title: Polycomb Underlies Transcriptional Heterogeneity in Lineage Priming of Embryonic Stem Cells [ChIP-Seq]

first: Rob

last: Illingworth

summary: X-linked Chromatin Immunoprecipitation (ChIP) for the histone modification H3K27me3 was performed on subpopulations of the HexVenus reporter mouse ES cell line (clone HV1.5) grown under self-renewing conditions. Subpopulations were identified and isolated based on the expression of the ES cell surface marker SSEA 1 and the expression of the venus protein. At approximately 70% confluence, cells were trypsinised, resuspended in FACs buffer (10%FCS in PBS) and incubated with a mouse monoclonal antibody to SSEA 1 (MC-480, Developmental Hybridoma Studies Bank, University of Iowa). Cells were then incubated with an Alexa-647 conjugated anti-mouse IgM antibody (Invitrogen) and subpopulations were fractionated by flow cytometry prior to further processing specific to each method. The aim was to determine if subtle changes in priming gene transcription were associated with changes in the magnitude of H3K27me3.

overall_design: mESCs carrying a fluorescently tagged Hhex-Venus (HV) reporter construct were FACS sorted and immediately cross-linked with formaldehyde and then stored at -80°C prior to performing ChIP. ChIP was performed on two independent biological replicates for both the primed and re-sorted populations in addition to a single replicate for the minor HV+S- (spontaneously differentiated) population. Sequencing libraries were generated for each sample and deep sequenced.

first: Robert

first: Jurriaan

last: Hölzenspies

first: Wendy

last: Bickmore

first: Joshua

last: Brickman


title: USP15 regulates type I interferon response in vivo and is required for pathogenesis of microbial and autoimmune neuroinflammation

status: Public on Oct 10 2016

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

type: Expression profiling by high throughput sequencing

summary: Genes and pathways in which inactivation dampens tissue inflammation present new opportunities for understanding the pathogenesis of common human inflammatory diseases, including inflammatory bowel disease, rheumatoid arthritis and multiple sclerosis. We identified a mutation in the gene encoding the deubiquitination enzyme USP15 (Usp15L749R) that protected mice against both experimental cerebral malaria (ECM) induced by Plasmodium berghei and experimental autoimmune encephalomyelitis (EAE). Combining immunophenotyping and RNA sequencing in brain (ECM) and spinal cord (EAE) revealed that Usp15L749R-associated resistance to neuroinflammation was linked to dampened type I interferon responses in situ. In hematopoietic cells and in resident brain cells, USP15 was coexpressed with, and functionally acted together with the E3 ubiquitin ligase TRIM25 to positively regulate type I interferon responses and to promote pathogenesis during neuroinflammation. The USP15-TRIM25 dyad might be a potential target for intervention in acute or chronic states of neuroinflammation.

overall_design: Sequencing of RNA extracted from target tissue in two experimental neuroinflammation models in wild-type (B6), USP15(L749R) and Trim25 KO mutant mice: (1) brains at day 3 and 5 following Plasmodium berghei ANKA (PbA) infection for the cerebral malaria model (ECM); and (2) spinal cords at day 7 following induction of experimental autoimmune encephalomyelitis (EAE) for B6 and Usp15 mutant mice only.

first: Irena

last: Radovanovic

first: Maria

middle: J

last: Polyak

first: Sabrina

last: Torre

first: Philippe

last: Gros


title: Gene expression data for body versus head samples for detection of genes with enriched expression in salivary glands of the spider mite Tetranychus urticae

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

country: USA

institute: University of Utah

summary: Proteins produced in the salivary glands of arthropod herbivores can function as effectors to modify plant defense responses. To obtain a set of candidate, salivary gland specific genes for the mite herbivore Tetranychus urticae, mites were dissected and the head region was recovered. Specifically, the proterosoma was dissected from 250 mites. This includes the salivary glands, and other nearby tissue (given their small size, exact micro-dissection of salivary glands was not possible). As a reference for assessing differential expression to identify genes that might be salivary gland specific, three replicates of 100 whole mites were used. Female mites, which are much larger than males, were used in all cases for collection of RNA.

overall_design: mRNA profiles were generated for intact 100 adult female T. urticae mites (in triplicate) and for dissected proterosoma of 250 adult females

first: Wannes

last: Dermauw

first: Vladimir

last: Zhurov

last: Greenhalgh

first: Thomas

last: Van Leeuwen


title: Transcriptome of mouse preimplantation development

status: Public on Oct 11 2016

city: Worcester

first: Ingolf

last: Bach

state: MA

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

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

overall_design: Refer to individual Series


title: The transcription factor, Nuclear factor, erythoid 2 (Nfe2), is a regulator of the oxidative stress response during Danio rerio development

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

summary: Development is a complex and well-defined process characterized by rapid cell proliferation and apoptosis. At this stage in life, a developmentally young organism is more sensitive to toxicants and other stressors when compared to an adult. In response to pro-oxidant exposure, members of the Cap’n’Collar (CNC) basic leucine zipper (b-ZIP) transcription factor family (including the Nfe2-related factors, Nrfs) activate the expression of genes that contribute to reduced toxicity. Here, we studied the role of the Nrf protein, Nfe2, in the developmental response to pro-oxidant exposure in the zebrafish. Following acute waterborne exposures to diquat or tert-buytlhydroperoxide (tBOOH) at three developmental stages, wildtype (WT) and nfe2 knockout (KO) embryos and larvae were morphologically scored and their transcriptomes sequenced.

