department: College of Life Science

institute: Shanghai University

summary: Analysis of  gene expression level. The hypothesis tested in the present study was that pro1 mutant influence the cell cycle pathway. Results provide important information of the cell cycle-related gene expression level regulation of cell cycle transition from G1 to S phase.

overall_design: Seedling mRNA profiles of 14DAG wild type (WT) and pro1 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2000 (Zea mays).

first: Jushan

last: Zhang


title: Specific molecular signatures underlie response to decitabine in CMML [RNA-seq]

first: Maria

last: Figueroa

overall_design: mRNA profiling in bone marrow mononuclear cells (BM MNC) from 14 CMML patients (8 decitabine responders vs. 6 non-responders).

first: Kristen

last: Meldi

first: Tingting

last: Qin

first: Valeria

last: Santini


title: RNA-seq profiling of microdissected rat renal tubule segments

city: Bethesda

first: Jae Wook

last: Lee

address: 10 Center Drive, 6N314

institute: National Institutes of Health

summary: We sequenced mRNAs from glomeruli and 14 different rat renal tubule segments collected by hand microdissection.

overall_design: Collagenase-digested rat renal tubule segments were collected by hand microdissection. Poly(A)-mRNAs were captured from cell lysate and sequenced using paired-end protocol.

first: Jae

middle: W

first: Mark

last: Knepper


title: RNAseq analysis of murine ITPKB deficient versus wild type LT-HSC

city: La Jolla

first: Lana

last: Schaffer

state: CA

address: 10550 North Torrey Pines Road

department: DNA ARRAY CORE

institute: TSRI

summary: Tight regulation of hematopoietic stem cell (HSC) homeostasis is essential for life-long hematopoiesis, for preventing blood cancers and for averting bone marrow failure. The underlying mechanisms are incompletely understood. Here, we identify production of inositol-tetrakisphosphate (IP4) by inositoltrisphosphate 3-kinase B (ItpkB) as essential for HSC quiescence and function. Young ItpkB-/- mice accumulated phenotypic HSC and showed extramedullary hematopoiesis. ItpkB-/- HSC were less quiescent and proliferated more than wildtype controls. They downregulated quiescence and stemness associated mRNAs, but upregulated activation, oxidative metabolism, protein synthesis and lineage associated transcripts. Although they showed no significant homing defects, ItpkB-/- HSC had a severely reduced competitive long-term repopulating potential. Aging ItpkB-/- mice lost hematopoietic stem and progenitor cells and died with severe anemia. Wildtype HSC normally repopulated ItpkB-/- hosts, incidating a HSC-intrinsic ItpkB requirement. ItpkB-/- HSC had reduced cobblestone-area forming cell activity in vitro and showed increased stem-cell-factor activation of the phosphoinositide 3-kinase (PI3K) effector Akt, reversed by exogenous provision of the known PI3K/Akt antagonist IP4. They also showed transcriptome changes consistent with hyperactive Akt/mTOR signaling. Thus, we propose that ItpkB ensures HSC quiescence by limiting cytokine-induced PI3K signaling in HSC.

overall_design: For each of 3 replicate ItpkB-/- or wt samples, we enriched Lin- cells from BM of 4 pooled age-matched mice with Rapidspheres (Stemcell Technologies), FACS-sorted ≥10,000 LSK CD34-CD150+CD48-Flk2- LT-HSC into lysis buffer and prepared RNA with RNeasy Micro kits (Quiagen). RNA sequencing was done using an Illumina HISeq Analyzer 2000, Casava v1.8.2 genome analyzer pipeline, TopHat v1.4.1/Bowtie2 genome alignment and Partek v6.6 mRNA annotation software. Statistical analyses were done with edgeR (Bioconductor package), excluding genes with false discovery rates >0.15, fold-change magnitudes ≤1.4 and log2(counts per million) ≤4 to avoid undefined values and the poorly defined log fold-changes for low counts close to 0. Unsupervised clustering of 441 significantly changed genes was done with dChip using rank correlation and a centroid linkage method. Scatter plots were generated in Spotfire.  GSEA was performed with gene set permutation, using gene sets from MSigDB (www.broadinstitute.org/gsea/msigdb/index.jsp) or manually curated from, excluding genes without HUGO approved symbols

first: K

last: Sauer

first: S

last: Siegemund

first: L

middle: R

last: Head


title: Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic β-cell function (Insm1, Neurod1 and Foxa2 ChipSeq data from pancreatic beta cell)

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: Genome-wide Insm1 binding sites analysis revealed an overrepresentation of sequences predicted to bind bHLH and/or forkhead factors, and further analyses demonstrated that most Insm1 sites in the genome are co-occupied by Neurod1 and Foxa2. Binding regions co-occupied by all three factors but not single Insm1 sites explained a significant fraction of gene expression changes in Insm1 mutant β-cells. Together, our data provide evidence that an Insm1, Neurod1 and Foxa2 network maintains a mature gene expression program in β-cells.

