title: RNA-seq analysis reveals profound changes in transcript profiles between siCon- and siH19-transfected myotubes

city: Farmington

last: Zhang

address: 400 Farmington Ave

institute: UConn Health

summary: We used high throughput sequencing to analyze the transcriptional profiling of myotubes. By comparing the transcriptional profiling of myotubes with or without H19 knockdown,1131 genes or transcripts were found at least 1.5-fold up-regulated in siH19 relative to siCon cells, meanwhile 508 genes or transcripts were found at least 1.5-fold down-regulated in siH19 over siCon cells.

overall_design: 40h following initiation of differentiation, myotubes were transfected with either control siRNA or siH19. 48h later after transfection, total RNA was extracted for library preparation and RNA-seq analysis to compare trancript profiles between siCon and siH19 cells.

first: Gordon

middle: G

last: Carmichael

first: Yingqun

last: Huang


title: Genes Targeted by the Hedgehog-Signaling Pathway can be Regulated by Estrogen Related Receptor β

status: Public on Nov 06 2015

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

country: USA

institute: Xiphophorus Genetic Stock Center

type: Expression profiling by high throughput sequencing

summary:
We report Hedgehog signaling responsive genes with or without Esrrb in NI3T3 cells.
Using Hh-responsive cells, we used RNA-Seq to find Hh responsive genes.
In addition, we tested Esrrb's modification on Hh target genes' response.

overall_design: Control vector transfected cells with vehicle treatment, Esrrb expression vector transfected cell with vehicle treatment, control vector transfected cells with Hh conditioned medium treatment, Esrrb expression vector transfected cell with Hh conditioned medium treatment,

first: Dennis

middle: B

last: Lubahn


title: ChIP-Seq analysis to identify direct binding of ZNF165

status: Public on Nov 09 2015

city: Dallas

first: Angelique

last: Whitehurst

address: 5323 Harry Hines Blvd.

department: Simmons Cancer Center

institute: UT Southwestern

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We found that the cancer testis antigen, ZNF165, is required for viability and modulates TGFβ-induced gene expression in mesenchymal, Claudin-Low, TNBC. To begin to define ZNF165's role in TNBC tumorigenesis, we performed ChIP-Seq analysis in the mesenchymal TNBC tumor derived cell line, WHIM12, stably expressing ZNF165-V5. This analysis uncovered 381 peaks associated with 410 genes and included TGFβ target genes, SMURF2 and SMAD, that promote negative TGFβ feedback regulation.  Our results provide insight into how ZNF165 globally modulates TGFβ signaling and nominates ZNF165 candidate gene targets.

overall_design: WHIM12 cells were stably infected ZNF165-V5 were grown to 75% confluency. Chromatin was isolated, sonicated and immunoprecipitated using a V5 antibody. Purifed ChIP-ed DNA was then sequence, aligned to hg19 and HOMER was justed to identify significantly enriched peaks.

first: Kimberly

last: Maxfield


title: Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [RNA]

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: Upon recruitment to active enhancers and promoters, RNA polymerase II (Pol_II) generates short non-coding transcripts of unclear function. The mechanisms that control the length and the amount of ncRNAs generated by cis-regulatory elements are largely unknown. Here, we show that the adapter protein WDR82 and its associated complexes actively limit such non-coding transcription. WDR82 targets the SET1/COMPASS H3K4 methyltransferase and the nuclear Protein Phosphatase 1 (PP1) complexes to the initiating Pol_II. WDR82 and PP1 also interact with components of the transcriptional termination and RNA processing machineries. Depletion of WDR82, SET1 or the PP1 subunit required for its nuclear import caused distinct but overlapping transcription termination defects at highly expressed genes, active enhancers and promoters, thus enabling the increased synthesis of unusually long ncRNAs. These data indicate that transcription initiated from cis-regulatory elements is tightly coordinated with termination mechanisms that impose the synthesis of short RNAs.

overall_design: polyA-mRNAs or 4sU-labeled RNAs from BMDMs, either untreated or treated for with lipopolysaccharide (LPS) for the indicated time. Experiments were carried out in cells containing either a short hairpin targeting either of these: 1) Wdr82; 2) Set1a+Set1b; 3) Pnuts; or the empty vector (LMP) or a scrambled as a control. When specified, cells were pre-treated with 5,6-Dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) in order to prevent RNA polymerase II elongation.

first: Liv

middle: M

last: Austenaa

first: Marta

last: Simonatto

first: Silvia

last: Masella

first: Giulia

last: Della Chiara

first: Serena

last: Ghisletti

first: Alessia

last: Curina

first: Elzo

last: de Wit

first: Britta

middle: A

last: Bouwman

first: Stefano

last: de Pretis

first: Viviana

last: Piccolo

first: Alberto

last: Termanini

first: Elena

last: Prosperini

first: Mattia

last: Pelizzola

first: Wouter

last: de Laat

first: Gioacchino

last: Natoli


title: Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells

first: Yuan

last: Lu

summary:
We report nuclear receptor Esrrb's responsive genes with or without Esrrb ligand DY131 in DU145 cells.
Using Esrrb-null cells, we used RNA-Seq to find Esrrb responsive genes.
In addition, we tested DY131-driven Esrrb-dependent genes to test the ligand dependency of Esrrb in regulating gene expression.

overall_design: Control vector transfected cells with vehicle treatment, Esrrb expression vector transfected cell with vehicle treatment, control vector transfected cells with DY131 treatment, Esrrb expression vector transfected cell with DY131 treatment.

first: Dennis

last: Lubahn


title: On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA]

city: Woods Hole

first: Esther

middle: Jane

last: Pearl

state: MA

address: 7 MBL Street

department: National Xenopus Resource

institute: Marine Biological Laboratory

summary: A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs expressed over time during embryogenesis. Here we present a comprehensive characterization of protein and mRNA dynamics across early development in Xenopus. Surprisingly, we find that most proteins change very little and duplicated genes are expressed similarly. While the correlation between mRNA levels and protein expression is poor, a mass action kinetics model parametrized by the protein synthesis and degradation rates regresses protein dynamics to RNA dynamics, corrected for initial protein concentration. This study provides a rich resource for developmental biologists, unveiling detailed data for absolute levels of ~10K proteins and ~28K transcripts via convenient web portal. It underscores the lasting impact of maternal dowry, finds surprisingly few cases where degradation alone drives a change in protein level, and highlights the importance of transcription in shaping the proteome.

overall_design: mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification.

first: Leonid

last: Peshkin

first: Martin

last: Wuhr

middle: J

first: Wilhelm

last: Haas

first: Robert

last: Freeman

first: John

middle: C

last: Gerhart

first: Allon

last: Klein

first: Marko

middle: E

last: Horb

first: Steven

middle: P

last: Gygi

first: Marc

middle: W

last: Kirscher


title: Epigenetic profiling in CD4 and CD8 T cells from Graves’ disease patients reveals changes in genes associated with T cell receptor signaling [ChIP-seq]

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19

department: Department of Biomedicine

country: Estonia

institute: University of Tartu

summary: In Graves’ disease (GD), a combination of genetic, epigenetic and environmental factors causes an autoimmune response to the thyroid gland, characterized by lymphocytic infiltrations and autoantibodies targeting the thyroid stimulating hormone receptor (TSHR) and other thyroid antigens. To identify the epigenetic changes involved in GD, we performed a genome-wide analysis of DNA methylation and enrichment of H3K4me3 and H3K27ac histone marks in sorted CD4+ and CD8+ T cells. We found 365 and 3322 differentially methylated CpG sites in CD4+ and CD8+ T cells, respectively. Among the hypermethylated CpG sites, we specifically found enrichment of genes involved in T cell signaling (CD247, LCK, ZAP70, CD3D, CD3E, CD3G, CTLA4 and CD8A) and decreased expression of CD3 gene family members. The hypermethylation was accompanied with the active chromatin histone modifications as we found decreased signals of H3K4me3 and H3K27ac marks at several T cell signaling genes in ChIP-seq analysis. In addition, we found hypermethylation of the TSHR gene first intron, where several GD-associated polymorphisms are located. Our results demonstrate an involvement of dysregulated DNA methylation and histone modifications at T cell signaling genes in GD patients.

overall_design: Individuals were recruited from the Estonian Genome Center of the University of Tartu. Genomic DNA was extracted from sorted CD4+ (H3K4me3 ChIP: 15 controls and 14 GD patients; H3K27ac ChIP: 11 controls and 13 GD patients) and CD8+ (H3K4me3 ChIP: 17 controls and 14 GD patients; H3K27ac ChIP: 15 controls and 14 GD patients) T cells. The data collection was performed at the SNP&SEQ Technology Platform in Uppsala University, and data analysis was done at the Institute of Biomedicine and Translational Medicine in the University of Tartu.

first: Lili

last: Milani


title: microRNAs and isomiRs repertoire in poricne endometrium revealed by Illumina sequencing

city: Olsztyn

first: Monika

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Recently, microRNAs (miRNAs), known to modulate gene expression through post-transcriptional mechanisms, were implied in regulation of early pregnancy events including maternal recognition of pregnancy and implantation. To characterize complex transcriptomic changes in expression of miRNAs in pregnant and cyclic endometria collected on days 12, 16 and 20 was analyzed using Illumina deep sequencing. This research showed repertoire of pregnancy-related miRNAs in porcine endometrium during initial stages of conceptus implantation and during the estrous cycle and sheds light on miRNA-mediated gene expression regulation mechanism at the maternal-conceptus interface.

overall_design: miRNAs and isomiRs expression profiles were analyzed in samples collected from porcine endometrium on Days 12, 16 and 20 of pregnancy and estrous cycle. Each group was represented by 4 to 6 samples. Generated libraries were run in multiplex using specific barcodes to differentiate samples. Illumina sequencing was performed in duplicate (two runs) and after demultiplexing, the same samples from two independent runs were concatenated.

