title: Epigenetic landscape of olfactory receptor enhancers

city: San Francisco

first: Stavros

last: Lomvardas

institute: UCSF

summary: Distant enhancer elements are a major source of specificity in mammalian gene expression. Although enhancers that regulate broad developmental decisions and inducible gene expression have been studied extensively, little is known about regulatory elements that govern monogenic and monoallelic expression. Here, using high throughput epigenetic and genetic techniques we identified a plethora of distant enhancers that regulate monoallelic olfactory receptor (OR) gene expression. Potential OR enhancers have unique, cell type specific epigenetic marks that distinguish them from other neuronal enhancers and correlate with enhancer activity in vivo. Using sequence capture to enrich for these sequences we identified Dnase-protected footprints that reveal novel regulatory sequences and transcription factors required for OR gene activation. Our experiments provide insight to the regulation of OR expression, and describe novel principles and methodologies towards the understanding of transcriptional mechanisms that generate cellular diversity.

overall_design: In vivo examination of H3K79me3 enrichment and DNAse protected footprints on olfactory receptor enhancer sequences.  We performed ChIP-seq on native chromatin isolated from the mouse olfactory epithelium using antibodies against H3K79me3. To sequence accessible regions of the genome we treated nuclei with limiting amounts of DNAse I to digest accessible chromatin and perform Dnase Hypersensitivity (DHS)-seq.  In the olfactory epithelium, the H enhancer – the first described enhancer for olfactory receptors has a well-defined DNAse I hypersensitivity peak and is flanked by high levels of H3K79me3.  We find other intergenic sequences nearby olfactory receptor genes that share the same chromatin signature, and test their function in vivo.  TO uncover transcription factor footprints on olfactory receptor enhancers we performed sequence capture of the DHS-seq library to enrich for these sequences.  We find multiple DNAse-protected sequences and perform motif analysis on transcription factor footprints to reveal factors involved in olfactory receptor gene regulation.

first: Eirene

last: Markenscoff


title: Contribution of Veillonella parvula to Pseudomonas aeruginosa mediated pathogenicity in a murine tumor model system

status: Public on Nov 06 2014

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universität Braunschweig

type: Expression profiling by high throughput sequencing

summary: We investigated the specific interactions of the most dominant bacterial CF-pathogen, Pseudomonas aeruginosa, and the anaerobic bacterium Veilllonella parvula, that has been recovered at comparable cell numbers in the respiratory tract of CF patients. We used our recently established in-vivo murine tumor model to investigate mutual influences of the two pathogens during a biofilm-associated infection process. We found that although P. aeruginosa and V. parvula colonized distinct niches within the tumor, in mice that were co-infected with both bacterial species significant higher cell numbers of P. aeruginosa were recovered from the tumor tissue. Concordantly, in vivo transcriptional profiling implied that the presence of V. parvula supports P. aeruginosa growth at the infected host site, and the higher P. aeruginosa load correlated with clinical deterioration.

sample_organism:
Mus musculus
Veillonella parvula DSM 2008
Pseudomonas aeruginosa PA14

overall_design: We cultivated P. aeruginosa PA14 and V. parvula DSM No.:2008 in mono- and co-cultures in vivo using an established murine tumor model. Corresponding in vitro samples were generated under anaerobe growth conditions.

first: Christian

last: Pustelny

first: Uliana

last: Komor

first: Vinay

last: Pawar

first: Anne

last: Lorenz

first: Annette

last: Moter

first: Claudia

last: Grothe

first: Heinrich

last: Lünsdorf

first: Siegfried

last: Weiss

first: Susanne

last: Häussler


title: Loss of cytosine-5 methylation in tRNA triggers stress responses in a disease model for Intellectual Disability

city: Cambridge

first: Patrick

last: Lombard

state: Cambridgeshire

address: Tennis Court Road, Cambridge

country: United Kingdom

institute: University of Cambridge

type: Genome binding/occupancy profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Mutations in the cytosine-5 RNA methyltransferase NSun2 can cause Intellectual Disability (ID) and symptoms commonly found in patients with Dubowitz syndrome.   By analysing gene expression data with the global cytosine-5 RNA methylome in NSun2-deficient mice, we find that loss of cytosine-5 RNA methylation increases the fragmentation of transfer RNAs (tRNA) leading to an accumulation of 5’ halves. Cleavage of tRNAs by Angiogenin is a common cellular stress response to silence translational programmes, and we show that Angiogenin binds tRNAs lacking site-specific NSun2-methylation with higher affinity.  Furthermore, cells lacking functional NSun2 up-regulate stress markers, and deletion of NSun2 compromises cellular survival in response stress stimuli including UV-light and oxidative stress. The decreased tolerance of NSun2 null cells towards oxidative stress can be rescued through inhibition of Angiogenin.  In conclusion, cytosine-5 RNA methylation is an essential post-transcriptional mechanism during cellular stress responses and NSun2-mediated tRNA methylation protects from Angiogenin-dependent stress-induced RNA cleavage.

overall_design:
RNA Methylation profiling by high throughput sequencing
small non-coding RNA profiling by high throughput sequencing
Pol III Chromatin-IP profiling by high throughput sequencing

first: Sandra

last: Blanco


title: Genome-wide DNase hypersensitive sites during osteoclastogenesis

status: Public on Nov 05 2014

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

summary: Clarification of the mechanisms underlying osteoclast differentiation enable us to understand the physiology of bone metabolism as well as the pathophysiology of bone diseases, such as osteoporosis. Recently, it has been reported that epigenetics can determine the cell fate and regulate cell type specific gene expression. However, little is known about epigenetics during osteoclastogenesis. To reveal a part of epigenetics, especially focused on chromatin dynamics, during early osteoclastogenesis and identify novel transcription factors involved in osteoclastogenesis, we investigated genome-wide analysis of open chromatin during receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclastogenesis using DNase I hypersensitive sites sequencing (DNase-seq). DNase-seq was performed using the extracted nuclei obtained from RAW264 cells treated with or without RANKL for 24 hours, followed by several bioinformatic analyses. DNase I hypersensitive sites (DHSs) during RANKL-induced osteoclastogenesis were dynamically changed and accumulated in promoter regions, although the distributions of DHSs among cis-regulatory DNA regions were identical regardless of RANKL stimulation. Motif discoveries from DHSs successfully identified well-known osteoclastogenic transcription factors such as Jun, CREB1, FOS, ATF2 and ATF4, but also novel transcription factors for osteoclastogenesis such as Zscan10, Atf1 Nrf1 and Srebf2. siRNA knockdown of these identified novel transcription factors impaired osteoclastogenesis. Taken together, DNase-seq can be a useful tool for comprehension of epigenetics, especially chromatin dynamics during osteoclastogenesis and for identification of novel transcription factors involved in osteoclastogenesis. This study may reveal underlying mechanisms that determine cell-type specific differentiation of bone cells and may lead to investigate novel therapeutic targets for osteoporosis.

overall_design: Examination of genome-wide DNase Hypersensitive Sites in differentiated and undifferentiated RAW264 cells.

first: Kazuki

last: Inoue


title: TNFalpha signaling primes chromatin for NF-kappaB binding and induces rapid and widespread nucleosome repositioning

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

summary:
Background
The rearrangement of nucleosomes along the DNA fiber profoundly affects gene expression, but little is known about how signaling reshapes the chromatin landscape, in 3D space and over time, to allow the establishment of new transcriptional programs.

Results
Using micrococcal nuclease treatment and high-throughput sequencing, we map genome-wide changes in nucleosome positioning in primary human endothelial cells stimulated with tumour necrosis factor alpha (TNFalpha) - a proinflammatory cytokine that signals through nuclear factor kappaB (NF-kappaB). Within 10 minutes, nucleosomes reposition at regions both proximal and distal to NF-kappaB binding sites, before the transcription factor quantitatively binds thereon. Similarly, in long TNFalpha-responsive genes, repositioning precedes transcription by pioneering elongating polymerases and appears to nucleate from intragenic enhancer clusters resembling super-enhancers. By 30 minutes, widespread repositioning occurs throughout Mbp-long chromosomal segments, with consequential effects on 3D structure, detected using chromosome conformation capture.

Conclusions
Whilst nucleosome repositioning is viewed as a local phenomenon, our results point to effects occurring over multiple scales. Here, we present data in support of a TNFalpha-induced priming mechanism, mostly independent of NF-kappaB binding and/or elongating RNA polymerases, leading to a plastic network of interactions that affects DNA accessibility over large domains.

overall_design: MNase-Seq of HUVEC cells after stimulation with TNFα for 0, 10 or 30 min. Biological replicates for 0 and 30 min.

first: Argyris

last: Papantonis

first: Gernot

last: Längst

first: Peter

middle: R

last: Cook


title: Ab initio identification of a marsupial-specific imprinted gene via genome-wide histone state profiling in opossum fibroblasts

status: Public on Nov 07 2014

city: College Station

first: Kory

last: Douglas

state: TX

address: 4458 TAMU

country: USA

institute: Texas A&M University

summary: We generated genome-wide histone maps of four histone modifications, H3K4me3, H3K9Ac, H3K9me3, and H3K27me3, by ChIP-seq in male fibroblasts isolated from a model marsupial, Monodelphis domestica. We assayed the correlation and association of these histone modifications with each other, certain genomic elements such as CpG islands and predicted promoters, and the transcriptional states of the genes they mark. Generally, we found that promoters of actively transcribed genes are associated with H3K4me3 and H3K9Ac and lack H3K9me3 and H3K27me3. We also show that transcriptionally opposing, mutually exclusive histone modifications mark monoallelically expressed and imprinted genes in our samples.

overall_design: Profiling of four histone modifications in adult ear fibroblasts of Monodelphis domestica by Illumina ChIP-seq.