overall_design: Wildtype animals were on the AB background and an additional germline nfe2 knockout strain were created by disruption of the nfe2 reading frame. Waterborne exposures to either diquat or tBOOH were carried out at three different developmental stages: 2 hours post fertilization (hpf), 48hpf, and 96hpf in 3 pools of 30 embryos per condition. Animals were exposed to no treatment, 20µM diquat or 1mM tBOOH for a 4-hour dosing period. Total RNA was isolated from pooled animals and 50 bp, paired end, libraries were sequenced using the Illumina HiSeq 2000 platform, with approximately 25 million reads per sample. Reads were then aligned to the Ensembl GRCz10 zebrafish reference genome using Tophat2 and raw counts data normalized using DESeq2. Gene annotation was from Ensemble for GRCz10.

first: Larissa

last: Williams

first: Briony

middle: A

last: Lago

middle: G

first: Amogelang

middle: R

last: Raphenya

first: Nicholas

last: Pray

first: Nabil

last: Saleem

first: Sophia

last: Salas

first: Katherine

last: Paulson

first: Roshni

middle: S

last: Mangar

first: Yang

last: Liu

first: Andy

last: Vo

first: Jordan

last: Shavit


title: otp90

city: evry

first: remi

last: bounon

state: essonne

address: 2 avenue Gaston Crémieux

department: BAP

country: France

institute: INRA

summary:
role of the otp90 protein
Comparison of the otp90 knock-out mutant with the corresponding WT genotype in regular growth conditions.

overall_design: mRNA seq on wild-type Col and otp90 mutants knock out.

first: Etienne

last: Delannoy

first: Sandrine

last: Balzergue

first: Rémi

last: Bounon

first: Véronique

last: Brunaud

first: Marie-Laure

last: Martin-Magniette


title: Early response of the fungus Pycnoporus coccineus to softwood and hardwood feedstocks

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

institute: INRAE - Aix Marseille University

summary: White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. The Polyporale fungus Pycnoporus coccineus CIRM-BRFM310 grows well on both coniferous and deciduous wood. In the present study we analyzed the early response of the fungus to softwood (pine) and hardwood (aspen) feedstocks.

overall_design: Examination of mRNA levels in fungal mycelium after 3 days growth in liquid cultures on pine or aspen.

first: François

last: Piumi

first: Igor

middle: V

last: Grigoriev

first: Anna

last: Lipzen


title: Abundant DNA 6mA methylation during early embryogenesis of zebrafish

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: DNA N6-methyldeoxyadenosine (6mA) is a well known prokaryotic DNA modification and has been shown to exist and play epigenetic roles in eukaryotic DNA. Here we report that 6mA accumulates up to 0.1% of total deoxyadenosine during early embryogenesis of vertebates, but diminishes with progression of the embryo development. During this process most 6mA locates in repetitive regions of the genome.

overall_design: The antibody-based  immunoprecipitation of 6mA‑containing DNA followed by next generation high-throughput sequencing (6mA‑IP‑seq) on early embryos of zebrafish.

first: Jianzhao

first: Guanzheng

first: Chuan

last: He


title: Comparative principles of DNA methylation reprogramming during human and mouse in vitro primordial germ cell specification [Mouse and Human RNA-seq and BS-seq]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

summary: Primordial germ cell (PGC) development is characterized by global epigenetic remodeling, which resets genomic potential and establishes an epigenetic ground state. Here we recapitulate PGC specification in vitro from naive embryonic stem cells and characterize the early events of epigenetic reprogramming during the formation of the human and mouse germline. Following rapid de novo DNA methylation during priming to epiblast-like cells, methylation is globally erased in PGC-like cells (PGCLCs). Repressive chromatin marks (H3K9me2/3) and transposable elements are enriched at demethylation resistant regions, while active chromatin marks (H3K4me3 or H3K27ac) are more prominent at regions that demethylate faster. The dynamics of specification and epigenetic reprogramming show species-specific differences, in particular markedly slower reprogramming kinetics in the human germline. Differences in developmental kinetics between species may be explained by differential regulation of epigenetic modifiers. Our work establishes a robust and faithful experimental system of the early events of epigenetic reprogramming and its regulation in the germline.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA-seq, BS-seq and PBAT of different time-points during human and mouse in vitro PGC-like cell specification

first: Ferdinand

last: von Meyenn

first: Simon

last: Andrews

first: Wolf

last: Reik


title: Genome-wide differential expression of genes and small RNAs in testis of two different porcine breeds and at two different ages

city: Wuhan

first: Yao

last: Li

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: College of Animal Sciences and Technology

country: China

institute: Huazhong Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Lu Chuan (LC, a Chinese local pig breed) and Yorkshire boars were generally considered as being pretty different in the time point and process of sexual maturation. Some documented evidences proved small RNAs (sRNA) and targeted genes are involved in mammalian testicular development and spermatogenesis. However, the detailed molecular regulation mechanisms of them remain largely unknown so far. We used the deep sequencing technology to characterize and identify the similarities and diversities of the expression and regulation of mRNAs, miRNAs and piRNAs which are possibly related to spermatogenesis and testicular development in different pig breeds at different stages of sexual maturity. In this study, we obtained a total of 10,716 mRNAs, 67 miRNAs and 16,953 piRNAs which were differentially expressed between LC and LW pig breeds or between the two sexual maturity stages. Of which, we identified 16 miRNAs and 28 targeted genes possibly related to spermatogenesis; 14 miRNAs and 18 targeted genes probably associated with cell adhesion related testis development. We also annotated 579 piRNAs which could potentially regulate cell death, nucleosome organization and other basic biology process, which implied that those piRNAs might be involved in sexual maturation difference. The integrated network analysis results suggested that some differentially expressed genes were involved in spermatogenesis through the ECM–receptor interaction, focal adhesion, Wnt and PI3K–Akt signaling pathways, some particular miRNAs have the negative regulation roles and some special piRNAs have the positive and negative regulation roles in testicular development. Our data provide novel insights into the molecular expression and regulation similarities and diversities of spermatogenesis and testicular development in different pig breeds at different stages of sexual maturity.