first: Kamil

last: Krawczynski

first: Stefan

last: Bauersachs


title: Epigenetic profiling in CD4 and CD8 T cells from Graves disease patients reveals changes in genes associated with T cell receptor signaling

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Trim33 binds and silences a class of young endogenous retroviruses in the mouse testis

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

summary: Transposable elements (TEs) have been active in the mammalian genome for hundreds of millions of years and each TE has had a distinct period of transpositional activity, followed by inactivation. Mice carrying reporter transgenes can be used to model transcriptional silencing at TEs. A mutagenesis screen for modifiers of epigenetic gene silencing produced a line with a null mutation in Trim33. Heterozygous mutants displayed increased expression of the reporter transgene. ChIP-seq of Trim33 in testis revealed 9,109 peaks, mostly at promoters, across the mouse genome. Trim33 was enriched at many RLTR10B elements that are among the youngest retrotransposons in the mouse genome.  RNA-seq revealed that testis of mice haploinsufficient for Trim33 had altered expression of a small group of genes. The gene with the most significant increase, Nmnat3, was found to be transcribed from an upstream RLTR10B element. We show that Trim33 is involved in repressing RLTR10B elements in mouse testis.

overall_design: Examination of Trim33 binding using ChIP sequencing and the result of Trim33 haploinsufficiency using RNA sequencing, in mouse testis

first: Harald

last: Oey

first: Alex

last: Spurling

first: Lucia

last: Daxinger

first: Emma

last: Whitelaw


title: The differentially expressed genes in rice jmj704 mutants revealed through RNA-Seq

status: Public on Nov 05 2015

city: Fuyang

first: Yuxuan

last: Hou

state: Zhejiang

address: 28 Shuidaosuo Road

country: China

institute: China National Rice Research Institute

summary: We sequenced mRNA from two-week old rice seedlings of  jmj704 and wild-type (ZH11) plants  to obtain the differntially expressed genes in jmj704 mutant.

overall_design: exzamination the differentially expressed genes between two-week old jmj704 and wild-type (ZH11) rice seedlings.

first: Shiwen

last: Huang


title: CD13 and ROR2 permit isolation of highly enriched cardiac mesoderm from differentiating human embryonic stem cells

city: Los Angeles

first: Rhys

middle: John Powling

last: Skelton

state: CA

address: 675 Charles E Young Dr S, Room 3645

department: Eli and Edythe Broad Stem Cell Research Center

institute: UCLA

summary: The resultant heat map demonstrates the maturation of CD13+/ROR2+ cells as they proceed through cardiac differentiation.

overall_design: RNA-seq analysis was preformed on RNA samples from undifferentiated hESCs, 13R2+ and 13R2- populations from day 3, 13R2+/NKX2-5+ and 13R2+/NKX2-5- from day 7, and 13R2+/NKX2-5+/α-MHC+ and 13R2+/NKX2-5+/MHC- from day 14

first: Debashis

last: Sahoo

first: James

last: Engel


title: Isolation of highly enriched cardiac mesoderm from differentiating human embryonic stem cells


title: Next Generation Sequencing Quantitative Analysis of steroid receptor RNA activator (SRA1) Transcriptomes

city: WINNIPEG

first: YI

last: YAN

state: MANITOBA

address: 5029 - 675 McDermot Ave Winnipeg, Mb

department: BIOCHEMISTRY AND MEDICAL GENETICS

country: Canada

institute: UNIVERSITY OF MANITOBA

summary: The steroid receptor RNA activator gene (SRA1) produces both a functional RNA (SRA) and a protein (SRAP), whose exact roles remain unknown. To identify cellular processes regulated by this unusual bi-faceted system, we characterized the transcriptome of two differenct cell lines upon depletion of these molecules.

overall_design: Two differenct cell lines including breast cancer MBD-MDA-231 and cervical cancer Hela cells upon SRA1 depletion and SRAP overexpression

first: Charlton

last: Cooper

first: Yi

last: Yan

first: Wayne

last: Xu

first: Deborah

last: Tsuyuki

middle: R

last: Davie

first: Etienne

last: Leygue


title: Two Distinct Promoter Nucleosome Architectures at Protein-Coding Genes in Yeast

city: Lausanne

first: Jacques

last: Rougemont

address: Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

summary: Previous studies indicate that eukaryotic promoters display a stereotypical chromatin landscape characterized by a well-positioned +1 nucleosome near the transcription start site and an upstream -1 nucleosome that together demarcate a nucleosome-free (or depleted) region. Here we present evidence that there are two distinct types of promoters distinguished by the resistance of the -1 nucleosome to micrococcal nuclease digestion. These different architectures are characterized by two sequence motifs that are broadly deployed at one set of promoters where a nuclease-sensitive ("fragile") nucleosome forms, but concentrated in a more narrow, nucleosome-free region at all other promoters. The RSC nucleosome remodeler acts through the motifs to establish stable +1 and -1 nucleosome positions, while binding of a small set of general regulatory (pioneer) factors at fragile nucleosome promoters plays a key role in their destabilization. We propose that the fragile nucleosome promoter architecture is adapted for regulation of highly expressed, growth-related genes.

overall_design: MNase-seq profiles obtained with various MNase concentrations from wild-type cells and cells depleted of different factors. ChIP-seq using anti-RNA polymerase II antibody, anti-histone H2A antibody, and anti-histone H3 antibody.

first: Slawomir

last: Kubik

first: Maria

last: Bruzzone

first: Philippe

last: Jacquet

first: Jean

middle: L

last: Falcone

first: David

last: Shore


title: Genome-wide Binding of Acetylated-STAT3 Demonstrates Negative Regulation of Dendritic Cells

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

summary: Dendritic cells (DC) play a vital role in the induction of activation or tolerance of immune response.  STAT3 is a master transcriptional regulator of immune response in DCs by positively or negatively regulating DC function, but the mechanisms are unknown. STAT3 is post-translationally modified by acetylation or phosphorylation. While much is understood about transcriptional targets of phosphorylated STAT3, the gene targets and the functional impact of acetylated-STAT3 remain unclear. We aimed to answer the gene targets of acetylated-STAT3 and test the hypothesis that acetylation of STAT3 plays a key role in negative regulation of DCs. We performed genome-wide binding analysis of acetyl-STAT3 by ChIP-Seq coupled with gene expression microarrays.   Acetylation of STAT3 induced by SAHA increased its capability to bind to target DNA sites in genome.  Theses binding sites were mostly proximal but some were also distal up to over 100 kb from transcription start site. Gene expression array showed 1701 genes up-regulated and 1668 genes down-regulated. Proximal binding of acety-STAT3 showed more effective transcription function than distal binding.  In top 500 binding peaks, the frequency of canonical motifs bound by acetyl-STAT3 were significantly higher than that for noncanonical motifs (p<0.00001).  Functional analysis revealed that acetyl-STAT3 regulates target genes by upregulating genes that are primarily involved in negative regulation of cytokine production and IL-10 signaling, or downregulating genes that are primarily involved in immune effector process and antigen processing/presentation. Upregulation of IL-10Ra by acetyl-STAT3 contributes to the enhanced sensitivity of IL-10 signaling and negative regulation of DC function.

overall_design: Bone marrow derived dendritic cells were treated with SAHA (500 nm) or diluent for 12 hours.  ChIP was performed using antibodies against STAT3, H3K4me3 and matched IgG control. DNA binding profiles were generated by deep sequencing using Illumina HiSeq 2000.

first: Yaping

last: Sun

first: Pavan

last: Reddy


title: Stable Chromosome Condensation Revealed by Chromosome Conformation Capture

city: Houston

first: Kyle

last: Eagen

address: 1 Baylor Plaza

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

summary:
Chemical cross-linking and high-throughput sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no such interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of chromatin folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes.

This SuperSeries is composed of the SubSeries listed below.


title: SOX9 modulates the expression of key transcription factors required for heart valve development

city: Vancouver

first: Pamela

middle: A.

last: Hoodless

state: British Columbia

address: 675 West 10th Avenue

department: Terry Fox Laboratories

institute: BC Cancer Agency

summary: Heart valve formation initiates when endothelial cells of the heart transform into mesenchyme and populate the cardiac cushions. The transcription factor, SOX9, is highly expressed in the cardiac cushion mesenchyme, and is essential for heart valve development. Loss of Sox9 in mouse cardiac cushion mesenchyme alters cell proliferation, embryonic survival, and disrupts valve formation. Despite this important role, little is known regarding how SOX9 regulates heart valve formation or its transcriptional targets. Therefore, we mapped putative SOX9 binding sites by ChIP-Seq in embryonic day (E) 12.5 heart valves, a stage at which the valve mesenchyme is actively proliferating and initiating differentiation. Embryonic heart valves have been shown to express a high number of genes that are associated with chondrogenesis, including several extracellular matrix proteins and transcription factors that regulate chondrogenesis. Consequently, we compared regions of putative SOX9 DNA-binding between E12.5 heart valves and E12.5 limb buds. We identified context-dependent and context–independent SOX9 interacting regions throughout the genome. Analysis of context-independent SOX9 binding suggests an extensive role for SOX9 across tissues in regulating proliferation-associated genes including key components of the AP-1 complex. Integrative analysis of tissue-specific SOX9 interacting regions and gene expression profiles on Sox9-deficient heart valves demonstrated that SOX9 controls the expression of several transcription factors with previously identified roles in heart valve development, including Twist1, Sox4, Mecom/Evi1 and Pitx2. Together, our data identifies SOX9 coordinated transcriptional hierarchies that control cell proliferation and differentiation during valve formation.

