title: Genome-wide analysis of full-length Androgen Receptor (AR) and AR Splice Variant (ARv567es) cistromes

city: Minneapolis

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

summary: Androgen Receptor (AR) variants (AR-V) drive prostate cancer (PCa) resistance to first and second-generation therapies targeting endocrine regulation of AR. To understand the sets of genomic targets of full-length AR vs. AR-Vs, we conducted genome-wide ChIP-seq using isogenic pairs of genome engineering cell lines expressing either ARv567es (R1-D567) or full-length AR (R1-AD1).  Our data demonstrate that androgen-activated full-length AR and AR-Vs both bind to similar genomic targets, which are enriched for high affinity androgen response elements (AREs).  Overall, this study demonstrates that AR-Vs restore the broad AR cistrome that is otherwise lost during endocrine-targeted therapy.

overall_design: ChIP-Seq of full-length Androgen Receptor (AR)  or AR splice variant (ARv567es) binding to genomic DNA

middle: M

first: Siu

last: Chan


title: Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (ChIRP-seq)

status: Public on Mar 13 2015

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

country: USA

institute: Texas A&M University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNAs) have recently emerged as new players in gene expression regulation. Whether and how lncRNAs might control hematopoietic stem cell (HSC) function remains largely unknown. Here, we profiled the transcriptome of purified long-term HSCs by deep RNA-sequencing and identified thousands of un-annotated transcripts of which 323 are predicted to be lncRNAs. Comparison of their expression in differentiated lineages represented by B cells (B220+) and Granulocytes (Gr1+), revealed that 159 are likely to be HSC-specific. Knockdown of two such non-coding genes (LincHSC-1 and LincHSC-2) indicated that they regulate HSC lineage differentiation, possibly via targeting cell cycle regulators and chromatin modification enzymes. Taken together, we comprehensively identify lncRNAs in HSC and show to examples that play important roles in HSC function.

overall_design: (I) Mouse Granulocytes mRNA profile were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. (II) To identify LncHSC target gene, mouse progenitor Sca-1+ cells were isolated from 5-FU injected mice and transduced with GFP+ retrovitus construct to knockdown lncHSC expression, and after in vitro culture for 2 days, KSL-GFP+ cells were sorted for mRNA profiling. (III) Mouse B-cells mRNA profile were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. (IV) Mouse HSC H3K4me1 and H3K27ac ChIP-seq were generated using 50,000-100,000 primary HSCs by deep sequencing using Illumina Hiseq 2000. (V) LincHSC-2 binding sites were interrogated in HPC5 mouse bone marrow progenitor cells by chromatin isolation by RNA purification sequencing (ChIRP-seq) using Illumina HiSeq 2500.

first: Benjamin

last: Rodriguez

first: Deqiang

last: Sun

first: Wei

last: Li

first: Margaret

last: Goodell


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

status: Public on Mar 12 2015

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

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

overall_design: MeCP2 ChIP-seq from the forebrain and cerebellum of wild-type mice.

middle: W

first: Benyam

middle: Z

last: Kinde

first: Michael

middle: E

last: Greenberg


title: Linking the aryl hydrocarbon receptor with altered DNA methylation patterns and developmentally induced aberrant antiviral T cell responses

status: Public on Mar 16 2015

city: Rochester

first: B Paige

last: Lawrence

state: NY

address: 575 Elmwood Ave.

department: Environmental Medicine

institute: University of Rochester Medical Center

type: Methylation profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptome profiling of human lung cancer cell lines.

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary:
Purpose: The aim of this study is to compare different RNA extraction methods using a mixture design that allows the relative changes of the majority of genes profiled to be estimated. A number of samples were degraded to allow us to compare methods for dealing with more variable samples.
Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 from a range of passages (2-4) were grown on 3 separate occasions in RPMI media (Gibco) supplemented with Glutamax and 10% fetal calf serum to a 70% confluence. To replicate common experimental conditions cell lines were treated with 0.01% Dimethyl sulfoxide (Sigma), which is commonly used as a vehicle in drug treatment experiments. After 6 hours of treatment, cells were collected, snap-frozen on dry ice and stored at -80 degrees C until required.
Methods - RNA preparation: Total RNA was extracted from between half a million and million cells using Total RNA Purification Kit (Norgen Biotek) with on-column DNAse treatment accorting to the kit instructions. RNA concentration for each pair of samples to be mixed was equalised to ~100 ng/μl using Qubit RNA BR Assay Kit (Life Technologies). Replicates were pooled in known proportions to obtain mixtures ranging from pure NCI-H1975 (100:0) to pure HCC827 (0:100) and intermediate mixtures ranging from 75:25 to 50:50 to 25:75  NCI-H1975:HCC827. All mixtures corresponding to the second replicate were split into two equal aliquots. One aliquot was left intact (we refer to this as the 'good' replicate), while the second aliquot was degraded to produce known outlier samples by incubation at 37 degrees C for 7 days in a thermal cycler with a heated lid.
10 μl from each replicated mixture (both good and degraded) were used for Next Generation Sequencing library preparation using two kits: Illumina TruSeq Total Stranded RNA with Ribozero (TotalRNA) and Illumina TruSeq RNA v2 (mRNA) according to the manufacturer's instructions. Completed libraries were sequenced on HiSeq 2500 with TruSeq SBS Kit v4- HS reagents (Illumina) as 100 bp single-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Approximately 30 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the human reference genome hg19 and mapped to known genomic features at the gene level using the Rsubread package (version 1.16.1) (Liao et al. 2013). Single reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014).

overall_design: Total RNA was extracted from lung adenocarcinoma cell lines NCI-H1975 and HCC827 (3 independent samples for each cell line) and mixed in known ratios. Both mRNA and Total RNA transcriptomes from these mixtures were profiled by RNA-Seq.

first: Aliaksei

last: Holik


title: RNA-seq analysis of gene expression patterns responding to TSA treatment during hESC neural differentiation

status: Public on Mar 11 2015

city: Shanghai

first: Naihe

last: Jing

state: Shanghai

address: 320 Yueyang road

country: China

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: We report the differential roles of an HDAC inhibitor-TSA during hESC nerual commitment. In the initiation of hESC differentiation, TSA could inhibit the downregulation of pluripotency genes to maintain pluripotency, whereas in the neural commitment stage, TSA could promote neural gene expression to assist hESC nerual determination.

overall_design: Examination of gene expression patterns in hESCs, day 4 or day 8 differentiated cells without or with TSA treatment

first: Yunbo

last: Qiao

first: Ran

last: Wang


title: SF3B1 Degron knockdown RNA-seq

city: Dedham

first: Adnan

last: Derti

state: MA

address: 100 Alden Street

department: Bioinformatics

institute: personal

summary: Knockdown of mutant and/or wild-type SF3B1 in MEL202 cell line by Degron knock-in, followed by RNA-seq, to identify splicing events governed by mutant SF3B1.

overall_design: Control: parental MEL202 cell line. Experiments: mutant-SF3B1 knockdown; wildtype-SF3B1 knockdown; mutant SF3B1 knockout. Treatments: each of these four conditions plus and minus shld.

first: Qianhe

last: Zhou

first: Frank

last: Stegmeier

first: David

last: Ruddy


title: Primary duck hepatocyte transcriptome analysis provides insight into the host innate immune response and hepadnavirus infection

first: LIANG

last: YAN

address: NO 131, Dongan Road

institute: Fudan University

summary:
Our aim was to classify and quantify transcripts identified in 24-h-cultured primary duck hepatocytes and construct a protein–protein interaction network to serve as a reference for host factors associated with hepadnavirus infection.
Methods: The transcriptome of 24h-cultured PDHs was analyzed by the pair-end sequencing on the Illumina Solexa platform. High-quality reads were mapped to the Anas platyrhynchos genome with TopHat v2.0.12 software. TopHat allows multiple alignments per read and default parameters were used. Cufflinks v2.2.1 software was later used for analyses that included transcript assembly and FPKM value calculations to quantify gene expression; this program was also run with default parameters.
Results: A total of 87.8 million high-quality reads were obtained from three primary duck hepatocyte samples isolated from three separate 1-day-old Anas domesticus ducklings. The reads (mean length 92.21 bases) were mapped to the Anas platyrhynchos genome. A total of 13,541 genes with > 1 fragments per kilobase of transcript per million mapped reads values were expressed in the 24-h-cultured primary duck hepatocyte samples.Using gene ontology analysis, expressed genes were assigned to functional categories. A total of 182 genes expressed in all three separate primary duck hepatocyte samples were identified as liver-specific genes.
Conclusions: Transcriptome and gene ontology analyses of 24-h-cultured primary duck hepatocytes indicate that these cells retain hepatocyte-specific biological characteristics and can be used as a model system for hepadnavirus infection. A novel protein–protein interaction network suggests that host factors regulating or inhibiting innate immunity are directly associated with hepadnavirus.

overall_design: The transcriptome of 24h-cultured PDHs was analyzed by the paired-end sequencing on the Illumina Solexa platform.