first: Paul

middle: B

last: Samollow

middle: C


title: Engineering acetyl-CoA supply: Functional expression of a bacterial pyruvate-dehydrogenase complex in the cytosol of Saccharomyces cerevisiae

status: Public on Nov 04 2014

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: The energetic (ATP) cost of biochemical pathways critically determines the maximum yield of metabolites of vital or commercial relevance. Cytosolic acetyl-CoA is a key precursor for biosynthesis in eukaryotes and for many industrially relevant product pathways that have been introduced into Saccharomyces cerevisiae, such as isoprenoids or lipids. In this yeast, synthesis of cytosolic acetyl-CoA via acetyl-CoA synthetase (ACS) involves hydrolysis of ATP to AMP and pyrophosphate. Here, we demonstrate that expression and assembly in the yeast cytosol of a pyruvate dehydrogenase complex (PDH) from Enterococcus faecalis can fully replace the ACS-dependent pathway for cytosolic acetyl-CoA synthesis. In vivo activity of E. faecalis PDH required the simultaneous expression of E. faecalis genes encoding its E1α, E1β, E2 and E3 subunits, as well as genes involved in lipoylation of E2 and addition of lipoate to growth media. A strain lacking ACS, that expressed these E. faecalis genes, grew at near-wild-type rates on glucose synthetic medium supplemented with lipoate, under aerobic and anaerobic conditions. A physiological comparison of the engineered strain and an isogenic Acs+ reference strain showed small differences in biomass yields and metabolic fluxes. Cellular fractionation and gel filtration studies revealed that the E. faecalis PDH subunits were assembled in the yeast cytosol, with a subunit ratio and enzyme activity similar to values reported for PDH purified from E. faecalis. This study indicates that cytosolic expression and assembly of PDH in eukaryotic industrial micro-organisms is a promising option for minimizing the energy costs of precursor supply in acetyl-CoA-dependent product pathways.

overall_design: For both strains - mutant strain IMY104 and reference strain CEN.PK113-7D' three independent chemostat cultures were performed. Each of the chemosta was sampled for transcriptome analysis. Samples were processed as described  below.

first: Barbara

middle: U

last: Kozak

first: Harmen

middle: M

last: van Rossum

first: Marijke

middle: A

last: Luttik

first: Kirsten

last: Benjamin

first: Liang

last: Wu

first: Simon

last: de Vries

first: Jack

middle: T

last: Pronk

first: Antonius

middle: J

last: van Maris


title: Epigenetic and transcriptional landscapes of Dnmt3a-deficient olfactory sensory neurons

first: Michael

last: Brainard

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

type: Methylation profiling by high throughput sequencing

summary: During differentiation, neurons experience a reorganization of DNA modification patterns within their genomes. However, the mechanisms underlying this developmental patterning and its role in defining the neuronal state are currently unclear. Here, we find that the de novo DNA methyltransferase Dnmt3a is necessary for elevated levels of 5-hydroxymethylcytosine (5hmC), a derivative of 5-methylcytosine (5mC), in olfactory sensory neurons (OSNs). Through an analysis of genome-wide 5mC and 5hmC distributions in isolated OSNs, we find that Dnmt3a-dependent 5mC and 5hmC occurs within regions of high accessibility, neural enhancers, and the transcription start sites of transcribed genes. Its loss results in the global disruption of gene expression patterns, including the upregulation of silent genes, the downregulation of mOSN-expressed genes, and the alteration of odorant-induced transcriptional responses of immediate early genes. Together, these results demonstrate that Dnmt3a is necessary to define the neuronal transcriptional state and may be broadly involved in refining expression profiles within differentiated cells.

overall_design: To determine the contributions of Dnmt3a to the DNA modification and transcriptional landscapes of a post-mitotic neuronal population, we performed DNA immunoprecipitation (DIP-seq) using antibodies specific for 5mC and 5hmC and rRNA-depleted transcriptional profiling (RNA-seq) coupled to high-throughput sequencing using genomic DNA or RNA from FACS-isolated mature olfactory sensory neurons (mOSNs) from main olfactory epithelium (MOE) of Dnmt3a wildtype (WT), heterozygous-null (Het), or homozygous-null (KO) 3-week old mice. Similarly, to compare this information with other epigenetic features of the MOE, we performed H3K4me1 (WT), H3K27ac (WT), and H3K27me3 (WT and KO) chromatin immunoprecipitation (ChIP)-seq and DNase I hypersensitivity assays (DNase-seq) using MOE nuclei from 3-week old mice. In addition, we assayed the influence of Dnmt3a-deficiency on the induction of odorant-responsive genes by exposing 3-week old Dnmt3a WT, Het, and KO mice to either water or a 1:1:1 mixture of amyl acetate:acetophenone:octanal for 1 hour and performed rRNA-depleted RNA-seq using RNA isolated from their MOEs.

first: Bradley

last: Colquitt

first: Stavros

last: Lomvardas


title: Next-generation sequencing facilitates quantitative analysis of diaphysis and metaphysis from femur of 5-week-old Dlx3Oc-cKO and wild type (WT=Dlx3+/+) mice transcriptomes

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived femoral diaphysis and metaphysis transcriptome profiling (RNA-seq) to determine pathways and networks dependent on Dlx3 during bone development and homeostasis.
Methods: mRNA profiles of diaphysis and metaphysis isolated from the femur of 5-week-old wild-type (WT) and Dlx3Oc-cKO (OC-cre;Dlx3f/-) conditional knockout mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level by ANOVA (ANOVA) and TopHat. qRT-PCR validation was performed using SYBR Green assay.
Results: RNA-Seq data were generated with Illumina's HiSeq 2000 system. Raw sequencing data were processed with CASAVA 1.8.2 to generate fastq files. Reads of 50 bases were mapped to the mouse transcriptome and genome mm9 using TopHat 1.3.2. Gene expression values (RPKM) were calculated with Partek Genomics Suite 6.6, which was also used for the ANOVA analysis to determine significantly differentially expressed genes.
Conclusions: Our study represents the first detailed analysis of Dlx3Oc-cKO diaphysis and metaphysis from femurs, with biologic triplicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Diaphysis and metaphysis mRNA profiles of metaphysis and diaphysis from femurs of 5-wk-old (WT) and Dlx3Oc-cKO male mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Maria

middle: I

last: Morasso

first: Juliane

last: Isaac

first: Julie

last: Erthal

first: Jonathan

last: Gordon

first: Olivier

last: Duverger

first: Hong

middle: W

first: Alexander

last: Lichtler

first: Gary

middle: S

last: Stein

first: Jane

last: Lian


title: Coilin's RNA, DNA and protein interactomes redefine the Cajal body as a hub for small non-coding RNAs

city: New Haven

first: Karla

last: Neugebauer

state: CT

address: 333 Cedar Street

department: Molecular Biophysics & Biochemistry

institute: Yale University

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: Transfer of Non-coding DNA Drives Regulatory Rewiring in Bacteria

first: Yaara

last: Oren

state: Massachusetts

address: 415 Main street cambridge

institute: Broad institute

summary: The rapid pace of evolution in bacteria is widely attributed to the promiscuous horizontal transfer and recombination of protein-coding genes. However, it is not known whether the same forces also drive the evolution of non-coding regulatory regions. Here we demonstrate that regulatory region can ‘switch’ between non-homologous alternatives and that such switching is ubiquitous, occurring across the bacterial domain. We show that such regulatory switching strongly impacts promoter architecture and expression divergence. We further show that regulatory transfer facilitates rapid phenotypic diversification of a human pathogen. This regulatory mobility enables bacterial genes to access a vast pool of potential regulatory elements, facilitating efficient exploration of the regulatory landscape.

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

overall_design: Examination of 2 E. coli strains in 2 conditions

first: Tal

last: Pupko


title: A Y-chromosome-encoded small RNA acts as sex determinant in persimmons

city: Davis

first: Luca

last: Comai

state: Calif

address: 451 Health Sciences Dr

department: Genome Center

institute: UC Davis

summary: In plants, multiple lineages have evolved sex chromosomes independently, providing a powerful comparative framework, but few specific determinants controlling the expression of a specific sex have been identified. We investigated sex-determinants in Caucasian persimmon, Diospyros lotus, a dioecious plant with heterogametic males (XY). Male-specific short nucleotide sequences were used to define a male determining region. A combination of transcriptomics and evolutionary approaches detected a Y-specific sex-determinant candidate, OGI, that displays male-specific conservation among Diospyros species. OGI encodes a small RNA targeting the autosomal MeGI gene, a homeodomain transcription factor regulating anther fertility in dosage-dependent fashion. This identification of a feminizing gene suppressed by a Y-chromosome-encoded small RNA contributes to our understanding of the evolution of sex chromosome systems in higher plants.

overall_design: For expression analyses, mixed buds were sampled on June 17, and July 4, 2013, corresponding to the early differentiation stages of male/female primordia, respectively.

first: Takashi

last: Akagi

first: Isabelle

last: Henry

first: Ryutaro

last: Tao


title: GATA2 shRNA Expression in Castration Resistant Prostate Cancer Cell Lines

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

summary: The transcription factor GATA2 regulates chemotherapy resistance in prostate cancer. We report a novel GATA2 transcriptional program that has implications for chemotherapy resistance disease and aggressiveness in castration resistant prostate cancer.

overall_design: Examination of the transcriptional network changes induced in human Ch-CRPC cell lines by two shRNA mediated knock down of GATA2 versus random shRNA control

first: Josep

last: Domingo-Domenech


title: The general mode of translation inhibition by macrolide antibiotics

status: Public on Nov 03 2014

city: Chicago

first: Krishna

last: Kannan

state: IL

address: 900 S Ashland Avenue

department: Center for Pharmaceutical Biotechnology

institute: University of Illinois at Chicago

summary: Macrolides are clinically important antibiotics thought to inhibit bacterial growth by impeding the passage of newly synthesized polypeptides through the nascent peptide exit tunnel of the bacterial ribosome. Recent data challenged this view by showing that macrolide antibiotics can differentially affect synthesis of individual proteins. In order to understand the general mechanism of macrolide action, we used genome-wide ribosome profiling and analyzed the redistribution of ribosomes translating highly expressed genes in bacterial cells treated with high concentrations of macrolide antibiotics. The metagene analysis indicated that inhibition of early rounds of translation, which would be characteristic of the conventional view of macrolide action, occurs only at a limited number of genes. Translation of most genes proceeds past the 5' proximal codons and can be arrested at more distal codons when the ribosome encounters specific short sequence motifs. The sequence motifs enriched in the sites of arrest are confined to the nascent peptide residues in the peptidyl transferase center but not to the peptide segments that contact the antibiotic molecule in the exit tunnel. This led to the conclusion that the general mode of macrolide action involves selective inhibition of peptide bond formation between specific combinations of donor and acceptor substrates. Additional factors operating in the living cell but not during in vitro protein synthesis may modulate site-specific action of macrolide antibiotics.