overall_design: 6 samples include, replicates of Insm1 and Foxa2, IgG pull down as a control

first: Shiqi

last: Jia


title: Developmental Competence Encoded at the Level of Enhancers

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

summary: The emergence of distinct cell types during embryonic development relies on the ability of progenitor cells to properly interpret environmental cues; yet how this developmental competence is established is unknown. Here we show that epigenetic priming of enhancers signifies developmental competence. Chromatin mapping during endodermal lineage diversification of human pluripotent stem cells revealed en masse acquisition of a poised chromatin state at enhancers for multiple descendant lineages in developmental intermediates. The responsiveness of developmental intermediates to lineage-inductive signals is dependent on a poised enhancer state. We further find that lineage-specific enhancers are first recognized by transcription factors involved in chromatin priming, while subsequent recruitment of lineage-inductive transcription factors leads to enhancer and target gene activation. Together, our results identify acquisition of a poised chromatin state at enhancers as a general mechanism by which progenitor cells gain the competence to rapidly activate lineage-specific genes in response to inductive signals.

overall_design: The overall goal of this study was the examine the dynamic changes in the enhancer landscape during endodermal and pancreatic differentiation of hESCs. Specifically we performed ChIP-seq of enhancer related histone modifications (H3K4me1 and H3K27ac) during a five stage differentiation (ES, DE, GT, FG and PE) of hESCs to the pancreatic lineage with two independent biological replicates. To further investigate enhancer activity we performed GRO-seq analysis during the same time course. Additionally, we performed ChIP-seq of the pancreatic regulator PDX1 in hESC derived pancreatic endoderm. To assess its effect on enhancers we also performed H3K27ac ChIP-seq on hESC derived PE transduced with shRNA targeting PDX1 as well as a scrambled control. H3K27ac ChIP-seq was also performed on hESC derived hepatic endoderm using two different protocols to examine enhancer activity during the liver/pancreas lineage decision. Lastly, to investigate the role of pioneer transcription factors at enhancers, we performed ChIP-seq of FOXA1 and FOXA2 during the same five stage pancreatic timecourse.

first: Allen

first: Feng

last: Yue

first: Yan

last: Li


title: Transcriptome analysis of post-hatch breast muscle in legacy and modern broiler chickens reveals enrichment of several regulators of myogenic growth

city: Newark

first: Carl

middle: Joseph

last: Schmidt

state: De

address: 531 S. College Ave.

department: Animal and Food Sciences

institute: University of Delaware

summary: We report the results of comparative transcriptional profiling in the pectoralis major muscle of a modern production broiler line (Ross 708) and a legacy broiler line inbred since the late 1940s (Illinois) focusing on metabolic differences and differences in myogenic growth regulators

overall_design: Differential gene expression analysis between Ross 708 and Illinois pectoralis major at two post-hatch time points (D6 and D21) that bracket critical inflection point in the allometric growth characteristics of the muscle

first: Richard

last: Davis


title: Targeted disruption of DNMT1, 3A and 3B in human embryonic stem cells [DNMT1]

status: Public on Mar 30 2015

city: Cambridge

first: Rahul

last: Karnik

state: MA

address: 419 Broadway

summary: DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Somatic patterns of DNA methylation are largely static, apart from focal dynamics at gene regulatory elements. To further advance our understanding of the role of DNA methylation in human development and disease, we inactivated all three catalytically active DNA methyltransferases in human embryonic stem cells (ESCs) using CRISPR/Cas9 genome editing. Disruption of DNMT3A or DNMT3B individually, as well as of both enzymes in tandem, creates viable, pluripotent cell lines with distinct effects on their DNA methylation landscape as assessed by whole-genome bisulfite sequencing. Surprisingly, in contrast to mouse, deletion of DNMT1 resulted in rapid cell death in human ESCs. To overcome the immediate lethality, we generated a doxycycline (DOX) responsive tTA-DNMT1* rescue line and readily obtained homozygous DNMT1 mutant lines. However, DOX-mediated repression of the exogenous DNMT1* initiates rapid, global loss of DNA methylation, followed by extensive cell death, demonstrating that DNA methylation is essential for human ESCs cultured in standard conditions. In summary, our data provide a comprehensive characterization of DNMT mutant ESCs, including single base genome-wide maps of their targets.

overall_design: RRBS methylation profiling of a time course of DNMT1* withdrawal in human ES cells

first: Alex

last: Meissner


title: Targeted disruption of DNMT1, 3A and 3B in human embryonic stem cells [DNMT3A/3B DKO]

overall_design: RRBS methylation profiling of DNMT3A/3B DKO human ES cells


title: Targeted disruption of DNMT1, 3A and 3B in human embryonic stem cells [WGBS]

overall_design: WGBS profiling of DNMT3A, DNMT3B, and DNMT3A/3B double knockout human ES cells


title: DOT1L Inhibits SIRT1 and SUV39H1-Mediated H3K9 Modification to Maintain Gene Expression (ATACseq)

city: New York

last: Koche

institute: Memorial Sloan Kettering Cancer Center

summary: Methylation of histone 3 on lysine 79 (H3K79) is broadly associated with active gene expression in eukaryotes, and the H3K79 methyltransferase DOT1L is indispensable for specific leukemia subtypes like those with MLL-translocations. We found that suppression of the histone deacetylase SIRT1 rescued MLL-AF9 leukemia cells from their dependence on DOT1L. We show that upon DOT1L inhibition, SIRT1 is required for the acquisition of a repressive chromatin state consistent with facultative heterochromatin around MLL-AF9 target genes in leukemia and other genes possess an H3K79me2(hi), H3K9ac(hi), H3K9me2(low) histone modification profile in normal hematopoietic stem and progenitor cells.