first: Liang

last: Yan

first: Di

last: Qu


title: The Histone Deacetylase Sirt6 Controls Embryonic Stem Cell Fate Via Tet-Mediated Production of 5-Hydroxymethylcytosine

city: Boston

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: How embryonic stem cells (ESC) commit to specific cell lineages and ultimately yield all cell types of a fully formed organism remains a major question. ESC differentiation is accompanied by large-scale histone and DNA modifications, but the relations between these two categories of epigenetic changes are not understood. Here we demonstrate the hierarchical interplay between the histone deacetylase, sirtuin 6 (Sirt6), which targets acetylated histone H3 at lysines 9 and 56 (H3K9ac and H3K56ac), and the Tet (Ten-eleven translocation) enzymes, which convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). ESCs derived from Sirt6 knocSirt6 KOut (S6Sirt6 KO) mice are skewed towards neuroectoderm development. This phenotype is associated with derepression of Oct4, Sox2 and Nanog, which in turn causes an upregulation of Tet enzymes and elevated production of 5hmC. Genome-wide analysis revealed an upregulation of neuroectoderm genes marked with 5hmC in S6Sirt6 KO ESCs, thereby implicating Tet enzymes in the neuroectoderm-skewed differentiation phenotype of S6Sirt6 KO ESCs, which is fully rescued upon knockdown of Tets. We demonstrate a new role for Sirt6 as a chromatin regulator safeguarding the balance between pluripotency and differentiation through Tet-dependent regulation of 5hmC levels.

overall_design:
ChIP-Seq experiments to examine two different histone modifications (H3K9ac and H3K56ac) and Sirt6 binding in Sirt6 wild type (WT) and knock-out (Sirt6 KO) mouse embryonic stem cells with and without treatment using differentiating agent retonic acid (RA).
CMS-IP 5-Hydroxymethylation mapping in wild type (WT, 129 mouse strain) and Sirt6 knockout (S6KO, 129 mouse strain) mouse embryonic stem cells.

first: Jean-Pierre

last: Etchegaray

first: Raul

last: Mostoslavsky

first: Alon

last: Goren


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

first: Harrison

last: Gabel

overall_design: Bisulfite-seq from mouse cortex and cerebellum

first: Benyam

last: Kinde

first: Hume

last: Stroud

first: Michael

last: Greenberg


title: Dual Roles of Histone H3 Lysine 9 Acetylation in Human Embryonic Stem Cell Pluripotency and Neural Differentiation

first: Naihe

last: Jing


title: Epigenome Editing by a CRISPR/Cas9-Based Acetyltransferase Activates Genes from Promoters and Enhancers

city: Durham

first: Christopher

last: Vockley

state: NC

address: 101 science drive rm 2193

institute: Duke University

summary: Epigenetic modifications determine the structure and regulation of eukaryotic genomes and define key signatures of cell lineage specification. Technologies that facilitate the targeted manipulation of epigenetic marks could be used to precisely control cell phenotype or interrogate the relationship between the epigenome and transcriptional control. Here we have generated a programmable acetyltransferase based on the CRISPR/Cas9 gene regulation system, consisting of the nuclease-null dCas9 protein fused to the catalytic core of the human acetyltransferase p300. This fusion protein catalyzes acetylation of histone H3 lysine 27 (H3K27) at its target sites, leading to robust transcriptional activation of target genes from promoters, proximal enhancers, and distal enhancers. In contrast to conventional dCas9-based activators, the acetyltransferase fusion effectively activated genes from enhancer regions and with individual guide RNAs. The core p300 domain was also portable to other programmable DNA-binding proteins. This technology enables the targeted perturbation of native epigenetic architecture and will be useful for reprogramming the epigenome for applications in genomics, genetics, disease modeling, and manipulating cell fate.

overall_design: HEK293T cells were transfected in triplicate with plasmids expressing synthetic transcription factors. The synthetic TFs were either (a) dCas9-VP64 fusion protein and a targeting guide RNA (gRNA), or (b)dCas9-p300 fusion protein containing the catalytic domain of p300 and a targeting guide RNA (gRNA).  As a control, cells were transfected with plasmids expressing dCas9 alone and dCas9 fused with a aceryltransferase null mutatnt form of the p300 catalytic domain (D1399Y, as in text). After transfection, RNA-seq was used to identify differential expressin at on-target and off-target  sites.

first: Isaac

middle: B

last: Hilton

first: Anthony

last: D'Ippolito

first: Gregory

last: Crawford

first: Timothy

last: Reddy

first: Charles

middle: A

last: Gersbach


title: ChIP-seq analysis of H3K9 acetylation enrichment in hESCs and day 8 neural progenitor cells

summary: H3K9 acetylation was enriched in pluripotency genes in hESCs and in neural genes in neural progenitor cells

overall_design: Examination of H3K9 acetylation distributions in hESCs and neural progenitor cells

first: Yunbo

last: Qiao

first: Ran

last: Wang


title: Pausing of RNA polymerase II regulates mammalian developmental potential

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

summary: The remarkable capacity for pluripotency and self-renewal in embryonic stem cells (ESCs) requires a finely-tuned transcriptional circuitry wherein the genes and pathways that initiate differentiation are suppressed, but poised to respond rapidly to developmental signals. To elucidate transcriptional control in mouse ESCs in the naïve, ground state, we defined the distribution of engaged RNA polymerase II (Pol II) at high-resolution. We find that promoter-proximal pausing of Pol II is widespread at genes encoding signaling molecules that control ESC proliferation, differentiation and metabolism, but is not enriched at developmental control genes. Accordingly, ablation of the primary pause-inducing factor, NELF, causes proliferation defects, early embryonic lethality and dysregulation of critical ESC signaling pathways. Moreover, loss of NELF in ESCs causes resistance to cell fate commitment through dramatic attenuation of FGF/ERK activity. This work thus uncovers an unanticipated role for NELF-mediated pausing in establishing the responsiveness of ESCs to developmental cues.

overall_design: RNA-seq, GRO-seq, and Start-RNA-seq from mouse embryonic stem cells (mESCs). For RNA-seq, two biological replicates are included for each of two treatment conditions; control, and 4-hydroxytamoxifen (4OHT) treated to ablate expression of NELF-B. For GRO-seq, data from two biological replicates of untreated mESCs are included. For Start-RNA-seq, three biological replicates are included for each of two treatment conditions; control and 4OHT.

first: Lucy

middle: H

last: Williams

first: George

last: Fromm

first: Nolan

middle: G

last: Gokey

first: Telmo

last: Henriques

first: Ginger

last: Muse

first: Adam

last: Burkholder

first: David

middle: C

last: Fargo

first: Guang

last: Hu


title: Systematic Mapping of ADAR1 Binding Reveals its Regulatory Roles in Multiple RNA Processing Pathways [CLIP-seq]

city: LA

first: Jaegyoon

last: Ahn

state: CA

address: 611 Charles E. Young Drive

department: IBP

institute: UCLA

summary: ADARs are the primary factors underlying A-to-I editing in metazoans. We conducted the first global study of ADAR1-RNA interaction in human cells using CLIP-Seq. In contrast to the expected predominant binding of ADAR1 to Alu repeats, thousands of CLIP sites were located in non-Alu regions. This unexpectedly frequent non-Alu binding enabled discovery of transcriptome-wide functional and biophysical targets of ADAR1 in the regulation of mRNA processing including alternative 3' UTR usage and alternative splicing. In addition, a global analysis of ADAR1 binding to non-Alu regions also revealed its primary interaction with microRNA (miRNA) transcripts in the nucleus, which subsequently affected expression levels of mature miRNAs. A complex global picture was revealed regarding the dependence of this function on the double-stranded RNA binding domains or deaminase activity. Our study unfolded a broad landscape of the diverse functional roles of ADAR1.

overall_design: To charaterize ADAR1 binding profiles in U87 cells, we performed CLIP-seq using two different ADAR1 monoclonal antibodies.

first: X

last: Xiao

first: J

last: Bahn


title: A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depend on histone recycling in transcribed chromatin

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

type: Genome binding/occupancy profiling by genome tiling array


title: A Grhl2-dependent gene network controls trophoblast branching morphogenesis

status: Public on Mar 10 2015

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School


title: Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation [iCLIP]

status: Public on Mar 18 2015

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265

institute: Stanford University

summary: Visualizing the physical basis for molecular behavior inside living cells is a grand challenge in biology. RNAs are central to biological regulation, and RNA’s ability to adopt specific structures intimately controls every step of the gene expression program.1 However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles predominantly viewed only two of four nucleotides that make up RNA.2,3 Here we present a novel biochemical approach, In Vivo Click SHAPE (icSHAPE), that enables the first global view of RNA secondary structures of all four bases in living cells. icSHAPE of embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguishes different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved in vitro, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA binding or modification proteins that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N6-methyladenosine (m6A) modification genome-wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.

overall_design: Development and implementation of a chemoaffinity method to study the in vivo secondary structure of the transcriptome

first: Robert

last: Spitale

first: Qiangfeng

last: Zhang

first: Pete

last: Crisalli

first: Jong-Wha

last: Jung

first: Hannes

middle: Y

last: Kuchelmeister

first: Eduardo

last: Torre

first: Pedro

middle: J

last: Batista

first: Eric

middle: T

last: Kool

first: Howard

last: Chang


title: RNA-seq of Maternal Kdm1a mutant 2C embryos and eggs

city: Bethesda

first: Todd

last: Macfarlan

address: 6 Center Drive, Building 6B, Room 2B-211

institute: NIH

summary: 2C embryos were generated from Kdm1a FL/Fl Zp3Cre females mated to wild type males for RNA-seq analysis using the Nugen Ovation RNA-seq system V2. Ovulated eggs from Kdm1a FL/Fl Zp3Cre females were isolated for RNA-seq analysis using the Nugen Ovation RNA-seq system V2.