overall_design: Comparing ribosome distribution in bacterial cells treated with macrolide antibiotics against the control cells.

last: Mankin

first: Eugene

last: Oh

last: Weissman

first: Pinal

last: Kanabar

first: David

last: Schryer

first: Tanel

last: Tenson

first: Tanja

last: Florin

first: Neil

last: Bahroos


title: The exon junction complex is restricted to a specific subset of splice junctions

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

summary: We employ multi-step affinity purification followed by high-throughput sequencing  to determine the location of EJC complexes assembled on a cellular transcriptome in Drosophila S2 cells, finding 6% of the intron-containing genes were not associated with EJCs, and within genes with multiple introns, only specific exon-exon junctions assembled an EJC.

overall_design: RIP-Seq, 3 samples

first: Nazmul

last: Haque

first: Scot

last: Harms

first: Malcolm

middle: E

last: Cook


title: RNAseq on lungs from WT vs claudin 4 KO mice that underwent ventilator-induced lung injury

city: Los Angeles

first: Zea

last: Borok

address: 2011 Zonal Avenue HMR911

department: Division of Pulmonary, Critical Care and Sleep Medicine

institute: University of Southern California

summary: WT mice and claudin 4 KO mice were exposed to ventilator-induced lung injury (VILI) for 2 hours. We found that in some Cldn4 KO mice, injury was similar to WT, while in others, injury was higher, as assessed by amount of protein leak into broncho-alveolar lavage fluid. We performed RNAseq to find which genes were responsible for higher injury in Cldn4 KO mice.

overall_design: WT mice and claudin 4 KO mice were exposed to ventilator-induced lung injury (VILI) for 2 hours. RNA were extracted from whole lungs and RNA sequencing was performed. The samples are (all in duplicates): WT no VILI, Cldn4 KO no VILI, WT VILI, Cldn4 KO VILI with similar injury to WT (Cldn4 KOlow), and Cldn4 KO VILI with higher injury than WT (Cldn4 KOhigh)

first: Hidenori

last: Kage

first: Crystal

middle: N

last: Marconett


title: Genome-wide analysis of the lsm4 and lsm5 mutant transcriptomes

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

summary: The goal of this study was to compare the transcriptional profile (RNA-seq) of lsm4 and lsm5 Arabidopsis mutants with their respective wild type plants grown under continous light conditions

overall_design: lsm4 and lsm5 mutant plants were grown together with their respective wild type plants for two weeks under continuous white light at 22 degrees centigrades and the transcriptional profile of these plants was analyzed using RNA-seq.


title: Sequence selectivity of macrolide-induced translational regulation

first: Mee-Ngan

middle: F.

last: Yap

address: 320 E Superior St

department: Microbiology-Immunology

institute: Northwestern University Feinberg School of Medicine

summary: We sequenced a total of 12 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from azithromycin-treated and -untreated S. aureus samples. The data represented 2 independent biological replicates.

sample_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: Examination of the impact of azithromycin on global translatome, mRNA abundance and the ribosome density along the transcripts.

first: A

last: Davis

first: M

middle: F


title: Allelic expression mapping across cell lineages reveal repressor disruption among disease SNPs

city: Montreal

first: Tony

last: Kwan

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

summary: Most variants associated to diseases are located in non-coding regions of the genome, and are thought to be regulatory in nature. Cis-regulatory SNPs (cis-rSNPs) impacting transcription can be identified through the mapping of differences in allelic expression (AE). We mapped common cis-rSNPs of protein coding and non-coding genes in 3 distinct cell-types. We show 70% sharing across tissues and similar genetically controlled transcription for protein-coding genes and lincRNAs. Candidate cis-rSNPs altering the expression of 42 non-coding RNA overlap SNPs underlying GWAS associations for 39 diseases. We uncover a new class of cis-rSNPs leading to disruption of footprint-derived de novo motifs, predominantly bind by repressive factors and implicated in disease susceptibility through overlaps with GWAS SNPs. Finally, we provide proof-of-principle for a new approach for genome-wide functional validation of transcription factor – SNP interactions. We perturbed NFκB action in lymphoblasts and identified 489 cis-regulated transcripts with altered AE after NFkB perturbation. Altogether, we performed a comprehensive analysis of cis-variation in four cell-populations, and provide new tools for the identification of functional variants associated to complex diseases.

overall_design: Mapping cis-rSNPs across 3 distinct cell types in humans

first: Veronique

last: Adoue


title: Epstein-Barr Virus oncoprotein super-enhancers control B cell growth

status: Public on Nov 01 2014

city: Boston

first: Hufeng

last: Zhou

address: 181 Longwood Ave,

department: Department of Microbiology and Molecular Genetics

institute: Harvard Medical School

summary: Super-enhancers are principal determinants of cell transcription, development, phenotype, and oncogenesis, not yet implicated in host-pathogen interactions. We found four Epstein-Barr virus (EBV) oncoproteins and five EBV-activated NF-B subunits co-occupying thousand of enhancer sites in EBV-transformed lymphoblastoid cells (LCLs). Of these, 187 had markedly higher and broader histone H3K27ac signals characteristic of super-enhancer formation, and were designated “EBV super-enhancers”. EBV super-enhancer associated genes included MYC and BCL2, which enable LCL proliferation and survival. EBV super-enhancers were enriched for specific B cell transcription factor motifs and had high STAT5 and NFAT co-occupancy. EBV super-enhancer associated genes were more highly expressed than other LCL genes. Disruption of EBV super-enhancers by the bromo-domain inhibitor, JQ1, by conditional inactivation of an EBV oncoprotein or NF-B, decreased MYC or BCL2 gene expression and arrested LCL growth. These findings provide novel insights into the mechanisms by which EBV causes lymphoproliferation and identify opportunities for therapeutic intervention.

overall_design: ChIP-seq was used to define the BRD4 genome-wide landscape in GM12878 lymphoblastoid cells.

first: Stefanie

last: Schmidt

first: Sizun

last: Jiang

first: Bradford

last: Willox

first: Katharina

last: Bernhardt

first: Jun

last: Liang

first: Eric

last: Johannsen

first: Peter

last: Kharchenko

first: Benjamin

last: Gewurz

first: Elliott

last: Kieff

first: Bo

last: Zhao


title: Identifying the targets of the pair-rule transcription factors Even-skipped and Runt in the late Drosophila blastoderm

status: Public on Nov 02 2014

first: Adam

last: Paré

address: 1275 York Avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: It has long been appreciated that striped pair-rule transcription factor expression is necessary for convergent extension in the early Drosophila embryo, although the mechanisms that link these transcriptional regulators to planar polarity in this tissue have long been elusive. The goal of this study was to determine the transcriptional tragets of the pair-rule transcription factors Eve and Runt in Drosophila blastoderm embryos. We compared the transcriptional profiles of late blastoderm embryos injected with either water or dsRNAs against both eve and runt to identify differentially expressed genes that may directly contribute to the establishment of planar polarity during Drosophila convergent extension.

overall_design: Comparing the mRNA profiles from late blastoderm Drosophila embryos injected with either water (Water) or eve+runt dsRNAs (Eve), in triplicate, using Illumina HiSeq.

last: Pare

first: Jennifer

last: Zallen


title: Ssu72 and Ser5P-RNAPII ChIPseq in hESCs. GROseq analysis in siCtrl and siSSu72 transfected hESCs.

city: La Jolla, San Diego

first: conchi

last: estaras

address: 10010 N Torrey Pines Rd

department: Regulatory Biology

institute: The Salk Institute

summary: Ssu72 is a Ser5P-RNAPII phosphatase, nevertheless few targets have been characterized and  its role in mammal cells remains elusive. Using ChIPseq and GROseq technologies we aimed to identify Ssu72 targets in human embryonic stem cells.

overall_design: For the ChIPseq experiments, H1 hESCs growing in mTeSR media were doubled fixed with DSG 2mM (45min) and FA 1% (20min) and processed to chromatin immunoprecipitation. For GROseq experiments, H1 hESCs were transfected with siCtrl or siSsu72 siRNAs using RNAimax (Invitrogene) for 48h. Then, run-on experiment was done with isolated nuclei. Nascent RNA purification and subsequent steps needed before sequencing were carried out essentially as described in Core et al, 2008, Science 319(5871): 1791-1792.

first: Conchi

last: Estaras

first: Yupeng

last: Chen

first: Lirong

last: Zhang

first: Kathy

last: Jones


title: DMRT6 coordinates the transition between mitotic and meiotic developmental programs during mamalian spermatogenesis

status: Public on Oct 31 2014

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: In mammals, a key transition in spermatogenesis is the exit from spermatogonial differentiation and mitotic proliferation and the entry into spermatocyte differentiation and meiosis. Although several genes that regulate this transition have been identified, how it is controlled and coordinated remains poorly understood. Here we examine the role in male gametogenesis of the Doublesex-related gene Dmrt6 (Dmrtb1) and find that Dmrt6 plays a critical role in directing germ cells through the mitotic to meiotic germ cell transition. DMRT6 protein is expressed in late mitotic spermatogonia. In mice of the C57BL/6J strain a null mutation in Dmrt6 disrupts spermatogonial differentiation, causing expression in inappropriate cell types of spermatogonial differentiation factors including SOHLH1, SOHLH2 and DMRT1 and the meiotic initiation factor STRA8 and causing most late spermatogonia to undergo apoptosis. In mice of the 129Sv background, most Dmrt6 mutant spermatogonia can complete differentiation and enter meiosis, but they show defects in chromosome pairing, establishment of the XY body, and processing of recombination foci, and mainly arrest in mid-pachynema. mRNA profiling of Dmrt6 mutant testes together with DMRT6 ChIP-seq suggest that DMRT6 represses genes involved in spermatogonial differentiation and activates genes required for meiotic prophase. Our results indicate that Dmrt6 plays a key role in coordinating the transition in gametogenic programs from spermatogonial differentiation and mitosis to spermatocyte development and meiosis.

overall_design: Six samples for RNA-Seq with three biological replicates in each group.  Two samples for ChIP-Seq (one input and one ChIP).

first: David

last: Zarkower

middle: D


title: Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

city: Ames

first: Steven

last: Cannon

state: IA

address: Crop Genome Informatics Laboratory #1017, Iowa State University

institute: United States Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit

summary:
Background

The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement.

Results

In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~10 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses.