overall_design: Examination of histone modifications and a chromatin modifier with and without drug treatment and RNA interference.

middle: P

first: Chun-Wei

last: Chen

first: Scott

last: Armstrong


title: DOT1L Inhibits SIRT1 and SUV39H1-Mediated H3K9 Modification to Maintain Gene Expression [ChIP-seq 2]

overall_design: Examination of histone modifications via ChIP-seq in three human cancer cell lines.

first: Chun


title: Genome-wide analysis of ETS factor ER71/ETV2 chromatin occupancy

city: SAINT LOUIS

first: Daofeng

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: We discover that ER71/ETV2 initiates hemangiogenic program by activating blood and endothelial cell lineage specifying genes while enhancing FLK1 expression and expanding hemangioblast population. Furthermore, ER71/ETV2 establishes an ETS hierarchy by directly activating Ets genes in hematopoietic and endothelial cell lineage development. As such, ER71/ETV2-initiated blood and endothelial cell program is maintained by ER71/ETV2 downstream ETS factors through an ETS switching mechanism.

overall_design: ChIP-seq analysis of ER71 in differentiated embryonic stem cells

first: Fang

last: Liu

first: Kyunghee

last: Choi

first: Ting

last: Wang


title: DOT1L Inhibits SIRT1 and SUV39H1-Mediated H3K9 Modification to Maintain Gene Expression (ChIPseq)


title: Targeted disruption of DNMT1, 3A and 3B in human embryonic stem cells

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC

city: Nashville

first: Qingguo

state: TN

address: 2525 West End AVE Suite 808

department: Biomedical Informatics

institute: Vanderbilt University

summary: We report a comparison of the genome-wide binding patterns of MYC and WDR5, and the effects of a mutation in MYC (WBM) that disrupt the MYC-WDR5 interaction.

overall_design: The experimental design included two distinct experimental strategies. For comparison of genome-wide binding patters of wild-type (WT) and WDR5 binding-deficient (WBM) MYC, HEK293 cells were engineered by retroviral transduction to express either FLAG-tagged WT-MYC, FLAG-tagged WBM-MYC, or an empty vector control ("vec") ChIP was performed on all samples using the anti-FLAG antibody, and co-precipitating DNAs subject to next-generation sequencing. Samples "2514-WPT-1_1", "2514-WPT-5_1" and "2514-WPT-13_1" are three independent biological replicates of ChIPs performed on the "vec" control cells (i.e., those not expressing any exogenous MYC). Samples "2514-WPT-2_1", "2514-WPT-6_1" and "2514-WPT-10_1" are three independent biological replicates of ChIPs performed on the WT-MYC expressing cells. "2514-WPT-3_1", "2514-WPT-7_1" and "2514-WPT-11_1" are three independent biological replicates of ChIPs performed on the WBM-MYC expressing cells. For comparison of these binding patterns with those of WDR5, we performed ChIP in HEK293 cells with either an antibody against WDR5, or with IgG (negative control). Samples "2514-WPT-23_1", "2514-WPT-25_1", and "2514-WPT-27_1" are independent biological replicates of ChIPs performed with the anti-WDR5 antibody. Samples "2514-WPT-24_1", "2514-WPT-26_1", and "2514-WPT-28_1" are independent biological replicates of ChIPs performed with the negative IgG control.

first: Lance

last: Thomas

first: Zhongming

last: Zhao

first: William

last: Tansey


title: SRA of transcriptome of Hevea brasiliensis

status: Public on Mar 29 2015

city: Danzhou

first: Jinquan

last: Chao

address: Baodao Xincun

department: Rubber Research Institute

institute: Chinese Academy of Tropical Agricultural Sciences

summary: We report here the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of two Hevea brasiliensis clones (RY8-79 and PR107). The output of sequenced data showed that more than 26 million sequence reads with average length of 90nt were generated in both clones. Totally 51829 unigenes (mean size = 640 bp) were assembled through transcriptome de novo assembly, which represent more than 16-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Base on limit rule with FDR≤0.001 and |log2 Ratio|≥1, 6726 different expression unigenes (3018 up and 3708 down) were detected as PR107 versus RY8-79. Functional analysis showed mass of categories were reprogrammed between two clones, which relate latex generation and expelling difference between them. As a comparative transcriptome analysis, the results obtained here will greatly expand our understanding of physiological differences among varieties in molecular level and will contribute t

overall_design: The transcriptome of latex in Hevea brasiliensis

first: Yueyi

first: Weimin

last: Tian


title: Piwi proteins and piRNAs in mammalian oocytes and early embryos

status: Public on Mar 27 2015

city: Mainz

first: David

last: Rosenkranz

address: Anselm-Franz-von-Bentzel-Weg 7

department: Institute of Anthropology

institute: Johannes Gutenberg-University Mainz

summary: Germ cells of most animals critically depend on piRNAs and Piwi proteins. Surprisingly, piRNAs in mouse oocytes are relatively rare and dispensable. We present compelling evidence for strong Piwi-piRNA expression in oocytes of other mammals. Human fetal oocytes express PIWIL2 and transposon-enriched piRNAs. Oocytes in adult human ovary express PIWIL1 and PIWIL2, while those in bovine ovary just express PIWIL1. In human, macaque and bovine ovaries we find piRNAs that resemble testis-borne pachytene piRNAs. Isolated bovine follicular oocytes were shown to contain abundant, relatively short piRNAs that preferentially target transposable elements. Using label-free quantitative proteome analysis we show that these maturing oocytes strongly and specifically express the thus-far uncharacterized PIWIL3 protein, alongside other known piRNA-pathway components. In bovine early embryos these piRNAs are still abundant, revealing a potential impact of piRNAs on mammalian embryogenesis. Our results reveal unexpected, highly dynamic piRNA pathways in mammalian oocytes and early embryos.