overall_design: 3 replicates of maternal Kdm1a mutant 2C embryos and eggs were collected for RNA-seq, compared to wt 2C embryos and wt oocyte samples from Macfarlan TS et al,  Nature 2012 (GEO acession GSE33923)


title: Chromatin-wide profiling of the protein kinase DYRK1A reveals a role as a transcriptional activator of cell growth related genes

city: Barcelona

first: Chiara

last: Di Vona

state: Spain

address: Carrer Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: CRG

summary: DYRK1A is a dosage-sensitive protein kinase that fulfills key roles during development and in tissue homeostasis, and its dysregulation results in human pathologies. DYRK1A is present in both the nucleus and cytoplasm of mammalian cells, although its nuclear function remains unclear. Genome-wide analysis of DYRK1A-associated loci reveals that the kinase is recruited preferentially to promoters of genes actively transcribed by RNA polymerase II (RNAPII), which are functionally associated with translation, RNA processing and cell cycle. DYRK1A-bound promoter sequences are highly enriched in a conserved palindromic motif, which is necessary to drive DYRK1A-dependent transcriptional activation. DYRK1A phosphorylates the carboxy-terminal domain (CTD) of RNAPII at Ser2 and Ser5. Depletion of DYRK1A results in reduced association of RNAPII at the target promoters as well as hypophosphorylation of the CTD of RNAPII along the target gene bodies. Accordingly, we propose that DYRK1A acts as a transcriptional regulator by acting as a novel CTD kinase.

overall_design: Occupancy of the kinase DYRK1A in two different cell lines and in two different growing conditions.

first: Susana

last: de la Luna


title: Length-dependent gene misregulation in Rett syndrome

first: Harrison

last: Gabel


title: High Precision Analysis of Translational Pausing in Bacteria Lacking EFP by Ribosome Profiling

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Ribosome profiling is a powerful method for globally assessing the activity of ribosomes in a cell. Despite its application in many organisms, ribosome profiling studies in bacteria have struggled to obtain the resolution necessary to precisely define translational pauses. Here we report improvements that yield much higher resolution in E. coli profiling data, enabling us to more accurately assess ribosome pausing and refine earlier studies of the impact of polyproline motifs on elongation. We comprehensively characterize pausing at proline-rich motifs in the absence of elongation factor EFP. We find that only a small fraction of genes with strong pausing motifs have reduced ribosome density downstream and identify features that explain this phenomenon. These features allow us to predict which proteins likely have reduced output in the efp knockout strain.

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

overall_design: Ribosome profiling of E. coli MG1655 and mutants lacking EFP or its three modifiying enzymes


title: Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex

city: La Jolla

first: Anjana

last: Rao

address: 9420 Athena Circle

department: Department of Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

summary: ASXL1 is the obligate regulatory subunit of a deubiquitinase complex whose catalytic subunit is BAP1. Heterozygous mutations of ASXL1 that result in premature truncations are frequent in myeloid leukemias and Bohring-Opitz syndrome. Here, we demonstrate that truncated ASXL1 proteins confer enhanced activity on the ASXL1-BAP1 complex. Stable expression of truncated, hyperactive ASXL1-BAP1 complexes in a hematopoietic precursor cell line resulted in global erasure of H2AK119Ub, striking depletion of H3K27me3, selective upregulation of a subset of genes whose promoters bore both H2AK119Ub and H3K4me3, and spontaneous differentiation to the mast cell lineage. These outcomes required the catalytic activity of BAP1, indicating these events were downstream consequences of H2AK119Ub erasure. In bone marrow precursors, truncated ASXL1-BAP1 expression cooperated with TET2 loss-of-function to increase differentiation to the myeloid lineage in vivo. We propose that pathological ASXL1 mutations confer gain-of-function on the ASXL-BAP1 complex.

overall_design: ChIP-Seq for H2AK119Ub, H3K4me3, H3K27me3 on EML cells. RNA-Seq on EML cells expressing ASXL1(1-479)+BAP1 and control.

first: Antti

last: Larjo

first: Anand

last: Balasubramani


title: Systematic Mapping of ADAR1 Binding Reveals its Regulatory Roles in Multiple RNA Processing Pathways [small RNA-seq]

first: Jaegyoon

last: Ahn

type: Non-coding RNA profiling by high throughput sequencing

overall_design: To identify ADAR binding dependent miRNA defferential expression profiles, U87MG cells were transfected with ADAR1 overexpression vector, RNA binding mutant (EAA and E912A), siRNA of ADAR1 or controls.

first: X

last: Xiao

first: J

last: Bahn


title: Systematic Mapping of ADAR1 Binding Reveals its Regulatory Roles in Multiple RNA Processing Pathways

overall_design: Refer to individual Series


title: Target of Rapamycin Complex 2 regulates cell growth via Myc in Drosophila

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: To check the dMyc function, RNA profiling was achieved by the RNA-seq assay comparing mRNA levels of lst81, dm0, lst81dm0 and rictorΔ1 in the adult heads of male mutant animals with wild-type controls

overall_design: Compare the mRNA profiles of 5-day old adult head materials of mutants (lst81, dmP0, lst81dmP0 and rictor1) to wild type W1118 by Illumina suquencing.

first: Tao

last: Wang

first: Ying

last: Kuo

first: Huanwei

last: Huang


title: A Grhl2-dependent gene network controls trophoblast branching morphogenesis [ChIP-seq]

first: Christian

last: Hinze

summary: Healthy placental development is essential for reproductive success; failure of the feto-maternal interface results in preeclampsia and intrauterine growth retardation. We found that grainyhead-like 2 (GRHL2), a CP2-type transcription factor, is highly expressed in chorionic trophoblast cells, including basal chorionic trophoblast (BCT) cells located at the chorioallantoic interface in murine placentas. Placentas from Grhl2-deficient mouse embryos displayed defects in BCT cell polarity and basement membrane integrity at the chorioallantoic interface, as well as a severe disruption of labyrinth branchingmorphogenesis.Selective Grhl2 inactivation only in epiblastderived cells rescued all placental defects but phenocopied intraembryonic defects observed in global Grhl2 deficiency, implying the importance of Grhl2 activity in trophectoderm-derived cells. ChIPseq identified 5282 GRHL2 binding sites in placental tissue. By integrating these data with placental gene expression profiles, we identified direct and indirect Grhl2 targets and found a marked enrichment of GRHL2 binding adjacent to genes downregulated in Grhl2−/− placentas, which encoded known regulators of placental development and epithelial morphogenesis. These genes included that encoding the serine protease inhibitor Kunitz type 1 (Spint1), which regulates BCT cell integrity and labyrinth formation. In human placenta, we found that human orthologs of murine GRHL2 and its targets displayed co-regulation and were expressed in trophoblast cells in a similar domain as in mouse placenta. Our data indicate that a conserved Grhl2-coordinated gene network controls trophoblast branching morphogenesis, thereby facilitating development of the site of feto-maternal exchange. This might have implications for syndromes related to placental dysfunction.

overall_design: In vivo genome-wide examination of binding sites of the transcription factor GRHL2 by ChIP-seq using wild-type murine E17.5 placenta tissue. Two samples in total: one GRHL2 ChIP sample and one IgG ChIP sample using wild-type placentas tissue as antibody control.

first: Katharina

last: Walentin

first: Max

last: Werth

first: Nadine

last: Haase

first: Saaket

last: Varma

first: Robert

last: Morell

first: Annekatrin

last: Aue

first: Elisabeth

last: Pötschke

first: David

last: Warburton

first: Andong

last: Qiu

first: Jonathan

last: Barasch

first: Bettina

last: Purfürst

first: Christoph

last: Dieterich

first: Elena

last: Popova

first: Michael

last: Bader

first: Ralf

last: Dechend

first: Anne

last: Staff

first: Zeliha

last: Yurtdas

first: Ergin

last: Kilic

first: Kai

last: Schmidt-Ott


title: Retinoic acid signaling constrains the plasticity of Th1 cells and prevents development of pathogenic Th17 cells

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

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


title: Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacterial Serratia proteamaculans and Serratia plymuthica

city: Uppsala

first: Konstantia

last: Gkarmiri

institute: Swedish UNiversity of Agricultural Sciences

summary: Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. To understand the functional response of the fungal phytopathogen Rhizoctonia solani to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq. Transcriptome analysis revealed that approximately 10% of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had fold values exceeding 8x and for further analyses this cut-off value was used. Functional classification of DEGs revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation. In conclusion, it was found out that most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.

overall_design: Transcriptome profiling of fungal hyphae from treatments challenged with the bacteria and from control treatments containing only the fungus were generated by deep sequencing, in triplicate, by using Illumina® TruSeq.

first: Roger

middle: D

last: Finlay

first: Sadhna

last: Alström

first: Elizabeth

last: Thomas

first: Marc

last: Cubeta

first: Nils

last: Högberg


title: Defective structural RNA processing in relapsing-remitting multiple sclerosis

city: Nashville

first: Charles

middle: F

last: Spurlock III

state: Tennessee

address: 1161 21st Avenue South

department: Medicine

institute: Vanderbilt University School of Medicine

summary: It is fundamentally unknown how normal cellular processes or responses to extracellular stimuli may invoke polyadenylation and degradation of ncRNA substrates or if human disease processes exhibit defects in polyadenylation of ncRNA substrates as part of their pathogenesis. Our results demonstrate that mononuclear cells from subjects with relapsing-remitting multiple sclerosis (RRMS) exhibit pervasive increases in levels of polyadenylated ncRNAs including Y1 RNA, 18S and 28S rRNA, and U1, U2, and U4 snRNAs and these defects are unique to RRMS. Defects in expression of both Ro60 and La proteins in RRMS appear to contribute to increased polyadenylation of ncRNAs. Further, IFN-β1b, a common RRMS therapy, restores both Ro60 and La levels to normal as well as levels of polyadenylated Y1 RNA and U1 snRNA suggesting that aberrant polyadenylation of ncRNA substrates may have pathogenic consequences.

overall_design: We extracted RNA from peripheral whole blood in healthy control subjects and patients with established relapsing-remitting multiple sclerosis using PaxGene tubes.