overall_design: LC and LW boars considerably differ in sexual maturation time; LW boars reach maturity at ~180 days old (Egbunike 1979), whereas LC boars reach maturity at 90 days old (Huang Ya-qiong et al. 2013). We dissected the testes from three LC and LW boars aged 20 days (sexual immaturity, B) and 200 days ( maturity, A). No genetic linkage was present between the three LC boars or three LW boars at 20 or 200 days old. The similarities and diversities for the two pig breeds were analyzed from the RNA-seq and small RNA-seq.

first: Jialian

first: Chengchi

last: Fang

first: Liang

last: Shi

first: Jiajian

last: Tan

first: Yuanzhu

last: Xiong

first: Bin

last: Fan

first: Changchun


title: C9/ALS Human Embryonic Stem Cells  and C9/ALS Induced Pluripotent Stem Cells

status: Public on Oct 09 2016

city: Waltham

first: Sebastian

last: Kadener

address: 415 South Street

institute: Brandeis University

summary: We established two HESC lines with a C9 mutation (SZ-ALS1, SZ-ALS3) from embryos, which were obtained through preimplantation genetic diagnosis (PGD) and donated for cell line derivation by a family in which the mother was an expansion carrier (originally diagnosed as a carrier of an expansion with >40 repeats in blood by a repeat primed PCR). In addition, we generated halo-identical and unrelated C9/ALS iPSCs from a skin biopsies of the C9 carrier mother (patient H, 30 years-old), and from an unrelated C9/ALS patient, 2 years following disease-onset (patient M, 65 years-old).

overall_design: We established two HESC lines with a GGGGCC expansion in the C9orf72 gene (C9), and compared them with haplo-identical and unrelated C9 iPSCs.

first: Rachel

last: Eiges


title: Global gene expression profiles of Mycobacterium smegmatis under shock and mild nutrient starvation

city: Singapore

first: Thomas

last: Dick

address: Centre for Translational Medicine, Block MD6, 15-01, 14 Medical Drive

department: Microbiology

country: Singapore

institute: National University of Singapore

summary: Mycobacteria are known to be non-spore forming but very hardy: the bacilli can for instance survive starvation in zero-nutrient saline in a non-replicating state. Recently we reported that mycobacteria in fact can undergo cellular differentiation when exposed to different starvation conditions. The presence of traces of nutrients triggers the development of a new, ‘small resting cell’ form (SMRCs). Saline shock-starved large resting cells (LARCs), which did not show cell size or surface changes when observed by scanning electron microscopy, remodeled their internal structure to the septated, multi-nucleoided cells seen during differentiation to SMRCs. Here we conduct RNA-seq to gain greater insights into whether starvation elicited a distinct developmental pathway. Comparative transcriptome analysis of SMRC and LARC development revealed largely overlapping sets of differentially expressed regulatory and metabolic genes. These transcriptome data are consistent with a mycobacterial starvation-induced differentiation program in which at first septated, multi-nuceloided cells are generated. Under zero-nutrient conditions bacteria terminate development at this stage as LARCs. In the presence of traces of a carbon source, these multi-nucleoided cells continue differentiation into mono-nuleoided SMRCs.

overall_design: Exponentially growing M. smegmatis in rich 7H9 medium (0h sample, baseline) was transferred to PBS or PBS-Tween80 and RNA was sampled and sequenced after 1h and 3h to capture immediate responses, and after 24h when LARC formation in PBS cultures and SMRC formation in PBS-Tween80 culture are completed. In addition we sampled 14d old starved cultures to determine long term gene expression changes.

first: Mu-Lu

last: Wu

first: Martin

last: Gengenbacher

first: Jade

middle: C

last: Chung

first: Swaine

middle: L

last: Chen

first: Hans-Joachim

last: Mollenkopf

first: Stefan

middle: H

last: Kaufmann


title: Hepatocyte Nuclear Factor 1 coordinates multiple functions of intestinal epithelial cells