sample_organism:
Macaca fascicularis
Homo sapiens
Bos taurus

overall_design: Analyses of multiple small RNA libraries obtained from fetal/adult oocytes, cumulus cells, ovary, testis and 2-4 cell stage ivf embryos of multiple mammalian species.

first: Elke

last: Rovers

first: Mahdi

last: Mahdipour

first: Chung-Ting

last: Han

first: Nannan

last: He

first: Susana

last: Chuva de Sousa Lopes

first: Lucette

last: van der Westerlaken

first: Hans

last: Zischler

first: Falk

last: Butter

first: Bernard

last: Roelen

first: Rene

last: Ketting


title: Effect of Chromomethylase-2 and Dicer-like-3 knockouts on DNA methylation

status: Public on Mar 28 2015

city: Vienna

first: Manu

last: Dubin

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute, Austrian Academy of Sciences

summary: Whole genome bisulfite sequencing was performed on Chromomethylase-2 and Dicer-like-3 knockout mutants in order to confirm the results from genome wide association mapping and to identify the respective genomic regions that they target.

overall_design: Bisulfite sequencing of knockout mutants and WT controls

first: Magnus

last: Nordborg


title: Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus are Established in the Endosperm

city: Uppsala

first: Clement

last: Lafon-Placette

address: Almas Allé 5

country: Sweden

institute: SLU

summary: We described in this work the reproductive barrier between Capsella rubella and Capsella grandiflora leading to hybrid seed inviability. The transcriptome revealed a similar response to the one observed in interploidy hybrid seeds.

sample_organism:
Capsella rubella
Capsella grandiflora
Capsella grandiflora x Capsella rubella

overall_design: Study of seed transcriptome in Capsella rubella, Capsella grandiflora and reciprocal hybrid seeds

first: Carolin

last: Rebernig

first: Clément

first: Rocky

last: Hatorangan

first: Tanja

last: Slotte

first: Claudia

last: Köhler


title: DNA methylation variation in Arabidopsis has a genetic basis and appears to be involved in local adaptation

summary: Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions, demonstrating that methylation of transposable elements is temperature sensitive and associated with genetic polymorphism in both cis and trans, whereas gene body methylation is highly correlated with climate of origin and associated with genetic polymorphism in trans that shows evidence of local adaptation. While genome-wide surveys of naturally occurring DNA methylation have been published previously, the degree of genetic control revealed here is unprecedented. Furthermore, the observation that DNA methylation is associated with climate, and is apparently adaptively important, is completely novel.

overall_design: Bisulfite sequencing of 152 Swedish Arabidobsis accessions grown at 10 C and 121 grown at 16 C


title: Population epigenomics of Swedish Arabidopsis

summary: Plants display remarkable developmental and phenotypic plasticity in order to adapt to their environment. It has long been postulated that epigenetics plays a key role in these processes, but with one or two exceptions, solid evidence for the role of epigenetic variation in these processes is lacking. A key impediment to understanding these processes is the lack of information on the extent of epigenetic variation and how it relates to genetic and phenotypic variation in natural population, both over the lifecycle of an individual, and over evolutionary time. Here we show that genetic variants under selection in the north of Sweden appear to drive variation in DNA methylation, which in turn is highly correlated with local climate. Selective sweeps and genetic variants associated with adaptation to the local environment have previously been identified within the Swedish Arabidopsis population. Our finding that they harbour variants responsible for climate associated epigenetic variation strongly supports the role of epigenetic processes in local adaptation. These findings provide a basis for further dissecting the role of epigenetics in local adaptation at the molecular level

overall_design: Bisulfite sequencing of 113 F2 crosses between T550 and Brosarp-11-135.


title: DOT1L Inhibits SIRT1 and SUV39H1-Mediated H3K9 Modification to Maintain Gene Expression

first: Richard

last: Koche


title: DNMT inhibition in the Neonatal Preoptic Area

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: PN2 male and female rat pups were treated with vehicle or zebularine.  POA RNA was extracted and sequenced to deterime the effects of DNMT inhibition in POA gene expression.