first: John

last: Tossberg

first: Yan

last: Guo

first: Subramaniam

last: Sriram

first: Philip

middle: S

last: Crooke III

first: Thomas

middle: M

last: Aune


title: Quantitative profiling of long noncoding RNAs with targeted RNA sequencing.

city: Paris

first: Giovanni

last: Bussotti

address: 25-28 Rue du Dr Roux

country: France

institute: Institute Pasteur

summary: We compared the performance of conventional RNAseq with RNA Capture Sequencing (CaptureSeq) to assemble and quantify known RNA spike-Ins and human transcripts. We find CaptureSeq to be superior for the detection and quantification of the 37% lowest expressed genes, and comparable for the next 45% of moderately expressed genes. CaptureSeq contributes only minor technical variation and measures differential gene expression accurately. We demonstrate these advantages by the targeted sequencing of long noncoding RNAs across 20 human tissues, expanding previous annotations two-fold and simultaneously generating a quantitative atlas of expression. This analysis confirms the use of CaptureSeq as an important method for transcriptional profiling.

overall_design: Long noncoding RNA assembly and expression is analysed by targeted RNA sequencing for 20 human tissues and 4 human cell lines

first: Michael

last: Clark

first: Tim

last: Mercer

first: Tomasso

last: Leonardi


title: Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells [RNA-Seq]

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: In mammals, the nuclear lamina interacts with hundreds of large genomic regions, termed lamina-associated domains (LADs) that are generally in a transcriptionally repressed state. Lamins form the major structural component of the lamina and have been reported to bind DNA and chromatin. Here we systematically evaluated whether lamins are necessary for the peripheral localization of LADs in murine embryonic stem cells. Surprisingly, removal of essentially all lamins did not have any detectable effect on the genome-wide interaction pattern of chromatin with the inner nuclear membrane. This suggests that other components of the inner nuclear membrane mediate these interactions.

overall_design: 2 samples, each with a biological replicate: wt mESC, B type lamin null (dKO) dKO mESC

first: Mario

last: Amendola


title: m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency

first: Tong

last: Chen

address: No 16 Nan-xiao-jie Dong-zhi-men-nei

department: State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica

institute: China Academy of Chinese Medical Sciences

summary: N6-methyladenosine (m6A) has been recently identified as a conserved epitranscriptomic modification of eukaryotic mRNAs, but its features, regulatory mechanisms, and functions in cell reprogramming are largely unknown. Here, we report m6A modification profiles in the mRNA transcriptomes of four cell types with different degrees of pluripotency. Comparative analysis reveals several features of m6A, especially gene- and cell-type-specific m6A mRNA modifications. We also show that microRNAs (miRNAs) regulate m6A modification via a sequence pairing mechanism. Manipulation of miRNA expression or sequences alters m6A modification levels through modulating the binding of METTL3 methyltransferase to mRNAs containing miRNA targeting sites. Increased m6A abundance promotes the reprogramming of mouse embryonic fibroblasts (MEFs) to pluripotent stem cells; conversely, reduced m6A levels impede reprogramming. Our results therefore uncover a role for miRNAs in regulating m6A formation of mRNAs and provide a foundation for future functional studies of m6A modification in cell reprogramming.

overall_design: m6A-seq in ESC, iPSC, NSC and sertoli cells.

first: Yajuan

last: Hao

first: Ying

last: Zhang

first: Xiu-Jie

last: Wang

first: Yun-Gui

last: Yang

first: Qi

last: Zhou


title: Alteration in the transcriptome of the lung during TGFα-induced pulmonary fibrosis

status: Public on Mar 07 2015

city: Cincinnati

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Pulmonary fibrosis (PF) is associated with many chronic lung diseases including Systemic sclerosis (SSc), Idiopathic Pulmonary Fibrosis (IPF) and Cystic Fibrosis (CF) which are characterized by the progressive accumulation of stromal cells and formation of scar tissue.  Pulmonary fibrosis is a dysregulated response to alveolar injury which causes  a progressive decline in lung function and refractory to current pharmacological therapies.  Airway and alveolar epithelial cells and stromal cells contribute to pulmonary fibrosis but the cell-specific pathways and gene networks that are responsible for the pathophysiology are unknown. Recent animals models generated in our lab demonstrate clinical phenotypes seen in human fibrotic disease. The mouse model of transforming growth factor-α (TGFα)-induced fibrosis include conditionally expressing TGFα in the lung epithelium under control of the CCSP promoter driving rtTA expression (CCSP/TGFα).  This allow the TGFα is only expressed in airway and alveolar epithelial cells and only when mice fed doxycycline (Dox).  Similar to PF in humans, TGFα mice on Dox developed a progressive and extensive adventitial, interstitial and pleural fibrosis with a decline in lung mechanics. Thus, the TGFα transgenic mouse is a powerful model to determine lung cell-specific molecular signatures involved in pulmonary fibrosis.  In this study, we sought to determine changes in the transcriptome during  TGFα-induced pulmonary fibrosis. Our results showed that several pro-fibrotic genes increased in the lungs of TGFα mice. This study demonstrates that WT1 network gene changes associated with fibrosis and myfibroblast accumulation and thus may serve as a critical regulator fibrotic lung disease.

overall_design: mRNA profiles of CCSP/- and CCSP/TGFalpha mice treated with Dox

first: Vishwaraj

last: Sontake

first: Jenny

first: Satish

middle: K

last: Madala


title: Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells

status: Public on Mar 09 2015


title: Wide-type, brm, clf, and brm clf mutant seedlings

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university


title: Evaluating intra- and inter-individual variation in the human placental transcriptome

city: Leipzig

first: Mark

last: Stoneking

state: Saxony

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

summary:
Background: Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta.
Results: We estimate that on average, 33.2%, 58.9% and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals and among human groups, respectively.  Additionally, when technical and biological traits are included in models of gene expression they account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling and metabolism. Many biological traits demonstrated correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome (65% of expressed genes) exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection (26%), directional selection (4.9%), or diversifying selection (4.8%).
Conclusion: We apportion placental gene expression variation into individual, population and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.

overall_design: Placental mRNA was sequenced on an Illumina GAIIx. Samples were derived from 4 human groups, 10 individuals per group, 2 samples per individual

first: David

last: Hughes


title: TSS-seq analysis of K. marxianus

city: Yamaguchi

first: tomoyuki

last: kosaka

address: 1677-1 Yoshida

department: Agriculture

country: Japan

institute: Yamaguchi University

summary: Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. The transcriptome analysis clarified distinctive metabolic pathways under three different growth conditions, static culture, high temperature and xylose medium, in comparison to the control condition of glucose medium under a shaking condition at 30°C. Interestingly, the yeast appears to overcome the issue of reactive oxygen species, which tend to accumulate under all three conditions.

overall_design: 12 (3 samples each of 30D, 30DS, 45D and 30X conditions)

first: Mamoru

last: Yamada

first: Tomoyuki

last: Kosaka

first: Lertwattanasakul

last: Noppon

first: Rodrussamee

last: Nadchanok

first: Yuzuru

last: Suzuki

first: Terumi

last: Horiuchi


title: Nuclear orphan receptor TLX affects gene expression in pancreatic beta cells

status: Public on Mar 06 2015

city: WuHan

first: XiaoLi

last: Shi

address: DongHU road

institute: WuHan University

summary: Using Illumina’s digital gene expression (DGE) system, we investigated the transcriptional response to TLX overexpression in beta cells. Finally, an average of 13,791,918 and 12,476,623 reads of high quality clean tags were obtained from control and TLX-overexpressing beta cells, respectively. Results reveals that overexpression of TLX resulted in suppression of 176 genes by ≥50%, and also results in ≥2-fold upregulation of 49 genes.

overall_design: Expression profiling of stable TLX overexpressing MIN6 cells and control cells by high throughput sequencing

first: Xiao-Li

first: Yan-Cheng

last: Xu


title: m6a peak analysis in normal, FTO deficient and five stages of adipogenesis (D-2/0/2/5/10) in Mouse embryo fibroblast 3T3-L1 pre-adipocytes

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: Total RNA was extracted using TRI® Reagent (Sigma). cDNA was synthesized by RevertAid™ First Strand cDNA Synthesis Kit with Oligo dT primers (K1622, Fermentas) following manufacturer’s recommendations. PCR reactions were carried out on a DNAEngine® Thermal Cycler (PTC-0200G, Bio-Rad) in 25 μl reaction volume containing 1 μl cDNA, 200 nM primer pairs and components of TaKaRa Taq™ kit (R001A, Takara). All samples were analyzed in triplicate RT-qPCR.mRNAs were extracted using biotinylated poly(dT) oligo, followed by further removing of contaminated rRNA using RiboMinus Transcriptome Isolation Kit (K1550-02, Invitrogen). Then mRNAs were fragmented into 100-200nt length and subjected to immunoprecipitation with m6A specific antibody.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

overall_design: discovery of the binding motif of m6a in normal, FTO deficient and five stages of adipogensis (D-2/0/2/5/10) in Mouse embryo ﬁbroblast 3T3-L1 pre-adipocytes

first: Zhao

first: Yun-Gui

last: Yang

first: Baofa


title: Genome-wide characterization of cis-acting DNA targets of Opaque2 in maize

first: Chaobin

last: Li

state: Beijing

address: 2 Yuanmingyuan West Road, NMICC Building

institute: China Agricultural University

summary: Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds, but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). ChIP-Seq analysis detected 1,686 O2 DNA binding sites distributed over 1,143 genes. We identified 4 new O2 binding motifs; among them, TGACGTGG appears to be the most conserved and strongest. We confirmed that, except for the 16 kD and 18 kD zeins, O2 directly regulates expression of all other zeins. O2 directly regulates two transcription factors, genes linked to carbon and amino acid metabolism and abiotic stress resistance.