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

institute: Northwestern University

summary:
Background and Aims: Hepatocyte nuclear factor 1 (HNF1) transcription factors direct tissue specific gene regulation in liver, pancreas and kidney and are associated with diabetes. Here we investigate the transcriptional network governed by HNF1 in an intestinal epithelial cell line.
Methods: Chromatin immunoprecipitation followed by direct sequencing (ChIP-seq) was used to identify HNF1 binding sites genome-wide. Direct targets of HNF1 were validated using conventional ChIP assays. siRNA-mediated depletion of HNF1 followed by RT-qPCR further confirmed target genes.  The effect of HNF1 reduction on glucose uptake was measured by fluorescence activated cell sorting (FACS) following treatment of intestinal epithelial cells with 2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) amino]-2-deoxy-d-glucose (2-NBDG, a fluorescent glucose mimic).
Results: HNF1 controls multiple pathways that are critical for intestinal epithelial cell function, including properties of the cell membrane, cellular response to hormones, and regulation of biosynthetic processes. Approximately 50% of HNF1 binding sites are also occupied by hepatocyte nuclear factor 4A (HNF4A), caudal type homeobox 2 (CDX2), and forkhead box A2 (FOXA2). Depletion of HNF1 increases FOXA2 abundance and decreases levels of CDX2. Moreover, loss of HNF1 inhibits glucose uptake by the intestinal epithelial cell line.
Conclusions: These data show that HNF1 plays a critical role in regulating intestinal epithelial cell functions including glucose absorption. HNF1 interacts with other tissue-specific transcription factors to regulate differentiated properties of these cells.

overall_design: To determine the role of HNF1 in regulating gene expression in intestinal epithelial cells, ChIP-seq was performed for HNF1 in Caco2 (colorectal adenocarcinoma) cells.

first: Rui

last: Yang

first: Jenny

last: Kerschner


title: ZMYND8 co-localizes with NuRD on target genes and regulates recruitment of GATAD2A/NuRD to sites of DNA damage [RNA-seq]

status: Public on Oct 08 2016

city: Nijmegen

first: Cornelia

middle: Gijsbertha

last: Spruijt

address: Geert Grooteplein 26-28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: The NuRD complex is generally thought to repress transcription at both hyper- and hypomethylated regions in the genome. In addition, the complex is involved in the DNA damage response. Here, we show that ZMYND8 bridges NuRD to a number of putative DNA-binding zinc finger proteins. The ZMYND8 MYND domain directly interacts with PPPL? motifs in the NuRD subunit GATAD2A. Furthermore, GATAD2A and GATAD2B exclusively form homodimers and they thus define mutually exclusive NuRD subcomplexes. ZMYND8 and MBD3 share a large number of genome-wide binding sites, mostly active promoters and enhancers. Depletion of ZMYND8 does not affect NuRD occupancy genome-wide and expression of NuRD/ZMYND8 target genes in steady-state asynchronous cells. However, ZMYND8 facilitates immediate recruitment of GATAD2A/NuRD to induced sites of DNA damage. These results thus show that a specific substoichiometric interaction with a NuRD subunit paralogue provides unique functionality to a distinct NuRD subcomplex.

overall_design: RNA-seq samples for HeLa FRT-TO mock, ZMYND8KO, and ZMYND8KO-rescue cells


title: ZMYND8 co-localizes with NuRD on target genes and regulates recruitment of GATAD2A/NuRD to sites of DNA damage


title: ZMYND8 co-localizes with NuRD on target genes and regulates recruitment of GATAD2A/NuRD to sites of DNA damage [ChIP-seq]

overall_design: ChIP-seq samples for endogenous ZMYND8 (2 replicates), MBD3 (2 replicates), ZMYND8 in ZMYND8-KO cells, MBD3 in ZMYND8-KO cells, input of wild-type HeLa cells, GFP ChIP on WT HeLa cells, GFP ChIP on ZMYND8-GFP, GFP ChIP on GFP-GATAD2A and GFP ChIP on GFP-GATAD2B


title: RNA sequencing of Bifidobacterium longum subsp. longum SC596 in response to various substrates

city: Davis

first: Danielle

last: Lemay

state: CA

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

summary: The purpose of this project was to determine the whole transcriptome response of Bifidobacterium longum subsp. longum SC596 to pooled and individual human milk oligosaccharides (HMO) relative to lactose

overall_design: Bacterial isolates grown on lactose, pooled human milk oligosaccharides (HMO), lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), 2’fucosyllactose (2’FL), 3-fucosyllactose (3FL). RNA was extracted and sequenced, in duplicate, on an Illumina HiSeq. Early, mid, and late timepoints in response to pooled HMO were additionally sequenced in duplicate.

first: David

last: Mills

first: Daniel

last: Garrido

first: Nina

last: Kirmiz


title: Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

status: Public on Oct 07 2016

first: Vijay

last: Sankaran

address: 7 Cambridge Center

institute: Broad Institute

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens


title: Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits [MPRA]

summary: Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay (MPRA) to simultaneously screen 2,756 variants in strong linkage disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with endogenous erythroid regulatory activity. Across 23 sentinel variants, we conservatively identified 32 MPRA functional variants (MFVs). We used targeted genome editing to demonstrate endogenous enhancer activity across 3 MFVs that predominantly affect the transcription of SMIM1, RBM38, and CD164. Functional follow-up of RBM38 delineates a key role for this gene in the alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type-specific transcriptional regulatory pathways.

overall_design: Constructs containing SNPs in high LD with sentinel red blood cell GWAS hits were cloned upstream of a reporter gene in an MPRA plasmid. DNA from the plasmid and RNA 48 hours after transfection into K562 cells were isolated, RT-PCR was performed, reads containing barcodes were sequenced, and these barcodes were counted and a RNA/DNA ratio was derived to measure the relative activity of the construct.