overall_design: Males and Females were treated with either vehicle (0.1% DNMSO in saline) or Zebularine

first: Bridget

middle: M

last: Nugent

first: Margaret

last: McCarthy

middle: C


title: RNA Polymerase II Pausing Can Be Retained or Acquired During Activation of Genes Involved in the Epithelial to Mesenchymal Transition

city: Grand Forks

first: Tim

last: Casselli

state: ND

address: UND School of Medicine & HS 1301 N Columbia Road Stop 9037

department: Basic Sciences

institute: University of North Dakota

summary: Promoter-proximal RNA polymerase II (Pol II) pausing is implicated in the regulation of gene transcription. However, the mechanisms of pausing including its dynamics during transcriptional responses remain to be fully understood. We performed global analysis of short capped RNAs and Pol II Chromatin Immunoprecipitation sequencing in MCF-7 breast cancer cells to map Pol II pausing across the genome, and used permanganate footprinting to specifically follow pausing during transcriptional activation of several genes involved in the Epithelial to Mesenchymal Transition (EMT). We find that the gene for EMT master regulator Snail (SNAI1), but not Slug (SNAI2), shows evidence of Pol II pausing before activation. Transcriptional activation of the paused SNAI1 gene is accompanied by a further increase in Pol II pausing signal whereas activation of non-paused SNAI2 gene results in the acquisition of a typical pausing signature. The increase in pausing signal reflects increased transcription initiation without changes in Pol II pausing. Activation of the heat shock HSP70 gene involves pausing release that speeds up Pol II turnover, but does not change pausing location. We suggest that Pol II pausing is retained during transcriptional activation and can further undergo regulated release in a signal-specific manner.

overall_design: Untreated MCF-7 cells were analyzed for the distribution of Pol II using ChIP-sequencing with Anti-Pol II N-20 antibody (two independent biological replicates, A, B), and for the distribution of paused RNA polymerase II by sequencing of short capped RNAs (scRNAs) prepared from nuclei (three independent biological replicates, 1-3). All samples were sequenced on a MiSeq instrument in paired-end format

first: Sergei

last: Nechaev

first: Adam

last: Scheidegger

first: Archana

last: Dhasarathy


title: Replicative senescence is associated with nuclear reorganization and DNA methylation at specific transcription factor binding sites (MBD-seq)

status: Public on Mar 26 2015

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Primary cells enter replicative senescence after a limited number of cell divisions. This process is associated with reproducible changes in DNA methylation (DNAm) at specific sites in the genome. The mechanism that drives senescence-associated DNAm changes remains unknown and may arise through drift in DNAm or through regulated, senescence dependent modifications at specific sites in the genome. In this study, we analyzed the reorganization of nuclear architecture and DNA methylation during long-term culture of human fibroblasts and mesenchymal stromal cells (MSCs). [MethylCap-seq]

overall_design: Fibroblasts of two female donors (both 43 years old) were culture expanded and DNA was harvested of 10,000,000 cells at early passage (P3 or P5) and late passage (P30 and P33). DNA methylation changes were subsequently analyzed by MethylCap-Seq.

first: Sonja

last: Hänzelmann

first: Fabian

last: Beier

first: Eduardo

last: Gusmao

first: Carmen

last: Koch

first: Sebastian

last: Hummel

first: Iryna

last: Charapitsa

first: Sylvia

last: Joussen

first: Vladimir

last: Benes

middle: H

last: Brümmendorf

first: George

last: Reid

first: Ivan

last: Costa


title: Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis

last: Marazzi

address: 1468 Madison Avenue

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary:
The human helicase senataxin (SETX) has been linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS4) and ataxia with oculomotor apraxia (AOA2). Here we identified a role for SETX in controlling the antiviral response. Cells that had undergone depletion of SETX and SETX-deficient cells derived from patients with AOA2 had higher expression of antiviral mediators in response to infection than did wild-type cells. Mechanistically, we propose a model whereby SETX attenuates the activity of RNA polymerase II (RNAPII) at genes stimulated after a virus is sensed and thus controls the magnitude of the host response to pathogens and the biogenesis of various RNA viruses (e.g., influenza A virus and West Nile virus). Our data indicate a potentially causal link among inborn errors in SETX, susceptibility to infection and the development of neurologic disorders.

This SuperSeries is composed of the SubSeries listed below.


title: Length-dependent gene misregulation in Rett syndrome (ChIP-Seq 2)

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

summary: Disruption of the MECP2 gene leads to Rett syndrome (RTT), a severe neurological disorder with features of autism. MECP2 encodes a methyl-DNA-binding protein that is proposed to function as a transcriptional repressor, but, despite numerous studies examining neuronal gene expression in MeCP2 mutants, no coherent model has emerged for how MeCP2 regulates transcription. Here we identify a genome-wide length-dependent increase in the expression of long genes in neurons lacking MeCP2.  This gene misregulation occurs in human RTT brains and correlates with onset and severity of phenotypes in Mecp2 mutant mice, suggesting that the disruption of long gene expression contributes to RTT pathology. We present evidence that MeCP2 represses long genes by binding to brain-enriched, methylated CA dinucleotides within genes and show that loss of methylated CA in the brain recapitulates gene expression defects observed in MeCP2 mutants. We find that long genes encode proteins with neuronal functions, and overlap substantially with genes that have been implicated in autism and Fragile X syndrome. Reversing the overexpression of long genes in neurons lacking MeCP2 can improve some RTT-associated cellular deficits.  These findings suggest that a function of MeCP2 in the mammalian brain is to temper the expression of genes in a length-dependent manner, and that mutations in MeCP2 and possibly other autism genes may cause neurological dysfunction by disrupting the expression of long genes in the brain.