overall_design: Examination of 15 days after pollination(DAP) wild type maize endosperm with O2 specific antibody and IgG serves as control.

first: Rentao

last: Song


title: Transcriptomics analysis of gene expression in normal and FTO, METTL3 deficient Mouse embryo fibroblast 3T3-L1 pre-adipocytes

summary: RNA was isolated from control and FTO,METTL3 deficient mouse 3T3-L1 cells using the TRIzol (Invitrogen) reagent by following the company manual.Total RNA was isolated from transiently transfected cells with TRI® Reagent (Sigma). mRNA was extracted using biotinylated poly(dT) oligo, followed by further removing of contaminated rRNA using RiboMinus Transcriptome Isolation Kit (K1550-02, Invitrogen). mRNA quality was analyzed by NanoDrop. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

overall_design: Examination of gene expressive levels in normal and FTO, METTL3 deficient mouse 3T3-L1 cells


title: Genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in wide-type, brm, clf, and brm clf mutant seedlings

first: Lei

summary: By using ChIP-seq, we found that loss of BRM activity in developing seedlings leads to ectopic and increased H3K27me3 deposition at several hundred genes, indicating the critical role of BRM in preventing the inappropriate deposition of this histone mark. Removal of CLF in brm mutant could partcially suppress the increased H3K27me3.

overall_design: Examination of H3K27me3 in 14-day-old wt, brm, clf, and brm clf seedlings. Two biological replicates for each one.

first: Chenlong

first: Yuhai

last: Cui


title: Identification of the global transcriptional regulator All3953 (RbcR) in the cyanobacterium Anabaena sp. PCC 7120 by ChIP-Seq analysis

city: Sevilla

first: Silvia

last: Picossi

address: Avda. Americo Vespucio 49

department: Instituto de Bioquímica Vegetal y Fotosíntesis

institute: CSIC

summary: The whole regulon of the LTTR All3953 was determined at 3 h after Ci deficiency in the cyanobacterium Anabaena sp. PCC 7120 by ChIP-Seq analysis. A TAP-tagged version of the protein was used for the chromatin immunoprecipitation. A total of 142 peaks were found, mainly located in the chromosome of Anabaena.

overall_design: Two Anabaena sp PCC 7120 strains were constructed: one containing a TAP-tagged version of protein All3953 (strain CSS57), and a control strain expressing the TAP-tag under the all3953 promoter (strain CSS68). Cells of the two strains were grown in BG110 medium supplmented with 6 mM NH4Cl and 10 mM NaHCO3, and bubbled with 1% CO2-containing air. When the cultures had reached exponential phase (3-5 µgChl/ml), the cells were collected, washed with BG110, and resuspended in the same volume of BG110 supplemented with 6 mM NH4Cl and bubbled with air (low Ci conditions) for 3 h. Chromatin immunoprecipitation was carried out using extracts of both strains and IgG-conjugated dynabeads, and the resultant DNA was subjected to massive sequencing. The Triform algorithm method (Kornacker et al, 2013) was used to analyze the data. To identify the specific peaks found in strain CSS57, the CSS68 (control strain) ChIP data was used as the background for analysis of the CSS57 ChIP data.

first: Enrique

last: Flores

first: Antonia

last: Herrero


title: The Crc/CrcZ-CrcY global regulatory system helps integrating gluconeogenic and glycolytic metabolism in Pseudomonas putida

city: Madrid

first: Ruggero

last: La Rosa

address: C/ Darwin 3, Campus de Cantoblanco

department: Department of Microbial Biotechnology

institute: National Centre for Biotechnology CNB-CSIC

summary: In metabolically versatile bacteria, carbon catabolite repression (CCR) facilitates the preferential assimilation of the most efficient carbon sources, improving growth rate and fitness. In Pseudomonas putida, the Crc protein and the CrcZ and CrcY small RNAs (sRNAs), which are believed to antagonise Crc, are key players in CCR. Contrary to what occurs in other bacterial species, succinate or glucose elicit a weak CCR in this bacterium. We combined metabolic, transcriptomics and constraints-based metabolic flux analyses to clarify whether P. putida prefers succinate or glucose, and the role of the Crc/CrcZ-CrcY regulatory system in their metabolization. Succinate was consumed faster than glucose and allowed a higher growth rate. However, both compounds were co-metabolised when provided simultaneously. The levels of CrcZ and CrcY were lower when both substrates were present than when only one of them was provided, suggesting a role for Crc in coordinating metabolism. Metabolic reconstructions suggested that, when both substrates are present, Crc works to organize a metabolism in which carbon compounds flow in two opposite directions: from glucose to pyruvate, and from succinate to pyruvate. Therefore, Crc serves not only to favour the assimilation of preferred compounds, but also to balance the carbon fluxes, optimising metabolism and growth.

overall_design: mRNA profiles of Pseudomonas putida KT2440, KTCRC and KT2440-ZY during glucose and succinate co-feeding generated by deep sequencing, in duplicate, using Illumina technology

first: Fernando

last: Rojo


title: Evolutionary changes in promoter and enhancer activity during human corticogenesis

city: New Haven

first: Steven

last: Reilly

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptome analyses reveal enrichment of specific lncRNAs in specific brain regions and neuronal populations

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: Scripps Research

summary: Despite the availability of large-scale transcriptomics data, specific long noncoding RNAs (lncRNAs) expressed in specific brain regions and populations of neurons are poorly understood. Here we report analysis of expression of lncRNAs and mRNAs expressed in hippocampus and prefrontal cortex (PFC), two regions of brain that are involved in memory storage and neuropsychiatric disorders. Our unbiased analyses have identified specific lncRNAs and mRNAs that are enriched in hippocampus and PFC. We have identified several regions in the chromosomes characterized by clustered lncRNA expression suggesting the transcriptional hotspots of lncRNA in the genome. We find that, a subset of lncRNAs and protein coding genes in their vicinity are uniquely co-expressed in specific brain regions and thus presumably co-regulated. Furthermore, specific brain regions and neuronal populations have characteristic lncRNA expression profile. These studies reveal unexpected complexity in the expression profiles of lncRNAs in the mammalian brain.

overall_design: Examination of mRNAs and long noncoding RNAs in mouse hippocampus and prefrontal cortex of 8 adult mice.

first: Beena

last: Kadakkuzha

first: Mohammad

last: Fallahi

first: Gautam

last: Shankar


title: HP1 is involved in regulating the global impact of DNA methylation on alternative splicing

status: Public on Mar 08 2015

city: Tel- aviv

first: Ahuvi

last: Yearim

address: Ramat Aviv

department: Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel-Aviv University

summary: The global impact of DNA methylation on alternative splicing is largely unknown. Using a genome-wide approach in wild-type and methylation-deficient embryonic stem cells, we found that DNA methylation can act both as an enhancer and as a silencer of splicing, and affects the splicing of more than 20% of alternative exons. These exons are characterized by distinct genetic and epigenetic signatures. Alternative splicing regulation of a subset of these exons can be explained by Heterochromatin protein 1 (HP1), which silences or enhances exon recognition in a position-dependent manner. We constructed an experimental system using site-specific targeting of a methylated/unmethylated gene, and demonstrate a direct causal relationship between DNA methylation and alternative splicing. HP1 regulates this gene’s alternative splicing in a methylation-dependent manner by recruiting splicing factors to its methylated form. Our results demonstrate DNA methylation's significant global influence on mRNA splicing, and identify a specific mechanism of splicing regulation mediated by HP1.

overall_design: BS-seq on WT mouse ES cells (2 replicates), MNase-seq on WT and TKO cells (3 replicates), mRNA-seq on WT and TKO cells as well as HP1 knock-down cells (2 replicates for each sample)

first: Sahar

last: Gelfman

first: Ronna

last: Shayevitch

first: Shai

last: Melcer

first: Ohad

last: Glaich

first: Jan-Philipp

last: Mallm

first: Malka

last: Nissim-Rafinia

first: Ayelet-Hashahar

last: Cohen

first: Karsten

last: Rippe

first: Eran

last: Meshorer

first: Gil

last: Ast


title: Retinoic acid signaling constrains the plasticity of Th1 cells and prevents development of pathogenic Th17 cells [ChIP-Seq experiments]

first: Venu

last: Pullabhatla

address: Great Maze Pond

institute: Biomedical Research Centre

summary: CD4+ T cells differentiate into phenotypically distinct T-helper cells upon antigenic stimulation. Regulation of plasticity between these CD4+ T-cell lineages is critical for immune homeostasis and prevention of autoimmune diseases. However, the factors that regulate lineage stability are largely unknown. Here we investigate a role for retinoic acid (RA) in the regulation of lineage stability using T helper 1 (Th1) cells, traditionally considered the most phenotypically stable Th subset. We found that RA, through its receptor RARa, sustains stable expression of Th1 lineage specifying genes as well as repressing genes that instruct Th17 cell fate. RA signaling is essential for limiting Th1 cell conversion into Th17 effectors and for preventing pathogenic Th17 responses in vivo. Our studies identify RA-RARa as a key component of the regulatory network governing Th1 cell fate and define a new paradigm for the development of pathogenic Th17 cells. These findings have important implications for autoimmune diseases in which dysregulated Th1-Th17 responses are observed.

overall_design: Identification of RARa binding in wild-type Th1 cells and mapping of enhancers using chromatin IP against p300, H3k4me1, H3k4me3, and H3k27ac in wild-type and dnRara Th1 cells.