overall_design: Examination of SOX9 binding sites in E12.5 atrioventricular canal (AVC) and E12.5 embryonic limb and mRNA expression profiling in E12.5 WT and Sox9 mutant AVCs, in duplicate.

first: Rebecca

last: Cullum

first: Victoria

last: Garside


title: Polytene underreplication

summary: Chemical cross-linking and high-throughput sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no such interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of chromatin folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes.

overall_design: Male Drosophila salivary glands are compared to normally replicated 0-6 hour embryos to determine the differentially underreplicated regions of polytene chromosomes.

first: Roger

middle: D

last: Kornberg


title: Polytene Hi-C

overall_design: Hi-C experiments where ligation is performed on beads (tethered) on male Drosophila salivary glands from three independent biological replicates.  Also one Hi-C experiment where the ligation is performed in solution (conventional).


title: The bacterial cell-cycle regulator GcrA is a σ70 co-factor that drives gene expression from a subset of methylated promoters.

status: Public on Nov 10 2015

city: Berkeley

first: Diane

last: Haakonsen

address: 330 Li Ka Shing

department: MCB

institute: Berkeley

summary: Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we find that the essential cell cycle regulator GcrA in Caulobacter crescentus activates the transcription of target genes in a fundamentally different manner. GcrA forms a stable complex with RNA polymerase and localizes to almost all active σ70-dependent promoters in vivo, but activates transcription primarily at promoters harboring certain DNA methylation sites. Whereas most transcription factors that contact σ70  interact with domain 4, GcrA interfaces with domain 2, the region that binds the -10 element during strand separation. Using kinetic analyses and a reconstituted in vitro transcription assay, we demonstrate that GcrA can stabilize RNA polymerase binding and directly stimulate open complex formation to activate transcription. Guided by these studies, we identify a regulon of ~200 genes, providing new insight into the essential functions of GcrA. Collectively, our work reveals a new mechanism for transcriptional regulation, and we discuss the potential benefits of activating transcription by promoting RNA polymerase isomerization rather than exclusively recruitment.

overall_design: Examination of GcrA, RNAP, Sigma70 ChIP in PYE and in PYE + rifampicin-treated for 30 min; sigma32 and sigma54 in PYE + rifampicin-treated for 30 min

first: Michael

middle: T

last: Laub


title: Serine and SAM responsive complex SESAME regulates histone modification crosstalk by sensing cellular metabolism

status: Public on Nov 04 2015

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: We report the genome-wide localization of SESAME and found that three SESAME subunits localized in the gene body.

overall_design: Examining the genome-wide localization of SESAME subunits (Sam1, Ser33, Pyk1) and Set1

first: Shanshan

last: Li


title: IFN-kappa inhibits HPV31 transcription by inducing Sp100 proteins

city: Tübingen

first: Günter

last: Jäger

address: Calwerstr. 7

country: Germany

institute: Institute of Medical Genetics Tübingen

summary: Using doxycycline-inducible IFN-kappa expression in CIN612-9E cells, which maintain extrachromosomally replicating HPV31 genomes, we demonstrate that IFN-kappa inhibits the growth of these cells and reduces viral transcription and replication. Interestingly, the initiation of viral early transcription was already inhibited 4-6h after IFN-kappa expression. This was also observed with recombinant IFN-beta suggesting a common mechanism of IFNs. RNA-seq analysis identified 1367 IFN-kappa regulated genes of which 221 were modulated >2-fold. The majority of those (71%) matched known ISGs confirming that IFN-kappa acts as a bona fide type I IFN in hr-HPV-positive keratinocytes. RNAi and co-transfection experiments indicate that the inhibition of viral transcription is mainly due to the induction of Sp100 proteins by IFN-kappa.

overall_design: CIN612-9E/pInd-IFN-kappa were induced for 4h with 1µg/ml doxycyclin or not. Three biological replicates were analyzed.

first: Christina

last: Habiger

last: Walter

first: Thomas

last: Iftner

first: Frank

last: Stubenrauch


title: Transcriptome of iPSC-derived Neural Cells with Heterozygous Knockout in CHD8

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: CHD8, encoding Chromodomain helicase DNA binding protein 8, is a top autism spectrum disorders (ASDs) risk gene. To better understanding the molecular links between CHD8 functions and ASD, we have applied the CRISPR/Cas9 technology to knockout one copy of CHD8 in induced pluripotent stem cells (iPSCs) to mimic the loss of function status that would exist in the developing human embryo prior to neuronal differentiation. Transcriptome profiling (RNA-seq) in neural progenitors and early differentiating neurons revealed that CHD8 hemizygosity (CHD8+/-) affected the expression of several thousands of genes, enriched for functions of neural development, β-catenin/Wnt signaling, extracellular matrix, and skeletal system development. Moreover, CHD8 regulates multiple genes implicated in ASD, schizophrenia and genes associated with brain volume.

overall_design: iPSCs derived from a healthy subject were transduced with CRISPR/Cas9 vectors with  single guide RNA sequences to target the N-terminal of CHD8 protein to generate truncated mutation seach of the two target sequences. Two clones, one with a 2-bp (KO1) and the other with a 10-bp (KO2) heterozygous deletion were found.The CHD8+/- iPSC lines were used to generate NPCs and early differentiating neurons for RNA-seq analysis, together with samples prepared from the parental clones, for a total of 8 samples (two biological replicates of wild-type (WT) and CHD8+/- at two neurodevelopmental stages).

first: Ping

last: Wang

first: Mingyan

last: Lin

first: Erika

last: Pedrosa

first: Anastasia

last: Hrabovsk

first: Zheng

last: Zhang

first: Wenjun

last: Guo

first: Herbert

last: Lachman


title: Post-transcriptional microRNA modifications in the Dengue mosquito vector, Aedes aegypti

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

summary: MicroRNAs (miRNA) have alternative forms known as isomiRs, which differ from each other by a few nucleotides. Next generation sequencing platforms facilitate identification of these isomiRs and recent discoveries regarding their functional importance have increased our understandings of the regulatory complexities of the microRNAome. Observed changes in the miRNA profiles in mosquitoes infected with flaviviruses have implicated small RNAs in the interactions between viruses and their vectors. Here we analysed the isomiR profiles of both uninfected and infected blood fed Aedes aegypti mosquitoes with a major human pathogen, Dengue virus at two time points post-infection. We found noticeable changes to the isomiR expression profile in response to infection and aging. Data analysis revealed a distinct bias towards isomiR production in the mature miRNA as opposed to the star strand. Furthermore, we noticed that only in 40% of Ae. aegypti miRNAs, the most abundant reads for each particular miRNA match the exact sequence reported in the miRbase. The isomiR expression variations between an Ae. aegypti embryonic cell line (Aag2) and whole mosquitoes demonstrated a tissue-specific pattern of isomiR production. Our results illustrated a bias for certain types of isomiRs for each miRNA. The findings presented in this study also provide evidence that isomiR production is not a random phenomenon and may be important in DENV colonisation of its vector.

overall_design: Examination of isomiR production rate in DENV infected and non infected mosquitoes

first: Sassan

last: Asgari


title: CBP occupancy in Drosophila S2 cells

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

summary: CREB-binding protein (CBP, also known as nejire) is a transcriptional co-activator that is conserved in metazoans. We have generated CBP ChIP-seq data from Drosophila S2 cells and compared it to modENCODE data. This shows that CBP is bound at genomic sites with a wide range of functions. As expected, we find that CBP is bound at active promoters and enhancers. In addition, we find that the strongest CBP sites in the genome are found at Polycomb Response Elements embedded in histone H3 lysine 27 trimethylated (H3K27me3) chromatin, where they correlate with binding of the Pho repressive complex. Interestingly, we find that CBP also binds to most insulators in the genome. At a subset of these, CBP may regulate insulating activity, measured as the ability to prevent repressive H3K27 methylation from spreading into adjacent chromatin.

overall_design: ChIP seq in Drosophila S2 cells using two different antibodies against CBP (nejire), one raised in rabbit against amino acids 2540-3190 (CBP rb), and one raised in guinea-pig against amino acids 1-178 (CBP gp)

first: Ann

last: Boija

first: Per

last: Stenberg


title: Analysis of transcriptome changes in Kmt2d deletion in cardiac mesoderm, anterior heart field precursors and cardiomyocytes

city: San Francisco

first: Siang-Yun

last: Ang

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

summary: KMT2D is required in the cardiac mesoderm, anterior heart field precursors and cardiomyocytes. Kmt2d deletion in cardiac mesoderm (Mesp1Cre) is embryonic lethal at E10.5 and mutants have hypoplastic hearts; Kmt2d deletion in anterior heart field precursors (Mef2cAHF::Cre) deletion is embryonic lethal at E13.5 and mutants have defects in septation of outflow tract and interventricular septum (IVS); Kmt2d deletion in cardiomyocytes (Tnnt2::Cre) deletion is embryonic lethal at E14.5 and mutants have defects in IVS septation and compact myocardium. The goal of this study is to compare changes in gene expression in these Kmt2d conditional deletion mutants and understand common or distinct pathways dysregulated in absence of KMT2D.

overall_design: Whole genome gene expression analysis was performed on RNA isolated from control and mutant embryonic hearts (or right ventricles and outflow tract for anterior heart field deletion samples). Libraries were prepared using Illumina TruSeq Paired-End Cluster Kit v3, and sequenced with the Illumina HiSeq 2500 system for pair-ended 100 base pairs (PE 100 bp).