Conclusions

We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.

overall_design: We sequenced mRNA from soybean cv. "Williams 82" root samples that includes three control samples (0 hr), and three biological replicates for each of the three time points 1, 6 and 12 hr under dehydration and salt stress

first: Vikas

last: Belamkar

first: Nathan

last: Weeks

first: Arvind

middle: K

last: Bharti

first: Andrew

last: Farmer

first: Michelle

last: Graham


title: Gene expression profiling of mouse bone marrow-derived macrophages (RNA-Seq)

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Bone marrow (BM) cells were obtained by flushing the long bones of 8-week old  C57BL/6 mice. BM cells were then were plated in macrophage SFM medium (Life Technologies) supplemented with penicillin-streptomycin and CSF-1 (Peprotech, 100 ng/ml) and cultured for one week to allow macrophage differentiation. BMDMs were polarized by adding IL-4 to the medium (40 ng/ml, Peprotech) for 72h or left untreated.

overall_design: 8 samples total, 2 groups, 4 biological replicates in each group

first: Mario

middle: L

last: Squadrito

first: Caroline

last: Baer

first: Frédéric

last: Burdet

first: Claudio

last: Maderna

first: Gregor

last: Gilfillan

first: Robert

last: Lyle

first: Michele

last: De Palma


title: Genome-wide mapping of Rad21 binding sites and gene expression profiling in wild type mouse small intestinal epithelial crypts and Apc Min adenomas

city: East Melbourne

first: Huiling

last: Xu

state: Victoria

address: St Andrew Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

summary: To investigate the role of RAD21 in the transcriptional regulation of global gene expression at early stage of colorectal cancer developments, we peformed the genome-wide analysis to map genomic regions bound by Rad21 in normal small testinal crypts and tumors (adenomas) harvested from Apc Min/+ mice using ChIP-seq. ChIP-seq naalysis identified high confidence RAD21 binding sites unique to normal crypts or adenomas, as well as those common to both tissues. We further performed RNA-seq to profile the changes in gene expression from normal WT crypts to adenomas at the very early stage of adenomagenesis in the context of Rad21 heterozygous loss.

overall_design: mRNA profiles of normal small intestinal crypts (WT) and adenomas from Apc Min/+ and Apc Min/+:Rad21+/- double mutant mouse; Mapping of Rad21 genomic binding sites in normal intestinal crypts (WT) and Apc Min/+ adenomas

middle: G

last: Ramsay


title: Dissecting neural differentiation regulatory networks through epigenetic footprinting

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

summary: Human pluripotent stem cell derived models that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community.  Notch signaling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells (NPCs) in the embryonic and adult nervous system1-3. Use of a HES5 reporter enables the isolation distinct populations of human embryonic stem (ES) cell derived NPCs that represent building blocks of cortical development in vitro4. Here, we report the transcriptional and epigenomic analysis of six consecutive stages of human ES cell differentiation along the neural lineage aimed at modeling key cell fate decisions including specification, expansion and patterning during the ontogeny of neural stem and progenitor cells. In order to dissect the regulatory mechanisms that orchestrate the stage-specific differentiation process we developed a computational framework to infer key regulators of each cell state transition based on the progressive remodeling of the epigenetic landscape and then validated these through a pooled shRNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and show here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our reference maps and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation.

overall_design: hESC were differentiated in vitro into 5 different NPC populations (NE, ERG, MRG, LRG and LNP) over a time period of 220 days. The hESCs and the first 3 NPC populations (NE, ERG, MRG) were subjected to ChIP-Seq for H3K4m3, H3K4me1, H3K27ac and H3K27me3 as well as RNA-Seq with two biological replicates each as well as whole genome bisulfite sequencing in singlicate. The last two populations (LRG, LNP) were both profiled by RRBS and the LRG populations also by RNA-Seq. In addition, each of the first three NPC populations were differentiated into more mature neuronal populations (NEdN, ERGdN, MRGdN). The LRG population was differentiated along the astrocyte fate (LRGdA). Each of these more mature populations was subjected to RNA-Seq in replicate. Finally, the NE and MRG populations were profiled for the transcription facctor OTX2 by ChIP-Seq.

first: Alex

last: Meissner

first: Yechiel

last: Elkabetz


title: Aging-induced type I interferon response at the choroid plexus negatively affects brain function.

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: We investigated  gene expression profile of the Brain's choroid plexus and other organs of young and aged mice. Additionally, we analysed gene expression profile of the choroid plexus in iso- and heterochronic- parabiosis settings of young and aged mice.

overall_design: 75 samples

first: Kuti

last: Baruch

first: Aleksandra

last: Deczkowska

first: David

last: Eyal


title: Overexpression of ERG in cord blood progenitors promotes expansion and recapitulates molecular signatures of high ERG leukemias

city: Sydney

first: Jason

last: Wong

state: NSW

address: Level 2, Lowy Cancer Research Centre, University of New South Wales

institute: UNIVERSITY OF NEW SOUTH WALES

summary: High expression of the ETS family transcription factor ERG is associated with poor clinical outcome in acute myeloid leukemia (AML) and acute T-cell lymphoblastic leukemia (T-ALL). In murine models, high ERG expression induces both T-ALL and AML. However, no study to date has defined the effect of high ERG expression on primary human hematopoietic cells. In the present study, human CD34+ cells were transduced with retroviral vectors to elevate ERG gene expression to levels detected in high ERG AML. RNA sequencing was performed on purified populations of transduced cells to define the effects of high ERG on gene expression in human CD34+ cells. Integration of the genome-wide expression data with other data sets revealed that high ERG drives an expression signature that shares features of normal hematopoietic stem cells, high ERG AMLs, early T-cell precursor-ALLs and leukemic stem cell signatures associated with poor clinical outcome. Functional assays linked this gene expression profile to enhanced progenitor cell expansion. These results support a model whereby a stem cell gene expression network driven by high ERG in human cells enhances the expansion of the progenitor pool, providing opportunity for the acquisition and propagation of mutations and the development of leukemia.

overall_design: RNA sequencing in ERG overexpressing human CD34+ cells

first: John

last: Pimanda

first: Dominik

last: Beck

first: Julie

last: Thoms

first: Yizhou

last: Huang


title: Transcriptomics of Bacillus amyloliquefaciens SQR9 to maize root exudates

city: Nanjing

first: Dongqing

last: Yang

state: Jiangsu

address: Weigang 1#, Xuanwu district

country: China

institute: Nanjing Agricultural University

summary: Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates.

overall_design: 4 treatments, including 2 blank control (24 h and 48 h-post inoculation, named as 5 and 15, respectively), and 2 treatments with maize root exudates (24 h and 48 h-post inoculation, named as 7 and 17, respectively)

last: Zhang

first: Ruifu

first: Qirong

last: Shen


title: Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing

first: Hao

last: Wu

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: Genetics

institute: Harvard Medical School/HHMI

summary: Active DNA demethylation in mammals involves TET-mediated iterative oxidation of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) and subsequent excision repair of highly oxidized cytosine bases 5-formylcytosine (5fC)/5-carboxylcytosine (5caC) by Thymine DNA glycosylase (TDG). However, quantitative and high-resolution analysis of active DNA demethylation activity remains challenging. Here we describe M.SssI methylase-assisted bisulfite sequencing (MAB-seq), a method that directly maps 5fC/5caC at single-base resolution. Genome-wide MAB-seq allows systematic identification of 5fC/5caC in Tdg-depleted embryonic stem cells, thereby generating a base-resolution map of active DNA demethylome. A comparison of 5fC/5caC and 5hmC distribution maps indicates that catalytic processivity of TET enzymes correlates with local chromatin accessibility. MAB-seq also reveals strong strand asymmetry of active demethylation within palindromic CpGs. Integrating MAB-seq with other base-resolution mapping methods enables quantitative measurement of cytosine modification states at key transitioning steps of active demethylation pathway, and reveals a regulatory role of 5fC/5caC excision repair in active DNA demethylation cascade.

overall_design: Analysis of 5fC/5caC excision repair-dependent active DNA demethylome by MAB-seq in mouse embryonic stem cells.

first: Xiaoji

first: Yi


title: RNA-seq of Procr-expressing mouse mammary myoepithelium

city: Shanghai

first: Qing Cissy

last: Yu

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institute of Biological Sciences

summary: Procr, also known as EPCR, is a protein C receptor known to function in the platelet coagulation cascade. We have used RNA-seq to examine RNA differential expression between Procr+ and Procr- myoepithelium in mouse mammary gland.

overall_design: Examine RNA differential expression among subsets of freshly sorted mouse mammary gland myoepithelium.

last: Zeng

first: Qing

middle: C

first: Xiao

middle: O

first: Li


title: Systems biology with high-throughput sequencing revealed genetic mechanisms underlying the Metabolic Syndrome in the Lyon Hypertensive Rat

first: Jinkai

last: Wang

address: 650 Charles E. Young Drive South, CHS 33-228

institute: University of California, Los Angeles

summary: The metabolic syndrome (MetS) is a collection of co-occurring complex disorders including obesity, hypertension, dyslipidemia, and insulin resistance. The Lyon Hypertensive (LH) and Lyon Normotensive (LN) rats are models of MetS sensitivity and resistance, respectively. To identify genetic determinants and mechanisms underlying MetS, 169 rats from an F2 intercross between LH and LN were studied. Multi-dimensional data were obtained including genotypes of 1536 SNPs, 23 physiological traits including blood pressure, plasma lipid and leptin levels, and body weight/adiposity, and more than 150 billion nucleotides of RNA-seq reads from the livers of 36 F2 individuals, 6 LH and 6 LN individuals. We identified 17 pQTLs (physiological quantitative trait loci) and 1200 eQTLs (gene expression quantitative trait loci). Systems biology methods were applied to identify 18 candidate MetS genes, including genes (Prcp and Aqp11) previously shown to be MetS-related. We found an eQTL hotspot on RNO17, which was also located within pQTLs for MetS-related traits. The genes regulated by this eQTL hotspot were mainly in two co-expression network modules (a mitochondria related module and a gene regulation related module) and were predicted to causally affect many MetS-related traits. Multiple evidences strongly and consistently support RGD1562963, a gene regulated in cis by this eQTL hotspot and possibly related to RNA stability, as the eQTL driver gene directly affected by genetic variation between LH and LN rats; the expression of this gene is also correlated with MetS-related traits. Our study sheds light on the intricate pathogenesis of MetS and proved that systems biology with high-throughput sequencing is a powerful method to study the etiology of complicated diseases.