overall_design: MeCP2 ChIP-seq from the frontal cortex and cortex of wild-type mice

first: Benyam

middle: Z

last: Kinde

first: Michael

last: Greenberg


title: Length-dependent gene misregulation in Rett syndrome (RNA-Seq)

overall_design: Total RNA-seq Data from the visual cortex of wild-type and MeCP2 knockout animals at 8-10 weeks of age

middle: E


title: Length-dependent gene misregulation in Rett syndrome (Bisulfite-Seq 2)

overall_design: Bisulfite-seq from mouse cortex and cerebellum

first: Hume

last: Stroud


title: Replicative senescence is associated with nuclear reorganization and DNA methylation at specific transcription factor binding sites (RNA-seq)

last: Wagner

summary: Primary cells enter replicative senescence after a limited number of cell divisions. This process is associated with reproducible changes in DNA methylation (DNAm) at specific sites in the genome. The mechanism that drives senescence-associated DNAm changes remains unknown and may arise through drift in DNAm or through regulated, senescence dependent modifications at specific sites in the genome. In this study, we analyzed the reorganization of nuclear architecture and DNA methylation during long-term culture of human fibroblasts and mesenchymal stromal cells (MSCs). [RNA-seq]

overall_design: RNA was isolated from 1,000,000 cells of three MSC donors (59, 64, and 73 years old) at passage 4 and passage 13 using the miRNeasy Mini Kit (Qiagen). Gene expression profiles were analzyed by  deep sequencing with IlluminaHiSeq 2000 technology with a read length of 50 bases at EMBL gene core facility (Heidelberg, Germany).

first: Tim


title: SETX attenuates the antiviral innate immune response and controls viral biogenesis (GRO-Seq)

summary: The innate immune response is the first line of defense against pathogens, and factors that control this cellular response represent targets for treating both infectious and inflammatory diseases. Here, we reveal a novel role for the human helicase SETX, also previously implicated in amyotrophic lateral sclerosis (ALS4) and ataxia with oculomotor apraxia (AOA2), in controlling the magnitude of the antiviral response. Cells depleted for SETX and AOA2 patient-derived SETX-null cells show increased expression of antiviral mediators in response to infection. Mechanistically, this effect is achieved through SETX-mediated inhibition of RNAPII transcription of antiviral genes, and depends on SETX helicase activity. Our results suggest that SETX helps maintain the delicate balance between controlling viral infection and avoiding the potentially detrimental effects of an excessive antiviral response. More broadly, the observation that SETX can regulate the transcriptional activity of specific genes may have important implications for disorders where SETX function is compromised.

overall_design: A549 cells that were transfected with either control non-targeting or SETX-specific siRNAs were infected with the Influenza A virus (A/PR/8/34(ΔNS1) strain) at a multiplicity of infection (MOI) of 3 for 4 hours. Nuclei were then extracted and used to prepare Global Run-On Sequencing (GRO-seq) libraries.

first: Matthew

middle: S

last: Miller

first: Alexander

last: Rialdi

first: Jessica

last: Ho

first: Micah

last: Tilove

first: Luis

last: Martinez-Gil

first: Natasha

last: Moshkina

first: Zuleyma

last: Peralta

first: Justine

last: Noel

first: Camilla

last: Melegari

first: Ana

last: Maestre

first: Panagiotis

last: Mitsopoulos

first: Joaquín

last: Madrenas

first: Sven

last: Heinz

first: Chris

last: Benner

first: John

middle: A

last: Young

first: Alicia

last: Feagins

first: Christopher

middle: F

last: Basler

last: Fernandez-Sesma

first: Olivier

last: Bequerel

first: Martin

last: Lavin

first: Harm

last: van Bakel


title: Replicative senescence is associated with nuclear reorganization and DNA methylation at specific transcription factor binding sites

first: Wolfgang

last: Wagner


title: The IDH2 mutation cooperates with the NPM1 mutation to activate Hoxa9/Meis1 and hypoxia pathways in acute myeloid leukemia (MeDip-seq)

status: Public on Mar 25 2015

city: Cho-ku

first: yoko

last: ogawara

state: Tokyo

address: 5-1-1, Tsukiji

country: Japan

institute: National Cancer Center Research Institute

summary: Mutations in IDH1 and IDH2 are frequently observed in various cancers, including acute myeloid leukemia (AML). Mutant IDHs convert α-ketoglutarate (α-KG) to 2-hydroxyglutarate (2-HG), which dysregulates a set ofα-KG-dependent dioxygenases. To determine whether mutant IDHs are valid targets for cancer therapy, we established a mouse AML model harboring an IDH2 mutation by transplanting mice with nucleophosmin1 (NPM1)+/- mouse hematopoietic stem/progenitor cells that had been co-transduced with four mutant genes (NPMc, IDH2/R140Q, DNMT3A/R882H and FLT3/ITD) that frequently occur simultaneously in human AML patients. IDH2/R140Q is necessary for the engraftment or survival of NPMc+ cells in vivo.　Gene-expression analysis indicated that NPMc increased the expression of Hoxa9, and that IDH2/R140Q increased the level of Meis1 and activated the hypoxia pathway in AML cells.　Conditional deletion of IDH2/R140Q blocked 2-HG production and maintenance of leukemia stem cells, resulting in survival of the AML mice. IDH2/R140Q reversibly decreased the levels of 5hmC modification and gene expression at some differentiation inducing genes (Ebf1, Pax5 and Spib). These results indicate that the IDH2 mutation is critical for the development and maintenance of AML stem cells, and that mutant IDHs are promising targets for anticancer therapy.