first: Benoit

last: Bruneau

first: Siang

middle: Y


title: Molecular Response of Chorioretinal Endothelial Cells to Complement Injury: Implications for Macular Degeneration

city: Iowa City

first: S. Scott

last: Whitmore

state: IA

address: 375 Newton Road

department: The University of Iowa Institute for Vision Research

institute: The University of Iowa

summary: Age-related macular degeneration (AMD) is a common, blinding disease of the elderly in which macular photoreceptor cells, retinal pigment epithelium, and choriocapillaris endothelial cells ultimately degenerate. Recent studies have found that degeneration of the choriocapillaris occurs early in this disease and that this endothelial cell dropout is concomitant with increased deposition of the complement membrane attack complex (MAC) at the choroidal endothelium. However, the impact of MAC injury to choroidal endothelial cells is poorly understood. To model this event in vitro, and to study the downstream consequences of MAC injury, endothelial cells were exposed to complement from human serum, compared to heat inactivated serum which lacks complement components. Cells exposed to complement components in human serum showed increased labeling with antibodies directed against the MAC, time and dose dependent cell death as assessed by lactate dehydrogenase assay, and increased permeability. RNA-Seq analysis following complement injury revealed increased expression of genes associated with angiogenesis including matrix metalloproteases (MMPs)  3 and 9, and VEGF-A. The MAC-induced increase in MMP9 RNA expression was validated using C5 depleted serum compared to C5 reconstitited serum. Increased levels of  MMP9  were also determined using Western blot and zymography. These data suggest that, in addition to cell lysis, complement attack on choroidal endothelial cells promotes an angiogenic phenotype in surviving cells.

overall_design: RNA-Seq of RF/6A (cultured choroidal endothelial cells from Rhesus macaque) treated with either 50% heat-inactivated human serum ([CONTROL], n=3) or 50% normal human serum (active complement membrane attack complex [MAC], n=3)

first: S

middle: S

first: Robert

middle: F

last: Mullins


title: RNAseq analysis of Mo17 seedlings

city: East Lansing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Road

institute: Michigan State University

summary:
Quantify gene expression by measurement of mRNA in maize inbred line Mo17
mRNA-seq used as part of the validation of CAGE results used for the genome-wide location and dynamic of maize core promoters obtained from the experimental establishment of the TSSs coordinates

overall_design: 4 samples

first: Maria

middle: K

last: Mejia-Guerra

first: Wei

last: Li

first: Narmer

last: Galeano

first: Mabel

last: Vidal

first: Jonh

last: Gray

first: Andrea

middle: I

last: Doseff


title: Nitric oxide regulates gene expression in cancers by controlling histone posttranslational modifications [HiSeq 2000]

city: Chicago

first: Douglas

middle: David

last: Thomas

state: IL

address: 900 S Ashland Ave Room 3306

department: Medicinal Chemistry & Pharmacognosy

institute: University of Illinois at Chicago

summary: Dynamic changes in histone posttranslational modifications (PTMs) are important regulators of chromatin structure and gene transcription in both normal and disease settings. Herein, we describe a novel signaling mechanism of nitric oxide (•NO) by demonstrating its ability to modulate gene expression via alteration of histone PTMs. Having established that •NO exposure induced differential expression of approximately 6500 genes, we set out to determine if there was an epigenetic component to their regulation. •NO exposure led to alterations in the global levels of acetyl and methyl modifications at numerous lysine residues on core histones H3 and H4. Residues H3K9me2/ac were examined further and determined to have differential distribution at various loci throughout the genome in response to •NO. Changes in the enrichment levels of H3K9me2/ac at specific genes correlated with changes in the expression levels of their transcripts. Molecular mechanisms contributing to phenotypic outcomes in •NO-associated cancers remain to be well understood since traditional modes of •NO-signaling do not explain a large proportion of its impact on tumor cell behavior. Our results reveal that •NO drives a significant amount of gene expression changes epigenetically by changing the distribution of numerous histone marks.

overall_design: Cultured cells were treated with 500uM DETA/NO to examine the effects of a physiologically relevant •NO concentration on differential distribution of H3K9ac/H3K9me2. A total of two untreated biological replicates and two •NO-treated biological replicates were harvested. The untreated samples served as control against which comparisons were made to elucidate •NO-mediated changes in the histone landscape.

first: Divya

last: Vasudevan

first: Jason

last: Hickok

first: Rhea

last: Bovee

first: Vy

last: Pham

first: Lin

last: Mantell

first: Neil

last: Bahroos

first: Pinal

last: Kanabar

first: Xing-Jun

last: Cao

first: Mark

last: Maienschein-Cline

first: Benjamin

middle: A

last: Garcia


title: ESRP2 Regulates A Conserved And Cell-Type-Specific Splicing Program to Support Postnatal Liver Maturation

city: LA

first: Jaegyoon

last: Ahn

address: 611 Charles E. Young Drive

department: IBP

summary: Alternative splicing greatly expands the proteomic diversity but its functional impact is often unclear. Here, we identify a highly conserved and temporally coordinated cell-type-specific splicing program, which is activated in part by ESRP2 during postnatal liver development. Consistent with failure of many neonatal-to-adult splicing transitions, Esrp2 null mice exhibit persistent expression of fetal markers and loss of mature hepatocyte characteristics. Conversely, ectopic expression of ESRP2 in immature mouse or human hepatocytes results in a reciprocal switch in splicing. Our findings define an essential role for ESRP2 in generation of conserved repertoires of adult splice isoforms that facilitate postnatal liver maturation.

overall_design: Mouse liver RNA was isolated with Trizol (Invitrogen). Hi-Seq libraries were prepared and paired-end 100bp Illumina sequencing was performed on mouse liver samples from different developmental stages.

first: A

last: Kalsotra

first: X

last: Xiao


title: Nitric oxide regulates gene expression in cancers by controlling histone posttranslational modifications

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Ribo_seq (aka ribosome profiling) analysis of control and Myc-induced U2OS cells

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: We used Ribo-seq to examine the effect of Myc activation on protein translation in U2OS cells and correalted these changes with alterations in RNA level measured by RNA-seq on tye same conditions. We also examined these effects in the presence of Torin-1, an inhibitor of mTOR

overall_design: We measure ribosome occupancy profiles in U2OS cells containing an inducible Myc expression vector that were induced or mock-treated in duplicates for 36 hours. In addition, we repeated the experiments in the presence of Torin-1, an inhibitor of mTOR.

first: R

last: Agami


title: GRO-seq analysis of control and Myc-induced U2OS cells

summary: We used GRO-seq to examine the effect of Myc activation on RNA transcription in U2OS cells.

overall_design: We measure in duplicates gene transcription rates in U2OS cells containing an inducible Myc expression vector that were induced or mock-treated in duplicates for 5 hours.


title: Ets-domain transcription factor Ets21c and nuclear receptor Ftz-F1 are novel effectors of JNK promoting tumor malignancy

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

institute: CECAD Research Center  Cologne

summary: Cancer represents a complex family of diseases, characterized by the uncontrolled malignant growth of a particular cell type and by metastatic dissemination of these transformed cells to secondary sites. The hallmark tumor features emerge as a result of aberrant cellular signaling and pathological gene expression driven by cooperating genetic lesions. Being the convergence points of signaling pathways, transcription factors play crucial roles in cancer. Here, we define a transcription factor network that triggers an abnormal gene expression program promoting malignancy of clonal tumors, generated in Drosophila imaginal disc epithelium by overexpressing oncogenic Ras (RasV12) in a background lacking the tumor suppressor gene scribble (scrib1). We show that the nuclear receptor Ftz-F1 and the ETS-domain transcription factor Ets21c are upregulated in the rasV12scrib1 tumors in response to activated Jun-N-terminal kinase (JNK) signaling. Depletion of either Ftz-F1 or Ets21c improves viability of Drosophila larvae suffering from tumors, and this effect can be further enhanced by simultaneous removal of the Jun-dimerizing partner Fos. We identified Fos as a key mediator of JNK-induced differentiation defects and further show that Ftz-F1 and Fos are required for tumor invasiveness. However, only Ets21c can efficiently substitute for JNK and cooperate with RasV12 to induce invasive tumors that recapitulate hallmarks of malignant rasV12scrib1 tumors including elevated matrix metalloprotease (MMP1) and insulin-like peptide 8 (Dilp8) expression. In conclusion, our study provides functional evidence for a network of cooperating transcription factor that dictates target gene expression and promotes tumor phenotypes in response to aberrant JNK signaling.

overall_design: 20 samples analyzed, 4 control samples

first: Eva

last: Külshammer

first: Juliane

last: Mundorf

first: Merve

last: Kilinc

first: Peter

last: Frommolt

first: Prerana

last: Wagle


title: Genome-wide studies identify a novel interplay between AML1 and AML1/ETO in t(8;21) acute myeloid leukemia

city: shanghai

first: Huanwei

last: Wang

state: shanghai

address: 197 Ruijin Rd II

department: Shanghai Institute of Hematology

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (RJH-SJTU-SM)

summary: The AML1/ETO fusion protein is essential to the development of acute myeloid leukemia (AML), and is well recognized for its dominant-negative effect on the co-existing wild-type protein AML1. However, the involvement of wild-type AML1 in AML1/ETO-driven leukemogenesis remains elusive. Through chromatin immunoprecipitation sequencing, computational analysis plus a series of experimental validations, we report here that AML1 is able to orchestrate the expression of AML1/ETO targets regardless of being activated or repressed, via forming a complex with AML1/ETO and via recruiting the cofactor.

overall_design: 4 ChIP-seq assays were used to identify the high confidence binding regions of AML1-ETO and AML1 in t(8;21) AML Kasumi-1 cell lines. The anti-AML1 (N20) antibody targets the N-terminus of AML1 and recognizes both AML1 and AML1/ETO; the anti-AML1 (C19) antibody targets the C-terminus of AML1 and recognizes AML1 but not AML1/ETO; the anti-ETO (C20) antibody targets the C-terminus of ETO and specifically recognizes AML1/ETO. 2 ChIP-seq assays were used to identify the binding regions of AML1 in human macrophage U937 cell lines. And the total input was used as control.