overall_design: RNA-Seq of the liver of 6 LH (Lyon Hypertensive) rats and 6 LN (Lyon Normotensive) rats and 36 F2 rats.

middle: M

last: Ma

first: Amanda

last: Mennie

first: Janette

last: Pettus

first: Yang

last: Xu

first: Lan

last: Lin

first: Matthew

last: Traxler

first: Jessica

last: Jakoubek

first: Santosh

last: Atanur

first: Timothy

last: Aitman

last: Xing

first: Anne

last: Kwitek


title: Maternal nutrition induces gene expression changes in fetal muscle and adipose tissues in sheep

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Maternal nutrition during different stages of pregnancy can induce significant changes in the structure, physiology, and metabolism of the offspring. These changes could have important implications on food animal production especially if these perturbations impact muscle and adipose tissue development. The objective of this study was to evaluate the effect of different maternal diets on the transcriptome of fetal tissues in sheep. Ewes were bred to a single sire and from days 67 ± 3 of gestation until necropsy (days 130 ± 1), they were fed one of three isoenergetic diets: alfalfa haylage (H; fiber), corn (C; starch), or dried corn distillers grains (D; fiber plus protein plus fat). Longissimus dorsi (M), subcutaneous adipose depot (S), and perirenal adipose depot (R) tissues from individual fetuses were pooled and then analyzed by RNA sequencing.

overall_design: A total of 26 fetuses were removed from 15 dams. From the fetuses three different tissues were collected including one muscle, longissimus dorsi muscle (M), and two adipose tissues, perirenal adipose depot (R) and subcutaneous adipose depot (S). The RNA samples from the 26 fetuses were pooled to generate four biological replicates per maternal diet and tissue. In particular, per each diet and tissue, two RNA pools were created from male fetuses and two RNA pools were created from female fetuses. Overall, a total of 36 pools (i.e., 12 pools per tissue, 3 tissues in total) underwent RNA extraction, library generation, and subsequent sequencing.

first: Amy

last: Radunz

first: Hasan

last: Khatib


title: Functional characterization of the TERRA transcriptome at damaged telomeres

first: Julien

last: Delafontaine

state: Vaud

address: Route Cantonale

department: SV

institute: EPFL

summary: We characterize the TERRA transcriptome at normal and TRF2-depleted telomeres by RNA-seq and we demonstrate that TERRA upregulation is occurring at all transcribed telomeres upon depletion of TRF2.

overall_design: RNA-sequencing of HeLa mRNA, 4 samples: with or without TERRA enrichment by IP (respectively "IP" and "input"), with or without TFR-2 knock-down (respectively "_T" and "_EV").

first: Antonio

last: Porro

first: Sasha

last: Feuerhahn

first: Harold

last: Riethman

first: Jacques

last: Rougemont

first: Joachim

last: Lingner


title: The role of HIF-1α and HIF-2α in hypoxic and M2-polarized macrophages

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

summary: Macrophages (MФ) skewn towards a regulatory-like phenotype are known to promote tumor progression. They tend to accumulate in hypoxic tumor areas and activate hypoxia-inducible factors (HIF-1 and HIF-2). HIFs are known to alter the gene expression profile of MФ. To define direct HIF-1 and HIF-2 target genes in hypoxic and IL-10 treated human MФ we used chromatin immuno-precipitation-sequencing (ChIP-seq) and microarray analysis on a genome-wide scale.

overall_design: ChIP-seq of HIF1a and HIF2a in human macrophages under hypoxic and normoxic conditions with and without Interleukin-10 treatment

first: Michaela

last: Tausendschön

first: Nathalie

last: Dehne

first: Bernhard

last: Brüne

first: Christian

last: Schmidl


title: RNAseq Analysis of Transcriptomic Response to Zn Resupply in Chlamydomonas reinhardtii

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

summary: Zn-limited cells accumulate Cu in intracellular structures in a reversable manner.  We used RNAseq analysis to monitor gene expression in Zn-limited cells, and during a time course (0 - 24 h) after Zn resupply.

overall_design: Comparison of Chlamydomonas reinhardtii gene expression when Zn deficient cells are resupplied with 2.5 µM Zn. Time points 0 (before resupply), 1.5, 3, 4.5, 12, and 24 hours after resupply.  Four biological replicates per condition.

last: Hong-Hermesdorf

first: Marcus

last: Miethke

first: Janette

last: Kropat

first: Sabeeha

last: Merchant


title: The Polycomb Group Gene EMF2B is required for meristem determinacy and organ specification in rice flowers.

city: Davis

first: Venkatesan

last: Sundaresan

state: CA

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

summary: The Polycomb Repressive Complex 2 (PRC2) represses the transcriptional activity of target genes through trimethylation of Lysine 27 of Histone H3. The functions of the plant PRC2 have been chiefly described in Arabidopsis but specific PRC2 functions in other plant species, especially the cereals, are still largely unknown. Here we characterize mutants in the rice EMF2B gene, an ortholog of the Arabidopsis PRC2 gene EMBRYONIC FLOWER2 (EMF2). Loss of EMF2B in rice results in complete sterility, and mutant flowers have severe floral organ defects and indeterminacy that resemble loss of function mutants in rice E-function floral organ specification genes. Transcriptome analysis identified the E-function genes OsMADS1, OsMADS6 and OsMADS34 that are involved in floral development as differentially expressed in the emf2b mutant compared to wild type. OsMADS1 and OsMADS6 are known to be required for meristem determinacy in rice, and are down-regulated in the emf2b mutant, whereas OsMADS34 which interacts genetically with OsMADS1 was up-regulated. Chromatin immunoprecipitation for H3K27me3 followed by deep sequencing showed that all three genes are amongst the presumptive targets of PRC2 in the meristem. We propose that the PRC2 operates through a mechanism that involves regulation of E-function genes to play a major role in floral organ specification and floral meristem determinacy in rice, and possibly in other cereals.

overall_design: RNA-seq: The transcriptome of WT and emf2b rice panicles were compared via RNA-seq.

first: Liza

middle: J

last: Conrad

first: Imtiyaz

last: Khanday

first: Cameron

last: Johnson

first: Sarah

last: Anderson

first: Ravi

last: Patel

first: Emmanuel

last: Guiderdoni

first: Gynheung

last: An

first: Usha

last: Vijayraghavan


title: White-to-brown metabolic conversion of human adipocytes by JAK inhibition

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

institute: F. Hoffmann-La Roche

summary: The rising incidence of obesity and related disorders such as diabetes and heart disease has  focused considerable attention on the discovery of novel therapeutics. One promising  approach has been to increase the number or activity of brown-like adipocytes in white  adipose depots, as this has been shown to prevent diet-induced obesity and reduce the  incidence and severity of type 2 diabetes. Thus, the conversion of fat-storing cells into  metabolically active thermogenic cells has become an appealing therapeutic strategy to  combat obesity. Here, we report a screening platform for the identification of small molecules  capable of promoting a white-to-brown metabolic conversion in human adipocytes. We  identified two inhibitors of Janus Kinase (JAK) activity with no precedent in adipose tissue  biology that permanently confer brown-like metabolic activity to white adipocytes.  Importantly, these metabolically converted adipocytes exhibit elevated UCP1 expression and  increased mitochondrial activity. We further found that repression of interferon signalling and  activation of hedgehog signalling in JAK-inactivated adipocytes contributes to the metabolic  conversion observed in these cells. Our findings highlight a novel role for the JAK/STAT  pathway in the control of adipocyte function and establish a platform to identify compounds  for the treatment of obesity.

overall_design: Human pluripotent stem-cell derived mesenchymal progenitor cells (PSC-MPCs), white adipose cells (PSC-WA), and brown adipose cells (PSC-BA) were treated with DMSO (as control), a JAK3-inhibitor compound, and a SYK-inhibitor compound respectively. Transcriptomic expression profiling was performed at 24 hours and 7 days respectively. Three biological replicates are available for each condition defined by cell type, compound, and time.

first: Annie

last: Moisan

first: Youn-Kyoung

last: Lee

first: Jitao

first: Carolyn

last: Hudak

first: Class

middle: A

last: Meyer

first: Michael

last: Prummer

first: Sannah

last: Zoffmann

first: Hoa

middle: H

last: Truong

first: Martin

last: Ebeling

first: Anna

last: Kiialainen

first: Régine

last: Gérard

first: Fang

last: Xia

first: Robert

middle: T

last: Schinzel

first: Kurt

last: Amrein

first: Chad

last: Cowan


title: Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

city: Riverside

first: Wenxiu

last: Ma

address: 900 University Ave

institute: University of California Riverside

summary: Characterizing the relationship between genome form and function requires methods both for zooming out, to globally survey the genomic architectural landscape, and for zooming in, to investigate regions of interest at high resolution. High throughput methods based on chromosome conformation capture (3C) have greatly advanced our understanding of the three-dimensional (3D) organization of genomes, but are limited in resolution by their reliance on restriction enzymes. Here we describe a method for comprehensively mapping global chromatin contacts that uses DNaseI for chromatin fragmentation, leading to greatly improved efficiency and resolution. Coupling this method with DNA capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture. We applied targeted DNase Hi-C to characterize the 3D organization of 1,030 lincRNA promoters in two human cell lines, and identified thousands of high-confidence lincRNA promoter-associated chromatin contacts at 1 kilobase pair (kbp) resolution. Detailed analysis of these contacts reveals that expression of lincRNAs is tightly controlled by complex mechanisms involving both super-enhancers and the polycomb repressive complex. Our results provide the first glimpse of the cell-type-specific 3D organization of lincRNA genes.

overall_design: DNase Hi-C assay (x1 replicate) in H1 and K562 cells, respectively. Targeted DNase Hi-C assays of the 220kb promoter-enhancer library (x1 replicate) and the 5Mb lincRNA promoter library (x2 replicate), in H1 and K562 cells, respectively.

first: Ferhat

last: Ay

first: Choli

first: Gunhan

last: Gulsoy

first: Xinxian

last: Deng

first: Savannah

last: Cook

first: Jennifer

last: Hesson

first: Carol

middle: B

last: Ware

first: Anton

last: Krumm

first: Jay

last: Shendure

first: C

last: Blau

first: Christine

last: Disteche

first: William

middle: S

last: Noble

first: Zhijun

last: Duan


title: Evolution of phenotypic plasticity and transgenerational effects of heat stress in the nematode Caenorhabditis remanei

status: Public on Oct 30 2014

city: Eugene

first: Patrick

middle: C.