overall_design: Map 5hmC in NIDF-AML cells

first: Yoko

last: Ogawara

first: Issay

last: Kitabayashi


title: Genome-wide identification of BATF2 binding sites in HeLa-BATF2 cells

city: Beijing

first: XueJia

last: Bai

address: 10 You’an Men West

department: Medical Genetics

institute: Capital Medical University

summary: Basic leucine zipper transcription factors (BATFs) play profound roles in the regulatory networks of gene expression in tumor cells. BATF2, also known as SARI (suppressor of AP-1, regulated by interferon), was able to suppress both growth and migration of various cancers. In searching for BATF2/SARI-specific regulatory DNA elements, we first established a stable BATF2 over-expression HeLa cell line, then employed ChIP-Sequencing in order to identify the responsive DNA motifs for BATF2/SARI.

overall_design: Examination of 2 different antibodies enrichment in HeLa-BATF2 cells.

last: BAI

first: Wei

last: DING


title: Therapy induced tumour secretomes promote resistance and tumour progression

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

summary: Drug resistance invariably limits the clinical efficacy of targeted therapy with kinase inhibitors against cancer. We found that targeted therapy with BRAF, ALK, or EGFR inhibitors induces a complex network of secreted signals in drug-stressed melanoma and lung adenocarcinoma cells. This therapy-induced secretome (TIS) stimulates the outgrowth, infiltration and metastasis of drug-resistant cancer clones in the tumour. Additionally, the TIS supports the survival of drug-sensitive cells, contributing to incomplete tumour regression. We used transcriptomic analysis of sensitive tumour cells and xenograft tumours treated with vehicle, vemurafenib, or crizotinib to identify the transcriptional drivers and to dissect the TIS in melanoma (A375, Colo800, UACC62) and lung adenocarcinoma (H3122). In addition, we utilize cell type–specific mRNA purification by translating ribosome affinity purification (TRAP) to identify pathways that are up-regulated in resistant cells (A375R) in response to the regressing tumour microenvironment.

overall_design: Analysis of the response of drug sensitive melanoma and lung adenocarcinoma cells to pharmacological inhibition of their driver oncogene and gene expression analysis of drug resistant cancer cells responding to different tumor microenvironments.

first: Joan

last: Massagué

first: Anna

last: Obenauf

first: Yilong

last: Zou


title: H3K18Ac and H3K18Cr ChIP-seq and RNA-seq analysis of LPS-stimulated RAW 264.7 cells

city: Dallas

first: Benjamin

last: Sabari

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: (1) We sought to characterize the genomic profiles of H3K18Ac and H3K18Cr before and after the activation of the LPS-induced inflamatory response to elucidate the role of differential acylation in the process of gene activation. We performed chromatin Immunoprecipitation followed by massively parallel sequencing (ChIP-seq) with two antibodies, anti-H3K18Ac and anti-H3K18Cr, in RAW264.7 cells +/- LPS stimulation. (2)  We also sought to characterize the effect of increasing the cellular concentration of crotonyl-CoA prior to LPS-stimulation on the expression of different classes of LPS-induced genes. We performed RNA-seq on mRNA isolated from RAW264.7 cells under four conditions a) untreated and unstimulated, b) untreated and LPS stimulated, c) crotonate pre-treated and unstimulated, d) crotonate pre-treated and LPS stimulated. Sequencing was performed on the HiSeq2000 (Illumina).

overall_design: ChIP-seq for H3K18Ac and H3K18Cr in RAW264.7 cells +/- LPS stimulation and RNA-seq of RAW264.7 cells +/- LPS stimulation and +/- sodium crotonate pretreatment


title: Transcriptome sequencing and analysis of rubber tree (Hevea brasiliensis Muell.) to discover putative genes associated with tapping panel dryness (TPD)

city: Haikou

first: xia

last: zhiqiang

address: 4 Xueyuan Road

institute: The Institute of Tropical Bioscience and Biotechnology

summary: This study is committed to de novo sequencing and comparative analysis of the transcriptomes of healthy (H) and Tapping panel dryness (TPD)-affected (T) rubber trees to identify the genes and pathways related to the TPD. Total raw reads of 34,632,012 and 35,913,020 bp were obtained from H and T library, respectively using Illumina Hiseq 2000 sequencing technology. De novo assemblies yielded 141,456 and 169,285 contigs, and 96,070 and 112,243 unigenes from H and T library, respectively. Among 66535 genes, 107021 genes were identified as differential expressed genes between H and T library via comparative transcript profiling. A majority of genes involved in natural rubber biosynthesis and jasmonate synthesis with most potential relevance in TPD occurrence were found to be differentially expressed. In TPD-affected trees, the expression of most genes related to the latex biosynthesis and jasmonate synthesis was severely inhibited and it probably the direct cause of the TPD. Our de novo transcriptome data sets provide a significant resource for the discovery of genes related to TPD and improve our understanding the occurrence and maintainace of TPD.

overall_design: De novo sequencing and comparative analysis of the transcriptomes of healthy (H) and Tapping panel dryness (TPD)-affected (T) rubber trees

first: Jin-Ping

last: Liu

first: Zhi-Qiang

last: Xia


title: Cis regulatory effects on A-to-I RNA editing in Drosophila melanogaster, Drosophila sechellia and their F1 hybrids

city: Stanford

first: Jin

middle: Billy

last: Li

address: 300 Pasteur Dr, Alway M341

institute: Stanford University

summary: We applied microfluidic multiplex PCR and deep sequencing (mmPCR-seq) to quantify RNA editing levels at targeted sites in Drosophila melanogaster, Drosophila sechellia and the species-specific alleles of their F1 hybrids to understand the contribution of cis and trans regulatory factors to regulating RNA editing levels.