first: Kankan

first: Yizhen

last: Li


title: Reversible Burst of Transcriptional Changes During Induction of Crassulacean Acid Metabolism (CAM) in Talinum triangulare

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

summary: Rapid, reversible induction of crassulacean acid metabolism in conjunction with pronounced reconfiguration of carbon metabolism enables T. triangulare to survive cycles of severe drought.

overall_design: RNA was extracted from leaves of Talinum triangulare plants (3 biological replicates) after plants were grown under 0, 4, 9 and 12 days of drought as well as after 2 days of re-watering. Paired-end samples were used for purposes of creating a de novo transcriptome assembly.

first: Dominik

last: Brilhaus

first: Andrea

last: Braeutigam

first: Tabea

last: Mettler-Altmann

first: Klaus

last: Winter


title: Myc activation coordinates gene transcription and protein translation responses


title: ChIP-seq after immunoprecipitation with either IgG or SOX2 antibodies in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells)

city: Toulouse

first: Nicolas

last: Chassaing

address: Place du Dr Baylac

department: Service de Génétique Médicale

country: France

institute: CHU Toulouse

summary: In order to identify target genes of the SOX2 transcription factor, we tried to identify SOX2 binding site in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) by ChIP-seq. SOX2 gene mutations are involved in anophthalmia and our hypothesis was that target genes of SOX2 transcription factor may also be candidate to be involved in ocular development.

overall_design: High throughput sequencing after chromatin immunoprecipitation using either an antibody against our target transcription factor (SOX2) or using control antobodies (IgG). These experiments were performed on only one immunoprecipitation with each antibody.

first: N


title: The Poly(C) binding protein Pcbp2, and its retrotransposed derivative Pcbp1, are independently essential to mouse development

city: Philadelphia

first: Ian

middle: M

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

department: Biology

institute: University of Pennsylvania

summary: RNA-binding proteins participate in a complex array of post-transcriptional controls essential to cell-type specification and somatic development.  Despite their detailed biochemical characterizations, the degree to which each RNA-binding protein impacts on mammalian embryonic development remains incompletely defined and the level of functional redundancy among subsets of these proteins remains open to question. The poly-(C) binding proteins, Pcbp’s (aCPs, hnRNPEs), are encoded by a highly conserved and broadly expressed gene family. The two major Pcbp isoforms, Pcbp2 and Pcbp1, are robustly expressed in a wide range of tissues and exert both nuclear and cytoplasmic controls over gene expression. Here we report that Pcbp1-null embryos are rendered nonviable in the peri-implantation stage. In contrast, Pcbp2-null embryos survive until mid-gestation at which time they undergo a loss in viability associated with cardiovascular and hematopoietic abnormalities. Adult mice heterozygous for either Pcbp1 or Pcbp2 null alleles display a mild and non-disruptive growth defect. These data reveal that Pcbp1 and Pcbp2 are individually essential for mouse embryonic development and post-natal growth, reveal a non-redundant in vivo role for Pcpb2 in hematopoiesis, and provide direct evidence that Pcbp1, a retrotransposed derivative of Pcpb2, has evolved essential function(s) in the mammalian genome.

overall_design: mRNA-seq on fetal liver tissue from 12.5 days post coitum. 4 replicates of WT and 3 replicates of PCBP2 Knockout

first: Louis

last: Ghanem

first: Andrew

last: Kromer

first: Brian

last: Gregory

first: Stephen

last: Liebhaber


title: Tip60 complex binds to active Pol II promoters and a subset of enhancers and co-regulates the c-Myc network in mouse embryonic stem cells

city: Illkirch

first: Sarina

last: Ravens

address: 1 Rue Laurent Fries

institute: IGBMC

summary:
Background
Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip60 as reflected in a genome-wide context is not yet well understood.

Results
Gel filtration of nuclear mESCs extracts indicate incorporation of Tip60 into large molecular complexes and exclude the existence of large quantities of “free” Tip60 within the nuclei of ESCs. Thus, monitoring of Tip60 binding to the genome should reflect the behaviour of Tip60-containing complexes. The genome-wide mapping of Tip60 binding in mESCs by chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) shows that the Tip60 complex is present at promoter regions of predominantly active genes that are bound by RNA polymerase II (Pol II) and contain the H3K4me3 histone mark. The coactivator HAT complexes, Tip60- and Mof (KAT8)-containing (NSL and MSL), show a global overlap at promoters, whereas distinct binding profiles at enhancers suggest different regulatory functions of each essential HAT complex. Interestingly, Tip60 enrichment peaks at about 200 bp downstream of the transcription start sites suggesting a function for the Tip60 complexes in addition to histone acetylation. The comparison of genome-wide binding profiles of Tip60 and c-Myc, a somatic cell reprogramming factor that binds predominantly to active genes in mESCs, demonstrate that Tip60 and c-Myc co-bind at 50–60 % of their binding sites. We also show that the Tip60 complex binds to a subset of bivalent developmental genes and defines a set of mESC-specific enhancer as well as super-enhancer regions.

Conclusions
Our study suggests that the Tip60 complex functions as a global transcriptional co-activator at most active Pol II promoters, co-regulates the ESC-specific c-Myc network, important for ESC self-renewal and cell metabolism and acts at a subset of active distal regulatory elements, or super enhancers, in mESCs.

overall_design: Genome- wide binding of Tip60 co-activator complexes

first: Changwei

last: Yu

first: Tao

last: Ye

first: Matthieu

last: Stierle

first: Laszlo

last: Tora


title: Transcriptomic analysis and ChIP-seq in CCE-Rx cells to identify SOX2 transcription factor target genes


title: High Mobility Group protein mediated transcription requires DNA damage marker γ-H2AX

city: Nancy Cedex

first: Guillermo

last: Barreto

address: 9, Avenue de la Forêt de Haye ‐ BP 20199

department: Campus Biologie-Santé. Faculté de Médecine

institute: CNRS Director of Research

summary: The eukaryotic genome is organized into chromatin, which constitutes the physiological template for DNA-dependent processes including replication, recombination, repair and transcription. Chromatin mediated transcription regulation involves histone modifications, chromatin remodeling and DNA methylation. However, the precise biological function of non-histone chromatin-associated proteins is still unclear. The high mobility group proteins are the most abundant non-histone chromatin-associated proteins. Here we combined proteomic, ChIP-seq and transcriptome data to decipher the mechanism of transcriptional regulation mediated by the high mobility group AT-hook protein 2 (HMGA2). We showed that HMGA2-induced transcription requires H2AX phosphorylation at S139 (H2AXS139ph; γ-H2AX), mediated by the kinase ataxia telangiectasia mutated (ATM). Furthermore, we demonstrated the relevance of this mechanism within the biological context of TGFB1-signaling. Our results link H2AXS139ph, a marker for DNA damage, to transcription, which is a new function for this histone modification. The interplay between HMGA2, ATM and H2AX is a novel mechanism of transcription initiation.

overall_design: Chip-seq data of HMGA2, H2AXS139ph and ATM obtained from Mouse embryonic Fibroblast cells in wt and Ko of Hmga2

first: Indrabahadur

last: Singh

first: Julio

last: Cordero

first: Nihan

last: Ozturk


title: RNA-seq analysis of control and Myc-induced U2OS cells

first: Ran

last: Elkon

summary: We used RNA-seq to examine the effect of Myc activation on U2OS cells transcriptome. We also examined these effects in the presence of Torin-1, an inhibitor of mTOR

overall_design: We measure gene expression profiles in U2OS cells containing an inducible Myc expression vector that were induced or mock-treated in duplicates for 36 hours. In addition, we repeated the experiments in the presence of Torin-1, an inhibitor of mTOR.

first: R

last: Agami


title: Cell-free DNA comprises an in vivo, genome-wide nucleosome footprint that informs its tissue(s)-of-origin

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

institute: University of Luebeck

summary: Nucleosomes are the basic unit of packaging of eukaryotic chromatin, and nucleosome positioning can differ substantially between cell types. Here, we sequence 14.5 billion plasma-borne cell-free DNA (cfDNA) fragments (700-fold coverage) to generate genome-wide maps of in vivo nucleosome occupancy. We identify 13 million local maxima of nucleosome protection, spanning 2.53 gigabases (Gb) of the human genome, whose positions and spacings correlate with nuclear architecture, gene structure and gene expression. We further show that short cfDNA fragments - poorly recovered by standard protocols - directly footprint the in vivo occupancy of DNA-bound transcription factors such as CTCF. The sequence composition of cfDNA has previously been used to noninvasively monitor cancer, pregnancy and organ transplantation, but a key limitation of this paradigm is its dependence on genotypic differences to distinguish between contributing tissues. We show that nucleosome spacing in gene bodies and cis-regulatory elements, inferred from cfDNA in healthy individuals, correlates most strongly with transcriptional and epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how in vivo nucleosome footprints can be used to infer the cell types that contribute to circulating cfDNA in pathological states such as cancer. Because it does not rely on genotypic differences, this strategy may enable the noninvasive cfDNA-based monitoring of a much broader set of clinical conditions than is currently possible.

overall_design: Sequencing of cfDNA libraries from healthy individuals, pooled healthy individuals and individuals with disease for the identification of nucleosomes and protection from other DNA binding proteins.