first: Chrysothemis

last: Brown

first: Emanuele

last: Rinaldis

first: Graham

last: Lord

first: Randolph

last: Noelle


title: Gene expression profiling of effect of Yap inhibition in a genetically engineered mouse model of hepatocellular carcinoma

city: Boston

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Defective Hippo/YAP signaling in the liver results in tissue overgrowth and development of hepatocellular carcinoma (HCC). Here, we uncover mechanisms of YAP-mediated hepatocyte reprogramming and HCC pathogenesis. We show that YAP functions as a rheostat maintaining metabolic specialization, differentiation and quiescence within the hepatocyte compartment. Importantly, treatment with siRNA-lipid nanoparticles (siRNA-LNPs) targeting YAP restores hepatocyte differentiation and causes pronounced tumor regression in a genetically engineered mouse HCC model (mice with liver-specific Mst1/Mst2 double knockout). Furthermore, YAP targets are enriched in an aggressive human HCC subtype characterized by a proliferative signature and absence of CTNNB1 mutations. Thus, our work reveals Hippo signaling as a key regulator of positional identity of hepatocytes, supports targeting YAP using siRNA-LNPs as a paradigm of differentiation-based therapy, and identifies an HCC subtype potentially responsive to this approach.

overall_design: Mice with liver-specific Mst1/Mst2 double-knockout (Adeno-Cre injected Mst1-/-; Mst2Flox/Flox mice) were monitored for the formation of HCC by ultrasound imaging.  Animals were then randomized to be treated by intravenous injection of either siYap-LNPs or siLuciferase-LNPs for a period of 9 days.

first: Julien

last: Fitamant

first: Nabeel

last: Bardeesy


title: Evolutionary changes in promoter and enhancer activity during corticogenesis (non-human)

first: Steven

last: Reilly

summary: Evolutionary changes in gene regulation during cortical development likely contributed to the expansion and specialization of the cortex. However, the lack of a regulatory map of the embryonic cortex has hindered identification of these changes and the biological processes they influenced. We performed genome-wide epigenetic profiling to compare promoter and enhancer activity during corticogenesis in rhesus and mouse. We identified 2,855 promoters and 8,996 enhancers that have gained activity in based on increased epigenetic marking. To detect biological pathways enriched for these changes, we mapped promoters and enhancers exhibiting epigenetic gains onto modules of co-expressed genes constructed using spatio-temporally rich expression data from developing cortex. We identified multiple modules enriched in lineage epigenetic gains. Gains in enriched modules were associated with genes functioning in neuronal proliferation and migration, cortical patterning, and the extracellular matrix. Gain-enriched modules also showed correlated gene expression patterns and similar transcription factor binding site enrichments in promoters and enhancers, suggesting they are connected by common regulatory mechanisms. Our results reveal coordinated patterns of potential regulatory changes associated with conserved developmental processes in corticogenesis, providing insight into cortical evolution.

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: For mouse samples, two biological replicates each from four cortical tissues (embryonic day 11.5 (E11.5), E14.5, E17.5 frontal, and E17.5 occipital. For Rhesus, two biological replicates each from 12 p.c.w. frontal and 12 p.c.w. occipital and one replicate from 8 p.c.w. Each replicate is comprised of H3K27ac and H3K4me2 ChIPs in addition to a shared input control.

first: James

middle: P

last: Noonan


title: Integrative transcriptome-wide analyses reveal critical HER2-regulated mRNAs and lincRNAs in HER2+ breast cancer

city: Cleveland

first: Ahmad

last: Khalil

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Breast cancer is a major health problem affecting millions of women worldwide. Over 200,000 new cases are diagnosed annually in the USA, with approximately 40,000 of these cases resulting in death. HER2-positive (HER2+) breast tumors, representing 20–30 % of early-stage breast cancer diagnoses, are characterized by the amplification of the HER2 gene. However, the critical genes and pathways that become affected by HER2 amplification in humans are yet to be specifically identified. Furthermore, it is yet to be determined if HER2 amplification also affects the expression of long intervening non-coding (linc)RNAs, which are involved in the epigenetic regulation of gene expression. We examined changes in gene expression by next generation RNA sequencing in human tumors pre- and post- HER2 inhibition by trastuzumab in vivo, and changes in gene expression in response to HER2 knock down in cell culture models. We integrated our results with gene expression analysis of HER2+ tumors vs matched normal tissue from The Cancer Genome Atlas. The integrative analyses of these datasets led to the identification of a small set of mRNAs, and the associated biological pathways that become deregulated by HER2 amplification. Furthermore, our analyses identified three lincRNAs that become deregulated in response to HER2 amplification both in vitro and in vivo. Our results should provide the foundation for functional studies of these candidate mRNAs and lincRNAs to further our understanding of how HER2 amplification results in tumorigenesis. Also, the identified lincRNAs could potentially open the door for future RNA-based biomarkers and therapeutics in HER2+ breast cancer.

overall_design: We compared changes in gene expression of both mRNAs and lincRNAs in BT474 cells that are treated with HER2 siRNAs vs cells treated with negative control siRNAs by RNA-seq.

first: Callie

last: Merry


title: BRD4 dynamics reveal novel acrosome-dependent chromatin reorganization during post-meiotic mammalian sperm development

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: During the post-meiotic phase of spermatogenesis, transcription is progressively repressed as the nuclei of haploid spermatids are compacted through a dramatic chromatin reorganization involving hyper-acetylation and replacement of most histones with sperm-specific protamines. Although BRDT has been shown to function in transcription as well as histone removal in post-meiotic spermatids, it is unknown whether other BET family proteins play a role.  Immunofluorescence of mouse testes revealed BRD4 in a complete ring around the nuclei of spermatids containing hyper-acetylated histones.  The BRD4 ring lies directly adjacent to the acroplaxome, or the cytoskeletal base of the acrosome, and does not form in acrosomal mutant mice.  ChIP sequencing in round spermatids revealed enrichment of BRD4 and acetylated histone H3 and H4 at the promoters of active genes.  GO Term analysis showed that BRD4 and BRDT bind to distinct subsets of spermatogenesis-specific genes.  Association of BRD4 with Cyclin T1 decreases as spermatogenesis progresses despite a persistence of association with acetylated H4.  Moreover, acetylated histones are removed from the condensing spermatid nucleus in a wave following the progressing acrosome.  These data provide evidence for an interesting mechanism in which BRD4 and perhaps acetylated histones are removed from the spermatid genome via the progressing acrosome as transcription is repressed.

overall_design: Single replicates each of Brd4, H3K9me3, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac, H4Kac (pan-acetyl antibody), and input in mouse round spermatid cells; input is used to control for local sonication efficiency bias.

first: Jessica

last: Bryant

first: Greg

first: Xiaoshi

last: Wang

first: Mirella

last: Meyer-Ficca

first: Gabriel

middle: L

last: Otte

first: Lacey

last: Luense

first: Marissa

last: Bartolomei

first: Gerd

middle: A

last: Blobel

first: Ralph

last: Meyer

first: Benjamin

last: Garcia

first: Shelley

last: Berger


title: Global discovery and characterization of small non-coding RNAs in marine microalgae

city: Norwich

first: Matthew

last: Beckers

state: Norfolk

address: Norwich Research Park

institute: University of East Anglia

summary:
Background: Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi.
Results: Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions.
Conclusions: This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and may be used for acclimation to environmental conditions.

sample_organism:
Thalassiosira pseudonana CCMP1335
Fragilariopsis cylindrus CCMP1102

overall_design: RNA-seq study of sRNA populations in two species of diatoms using Illumina GAII high-throughput sequencing

first: Sara

last: Lopez-Gomollon

first: Tina

last: Rathjen

first: Simon

last: Moxon

first: Florian

last: Maumus

first: Irina

last: Mohorianu

first: Vincent

last: Moulton

first: Tamas

last: Dalmay

first: Thomas

last: Mock


title: Transcriptome analysis of isolated stormal cells and tumor epithelial cells in mouse lung cancer by RNA-Seq

city: New York

first: Hyejin

last: Choi

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

summary: We sequenced mRNA from individual stormal cells (Macrophages, Monocytes, and Neutrophils) and tumor epithelial cells from KrasG12dD; p53-/- murine lung cancer model and WT control mouse to compare gene expressio profiles of lung cancer stroma and tumor cells to their counterparts of WT lugns. The tumor was generated by injecting HKP1 lung cancer cell line, which was driven by KrasG12D activation and loss of p53, via tail vein. The cells were sorted by their specific surface markers at day 20-25 after orthortopic lung cancer formation.

overall_design: Examination of mRNA levels in individual stormal cells and tumor cells from tumor lungs compared to their counterparts from WT lungs

first: DingCheng

last: Gao

first: Jianting

last: Sheng

first: Vivek

last: Mittal


title: Dynamic profiling of the protein life cycle in response to pathogens (RNA-seq)

first: Catherine

last: Wu

address: 450 Brookline Ave.

institute: Dana Farber Cancer Institute

summary: Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle.

overall_design: Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.

first: Marko

last: Jovanovic

first: Michael

last: Rooney

first: Nir

last: Hacohen

first: Aviv

last: Regev


title: CIITA regulated genes in human B cells

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: The MHC class II transactivator (CIITA) is essential for the expression of MHC-II genes. CIITA functions as a transcriptional activator when bound to genes although repressive roles have been reported at some loci in other cell types.  To define the role of CIITA in gene regulation in human B cells, we performed ChIP-seq for CIITA using three independent antibodies, the histone marks H3K4me3 and H3K27ac, and ATAC-seq in the Raji human B cell line.  Additionally, we profiled H3K27ac and ATAC-seq in the CIITA-null RJ2.2.5 cell line.  A core set of CIITA peaks were identified that overlapped in all antibodies.  Using the H3K27ac, H3K4me3, and ATAC-seq profiles generated in CIITA+ Raji and CIITA-null RJ2.2.5 cells CIITA dependent chromatin modifications were identified.  These data define the CIITA regulated genes in human B cells.