first: Jacob

last: Ulirsch


title: Histone H2A T120 phophorylation promotes oncogenic transformation via upregulation of cyclin D1 [ChIP-seq]

city: Nagasaki

first: TAKEYA

last: NAKAGAWA

address: 1-12-4 sakamoto

department: Biochemistry

country: Japan

institute: Nagasaki unversity

summary: It is well known that deregulation of chromatin modifiers, such as histone acetylases and methylases, causes malignancies. However, the possible role of histone phosphorylation in carcinogenesis has not yet been elucidated. Here, we found that histone phosphorylation by itself can be the causal event in carcinogenesis. First, we found that histone H2A T120 is phosphorylated in human cancer cell lines and proved that this phosphorylation is catalyzed by hVRK1. By knocking down VRK1, cyclin D1 was found to be downregulated by loss of H2A T120 phosphorylation and increased H2A K119 ubiquitylation of its promoter region, resulting in impaired cell growth. In human cancer tissues, we found that histone H2A is hyperphosphorylated, with upregulated cyclin D1. Mechanistically, histone H2A T120 phosphorylation and histone H2A K119 ubiquitylation, which repress transcription, are mutually inhibitory, suggesting that histone phosphorylation indirectly activates chromatin. Furthermore, mutated H2A T120D, which mimics phosphorylation, causes elevated H3K4 methylation in the same nucleosome. Subsequently, H3K4R, which functionally mimics H3K4 methylation, increases H3 S10 phosphorylation in the same nucleosome. Finally, both VRK1 and the H2A T120D mutant histone transformed NIH/3T3 cells. This suggests that histone H2A T120 phosphorylation by hVRK1 causes inappropriate gene and protein expression, including upregulated cyclin D1, resulting in carcinogenesis.

overall_design: ChIP-Seq analysis using 3 antibody (anti-H2A pT120, anti-VRK1, anti-H2A ubiquitylated K119 )  in siVRK1 or siControl treated HT1080 cells.

first: Hitoshi

last: Aihara

first: Takashi

last: Ito


title: AML1/ETO accelerates cell migration and impairs cell-to-cell adhesion and homing of hematopoietic stem/progenitor cells

city: Rozzano

first: Alberto

last: Termanini

state: MI

address: Via Manzoni, 113

country: Italy

institute: Istituto Clinico Humanitas

summary: The AML1/ETO fusion protein found in acute myeloid leukemias functions as a transcriptional regulator by recruiting co-repressor complexes to its DNA binding site. In order to extend the understanding of its role in preleukemia, we expressed AML1/ETO in a murine immortalized pluripotent hematopoietic stem/progenitor cell line, EML C1, and found that genes involved in functions such as cell-to-cell adhesion and cell motility were among the most significantly regulated as determined by RNA sequencing. In functional assays, AML1/ETO-expressing cells showed a decrease in adhesion to stromal cells, an increase of cell migration rate in vitro, and displayed an impairment in homing and engraftment in vivo upon transplantation into recipient mice. Our results suggest that AML1/ETO expression determines a more mobile and less adherent phenotype in preleukemic cells, therefore altering the interaction with the hematopoietic niche, potentially leading to the migration across the bone marrow barrier and to disease progression.

overall_design: RNA-sequencing of EML1 cell line after overexpression of AML1/ETO by retroviral cDNA transduction. Empty (No cDNA) vector was used as control.

first: Marco

last: Saia

first: Nicoletta

last: Rizzi

first: Massimiliano

last: Mazza

first: Elisa

last: Barbieri

first: Debora

last: Valli

first: Paolo

last: Ciana

first: Myriam

last: Alcalay


title: Histone H2A T120 phophorylation promotes oncogenic transformation via upregulation of cyclin D1 [RNA-seq]

overall_design: mRNA profiles of the five NIH/3T3 cell lines expressing wild-type as well as mutant H2A T120D were generated by deep sequencing using illumina MiSeq.

first: Hirofumi

last: Mizusaki


title: Comparative transcriptome analysis by RNAseq of Necrotic Enteritis Clostridium perfringens in ligated intestinal chicken loops and in vitro conditions.

city: Guelph

first: Valeria

middle: Regina

last: Parreira

state: ON

address: 50 Stone Rd E

department: Pathobiology

institute: University of Guelph

summary: Purpose: Analyze gene expression of necrotic enteritis C. perfringens in intestinal chicken loops comparing with in vitro conditions

overall_design: Comparison of differential gene expression using RNA seq of necrotic enteritis C. perfriegens CP1  type A of in vivo (chicken intestinal loops) and in vitro (lab cultures)

first: John

middle: F

last: Prescott


title: Cooperative Action Between SALL4A and TET Proteins in Stepwise Oxidation of 5-Methylcytosine

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

summary: TET family enzymes successively oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, leading to eventual demethylation. 5hmC and TET enzymes occupy distinct chromatin regions, suggesting unknown mechanisms controlling the fate of 5hmC within diverse chromatin environments. Here, we report that SALL4A preferentially associates with 5hmC in vitro and occupies enhancers in mouse embryonic stem cells in a largely TET1-dependent manner. While most 5hmC at SALL4A peaks undergoes further oxidation, this process is abrogated upon deletion of Sall4 gene, with a concomitant reduction of TET2 at these regions. Thus, SALL4A facilitates further oxidation of 5hmC at its binding sites, which requires its 5hmC binding activity and TET2, supporting a collaborative action between SALL4A and TET proteins in regulating stepwise oxidation of 5mC at enhancers. Our study identifies SALL4A as a 5hmC binder, which facilitates 5hmC oxidation by stabilizing TET2 association, thereby fine-tuning expression profiles of developmental genes in mouse embryonic stem cells.