first: Jay

last: Shendure


title: The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells

city: La Jolla

first: Thomas

middle: C

last: Whisenant

address: 10550 North Torrey Pines Rd

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute


title: Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue

first: Ian

last: Quigley

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

summary: V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their specification are poorly understood. Morphological and molecular evidence suggest that the zinc finger transcription factor Prdm12 may play a role in promoting V1 interneurons while repressing V2 and V0 fates. Here, we performed RNAseq on Xenopus laevis ectoderm converted to posteriorized neural tissue (with noggin and retinoic acid) in the presence or absence of a series of Prdm12 constructs (wild-type Prdm12, Prdm12-VP16, and Prdm12-engrailed-repressor). We also performed ChIPseq on a Prdm12-FLAG in wild-type or posteriorized neuralized (with noggin and retinoic acid) X. laevis ectoderm. Taken together, these data demonstrate Prdm12's genomic targets and their downstream transcription.

overall_design: X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP.

first: Kristine

last: Henningfeld

first: Chris

last: Kintner

first: Eric

middle: J

last: Bellefroid

first: Claude

last: Van Campenhout


title: The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells [RNA-seq]

summary: Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. We immunoprecipitated U2AF2 to identify what mRNA transcripts were bound as a function of activation by TCR crosslinking and costimulation. In parallel, mass spectrometry revealed the proteins incorporated into the U2AF2-centered RNA/protein interactome. Molecules that retained interaction with the U2AF2 complex after RNAse treatment were designated as “central” interactome members (CIMs). Mass spectrometry also identified a second class of activation-induced proteins, “peripheral” interactome members (PIMs), that bound to the same transcripts but were not in physical association with U2AF2 or its partners. siRNA knockdown of two CIMs and two PIMs caused changes in activation marker expression, cytokine secretion, and gene expression that were unique to each protein and mapped to pathways associated with key aspects of T cell activation. While knocking down the PIM, SYNCRIP, impacts a limited but immunologically important set of U2AF2-bound transcripts, knockdown of U2AF1 significantly impairs assembly of the majority of protein and mRNA components in the activation-induced interactome. These results demonstrated that CIMs and PIMs, either directly or indirectly through RNA, assembled into activation-induced U2AF2 complexes and play roles in post-transcriptional regulation of genes related to cytokine secretion. These data suggest an additional layer of regulation mediated by the activation-induced assembly of RNA splicing interactomes that is important for understanding T cell activation.

overall_design: RNAseq of total RNA from a primary CD4 T cell culture at rest and 48 hours after anti-CD3/CD28 bead activation

first: Eigen

last: Peralta

first: Lauren

last: Aarreberg

first: Nina

last: Gao

first: Steven

last: Head

first: Phillip

last: Ordoukhanian

first: Jamie

last: Williamson

first: Daniel

last: Salomon


title: Comparison between two different Pinus pinaster provenances (RNA-Seq)

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

summary: The transcriptome of needles from plants propagated by cuttings and cultured in the same conditions at SERIDA’s greenhouse at Villaviciosa (Asturias, Spain) were analyzed. The cuttings are from two different provenances of Pinus pinaster; Leiria (Portugal) and Tamrabta (Morocco). Their transcriptomes were analyzed using high throughput sequencing

overall_design: 4 samples

first: Concepción

last: Ávila

first: Francisco

last: Cánovas


title: The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells [RIP-Seq]

overall_design: U2AF2 RIPseq on a primary CD4 T cell culture at rest and 48 hours after anti-CD3/CD28 bead activation


title: Isolation and functional characterization of the arteriole hematopoietic stem cell niche

city: New York

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

summary: Hematopoietic stem cells (HSCs) inhabit distinct microenvironments within the adult bone marrow (BM) that govern the delicate balance between HSC quiescence, self-renewal, and differentiation. It has been suggested that quiescent HSCs localize adjacent to BM arteriole endothelial cells in a significant and non-random distribution. This data suggests that the arteriole BM vascular niche may be the primary HSC niche. Because the BM arteriole niche is composed of tightly-associated pericytes, including smooth muscle actin+, LepR+, Nestin+, NG2+, and nonmyelinating Schwann cells, we sought to begin to uncouple the arteriole BM EC niche by examining its capacity to support the maintenance and expansion of HSCs ex vivo and in vivo. We developed a method to isolate and culture BM arteriole endothelial cells in serum-/growth factor-free conditions, allowing for a non-biased approach to examining their instructive function. Utilizing our protocol, we demonstrate that BM endothelial cells, but not BM stromal cells, have the capacity to expand long-term repopulating, multi-lineage HSCs in lieu of complex serum and cytokine supplementation. In addition, transplantation of arteriole endothelial cells promoted rapid hematopoietic recovery and protected HSCs following an LD50 dose of myeloablative irradiation. These data demonstrate that arteriole-derived BM endothelial cells are endowed with the necessary signals to support the self-renewal and regenerative capacity of LT-HSCs and that transplantation of arteriole BM endothelial cells could be used as a therapeutic means to decrease pancytopenias associated with myeloablative treatments to treat a wide array of disease states.

overall_design: Transcriptome sequencing of bone marrow endothelial cells and bone marrow stroma, in vitro and in vivo, with and without HSC co-culture.

first: Michael

last: Poulos

first: Jason

last: Butler


title: Transcriptome profiling of planktonic stage to biofilm stage of deep sea bacterium Pseudoalteromonas sp. SM9913

status: Public on Nov 03 2015

city: Guangzhou

first: Xingsheng

last: Cai

state: Guangdong

address: Room 302, Building 2, #164 Xingang West Road, Haizhu District

department: Key laboratory of Tropical Marine Bio-resources and Ecology

institute: South China Sea Institute of Oceanology, Chinese Academy of Sciences

summary: We compared genetic profiles of  planktonic stage to biofilm stage of deep sea bacterium Pseudoalteromonas sp. SM9913 and revealed genetic features during switch from planktonic to pellicle stage in Pseudoalteromonas sp. SM9913.

overall_design: mRNA profiles of  Pseudoalteromonas sp. SM9913 planktonic cells, initial pellicle cells and mature pellicle cells were generated by Illumina Hiseq2000.

first: Pengxia

last: Wang

first: Biyuan

last: Li

first: Zhenshun

last: Zeng

first: Yunchang

last: Xie

first: Jie

first: Si

last: Zhang

first: Xiaoxue


title: Genome-wide microRNA-expression analysis after p53 activation in hepatocellular carcinoma

city: Chengdu

first: Ding

last: ruofan

address: southwest jiaotong university JiuLi campus

institute: southwest jiaotong university

summary: In order to characterize the differentially expressed miRNAs after the p53 activation , small RNA-seq were used after the overexpression of p53 in HepG2 cells.

overall_design: Four samples of HepG2 cells were subjected to small RNA-seq in two biological replicates.The HepG2 cells were treated with 1µg/ml doxorubicin for 24 hours to induce the expression of p53. The experimental group(dox-treated HepG2：HepG2_24h_rep1 and HepG2_24h_rep2) and control group(untreated HepG2: HepG2_0h_rep1 and HepG2_0h_rep2) were subjected to small RNA-seq to identify the p53-regulated miRNAs.

first: Zhiyun

last: Guo

first: Yalan

last: Yang

first: Ruofan

last: Ding

first: Wenrong

last: Liu

first: Yiming


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Cerebellum_miRNA]

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). Knock-in mouse models of HD with human exon 1 containing expanded CAG repeats inserted in the murine huntingtin gene (Hdh) provide a genetic reconstruction of the human causative mutation within the mouse model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.

overall_design: miRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the cerebellum of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.

first: Jim

last: Rosinski


title: Single cell RNA-Seq of Hira-KO and control MII oocytes

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

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

overall_design: Refer to individual Series


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Hippocampus_mRNA]

summary: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). Knock-in mouse models of HD with human exon 1 containing expanded CAG repeats inserted in the murine huntingtin gene (Hdh) provide a genetic reconstruction of the human causative mutation within the mouse model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the hippocampus of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.


title: Single cell RNA-Seq of Hira-KO and control MII oocytes [Zp3-Cre]

summary: The integrity of chromatin, which provides a dynamic template for all DNA-related processes in eukaryotes, is maintained through replication-dependent and -independent assembly pathways. To address the role of replication-independent histone deposition, we deleted the histone H3.3 chaperone Hira in developing mouse oocytes. We show that chromatin of non-replicative developing oocytes is highly dynamic, and that lack of continuous H3.3/H4 deposition alters chromatin structure, resulting in increased DNase I sensitivity, the accumulation of DNA damage, and, ultimately, a severe fertility phenotype. On the molecular level, abnormal chromatin structure leads to a dramatic decrease in the dynamic range of gene expression, the appearance of spurious transcripts, and inefficient de novo DNA methylation. In contrast to the only minor transcriptional phenotype observed in mouse pluripotent cells, we unequivocally show the importance of histone replacement and chromatin homeostasis for transcriptional regulation and normal developmental progression in an in vivo context.

overall_design: RNA-Seq on 4 Hiraf/f and 4 Hiraf/f, Zp3-Cre single MII oocytes.

first: Buhe

last: Nashun

first: Peter

last: Hill

first: Petra

last: Hajkova


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [cerebellum_mRNA]

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the cerebellum of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.


title: ATAC-Seq on Cohesin mutant HSPCs

city: Stanford

first: Howard

last: Chang

address: 269 Campus Dr. Stanford, CA

institute: Stanford University

summary: Understanding the impact of cohesin mutations on HSPC chromatin structure

overall_design: We examined chromatin structure using ATAC-seq in CD34+ enriched-human HSPC that were transduced with either cohesin WT, mutant or empty vector controls

first: Claire

last: Mazumdar

first: Ying

last: Shen

first: Ravi

last: Majeti


title: Single cell RNA-Seq of Hira-KO and control MII oocytes [Gdf9-Cre+]

summary: The integrity of chromatin, which provides a dynamic template for all DNA related processes in eukaryotes, is maintained through replication dependent and independent assembly pathways. To address the role of replication independent histone deposition, we deleted the histone H3.3 chaperone Hira in developing mouse oocytes. We show that chromatin of non-replicative developing oocytes is highly dynamic, and that lack of continuous H3.3/H4 deposition alters chromatin structure, resulting in increased DNase I sensitivity, the accumulation of DNA damage, and, ultimately, a severe fertility phenotype. On the molecular level, abnormal chromatin structure leads to a dramatic decrease in the dynamic range of gene expression, the appearance of spurious transcripts, and inefficient de novo DNA methylation. In contrast to the only minor transcriptional phenotype observed in mouse pluripotent cells, we unequivocally show the importance of histone replacement and chromatin homeostasis for transcriptional regulation and normal developmental progression in an in vivo context.