overall_design: Examination of CIITA binding sites and correlation with active histone modifiations and accessible chromatin in Raji and RJ2.2.5 cells

first: Christopher

first: Jeremy

last: Boss


title: JNK-mediated control of gene expression in liver

city: Worcester

first: Roger

last: Davis

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

summary: RNAseq analysis of gene expression in Liver of Control and JNK deficient mice fed a control or a High fat diet

overall_design: Contro(Albcre+)l and mice with liver-specific defiency of JNK (Alb Cre+ Jnk1flox/flox, Jnk2flox/flox or Jnk1flox/floxJnk2flox/flox) were fed a control or a high fat diet for 16 weeks. Gene expression analysis in liver was analyzed by RNAseq

first: Santiago

last: Vernia


title: Dynamic profiling of the protein life cycle in response to pathogens

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


title: MicroRNA profiling of glial progenitor cells in growth and differentiation conditions

status: Public on Mar 05 2015

city: San Francisco

first: Robert

last: Blelloch

address: 35 Medical Center Way

department: Urology

institute: University of California, San Francisco

summary: The molecular basis of astrocyte differentiation and maturation is poorly understood. As microRNAs have important roles in cell fate transitions, we set out to study their function during the glial progenitor cell (GPC) to astrocyte transition. Inducible deletion of all canonical microRNAs in GPCs in vitro led to a block in the differentiation to astrocytes. In an unbiased screen, the reintroduction of let-7 and miR-125 families of microRNAs rescued differentiation. Let-7 and miR-125 shared many targets and functioned in parallel to JAK-STAT signaling, a known regulator of astrogliogenesis. While individual knockdown of shared targets did not rescue the differentiation phenotype in microRNA-deficient GPCs, overexpression of these targets in wild-type GPCs blocked differentiation. This finding supports the idea that microRNAs simultaneously suppress multiple mRNAs that inhibit differentiation. The microRNA-regulated targets were enriched for genes downregulated during in vivo astrocyte differentiation and upregulated in glioblastomas, consistent with validity of using the in vitro model to study in vivo events. These findings provide insight into the microRNAs and the genes they regulate in this important cell fate transition.

overall_design: Small RNA profiling of 2 replicates of GPCs and astrocytes

first: Archana

last: Shenoy


title: ChIPseq measurement of transcriptional engagement and replication stress at the Drosophila Mid-blastula Transition

city: Evanston

first: Shelby

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

summary: These experiments measure genome-wide RNA Pol II binding in precisely staged wild-type embryos at five time points spanning the maternal to zygotic transition (nuclear cycles 12 through 14) of Drosophila melanogaster. In addition, RNA Pol II binding at nuclear cycle 13 is measured in embryos mutant for either mei-41/ATR or zelda. To correlate RNA Pol II binding with replication stress, genome-wide profiles of Replication protein A (70kDa subunit, RpA-70 EGFP) were generated in parallel with RNA Pol II for both wild-type and zelda at nuclear cycle 13.

overall_design: Two replicates each for 5 time points for wild type RNA Pol II. Two replicates for mei-41 RNA Pol II, nuclear cycle 13. Two replicates for zelda RNA Pol II, nuclear cycle 13. Two replicates each for Rpa70-EGFP in wild-type or zelda, nuclear cycle 13, matched to the corresponding RNA Pol II sample.

first: Eric

last: Wieschaus


title: ChIP-seq: Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain

status: Public on Mar 23 2015

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

summary: Embryogenesis requires the precise activation and repression of many transcriptional regulators. The Polycomb group proteins and the associated H3K27me3 histone mark are essential to maintain the inactive state of many of these genes. Mammalian Hox genes are targets of Polycomb proteins and form local 3D clusters centered on the H3K27me3 mark. More distal contacts have also been described, yet their selectivity, dynamics and relation to other layers of chromatin organization remained elusive. We report that repressed Hox genes form mutual intra- and inter-chromosomal interactions with other genes located in strong domains labeled by H3K27me3. These interactions occur in a central and active nuclear environment that consists of the HiC compartment A, away from peripheral Lamina Associated Domains. Interactions are independent of nearby H3K27me3-marked loci and determined by chromosomal distance and cell-type specific scaling factors, thus inducing a moderate reorganization during embryogenesis. These results provide a simplified view of nuclear organization whereby Polycomb proteins may have evolved to repress genes located in gene-dense regions whose position is restricted to central, active nuclear environments.

overall_design: Chromatin Immuno Precipitation (ChIP-seq) samples from mouse embryonic samples at different anatomical positions. Data based on 4 biological samples.

first: D

last: Noordermeer

first: M

last: Vieux-Rochas

last: Leleu

last: Duboule


title: Zebrafish foxc1a is required for appendage specific neural circuit development

first: Santanu

last: Banerjee

address: 421 Curie Blvrd

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: RNA-seq analysis of zebrafish foxc1a mutant

overall_design: For RNA-seq, mRNA was extracted from 38-40 hpf old embryos. We isolated wild type and foxc1a mutant samples by dissecting the entire first 6 anterior somitic segments (AS) through which the fin nerves migrate, and the adjacent posterior segments (PS; segments 7 through ~12) devoid of fin innervating nerves. Heads and yolks were excluded from all samples.  Tissues were stored in RNAlater solution (Life Technologies) for up to 2 days at 4 degree before RNA was extracted using the RNAeasy kit (Qiagen) according to the manufacture’s protocol. RNA was tested for integrity using a Bioanalyzer (Agilent technologies). RNA samples showing RIN value of 8 or higher were used for generating cDNA libraries as described in the TruSeq® Stranded mRNA sample preparation guide. At the final stage, 15 cycles of PCR amplifications was performed. Barcoded libraries representing duplicates of AS and PS samples of wild type and mutants were validated using Bionalyzer (Agilent Technology) and finally sequenced in Illumina HiSeq 2500 yielding paired end reads of 100bp. The RNA-seq Unified Mapper (RUM) (Grant et al., 2011) was used to align the reads to the Zv9/danRer7 reference genome and to assign each read uniquely to a transcript. We investigated transcripts that showed the highest fold changes of expression between the different groups. For Gene Ontology annotations, genes tagged by the GO term “axon guidance” were obtained from the gene ontology database (http://www.geneontology.org/). Next we filtered this list for the “Danio rerio” taxon (resulting in 116 unique genes) and used them to annotate our RNA-seq results.

last: Banarjee

first: Katharina

last: Hayer

first: John

last: Hogenesch

last: Granato


title: Blastomere-specific transcriptome sequencing reveals a determinant of anterior specification in C. elegans

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

summary: We sequenced amplified mRNA from 20 pooled AB and 20 pooled P1 blastomeres hand isolated from 2-cell stage C. elegans embryos three replicates each.

overall_design: Transcriptome profiles of each blastomere at the 2-cell stage of the C. elegans early embryo.

middle: O

last: Nishimura

first: Jason

last: Lieb


title: Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.

city: Leuven

first: Zeynep

last: Kalender Atak

address: Herestraat 49

country: Belgium

institute: KULeuven

summary: Understanding the molecular processes underlying intra-tumor heterogeneity is of critical importance to improve the efficiency of therapy and overcome drug resistance. In malignant melanoma, heterogeneity is though to arise -at least partly- through epigenetic rather than genetic reprogramming of proliferating cells, leading to the appearance within the primary tumors of a phenotypically distinct invasive cell subpopulation. The invasive melanoma cells are at the origin of metastatic spread and are thought to provide a reservoir of therapeutically resistant cells. To decipher the gene regulatory networks that underlie the proliferative and invasive cellular states we integrated publicly available gene expression and DNA methylation data from tumor biopsies with a newly generated compendium of open chromatin and histone modification profiling of melanoma cultures that are dominant in either of the two subpopulations. Extensive in silico analyses identified SOX10 and MITF, and AP-1 and TEADs as key upstream regulators of the proliferative and invasive transcriptomes, respectively. Knock-down experiments confirmed the implication of TEADs in the invasive gene network and, more importantly, established a causative link between activation of these transcription factors and melanoma cell invasion and sensitivity to MAPK inhibitors.

overall_design: Investigation of the epigenomic landscape of 11 melanoma cultures by using FAIRE-seq to map the open chromatin regions

first: Hana

last: Imrichova

last: Kalender-Atak

first: Valerie

last: Christiaens

first: Stein

last: Aerts


overall_design: Investigation of the epigenomic landscape of 11 melanoma cultures by using ChIP against the chromatin marker H3K27ac and H3K27me3, depicting active and silent enhancers respectively.

first: Annelien

last: Verfaillie


title: Fig and fig wasp mutualism

city: Rochester

first: Ellen

middle: O'Hara

last: Martinson

department: Biology

institute: University of Rochester

summary: A striking property of the ancient and obligate mutualism between figs and their pollinating wasps is that fig wasps consistently oviposit in the inner flowers of the fig syconium (gall flowers, which develop into galls that house developing larvae), but typically do not use the outer ring of flowers (seed flowers, which develop into seeds). To better understand differences between gall and seed flowers that might influence oviposition choices, and the unknown mechanisms underlying gall formation, we used a metatranscriptomic approach to analyze eukaryotic gene expression within fig flowers at the time of oviposition choice and early gall development. Consistent with the unbeatable seed hypothesis, which posits that only a portion of fig flowers are physiologically capable of responding to gall induction or supporting larval development, we found significant differences in gene expression assigned to defense and metabolism between gall- and seed flowers in receptive syconia. Transcripts assigned to flavonoids and defense were especially prevalent in receptive gall flowers, and carbohydrate metabolism was significantly up-regulated relative to seed flowers. In turn, high expression of the venom gene icarapin during wasp embryogenesis within galled flowers distinguishes it as a candidate gene for gall initiation. In response to galling, the fig significantly up-regulates the expression of chalcone synthase, which previously has been connected to gall formation in other plants. This study simultaneously evaluates the gene expression profile of both mutualistic partners in a plant-insect mutualism and provides evidence for a stability mechanism in the ancient fig-fig wasp association.