overall_design: In several cell lines, including TT2, Sall4 het, Sall4 KO, Sall1/Sall4 DKO, Tet1 KD, Tet1/2/3 TKO, Sall4a, Sall1 and Tet1 is ChIPed by antibody. ChIPed fragments were sequenced by Illumina GA II or Illumina HiSeq 2000 platform. 5mC and hmC were also immunoprecipitated by its antibody as well.

first: Jun

last: Xiong

first: Jiayu

last: Chen

first: Yali

last: Xu

first: Xiaojun

last: Ding

first: Ryuichi

last: Nishinakamura

first: Guo-Liang

first: She

first: Shaorong

last: Gao

first: Bing

last: Zhu


title: Intersectionally labeled Drd2-Pet1 single-neuron RNA-seq

city: Boston

first: Benjamin

last: Okaty

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Single-neuron transcriptome profiles of Dorsal Raphe neurons marked by a history of expression of Drd2::Cre and Pet1::Flpe (GFP+), as well as Dorsal Raphe neurons marked by a history of Pet1::Flpe expression only (mCherry+).

overall_design: GFP and mCherry expressing neurons from triple transgenic Drd2::Cre;Pet1::Flpe;RC:FrePe mice were acutely dissociated, manually sorted, and single-neuron RNA-seq was performed (17 GFP+ cells, 8 mCherry+ cells).

first: Tedi

last: Asher


title: p53 activity results in DNA replication fork processivity

status: Public on Oct 06 2016

city: Göttingen

first: Ina

last: Klusmann

address: Justus-von-Liebig-Weg 11

country: Germany

institute: Institute of Molecular Oncology

summary: p53 induces cell death upon DNA damage, but this may not confer all of its tumor suppressor activity. We report that p53 activation enhances the processivity of DNA replication, as monitored by multi-label fiber assays, whereas removal of p53 reduces fork progression. This was observed in tumor-derived U2OS cells, but also in murine embryonic fibroblasts with heterozygous or homozygous p53 deletion, and in freshly isolated thymocytes from mice with differential p53 status. Mdm2, a p53-inducible gene product, similarly supported DNA replication even in p53-deficient cells, suggesting that sustained Mdm2-expression is at least one of the mechanisms allowing p53 to prevent replicative stress. Thus, p53 helps to protect the genome during S phase, by preventing the occurrence of stalled or collapsed replication forks. These results expand p53’s tumor-suppressive functions, adding to the ex-post model (elimination of damaged cells) an ex-ante activity, i.e. the prevention of DNA damage during replication.

overall_design: Expression profiling by high throughput sequencing

first: Leonie

last: Müller

first: Matthias

last: Dobbelstein


title: Histone H2A T120 phophorylation promotes oncogenic transformation via upregulation of cyclin D1y

first: TAKEYA

last: NAKAGAWA

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

overall_design: Refer to individual Series


title: Identifying Nuclear Matrix-attached DNA across the Genome

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

institute: University of Vermont


title: Identifying Nuclear Matrix–attached DNA across the Genome (ChIP-seq)

summary: Experimental approaches to define the relationship between gene expression and nuclear matrix attachment regions (MARs) have given contrasting and method-specific results. We have developed a next generation sequencing strategy to identify MARs across the human genome (MAR-Seq). The method is based on crosslinking chromatin to its nuclear matrix attachment sites to minimize changes during biochemical processing. We used this method to compare nuclear matrix organization in MCF-10A mammary epithelial-like cells and MDA-MB-231 breast cancer cells and evaluated the results in the context of global gene expression (array analysis) and positional enrichment of gene-regulatory histone modifications (ChIP-Seq). In the normal-like cells, nuclear matrix–attached DNA was enriched in expressed genes, while in the breast cancer cells, it was enriched in non-expressed genes. In both cell lines, the chromatin modifications that mark transcriptional activation or repression were appropriately associated with gene expression. Using this new MAR-Seq approach, we provide the first genome-wide characterization of nuclear matrix attachment in mammalian cells and reveal that the nuclear matrix–associated genome is highly cell-context dependent.

overall_design: ChIP-seq of 3 histone modifications in 2 cell lines with 2 replicates

first: Jason

last: Dobson

first: Gary

last: Stein


title: Identifying Nuclear Matrix–attached DNA across the Genome (MAR-seq)

overall_design: MAR-seq, nuclear matrix associated DNA and digested background for 2 cell lines with 2 replicates


title: Nascent RNA sequencing reveals distinct features in Plant transcription

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Transcriptional regulation of gene expression is a major mechanism utilized by plants to confer phenotypic plasticity, yet compared to archaebacteria, eubacteria, and other eukaryotes, very little is known about the design principles of plant transcription. We generated an extensive catalog of nascent and steady state transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5'GRO-seq and RNA-seq and reanalyzed published maize data to capture the general characteristics of plant transcription. De novo annotation of nascent transcripts enabled accurate start site annotations and revealed novel unstable transcripts.  Coding and non-coding transcripts exhibit comparable promoter chromatin configurations. Motif analysis revealed new regulatory DNA elements including a conserved 'TGT core promoter motif' and unreported transcription factor (TF) binding sites. Mapping of engaged RNA polymerases revealed a lack of enhancer RNAs, promoter proximal pausing, and divergent transcription in Arabidopsis and maize, which are commonly present in humans and yeast. In contrast, Arabidopsis and maize genes accumulate RNA polymerases adjacent to the polyadenylation site immediately downstream of genes, a trend that correlated with increasing gene length and coincided with hypomethylation of CpG residues. Lack of promoter proximal pausing and a higher correlation of nascent and steady state transcripts indicates Arabidopsis regulates transcription predominantly at the level of initiation. Together, these findings provide insight into plant transcriptional mechanisms, but also eukaryotic transcription in general.