overall_design: RNA-Seq on 4 Hiraf/f and 4 Hiraf/f, Gdf9-Cre+ single MII oocytes


title: Cathepsin K Contributes to Cavitation and Collagen Turnover in Pulmonary Tuberculosis

city: Umeå

first: Christer

last: Larsson

address: Bldng. 6K

institute: Umeå universitet

summary: Cavitation in tuberculosis (TB) enables highly efficient person-to-person aerosol transmission. Currently, a number of hypotheses exist regarding the mechanisms underlying this process. To explore this process, we undertook an unbiased next-generation transcriptional analysis of samples from cavity walls, grossly normal tissue from the same lung, and uninfected control lungs. Of 17,318 mapped host transcripts, only 199 showed a significant >2-fold change in cavity wall versus normal infected and uninfected samples. Amongst 22 upregulated proteases, 5 type I collagenases were over-represented; these included cathepsin K (CTSK), mast cell chymase-1 (CMA1), matrix metalloproteinase (MMP)-1, MMP-13, and MMP-14. To determine if cavitation was associated with changes in collagen turnover, we assayed serum and urinary markers of collagen metabolism in rabbits with cavitary TB versus infected controls. Serum collagen type 1 C-terminal propeptide (CICP, a marker of collagen synthesis and degradation) and urinary deoxypyridinoline (DPD, a marker of degradation) were increased by 10- (p = 0.019) and 4-fold (p = 0.068), respectively; while urinary helical peptide (a marker of degradation) was decreased 3-fold (p=0.015). This indicates that cavitation in TB is associated with significant increases of both destruction and synthesis of collagen and that cleavage of type I collagen occurs outside the known cleavage sites of MMP-1, -13 and -14.

overall_design: Rabbit gene expression analysis in lung tissue from M. tuberculosis infected animals. Cavitary tissue, non cavitary tissue and lung tissue from non-infected animals are compared.

first: André

last: Kubler

first: Brian

last: Luna

first: Bruno

last: Andrade

first: Eduardo

middle: P

last: Amaral

first: Michael

last: Urbanowski

first: Marlene

last: Orandle

first: Kevin

last: Bock

first: Nicole

last: Ammerman

first: Laurene

last: Cheung

first: Kathryn

last: Winglee

first: Marc

last: Haluschka

first: Jin

last: Park

first: Alan

last: Sher

first: Jon

last: Friedland

first: Paul

last: Elkington

first: William

last: Bishai


title: Temporal transcriptomics suggest that twin-peaking genes reset the clock

city: Oxford

last: Pembroke

address: South Parks Road

institute: Functional Genomics Unit, Oxford University

summary: The mammalian suprachiasmatic nucleus (SCN) drives daily rhythmic behavior and physiology, yet a detailed understanding of its coordinated transcriptional programmes is lacking. To reveal the true nature of circadian variation in the mammalian SCN transcriptome we combined laser-capture microdissection (LCM) and RNA-Seq over a 24-hour light / dark cycle. We show that 7-times more genes exhibited a classic sinusoidal expression signature than previously observed in the SCN. Another group of 766 genes unexpectedly peaked twice, near both the start and end of the dark phase; this twin-peaking group is significantly enriched for synaptic transmission genes that are crucial for light-induced phase-shifting of the circadian clock. 342 intergenic non-coding RNAs, together with novel exons of annotated protein-coding genes, including Cry1, also show specific circadian expression variation. Overall, our data provide an important chronobiological resource (www.wgpembroke.com/shiny/SCNseq/) and allow us to propose that transcriptional timing in the SCN is gating clock resetting mechanisms.

overall_design: Pooled dissected tissue of the suprachiasmatic nucleus from five adult male mice provided one of three replicates for each of six timepoints over a 12:12 light/dark (LD) cycle (ZT2, 6, 10, 14, 18 and 22). Each biological replicate was sequenced over 3 seperate lanes using Illumina HiSeq.

middle: G

first: Arran

last: Babbs

first: Kay

middle: E

last: Davies

first: Chris

last: Ponting

first: Peter

last: Oliver


title: Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin

city: Eugene

first: Eric

last: Selker

state: OR

address: 1585 E 13th Ave

department: Institute of Molecular Biology

institute: University of Oregon

summary: Methylated lysine 27 on histone H3 (H3K27me) marks repressed "facultative heterochromatin", including developmentally regulated genes in plants and animals. The mechanisms responsible for localization of H3K27me are largely unknown, perhaps in part because of the complexity of epigenetic regulatory networks. We used a relatively simple model organism bearing both facultative and constitutive heterochromatin, Neurospora crassa, to explore possible interactions between elements of heterochromatin. In higher eukaryotes, reductions of H3K9me3 and DNA methylation in constitutive heterochromatin have been variously reported to cause redistribution of H3K27me3. In Neurospora, we found that elimination of any member of the DCDC H3K9 methylation complex (DIM-5, DIM-7, CUL4, DDB1/DIM-8 or DIM-9) caused massive changes in the distribution of H3K27me; regions of facultative heterochromatin lost H3K27me3 while regions that are normally marked by H3K9me3 became methylated at H3K27. Elimination of DNA methylation by deletion of the DNA methyltransferase gene, dim-2, had no obvious effect on the distribution of H3K27me. Elimination of HP1, which "reads" H3K9me3, also caused major changes in the distribution of H3K27me, indicating that HP1 is important for normal localization of facultative heterochromatin. Because loss of HP1 caused redistribution of H3K27me2/3 but not H3K9me3, these normally non-overlapping marks became superimposed. Indeed, mass spectrometry revealed substantial cohabitation of H3K9me3 and H3K27me2 on H3 molecules from an hpo strain. Loss of H3K27me machinery (e.g. the methyltransferase SET-7) did not impact constitutive heterochromatin, but partially rescued the slow growth of the DCDC mutants, suggesting that the poor growth of these mutants is partly attributable to ectopic H3K27me. Altogether, our findings with Neurospora clarify interactions of facultative and constitutive heterochromatin in eukaryotes.

overall_design: ChIP-seq was performed on 27 samples (H3K27me2me3 ChIP: 16 samples, H3K9me3 ChIP: 7 samples, GFP ChIP: 4 samples).  Each type of histone modification and GFP ChIP-seq includes a wild-type sample.  For H3K27me2me3 ChIP-seq, biological replicates are included for the dim-5 and dim-8 deletion strains.  H3K27me2me3 ChIP-seq also includes samples from 2 independent dim-2 strains.

first: Kirsty

last: Jamieson

first: Elizabeth

last: Wiles

last: McNaught

first: Yanchun

last: Shao

last: Rountree

first: Neena

last: Leggett


title: Proper chromatin programming during spermatogenesis is required for embryonic development

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: Epigenetic mechanisms including DNA methylation, non-coding RNAs and histone modifications control gene expression. Studies suggest that a father's lifetime experiences can be transmitted to his offspring to affect development and health. The mechanisms underlying such epigenetic inheritance are unknown. A potential route for paternal transmission is the unique chromatin composition of spermatozoa. Unlike somatic cells and oocytes, most nucleosomes in sperm are replaced with protamine nucleoproteins. The role of residual nucleosomes, residing at gene regulatory sequences, for epigenetic control of embryonic development is unknown. Here we generated a transgenic mouse model in which over-expression of the histone H3 lysine 4 (H3K4) demethylase LSD1/KDM1A during spermatogenesis alters H3K4 methylation in sperm. Strikingly, KDM1A over-expression in one generation causes severe embryonic defects in non-transgenic descendants spanning three subsequent generations. We show for the first time that correct histone methylation homeostasis during spermatogenesis is critical for offspring development and survival over multiple generations.

overall_design: Identification of H3K4me2 and nucleosome occupancies in sperm of wildtype mice, KDM1A transgenic mice and their non-transgenic littermates.

first: Keith

last: Siklenka

first: Serap

last: Erkek

middle: H

first: Sarah

last: Kimmins


title: Targeting the SIN3A-PF1 Interaction inhibits Epithelial to Mesenchymal Transition and Maintenance of a Stem Cell Phenotype in Triple Negative Breast Cancer (MNase-seq)

status: Public on Nov 02 2015

city: Stirling

first: Kevin

last: Petrie

state: Stirling

address: Stirling

department: Biological and Environmental Sciences

institute: University of Stirling

type: Methylation profiling by high throughput sequencing

summary: Triple negative breast cancer (TNBC) is characterized by a poorly differentiated phenotype and limited treatment options. Aberrant epigenetics in this subtype represent a potential therapeutic opportunity, but a better understanding of the mechanisms contributing to the TNBC pathogenesis is required. The SIN3 molecular scaffold performs a critical role in multiple cellular processes, including epigenetic regulation, and has been identified as a potential therapeutic target. Using a competitive peptide corresponding to the SIN3 interaction domain of MAD (Tat-SID), we investigated the functional consequences of selectively blocking the paired amphipathic helix (PAH2) domain of SIN3. Here, we report the identification of the SID-containing adaptor PF1 as a factor required for maintenance of the TNBC stem cell phenotype and epithelial to mesenchymal transition (EMT). Tat-SID peptide blocked the interaction between SIN3A and PF1, leading to epigenetic modulation and transcriptional downregulation of TNBC stem cell and EMT markers. Importantly, Tat-SID treatment led to a reduction in primary tumor growth and disseminated metastatic disease in vivo. In support of these findings, knockdown of PF1 expression phenocopied treatment with Tat-SID both in vitro and in vivo. These results demonstrate a critical role for a complex containing SIN3A and PF1 in TNBC and provide a rational for its therapeutic targeting.