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

institute: University of Oregon

summary: Analysis of evolved changes in transcriptional plasticity and parental effects on plasticity induced by mild heat stress in the nematode Caenorhabditis remanei. Results of this study highlight the importance of the broad environmental context of an organism and its influence on phenotypic plasticity, parental effects, and evolutionary responses.

overall_design: mRNA profiles of ancestral and two experimentally evolved populations of C. remanei. Parents of the sampled worms were raised at either 20°C or 30°C, then the resulting embryos were divided and reared at either 20°C or 30°C prior to collection (as L1 larvae). 6 replicates/larval temperature for each population if the parents were raised at 20°C, and 2 replicates/larval temperature for each population if the parents were raised at 30°C.

first: Kristin

last: Sikkink

first: Rose

last: Reynolds

first: Catherine

last: Ituarte

last: Cresko


title: Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: During transcription the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout budding yeast genome. In wild-type strains, R-loops were readily detected over the 35S rDNA region transcribed by Pol I and over the 5S rDNA transcribed by Pol III. In strains lacking RNase H activity, R-loops were elevated over other Pol III genes notably tRNAs, SCR1 and U6 snRNA, and were also associated with the cDNAs of endogenous TY1 retrotransposons, which showed increased rates of mobility to the 5?-flanking regions of tRNA genes. Unexpectedly, R-loops were also associated with mitochondrial genes in the absence of RNase H1, but not of RNase H2. Finally, R-loops were detected on highly expressed protein-coding genes in the wild-type, notably over the second exon of spliced ribosomal protein genes.

overall_design: ChIP-seq of RNA-DNA hybrids using antibody S9.6

first: Aziz

last: El Hage


title: Transcriptome of Nkx2-5-null atria

city: Los Angeles

first: Atsushi

last: Nakano

address: 615 Charles E. Young Dr. South

department: MCDB/BSCRC

institute: UCLA

summary: Atrial specific knockout of Nkx2-5 results in hyperplastic atria with ASD and conduction defects. To examine how Nkx2-5 regulates cardiac proliferation at late gestational stages, RNA-seq was performed.

overall_design: Examination of expression profile of 2 Nkx2-5-null atria and 3 controls

first: Yasuhiro

last: Nakashima

first: Diana

last: Yanez

first: Marlin

last: Touma

first: Haruko

first: Artur

last: Jaroszewicz

first: Maria

last: Jordan

first: Matteo

last: Pellegrini

first: Kenneth

middle: P

last: Roos


title: An Ezh2 and Ezh1 dual inhibitor, UNC1999, re-shapes the landscape of H3K27me3 versus H3K27ac in MLL-AF9-transformed murine leukemia

city: Chapel Hill

first: Bowen

last: Xu

state: NC

address: 450 West Drive, CB7295, Lineberger Cancer Center, GREG WANG Lab, RM 31-331

department: Biochemistry and Biophysics

institute: UNC-Chapel Hill

summary: Ezh2 and EZH1 are histone H3 lysine 27 (H3K27)-specific methyltransferases. Their hyperactive mutations and overexpression were found in cancer including various hematological malignancies. UNC1999 is a highly selective inhibitor for both enzymes. It suppresses H3K27 tri- and di-methylation globally and inhibits growth of MLL-rearranged acute leukemia. Here we performed ChIP-Seq to profile how UNC1999 affects distribution of H3K27me3 and its antagonizing H3K27ac in MLL-AF9-immortalized leukemia cells. We also performed ChIP-seq of SUZ12, an essential common cofactor of EZH2 and EZH1 following compound treatments.

overall_design: We treated MLL-AF9 transformed murine leukemia cells with DMSO, UNC1999 or UNC2400 (an inactive analog compound of UNC1999). Cells were then collected and used for ChIP-Sequencing of Input, H3K27me3, SUZ12, and H3K27ac.

first: Doan

last: On

first: X

middle: U

last: Bowen

first: G

last: Wang


title: Impact of HP1gamma and HP1gamma S83 phosphorylation on the transcriptionnal effect of PMA stimulation of mouse fibroblasts

city: Paris cedex 15

first: Christian

last: MUCHARDT

address: 25 rue du Dr-Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur Paris

summary: We have here followed the transcriptional effect of stimulation with the phorbol ester PMA in mouse fibroblasts from HP1gamma null mice recomplemented with either wild-type HP1gamma or an HP1g with an S83A mutation

overall_design: Spontaneously immortalized mouse embryonic fibroblasts from HP1gamma null mice were used to stably integrate either an empty expression vector, or expression vectors for either WT or S83A mutant HP1gamma. These cells were then stimulated with PMA for 0 or 60 min. and used for transcriptome analysis by Next Generation sequencing.

first: Laurence

last: ARBIBE

first: Christophe

last: RACHEZ

first: Florence

last: CAMMAS


title: Smoking Status Impacts microRNA Mediated Prognosis and Lung Adenocarcinoma Biology

city: Vancouver

first: Kelsie

middle: L

last: Thu

state: British Columbia

address: 675 West 10th Avenue

institute: BC Cancer Research Centre

summary:
Cigarette smoke is associated with the majority of lung cancers: however, 25% of lung cancer patients are non-smokers, and half of all newly diagnosed lung cancer patients are former smokers. Lung tumors exhibit distinct epidemiological, clinical, pathological, and molecular features depending on smoking status, suggesting divergent mechanisms underlie tumorigenesis in smokers and non-smokers. MicroRNAs (miRNAs) are integral contributors to tumorigenesis and mediate biological responses to smoking. Based on the hypothesis that smoking-specific miRNA differences in lung adenocarcinomas reflect distinct tumorigenic processes selected by different smoking and non-smoking environments, we investigated the contribution of miRNA disruption to lung tumor biology and patient outcome in the context of smoking status.
Results: We discovered novel and distinct smoking-status-specific patterns of miRNA and miRNA-mediated gene networks, and identified miRNAs that were prognostically significant in a smoking-dependent manner.
Conclusions: We conclude that miRNAs disrupted in a smoking-status-dependent manner affect distinct cellular pathways and differentially influence lung cancer patient prognosis in current, former and never smokers. Our findings may represent promising biologically relevant markers for lung cancer prognosis or therapeutic intervention.

overall_design: We applied a whole transcriptome sequencing based approach to interrogate miRNA levels in 94 patient-matched lung adenocarcinoma and non-malignant lung parenchymal tissue pairs from current [CS], former [FS] and never smokers [NS].

first: Emily

last: Vucic


title: Genome-wide chromatin analysis of Ewing sarcoma

city: Charlestown

first: Martin

last: Aryee

state: MA

address: 149 13th Street

department: Pathology

institute: Massachusetts General Hospital

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

overall_design: Refer to individual Series


title: Genome-wide chromatin analysis of Ewing sarcoma (ATAC-seq)

summary: We show that EWS-FLI1, an aberrant transcription factor responsible for the pathogenesis of Ewing sarcoma, reprograms gene regulatory circuits by directly inducing or directly repressing enhancers. At GGAA repeats, which lack regulatory potential in other cell types and are not evolutionarily conserved, EWS- FLI1 multimers potently induce chromatin opening, recruit p300 and WDR5, and create de novo enhancers. GGAA repeat enhancers can loop to physically interact with target promoters, as demonstrated by chromosome conformation capture assays. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild-type ETS transcription factors and abrogating p300 recruitment.

overall_design:
Mesenchymal stem cells (MSCs) and a Ewing sarcoma cell line (SKNMC) were analyzed by ATAC-seq. EWS-FLI1 was expressed in MSCs using a lentiviral vector (pLIV EWSFLI1 or pLIV empty vector control).

* Raw data not provided for the MSC samples. *

first: Miguel

last: Rivera


title: Interrogation of a Context-Specific Transcription Factor Network Identifies Novel Regulators of Pluripotency

city: New York

first: Raju

last: Chaganti

state: NY

address: 430 East, 67 Street, RRL-337,New York

department: Cell Biology

institute: MSKCC

summary: The predominant view of pluripotency regulation proposes a stable ground state with coordinated expression of key transcription factors (TFs) that prohibit differentiation. Another perspective suggests a more complexly regulated state involving competition between multiple lineage-specifying TFs that define pluripotency.  These contrasting views were developed from extensive analyses of TFs in pluripotent cells in vitro. An experimentally-validated, genome-wide repertoire of the regulatory interactions that control pluripotency within the in vivo cellular contexts is yet to be developed.  To address this limitation, we assembled a TF interactome of adult human male germ cell tumors (GCTs) using the Algorithm for the Accurate Reconstruction of Cellular Pathways (ARACNe) to analyze gene expression profiles of 141 tumors comprising pluripotent and differentiated subsets.  The network (GCTNet) comprised 1305 TFs, and its Ingenuity Pathway analysis identified pluripotency and embryonal development as the top functional pathways.  We experimentally validated GCTNet by functional (silencing) and biochemical (ChIP-seq) analysis of the core pluripotency regulatory TFs POU5F1, NANOG, and SOX2 in relation to their targets predicted by ARACNe.  To define the extent of the in vivo pluripotency network in this system, we ranked all TFs in the GCTNet according to sharing of ARACNe-predicted targets with those of POU5F1 and NANOG using an Odds-Ratio analysis method.  To validate this network, we silenced the top 10 TFs in the network in H9 ES cells. Silencing of each led to downregulation of pluripotency and induction of lineage; 7 of the 10 TFs were identified as pluripotency regulators for the first time.

overall_design: ChIP for three TFs OCT4, SOX2 and NANOG in two pluripotent cell line

first: Ritu

last: Kushwaha

first: Manjunath

last: Kustagi

first: Nirmala

last: Jagadish


title: Genome-wide chromatin analysis of Ewing sarcoma (ChIP-seq)

overall_design:
ChIP-seq for of 4 histone modifications (H3K27ac, H3K4me1, H3K4me3 and H3K27me3), FLI1, p300, WDR5, ELF1 and GABPA in primary Ewing sarcomas, Ewing sarcoma cell lines (A673 and SKMNC cells), and mesenchymal stem cells (MSC). EWS-FLI1 was knocked down in Ewing sarcoma cell lines with lentiviral shRNAs (shFLI1 and shGFP control). EWS-FLI1 was expressed in MSCs with lentiviral expression vectors (pLIV EWSFLI1 or pLIV empty vector control).