overall_design: Transcriptional profiling by 5'GRO-seq, GRO-seq, and RNA-seq

last: Hetzel

first: Sascha

last: Duttke

first: Joanne

last: Chory


title: SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: RNA metabolism is controlled by an expanding yet incomplete catalog of RNA binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull-down of twelve nuclear and cytoplasmic RBPs followed by quantitative mass-spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1923 human, 489 fly and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.

overall_design: eCLIP-seq was performed in biological replicate for AIFM1, NUMA1, RANGAP1, RNF219, VIM, ZNF184. Each sample has a size-matched input control for analysis

first: Kristopher

middle: W

last: Brannan

first: Wenhao

last: Jin

first: Charles

last: Banks

first: Joshua

last: Gilmore

first: Laurence

last: Florens

first: Michael

middle: P

last: Washburn

first: Eric

last: Van Nostrand

first: Gabriel

last: Pratt

first: Marie

middle: K

last: Schwinn

first: Danette

last: Daniels


title: Super-enhancer reprogramming drives a B cell-epithelial transition and high-risk leukemia

city: Charlestown

first: Katia

last: Georgopoulos

address: 1st and 13th St

department: CBRC

summary: IKAROS is required for the differentiation of highly proliferative pre-B cell precursors and loss-of-IKAROS function indicates poor prognosis in precursor B-cell acute lymphoblastic leukemia (B-ALL). Here we show that IKAROS regulates this developmental stage by positive and negative regulation of super-enhancers with distinct lineage affiliation.  IKAROS together with B cell master regulators, such as PAX5, EBF1 and IRF4, defines super-enhancers at pre-B cell differentiation genes and is required for a highly permissive chromatin environment, a function that cannot be compensated for by the other transcription factors. IKAROS, is also highly enriched at inactive enhancers of genes normally expressed in stem-epithelial cells.  Upon IKAROS loss, expression of pre-B cell differentiation genes is attenuated, while a group of extra-lineage transcription factors, directly repressed by IKAROS, and dependent on EBF1 re-localization at their enhancers, are induced. LHX2, LMO2 and TEAD-YAP1 together with other native B cell transcription regulators induce a feed-forward transcriptional loop based on their direct cooperation within a de novo super-enhancer network normally kept separate by IKAROS. Induction of de novo super-enhancers antagonizes Polycomb repression and superimposes aberrant stem-epithelial cell properties in a B cell precursor. This dual mechanism of IKAROS regulation promotes differentiation while safeguarding against a hybrid stem-epithelial-B cell phenotype that underlies high-risk B-ALL.

overall_design: 35 CHiPseq samples including input controls from WT and IKDN stromal adherent preB cells


title: Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers is Suppressed by a MicroRNA

city: Aurora

first: Timothy

last: McKinsey

state: CO

department: Division of Cardiology

institute: University of Colorado Anschutz Medical Campus


title: RNA-sequencing of murine wildtype and E2F-2 knockout hematopoietic progenitors and mature erythroblasts

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: We identified a role for E2F-2 in the regulation of erythroblast nuclear condensation and enucleation.  To help define the mechanism by which E2F-2 regulates these processes, we performed RNA-sequencing on undifferentiated hematopoietic cells and sorted, orthochromatic erythroblasts obtained from wildtype and E2F-2 knockout animals. In undifferentiated progenitor cells we find a limited number of differentially expressed genes associated with E2F-2-loss, likely due to compensation by other E2F family members.  However, in late-stage erythroblasts, loss of E2F-2 results in the down-regulation of over 1200 genes. Our subsequent analyses focused on the role of a particular mitotic kinase, Citron Rho-interacting kinase, which we find is induced in an E2F-2-dependent manner during terminal erythroid maturation and identify as a novel regulator of erythroblast enucleation.

first: Kelsey

last: Swartz

first: Alex

last: Minella


title: Analysis  of active enhancers and direct androgen receptor target genes in VCaP prostate cancer cells

city: Kuopio

first: Sari

last: Toropainen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Androgen receptor (AR) is typically overexpressed in castration-resistant prostate cancer (CRPC). CRPC-derived VCaP cells display an excessive number of chromatin AR-binding sites (ARBs). This study analyzed direct transcription programs of the AR, the prevalence of AR enhancers and the transcriptional regulators involved in the regulation of at the enhancer regions. The analysis utilized global nuclear run-on sequencing (GRO-seq). The GRO-seq data were integrated with the ARB and VCaP cell-specific transcription factor-binding data. Androgen in 30 min activated and repressed transcription of a large number of genes including novel AR targets IGF-1 receptor and EGF receptor. GRO-seq analysis also revealed that only a fraction of the ARBs resides at functional enhancers. Activation of AR bound enhancers was most potent at the sites that also bound PIAS1, ERG and HDAC3. Our genome-wide data provide new insights how AR can directly control growth-signaling pathways in CPRC cells.