overall_design: Mononucleosomes from MDA-MB-231 cells were isolated and ChIP with H3K4me3 antibody. DNA from Input and ChIP samples was purified and sequenced on Illumina Hiseq.

first: Yordan

last: Sbirkov


title: Targeting the SIN3A-PF1 Interaction inhibits Epithelial to Mesenchymal Transition and Maintenance of a Stem Cell Phenotype in Triple Negative Breast Cancer


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [cerebellum; hippocampus]

first: Jeff

last: Aaronson


title: ChIP-Seq on Cohesin mutant TF-1 Cell Line

first: Howard

last: Chang

state: CA

summary: Understanding the binding of GATA2, RUNX1 and SMC3 in RAD21 WT vs. mutant TF-1 Cells

overall_design: We examined GATA2, RUNX1 and SMC3 using ChIP-seq in TF-1 erythroleukemia cells that were transduced with an inducible vector expression WT or mutant (Q592*) RAD21 after 6 days of DOX induction

first: Claire

last: Mazumdar

first: Ying

last: Shen

first: Ravi

last: Majeti


title: The transcription and translation landscapes during human cytomegalovirus infection reveal novel host-pathogen interactions

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

institute: Weizmann Institute

summary: During its long infection cycle, human cytomegalovirus (HCMV) extensively manipulates cellular gene expression to maintain conditions favorable for viral propagation. In order to reveal the signature of cellular genes that are manipulated by HCMV, we measured RNA abundance and rate of protein production through the course of HCMV infection. We characterized changes for most expressed cellular genes and although much of the regulation was transcriptional we uncover diverse and dynamic translational regulation for subsets of host genes, revealing unappreciated coordination in translational control that suggests common regulators

overall_design: Ribosome profiling and mRNA-seq along HCMV infection

first: Alina

last: Shitrit


title: Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [RNA-Seq P30]

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary:
Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse
Methods: RNA was extracted from decapsulated testes of 29-30 day old mixed background mice of either genotype. Deep sequencing was used to determine quantitative expression of the genomes from independent replicates of each genotype
Results: RNA-Seq analysis identified some 640 genes that are down regulated at least 2-fold in Rfx2-/- testes, with ~150 being reduced at least 10-fold
Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 640 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function.

overall_design: Testicular mRNA profiles were determined by deep sequencing using testes from 5 independent wild type and 4 independent Rfx2-/- mice

first: W

last: S Kistler

first: Dominique

last: Baas

last: Lemeille

first: Marie

last: Paschaki

first: Emmanuèle

last: Barras

first: Wenli

last: Ma

first: Jean-Luc

last: Duteyrat

first: Laurette

last: Morlé

first: Bénédicte

last: Durand

first: Walter

last: Reith


title: Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [ChIP-Seq]

summary:
Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse
Methods: DNA was extracted from decapsulated testes of 21 day old mice. ChIP sequencing was used to determine the binding sites of RFX2.
Results: ChIP-Seq analysis identified ~880 binding sites of RFX2 near TSS.
Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 105 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function.

overall_design: Testicular RFX2 binding sites were determined by deep sequencing using testes from 2 independentWT mice

last: Kistler


title: Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Aberrant transcription of the HSATII pericentromeric satellite repeat is present in a wide variety of epithelial cancers. We observed that HSATII expression is induced in colon cancer cells cultured as xenografts or under non-adherent conditions in vitro, but it is rapidly lost in standard 2D cultures. Unexpectedly, physiological induction of endogenous HSATII RNA, as well as introduction of synthetic HSATII transcripts, generate complementary DNA intermediates in the form of DNA:RNA hybrids. Single molecule sequencing of tumor xenografts shows that HSATII RNA-derived DNA (rdDNA) molecules are stably reincorporated within pericentromeric loci, leading to progressive expansion of these regions

overall_design: We analyzed the dynamics of HSATII RNA and DNA level changes using single molecule sequencing (Helicos/SeqLL) in SW620 colon cancer cells transitioned from 2D in vitro culture conditions to growth as mouse xenografts and vice versa.

first: Francesca

last: Bersani

first: Eunjung

last: Lee

first: Peter

middle: V

last: Kharchenko

first: Andrew

middle: W

last: Xu

first: Mingzhu

last: Liu

first: Kristina

last: Xega

first: Olivia

last: MacKenzie

first: Brian

last: Brannigan

first: Hyunchul

last: Jung

first: Sridhar

last: Ramaswamy

last: Park

first: Shyamala

last: Maheswaran

first: David

last: Ting

first: Daniel

last: Haber


title: Different exercise modalities have distinct effects on the transcriptome profile in the male rat femoral diaphysis

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary: Mechanical loading is a key determinant of bone mass, geometry and strength and is essential to maintain optimal skeletal health. We hypothesized that spontaneous low-impact exercise would affect global gene transcript levels in cortical bone of growing rats. We used RNA-Seq to analyse the transcriptome of the femoral mid-diaphysis in pre-pubertal male rats that were assigned to one of three exercise groups for 15 days: control (CON); bipedal stance (BPS); and wheel exercise (WEX). RNA-seq analysis identified 808 and 324 differentially expressed transcripts in the BPS and WEX animals, respectively. In WEX animals, the up-regulated transcripts were enriched for gene ontology terms associated with bone metabolism. Both BPS and WEX animals showed changes in transcripts that were enriched for muscle-related processes. However, in WEX these transcripts were down-regulated while in BPS such transcripts were up-regulated. Importantly, we observed that the exercise mode had diametrically opposite effects on transcripts for multiple genes within the integrin-linked kinase (ILK) and Ca2+ signalling pathways such that they were up-regulated in BPS and down-regulated in WEX. The findings are important for our understanding of possible ways in which different exercise regimens might affect bone when normal activities apply mechanical stimuli during post-natal growth and development.

overall_design: 24 weanling (21 day old) male Sprague-Dawley rats were assigned to three exercise groups .After the 15 day trial period, total RNA was extracted from the femoral diaphysis and mRNA profiles were analysed using RNA-seq

first: Dharani

last: Sontam

first: Elwyn

last: Firth

last: Tsai

first: Mark

last: Vickers


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Hippocampus_miRNA]

first: Jeff

last: Aaronson

summary: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). Knock-in mouse models of HD with human exon 1 containing expanded CAG repeats inserted in the murine huntingtin gene (Hdh) provide a genetic reconstruction of the human causative mutation within the mouse model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.

overall_design: miRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the hippocampus of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.

first: Jim

last: Rosinski


title: Ikaros mediates gene silencing in T cells through Polycomb Repressive Complex 2 [ChIP-seq]

city: Illkirch

first: Attila

last: Oravecz

address: 1 rue Laurent Fries

institute: IGBMC

summary: T cell development is accompanied by epigenetic changes that ensure the silencing of stem cell-related, and the activation of lymphocyte-specific programs. How transcription factors influence these changes remains unclear. We show that the Ikaros transcription factor interacts with the Polycomb Repressive Complex 2 (PRC2) in CD4-CD8- thymocytes, and allows its binding to >200 developmentally-regulated genes, many of which are expressed in hematopoietic stem cells. Loss of Ikaros in CD4-CD8- cells leads to diminished histone H3 Lys27 (H3K27) trimethylation and ectopic expression of these genes. Ikaros binding triggers PRC2 recruitment and H3K27 trimethylation. Furthermore, Ikaros interacts with PRC2 independently of the Nucleosome Remodeling and Deacetylation complex. Our results identify Ikaros as a fundamental regulator of PRC2 function in developing T cells.

overall_design: Genome-wide comparison of different histone modifications, Ikaros, Suz12 and NuRD binding in different stages of T cell development in WT and Ikaros mutant mice. Profiling of H3K27me3 in DN1, DN2, DN3, DN4 and DP thymocytes and hematopoietic stem and progenitor cells (LSK cells) of WT and Ikaros mutant mice. Profiling of H3K4me3 and H3ac in WT and Ikaros mutant DP thymocytes. Global analysis of Ikaros binding in WT DN3, DN4 and DP cells, Suz12 binding in WT and Ikaros mutant DN3 cells, and Mta2 and Mi2beta binding in WT DN3 cells. Genome-wide profiling of Ikaros binding and H3K27me3 upon Ikaros activation in Ikaros-deficient leukemic T cells.

first: Apostol

last: Apostolov

first: Katarzyna

last: Polak

first: Bernard

last: Jost

first: Stéphanie

last: Le Gras

first: Susan

last: Chan

first: Philippe

last: Kastner


title: EHMT1 and EHMT2 inhibition induce fetal hemoglobin expression

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

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

overall_design: Refer to individual Series


title: EHMT1 and EHMT2 inhibition induce fetal hemoglobin expression [ChIP-seq]

summary: Using UNC0638 and genetic assays to inhibit EHMT1/2 and derepress fetal hemoglobin in adult hematopoietic cells.

overall_design: ChIP-seq for 2 histone modifications and total H3 (for quantitative normalization) in biological triplicates of cord blood, adult bone marrow, and UNC0638-treated adult bone marrow.

first: Aline

last: Renneville

last: Van Galen

first: Matthew

last: Canver

first: Marie

last: McConkey

first: John

last: Krill-Burger

last: Dorfman

first: Edward

middle: B

last: Holson

first: Bradley

last: Bernstein

first: Stuart

last: Orkin

last: Bauer

first: Benjamin

middle: L

last: Ebert