* Raw data not provided for the MSC and Primary Ewing sarcoma samples. *


title: Differential expression of miRNAs in response to topping in tobacco roots

city: zhengzhou

first: hongxiang

last: guo

address: 95 wenhua road

institute: henan agricultural university

summary: Topping is an important cultivating measure for flue-cured tobacco, and many genes had been found to be differentially expressed in response to topping. But it is still unclear how these genes are regulated. MiRNAs play a critical role in post-transcriptional gene regulation, so we sequenced two sRNA libraries from tobacco roots before and after topping, with a view to exploring transcriptional differences in miRNAs.Two sRNA libraries were generated from tobacco roots before and after topping. Solexa high-throughput sequencing of tobacco small RNAs revealed a total of 12,104,207 and 11,292,018 reads representing 3,633,398 and 3,084,102 distinct sequences before and after topping. The expressions of 136 conserved miRNAs (belonging to 32 families) and 126 new miRNAs (belonging to 77 families) were determined. There were three major conserved miRNAs families (nta-miR156, nta-miR172 and nta-miR171) and two major new miRNAs families (nta-miRn2 and nta-miRn26). All of these identified miRNAs can be folded into characteristic miRNA stem-loop secondary hairpin structures, and qRT-PCR was adopted to validate and measure the expression of miRNAs. Putative targets were identified for 133 out of 136 conserved miRNAs and 126 new miRNAs. Of these miRNAs whose targets had been identified, the miRNAs which change markedly (>2 folds) belong to 53 families and their targets have different biological functions including development, response to stress, response to hormone, N metabolism, C metabolism, signal transduction, nucleic acid metabolism and other metabolism. Some interesting targets for miRNAs had been determined.

overall_design: 2 samples examined:roots before and after topping

first: Liu

last: Weiqun

first: Guo

last: Hongxiang

first: Kan

last: Yunchao


title: Identification of transcripts whose abundance changes in response to acute switches in DSX isoform

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: RNAseq of dissected adult fat body after DSX isoform is switched using temperature inducible alleles or constructs.

overall_design: Biological duplicates were sequenced for each genotype at each condition.

last: Clough

first: Erin

last: Jimenez

first: Yoo-Ah

last: Kim

first: Cale

last: Whitworth

first: Megan

last: Neville

first: Leonie

last: Hempel

first: Hania

last: Pavlou

first: Zhen-Xia

last: Chen

first: David

last: Sturgill

first: Ryan

last: Dale

first: Harold

middle: E

last: Smith

first: Teresa

last: Przytycka

first: Stephen

last: Goodwin

first: Mark

last: Van Doren


title: Genome-wide chromatin analysis of Ewing sarcoma (RNA-seq)

first: Martin

last: Aryee

overall_design: Ewing sarcoma cell lines (A673 and SKNMC) were analyzed by RNA-seq. EWS-FLI1 was depleted by infection with lentiviral shRNAs (shFLI1 and shGFP control).

first: Miguel

last: Rivera


title: Isolation and Transcriptome Analyses of Human Erythroid Progenitors: BFU-E and CFU-E

first: John

last: Hale

address: 310 East 67th Street

institute: New York Blood Center

summary: Burst-forming unit-erythroid (BFU-E) and colony-forming unit-erythroid (CFU-E) cells are erythroid progenitors traditionally defined by colony assays. We developed a flow cytometry-based strategy for isolating human BFU-E and CFU-E cells based on the changes in expression of cell surface markers during in vitro erythroid cell culture. BFU-E and CFU-E are characterized by CD45+GPA-IL-3R-CD34+CD36-CD71low and CD45+GPA-IL-3R-CD34-CD36+CD71high phenotypes, respectively. Colony assays validated phenotypic assignment giving rise to BFU-E and CFU-E colonies, both at a purity ~90%. The BFU-E colony forming ability of CD45+GPA-IL-3R-CD34+CD36-CD71low cells required SCF and erythropoietin, while the CFU-E colony forming ability of CD45+GPA-IL-3R-CD34-CD36+CD71high cells required only erythropoietin. Bioinformatic analysis of the RNA-seq data revealed unique transcriptomes in each differentiation stage. The sorting strategy was validated in uncultured primary cells isolated from bone marrow and peripheral blood, indicating that marker expression is not an artifact of in vitro cell culture, but represents an in vivo characteristic of erythroid progenitor populations. The ability to isolate highly pure human BFU-E and CFU-E progenitors will enable detailed cellular and molecular characterization of these distinct progenitor populations and define their contribution to disordered erythropoiesis in inherited and acquired hematological disease. Our data provide important resource for future studies.

overall_design:
Transcription profiles of Human erythroid progenitors at distinct developmental stages were generated by deep sequencing, in triplicate, using IlluminaHiSeq 2000.
The complete dataset comprises 4 sample types: CD34, BFU, CFU, and Pro (reanalysis of GSM1304777-GSM1304779).

first: Jie

last: Li

first: Pooja

last: Bhagia

first: Fumin

last: Xue

first: Lixang

first: Julie

last: Jaffray

first: Hongxia

last: Yan

first: Joseph

last: Lane

first: Patrick

middle: G

last: Gallagher

first: Narla

last: Mohandas

first: Jing

last: Liu

first: Xiuli

last: An


title: DECIDUALIZATION INDUCES A SECRETOME SWITCH IN THE PERIVASCULAR NICHE CELLS OF THE HUMAN ENDOMETRIUM

status: Public on Oct 29 2014

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

summary: The endometrial perivascular microenvironment is rich in mesenchymal stem-like cells that express type 1 integral membrane protein Sushi domain containing 2 (SUSD2) but the role of these cells in the decidual transformation of this tissue in pregnancy is unknown. We used an antibody directed against SUSD2 (W5C5) to isolate perivascular (W5C5+) and non-perivascular (W5C5-) fibroblasts from mid-luteal biopsies. We show that SUSD2 expression, and hence the ratio of W5C5+ to W5C5- cells, changes in culture depending on cell-cell contact and activation of the Notch signaling pathway. RNA sequencing revealed that cultures derived from W5C5+ progenitor cells remain phenotypically distinct by the enrichment of novel and established endometrial perivascular signature genes. In an undifferentiated state, W5C5+-derived cells produced lower levels of various chemokines and inflammatory modulators when compared to their W5C5- counterparts. This divergence in secretomes became more pronounced upon decidualization, which transformed perivascular W5C5+ cells into the dominant source of a range of trophic and immunomodulatory cytokines, including leukemia inhibitory factor (LIF). Our findings indicate that the decidual response is spatially organized with differentiating perivascular cells establishing distinct cytokine and chemokine gradients that could direct trophoblast towards maternal vessels and govern local immune responses in pregnancy.

overall_design: Analysis of paired human endometrial stromal cultures, originating from either W5C5+ or W5C5- cells, from four biological replicates - a total of 8 samples - by Illumina RNAseq.

first: Keisuke

last: Murakami

first: Yi-Wah

last: Chan

first: Emma

last: Lucas


title: Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation

city: Newark

first: Shawn

middle: R

last: Thatcher

state: DE

address: 15 Innovation Way

institute: University of Delaware

summary: Analysis of the maize alternative splicing landscape, including transcript discovery and mapping of genotype-dependent variations in alternative splicing using B73, Mo17 and the SX19 inbred mapping population

overall_design: Total RNA was isolated from 5 week old leaves of hydroponically grown maize plants and used to construct RNA seq libraries

first: Bailin


title: Genome-wide nucleosome, histone and Pol II maps for wild type Saccharomyces cerevisiae induced with 3-aminotriazole (3AT)

status: Public on Oct 28 2014

first: David

middle: Johannes

last: Clark

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

summary: Paired-end sequencing study of (1) nucleosome core particles and under-digested chromatin from MNase-treated nuclei; (2) ChIP samples for HA-tagged histone H4 and H2B; (3) ChIP for the Rpb3 subunit of Pol II.

overall_design: Nucleosomal DNA and immunopurified sonicated DNA fragments were subjected to paired-end sequencing.

first: Hope

last: Cole

first: Josefina

last: Ocampo


title: Identifying Targets of DSX with ChIP-seq

first: Brian

last: Oliver

summary: We have used ChIP-seq on Drosophila  S2 cells to characterize genome-wide DSX occupancy.

overall_design: We have perfomed ChIP-seq on S2 cells transfected with either V5-tagged DSXF or DSXM constructs. We performed three biological replicates for each ChIP sample and two biological replicates for the input samples.  For peak calling and analysis, the reads from all biological replicates were pooled before aligning them to the genome.

first: Emily

last: Clough

first: Erin

last: Jimenez

first: Yoo-Ah

last: Kim

first: Cale

last: Whitworth

first: Megan

last: Neville

first: Leonie

last: Hempel

first: Hania

last: Pavlou

first: Zhen-Xia

last: Chen

last: Sturgill

first: Ryan

last: Dale

first: Harold

last: Smith

first: Teresa

middle: M

last: Przytycka

first: Stephen

last: Goodwin

first: Mark

last: Van Doren


title: The transcription factor FOXL2 mobilizes estrogen signaling in the maintenance of ovarian granulosa cells identity

city: GIF SUR YVETTE

first: Adrien

last: Georges

address: CEA/SACLAY

institute: CNRS


title: Identifying targets of DSX with DamID-seq

summary: We have adapted the DamID protocol for use with high throughput sequencing.  We have used DamID to identify the positions within the Drosophila genome where the transcription factor DSX is bound. We sequenced DpnI-digested genomic DNA from fly tissues containing UAS-Dam (control) or UAS-Dam-DsxF or UAS-Dam-DsxM.

overall_design: We have performed DamID-seq on adult male and female fatbody and on ovary.  We used two biological replicates for each tissue and sex.

first: David


title: Altered DNA Methylation Patterns in Human Oral Squamous Cell Carcinoma Cells

first: Katarzyna

middle: Maria

last: Marcinkiewicz

address: 1300 York Ave. Room E405

department: Pharmacology

institute: Weill Cornell Graduate School of Medical Sciences

summary: To gain insight into the DNA methylation changes during OSCC carcinogenesis,  we utilized cytosine conversion and next generation sequencing based technique- enhanced reduced representation bisulfite sequencing (ERRBS) - to assess DNA methylation in  cultured, human TERT-immortalized, non-tumorigenic OKF6-TERT1R and OSCC SCC-9 cells.