overall_design: We examined two different Ficus flower types at two different time points. Each sample contained a pool of hundreds of individual flowers from multiple sycomia.


overall_design: Investigation of the transcriptomes of 11 different melanoma cultures & Investigation of the effects of the Knock down of all 4 TEADs in an invasive melanoma culture (MM047).


title: TNFα Signaling Exposes Latent Estrogen Receptor Binding Sites in Breast Cancer Cells [GRO-seq]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: The interplay between mitogenic and proinflammatory signaling pathways play key roles in determining the phenotypes and clinical outcomes of breast cancers.  We have used global nuclear run-on coupled with deep sequencing to characterize the immediate transcriptional responses of MCF-7 breast cancer cells treated with estradiol, TNFα, or both.  In addition, we have integrated these data with chromatin immunoprecipitation coupled with deep sequencing for estrogen receptor alpha (ERα), the pioneer factor FoxA1 and the p65 subunit of the NF-κB transcription factor. Our results indicate extensive transcriptional interplay between these two signaling pathways, which is observed for a number of classical mitogenic and proinflammatory protein-coding genes.  In addition, GRO-seq has allowed us to capture the transcriptional crosstalk at the genomic locations encoding for long non-coding RNAs, a poorly characterized class of RNAs which have been shown to play important roles in cancer outcomes.  The synergistic and antagonistic interplay between estrogen and TNFα signaling at the gene level is also evident in the patterns of ERα and NF-κB binding, which relocalize to new binding sites that are not occupied by either treatment alone.  Interestingly, the chromatin accessibility of classical ERα binding sites is predetermined prior to estrogen treatment, whereas ERα binding sites gained upon co-treatment with TNFα require NF-κB and FoxA1 to promote chromatin accessibility de novo.  Our data suggest that TNFα signaling recruits FoxA1 and NF-κB to latent ERα enhancer locations and directly impact ERα enhancer accessibility. Binding of ERα to latent enhancers upon co-treatment, results in increased enhancer transcription, target gene expression and altered cellular response.  This provides a mechanistic framework for understanding the molecular basis for integration of mitogenic and proinflammatory signaling in breast cancer.

overall_design: Using GRO-seq and ChIP-seq (ER, FoxA1 and p65) to assay the molecular crosstalk of MCF-7 cells treated with E2, TNFα or both E2+TNFα.

first: Hector

last: Franco

first: Anusha

last: Nagari

first: Lee

middle: W


title: Mre11 suppresses replication stress and gene amplification proficiency

city: West Hollywood

first: Hisashi

last: Tanaka

state: CA

address: 8700 Beverly Blvd

department: Surgery

institute: Cedars-Sinai Medical Center

summary: Gene amplification, copy-number increases of particular genes and surrounding genomic segments, promotes cancer progression and acquired therapy resistance.  Thus, understanding genetic traits that confer gene amplification proficiency is important.  The primary step for gene amplification is spontaneous DNA rearrangements initiated by DNA breaks.  Here we show that mammalian cells became gene amplification-proficient when we knocked down Mre11/Rad50/Nbs1 (MRN) complex, a multifunctional complex that guards the genome from DNA breaks.  Cells with reduced Mre11 experienced severe replication stress, with marked increases of single-stranded breaks followed by double-stranded breaks during DNA replication.  Such breaks underlay for the increase in spontaneous gene amplification.  Other traits associated with replication stress, such as impaired intra-S phase checkpoint and global transcriptional changes in DNA metabolism genes also contributed to gene amplification proficiency.  Our results define Mre11 deficiency as a cause of replication stress and gene amplification proficiency and provide a candidate marker for aggressive cancer phenotypes.

overall_design: We sequenced four samples: 2 control, GFP-expressing samples and 2 Mre11 knockdown cells

first: Anna

last: Kondratova

first: Takaaki

last: Watanabe

first: Michael

last: Marotta

first: Matthew

last: Cannon

first: Anca

last: Segall

first: David

last: Serre


first: Zeynep

last: Kalender Atak

overall_design: Refer to individual Series


title: EGFR and MEK pathway signature RNA-Seq datasets

city: Salt Lake City

first: Andrea

last: Bild

state: Utah

address: 201 Presidents Circle

institute: University of Utah

summary: EGFR and MEK pathways were activated alone or in combination in human mammary epithelial cells. We profiled the pathway gene expression signatures using RNA-Seq.

overall_design: mRNA was extracted from human mammary epithelial cells overexpressing EGFR gene, MEK gene, or EGFR and MEK genes in combination (or GFP control) for RNA-Seq analysis. Experiment was performed in six replicates per condition.

first: W

middle: E

last: Johnson


title: ErbB2 Pathway Activation upon Smad4 Loss Promotes Lung Tumor Growth and Metastasis [ChIP-seq]

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: Lung cancer remains the leading cause of cancer death. Genome sequencing of lung tumors from patients with Squamous Cell Carcinoma has identified SMAD4 to be frequently mutated. Here we used a novel mouse model to determine the molecular mechanisms regulated by loss of Smad4 which lead to lung cancer progression. Mice with ablation of Pten and Smad4 in airway epithelium developed metastatic adenosquamous tumors. Comparative transcriptomic and in vivo cistromic analyses determined that loss of PTEN and SMAD4 resulted in activation of the ELF3 and the ErbB2 pathway due to decreased ERRFI1’s expression, a negative regulator of ERBB2 in mice and human cells. The combinatorial inhibition of ErbB2 and Akt signaling attenuated tumor progression and cell invasion, respectively. Expression profiles analysis of human lung tumors substantiated the importance of the ErbB2/Akt/ELF3 signaling pathway as both prognostic biomarkers and therapeutic drug targets for treating lung cancer.

overall_design: Examination of genome-wide SMAD4 binding in 7-month-old Ptend/d mouse lung.

first: Sung

last: Cho

first: Bindu

last: Akkanti

first: Nili

last: Jin

first: Jianqiang

last: Mao

first: Weiwen

last: Long

first: Tenghui

last: Chen

first: Yiqun

last: Zhang

first: Ximing

last: Tang

first: Ignacio

middle: I

last: Wistuba

first: Chad

middle: J

last: Creighton

first: Farrah

last: Kheradmand

first: Francesco

last: DeMayo


title: MRTF-SRF signaling is required for seeding of HSC/Ps in bone marrow during development

status: Public on Mar 04 2015

city: London

last: Gualdrini

address: 44 Lincoln's Inn Fields

institute: Francis Crick Institute

summary: Chemokine signaling is important for the seeding of different sites by hematopoietic stem cells during development. Serum Response Factor (SRF) controls multiple genes governing adhesion and migration, mainly by recruiting members of the Myocardin-Related Transcription Factor (MRTF) family of G-actin regulated cofactors. We used vav-iCre to inactivate MRTF-SRF signaling early during hematopoietic development. In both Srf- and Mrtf-deleted animals, hematopoiesis in fetal liver and spleen is intact, but does not become established in fetal bone marrow. Srf-null HSC/Ps (hematopoietic stem/progenitor cells) fail to effectively engraft in transplantation experiments, exhibiting normal proximal signaling responses to SDF-1, but reduced adhesiveness, F-actin assembly, and reduced motility. Srf-null HSC/Ps fail to polarise in response to SDF-1, and cannot migrate through restrictive membrane pores to SDF-1 or Scf in vitro. Mrtf-null HSC/Ps were also defective in chemotactic responses to SDF-1. MRTF-SRF signaling is thus critical for the response to chemokine signaling during hematopoietic development.

overall_design: Strand specific RNA sequencing (RNA-seq) in sorted WT and SRF deleted LSK cells with or without a 30 minute SDF stimulation and validation by qRT-PCR

first: Patrick

last: Costello

first: Mathew

last: Sargent

first: Diane

last: Maurice

first: Cyril

last: Esnault

first: Katie

last: Foster

first: Fernando

last: Anjos-Afonso

first: Richard

last: Treisman


title: Genome-wide modelling of transcription kinetics reveals patterns of RNA processing delays

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: We descrive a joint model of transcriptional activation and mRNA accumulation, using estrogen receptor ERα activation in MCF-7 breast cancer cell line, which can be used for inference of transcription rate, RNA processing delay and degradation rate given data from high-throughput sequencing time course experiments.

overall_design:
MCF-7 cells were mock treated or with 10nM 17b-E2 to nine time points (5', 10', 20', 40', 80', 160', 320', 640' and 1280'). Genome-wide identification of RNA polymerase II (RNAPII) occupancy and transcriptome profiling (RNA-seq) following E2 induction of MCF-7 cells

Please note that the information in the wig.txt files is in gene-specific coordinates, not chromosomic coordinates, as this is the most sensible format for the associated project/paper.

first: Antti

last: Honkela

first: Jaakko

last: Peltonen

first: Hande

last: Topa

first: Iryna

last: Charapitsa

first: Filomena

last: Matarese

first: Korbinian

last: Grote

first: Hendrik

middle: G

first: George

last: Reid

first: Neil

last: Lawrence

first: Magnus

last: Rattray