sample_organism: Drosophila melanogaster x Drosophila sechellia

overall_design: Examination of RNA editing levels through RT-PCR amplification of 493 loci in female heads of two replicates of D. melanogaster parents, two replicates of D. sechellia parents, two replicates of a mixture of the two parent species (mixed parent control), three replicates of their F1 hybrids, and three replicates of hybrids mutant for D. melanogaster Adar.

first: Anne

middle: L

last: Sapiro

first: Patricia

last: Deng

first: Rui

last: Zhang

middle: B


title: Functional diversity and convergence of small non-coding RNAs in male germ cell differentiation and fertilization (piRNA and endo-siRNAs)

city: Madrid

first: Jesus

last: Garcia Lopez

address: C/Ramiro de Maeztu 9

department: Cellular and Molecular Biology

country: Spain

institute: Cib (CSIC)

summary: The small non-coding RNAs (sncRNAs) are considered as postranscriptional key regulators of male germ cell development. In addition to microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), other sncRNAs generated from small nucleolar RNAs (snoRNAs), tRNAs or rRNAs processing may also play important regulatory roles in spermatogenesis. By next generation sequencing (NGS), we characterized the different sncRNA populations detected at three milestone stages in male germ differentiation: primordial germ cells (PGCs) at 13.5 dpc, pubertal spermatogonia cells, and mature spermatozoa. In order to assess the potential transmission of the sncRNAs through the mature spermatozoa during fertilization, the sncRNA population detected in male germ cells was also compared with sncRNAs detected in unfertilized mouse oocytes and zygotes. Combining the data obtained by NGS and microarrays from whole PGC and spermatogonia transcriptome, we defined the potential regulatory roles of specific miRNAs and their validated targets. Similar to miRNAs, both the small RNAs derived from snoRNAs and the piRNAs, could be involved in the postranscriptional regulation of mRNA transcripts during the male germ development. Finally, our results strongly suggest that the small RNAs-derived from tRNAs and rRNAs are interacting with PIWI proteins, and specifically with MILI. These new classes of piRNAs are not generated by the ping-pong pathway and could be the source of primary piRNAs.

overall_design: Comparative analysis from deep sequencing of piRNAs and endo-siRNAs in mouse oocytes, spermatozoa and zygotes

first: J

last: García-López

first: D

last: Cárdenas

first: L

last: Alonso

first: H

last: Artaza

middle: D

last: Hourcade

first: S

last: Martínez

first: M

last: Brieño

last: del Mazo


title: Functional diversity and convergence of small non-coding RNAs in male germ cell differentiation and fertilization

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

overall_design: Refer to individual Series


title: GATA3/G9A/MTA3 sequencing in non-treated  MCF-7 cells

first: Wenzhe

last: Si

address: 38 Xue Yuan Road

department: Department of Biochemistry and Molecular Biology

institute: Peking University Health Science Center

summary: Transcription factor GATA3 is essential for the specification and maintenance of the luminal cell differentiation in the mammary gland, and its expression is progressively lost during luminal breast cancer progression. However, how loss-of-function of GATA3 contributes to the development of breast cancer is still poorly understood. Here, we report that GATA3 nucleates a transcription repression program composed of G9A and MTA3-, but not MTA1- or MTA2-, constituted NuRD complex. Genome-wide analysis of the GATA3/G9A/NuRD(MTA3) targets identified a cohort of genes that are critically involved in epithelial-to-mesenchymal transition and cell invasion.

overall_design: Examination of GATA3/G9A/NuRD(MTA3) target genes in MCF-7 cell line.

first: Yan

last: Wang


title: Overlapping and unique signatures in the proteomic and transcriptomic responses of the nematode Caenorhabditis elegans towards pathogenic Bacillus thuringiensis

status: Public on Mar 23 2015

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

summary: The innate immune system acts as an early line of defense against microbial infection in all animals. It relies on activation of multiple signaling cascades that ultimately alter the abundance of molecules in cells. In this study, we utilized RNA-Seq to investigate the immune response of C.elegans infected by the Gram-positive pathogen Bacillus thuringiensis (BT). With the help of previously published proteome data on same pathogen and worm strain, we presented a detail high throughput analysis about worm immune response at both protein and mRNA levels. As a result, we identified gene sets that reflect transcriptional and post-transcriptional mechanisms of immune response. Finally, we emphasize the important role of C-type lectin domain-containing proteins and propose that AMPKs are new regulators of the immune response to infection with BT and possibly other pathogens, which link the pathogen induced damage of cells to defence response.

overall_design: mRNA profiles of wild type (WT) C.elegans exposed to either pathogenic Bacillus thuringiensis (BT) B-18247 (BT-247), non-pathogenic BT B-18407 (BT-407) or standard lab food E. coli OP50 at 6h or 12h were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Wentao

last: Yang

first: Katja

last: Dierking


title: Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells

status: Public on Mar 24 2015

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

summary: Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types.

overall_design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.

first: Diego

last: Miranda-Saavedra