overall_design: OKF6-TERT1R cells and SCC-9 cells were plated in 10 cm2 tissue culture plates at the density of 2 × 106 cells/plate. Total genomic DNA was extracted from OKF6-TERT1R and SCC-9 cells using DNeasy Blood & Tissue Kit (Qiagen, Germantown, MD, USA), including an RNAse treatment step.

first: Lorraine

last: Gudas


title: Global Transcriptome Analysis and Enhancer Landscape of Human Primary T Follicular Helper and T Effector Lymphocytes (RNA-Seq)

status: Public on Oct 27 2014

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary: T follicular helper (Tfh) cells are a subset of CD4+ T helper (Th) cells that migrate into germinal centers and promote B cell maturation into memory B and plasma cells. Tfh cells are necessary for promotion of protective humoral immunity following pathogen challenge, but when aberrantly regulated, drive pathogenic antibody formation in autoimmunity and undergo neoplastic transformation in angioimmunoblastic T-cell lymphoma and other primary cutaneous T-cell lymphomas. Limited information is available on the expression and regulation of genes in human Tfh cells. Using a fluorescence activated cell sorting-based strategy, we obtained primary Tfh and non-Tfh T effector (Teff) cells from tonsils and prepared genome-wide maps of active, intermediate, and poised enhancers determined by ChIP-seq, with parallel transcriptome analyses determined by RNA-seq. Tfh cell enhancers were enriched near genes highly expressed in lymphoid cells or involved in lymphoid cell function, with many mapping to sites previously associated with autoimmune disease in genome-wide association studies. A group of active enhancers unique to Tfh cells associated with differentially expressed genes was identified. Fragments from these regions directed expression in reporter gene assays. These data provide a significant resource for studies of T lymphocyte development and differentiation and normal and perturbed Tfh cell function.

first: Jason

last: Weinstein

first: Kimberly

last: Lezon-Geyda

first: Yelena

last: Maksimova

first: Sam

last: Craft

first: Yaoping

last: Zhang

first: Mack

last: Su

first: Vincent

first: Joseph

first: Patrick

last: Gallagher


title: Genome-wide ChIP sequence analysis of KSHV-infected primary effusion lymphoma (PEL) cell line BCBL-1 and human umbilical vein endothelial TIVE-LTC cells.

city: Gainesville

first: Rolf

last: Renne

state: FL

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Kaposi’s sarcoma-associated herpesvirus (KSHV) is a g-herpesvirus which persists as circular extrachromasomal DNA in the nucleus during latent infection.  During latency a limited number of viral proteins are expressed, including LANA (latency-associated nuclear antigen). LANA is a multi-functional protein known to interact with transcriptional regulators and chromatin remodelers, and to regulate the LANA and RTA promoters.  We hypothesized that LANA may contribute to the establishment of latency through controlling chromatinization and histone modification of KSHV episomes. We performed ChIP-seq analysis and correlated H3K4me3, H3K27me3, polII, and LANA occupancy of the KSHV genome at nucleotide resolution. Epigenetic marks were analyzed in BCBL-1 lymphoid cells and in telomerase-immortalized vein endothelial TIVE-LTC cells.  We found that the transcription active mark H3K4me3, but not silencing mark H3K27me3, was enriched at KSHV regions where LANA is bound. Co-occupancy of LANA and H3K4 was also detected on 167 host genes, of which 89 are actively transcribed. By comparing LANA occupancy with the profiling of 43 transcription factors from ENCODE, a subset of transcription factors was enriched at regions where LANA is bound, including znf143, CTCF, and Stat1. These results indicate that LANA also plays a role in modulating expression of host genes. Co-immunoprecipitation of LANA with the H3K4 methyltransferase hSET1 suggests that LANA recruits hSET1 to specific loci on the viral genome, leading to H3K4 methylation and ensuring transcription of latency-associated genes.  Host gene expression may be regulated by the same mechanism.

overall_design: LANA binding was correlated with the distribution in the latent KSHV genome of the transcription active histone modification H3K4me3, the silencing mark H3K27me3, and RNA polymerase II, using cells of lymphoid and endothelial origin.  A similar analysis was done for the human genome.  Biological replicates (BR) and technical replicates (TR) were included.

first: Jianhong

last: Hu

first: Yajie

last: Yang

first: Lauren

last: McIntyre


title: RNA-sequencing of CD34+ thymocytes that were cultured on an OP9-GFP or OP9-DLL1 feeder layer.

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

summary: Genetic studies in T-cell acute lymphoblastic leukemia have uncovered a remarkable complexity of oncogenic and loss-of-function mutations. Amongst this plethora of genetic changes, NOTCH1 activating mutations stand out as the most frequently occurring genetic defect, identified in more than 50% of T-cell acute lymphoblastic leukemias, supporting an essential driver role for this gene in T-cell acute lymphoblastic leukemia oncogenesis. In this study, we aimed to establish a comprehensive compendium of the long non-coding RNA transcriptome under control of Notch signaling. For this purpose, we measured the transcriptional response of all protein coding genes and long non-coding RNAs upon pharmacological Notch inhibition in the human T-cell acute lymphoblastic leukemia cell line CUTLL1 using RNA-sequencing. Similar Notch dependent profiles were established for normal human CD34+ thymic T-cell progenitors exposed to Notch signaling activity in vivo. In addition, we generated long non-coding RNA expression profiles (array data) from GSI treated T-ALL cell lines, ex vivo isolated Notch active CD34+ and Notch inactive CD4+CD8+ thymocytes and from a primary cohort of 15 T-cell acute lymphoblastic leukemia patients with known NOTCH1 mutation status. Integration of these expression datasets with publically available Notch1 ChIP-sequencing data resulted in the identification of long non-coding RNAs directly regulated by Notch activity in normal and malignant T-cell context. Given the central role of Notch in T-cell acute lymphoblastic leukemia oncogenesis, these data pave the way towards development of novel therapeutic strategies that target hyperactive Notch1 signaling in human T-cell acute lymphoblastic leukemia.

overall_design: CD34+ cells of 2 healthy donors are cultured on a OP9-GFP or OP9-DLL1 feeder layer.

first: Kaat

last: Durinck

first: Inge

last: Van de Walle

first: Wouter

last: Van Loocke

first: Ellen

last: Geerdens

first: Jan

last: Cools

first: Tom

last: Taghon

first: Frank

last: Speleman


title: Global Transcriptome Analysis and Enhancer Landscape of Human Primary T Follicular Helper and T Effector Lymphocytes

first: Vince

last: Schulz


title: Control of VEGF-A trancriptional programs by pausing and genomic compartmentalization

city: Kuopio

first: Minna

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

summary: Vascular endothelial growth factor A (VEGF-A) is a master regulator of vascular development and function. Consequently, VEGF-A regulated gene expression programs have been under heavy research. In this study we study the transcriptional regulation of VEGF-A-responsive genes in primary aortic endothelial cells (HAEC) and vein endothelial cells (HUVEC) using genome wide global run-on sequencing (GRO-Seq). We show that half of VEGF-A induced genes display a paused phenotype under basal conditions and are thus poised for rapid gene activation. Promoters of paused genes are distinguished from those of non-paused by higher basal enrichment for active histone marks H3K4me3, H3K9ac and H3K27ac. We also show that nearly 100% of the VEGF-upregulated genes are induced at the level of elongation, whereas 38-53% are also induced at the level of initiation. We also report a comprehensive chromatin interaction map generated in HUVECs using tethered conformation capture (TCC) and characterize chromatin interactions in relation to transcriptional activity. We demonstrate that sites of active transcription are more likely to engage in chromatin looping and identify chromatin compartments enriched for VEGF-regulated genes. Cell-type specific transcriptional activity was also shown to reflect boundaries of chromatin interactions within the HOXA cluster. Collectively, these findings provide new insight into mechanisms behind VEGF-A-regulated transcriptional programs in endothelial cells.

overall_design: ChIP-Seq (H3K4me2), GRO-Seq and HiC profiling was performed in HUVECs and HAECs.

first: Henri

last: Niskanen

first: Casey

last: Romanoski


title: Global Transcriptome Analysis and Enhancer Landscape of Human Primary T Follicular Helper and T Effector Lymphocytes (ChIP-Seq)

overall_design: Using a fluorescence activated cell sorting-based strategy, we obtained primary Tfh and non-Tfh T effector (Teff) cells from tonsils and prepared genome-wide maps of active, intermediate, and poised enhancers determined by ChIP-seq, with parallel transcriptome analyses determined by RNA-seq.

first: Jason

last: Weinstein

first: Kimberly

last: Lezon-Geyda

first: Yelena

last: Maksimova

first: Sam

last: Craft

first: Yaoping

last: Zhang

first: Mack

last: Su

first: Vincent

first: Joseph

first: Patrick

last: Gallagher


title: FOXL2 binding sites in primary cells from mouse ovarian follicles

first: Adrien

last: Georges

summary: FOXL2 is a lineage determining transcription factor in the ovary, but its direct targets and modes of action are not fully characterized. Here, we explore the genomic targets of FOXL2. We found in particular that FOXL2 directly modulates Esr2 expression through a newly identified intronic element.

overall_design: Input DNA and FOXL2 ChIP

first: David

last: L'Hôte

first: Anne

last: Todeschini

first: Aurélie

last: Auguste

first: Bérangère

last: Legois

first: Alain

last: Zider

first: Reiner

last: Veitia


title: Identifying targets of DSX with ChIP-seq, DamID-seq and DamID-chip and transcriptional response to DSX isoform switch

first: Brian

last: Oliver

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: RNA-sequencing of the GSI treatment of the CUTLL1 cell line

first: Annelynn

last: Wallaert

overall_design: CUTLL1 cell lines were treated with Compound E (GSI) or DMSO (solvent control). Cells were collected 12 h and 48 h after treatment. This was performed for 3 replicates. RNA-sequencing was performed on these samples.

first: Kaat

last: Durinck

first: Wouter

last: Van Loocke

first: Ellen

last: Geerdens

first: Jan

last: Cools

first: Frank

last: Speleman