overall_design: ChIP-seq samples were collected from cells treated with vehicle (ethanol, EtOH) or 10 nM R1881 (synthetic androgen methyltrienolone). IgG sample was collected from EtOH- and R1881-treated cells and used as background control. Biological duplicate samples of the AR (R1881-treated) and CTCF (vehicle- and R1881-treated) ChIP-seq samples were analyzed by using Illumina HiSeq 2000 platform 1.9. Single IgG and H3K9me3 (R1881-treated) samples were analyzed with the same platform. GRO-seq was used to determine androgen-induced changes in nascent transcription in VCaP and LNCaP cells.

first: Einari

last: Niskanen

first: Marjo

last: Malinen

first: Päivi

last: Sutinen

first: Minna

middle: U

last: Kaikkonen

first: Jorma

middle: J

last: Palvimo


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type APC and OX40L-TG APC induced T helper 17 cell Transcriptomes [RNA-seq]

city: Houston

first: xiang

last: xiao

state: Texas

address: 6670 Bertner Avenue, R7-217

institute: Houston Methodist Hospital and Houston Methodist Research Institute

summary:
Purpose:The goals of this study are to evaluate the effect of OX40 ligation on  transcriptome profiling of in vitro polarized T helper 17 cell (RNA-seq).
Methods: mRNA profiles of CD4+ T cells cultured in vitro under Th17-polarizing conditions for 48hrs (both Ctrl and OX40L treated groups) were generated by deep sequencing, using Illumina RapidRun. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) and TopHat followed by CuffDiff. qRT–PCR validation was performed using SYBR Green assays
Results: Among the 398 genes that were significantly affected by OX40, only about 11% were previously identified as RORγt target genes in Th17 cells.
Conclusions: Our study suggests that OX40 unlikely affects Th17 commitment, but most likely impairs their effector differentiation. As IL-17A and IL-17F are  Th17-defining cytokines, their suppression suggests that OX40 may inhibits effector functions of Th17 cells.

overall_design: mRNA profiles of CD4+ T cells cultured in vitro under Th17 differentiation conditions for 48 hours in the presence of WT-APCs or OX40L-TG APCs were generated by deep sequencing using Illumina RapidRun.

first: Xian

last: Li

first: Xiang

last: Xiao


title: Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits [mRNA-Seq]

city: Cambridge

first: Vijay

last: Sankaran

overall_design: RNA-seq for control (shLuc) and RBM38 knockdown (shRBM38-1 and shRBM38-2) was performed for primary human erythroid cells in Day 16 of in vitro culture.

first: Jacob

last: Ulirsch


title: Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs)

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health


title: Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) (RNA-seq)

summary: Genome-scale methods have identified subchromosomal structures so-called topologically associated domains (TADs) that subdivide the genome into discrete regulatory units, establish with their target genes. By re-engineering human duplications at the SOX9 locus in mice combined with 4C-seq and Capture Hi-C experiments, we show that genomic duplications can result in the formation of novel chromatin domains (neo-TADs) and that this process determines their molecular pathology.

overall_design: RNA-seq of embryonic limb buds for WT and mutant animals carrying structural variations at the Sox9/Kcnj locus.

middle: M

first: Martin

last: Franke

first: Robert

last: Schöpflin

first: Verena

last: Heinrich

first: Guillaume

last: Andrey

first: Stefan

last: Mundlos


title: Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) [Hi-C]

overall_design: Capture Hi-C experimetns at the Sox9/Kcnj locus in developing distal limbs of mutants and WT animals at E12.5 as well as from patient fibroblasts


title: Mechanistic evaluation and transcriptional signature of a Glutathione S-transferase Omega 1 inhibitor

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Glutathione S-transferase omega 1 (GSTO1) is an atypical GST isoform that is overexpressed in several cancers and has been implicated in drug resistance. Currently, no small-molecule drug targeting GSTO1 is under clinical development. In this study we show that silencing of GSTO1 with siRNA significantly impairs cancer cell viability, validating GSTO1 as a potential new target in oncology. We report on the development and characterization of a series of chloroacetamide-containing potent GSTO1 inhibitors. Co-crystal structures of GSTO1 with our inhibitors demonstrate covalent binding to the active site cysteine. These potent GSTO1 inhibitors suppress cancer cell growth, enhance the cytotoxic effects of cisplatin, and inhibit tumor growth in colon cancer models as single agent. Bru-seq-based transcription profiling unraveled novel roles for GSTO1 in cholesterol metabolism, oxidative and endoplasmic stress responses, cytoskeleton, and cell migration. Our findings demonstrate the therapeutic utility of GSTO1 inhibitors as anticancer agents and identify novel cellular pathways under GSTO1 regulation in colorectal cancer.

overall_design: HCT116 (human colorectal carcinoma) cells were exposed to DMSO, C1-27 or C1-14 for 4 h and GSTO1 siRNA or C1-27 for 24 h, followed by labeling of nascent RNA using bromouridine.

first: Kavya

last: Ramkumar

first: Soma

last: Samanta

first: Anahita

last: Kyani

first: Suhui

last: Yang

first: Shuzo

last: Tamura

first: Libby

last: Ziemke

first: Jeanne

middle: A

last: Stuckey

first: Si

first: Krishnapriya

last: Chinnaswamy

first: Hiroyuki

last: Otake

first: Bikash

last: Debnath

first: Vladimir

last: Yarovenko

first: Judith

last: Sebolt-Leopold

first: Nouri

last: Neamati


title: Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high-fat or low-fat meal

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

summary: We report the transcriptional response of the zebrafish digestive organs to an acute high-fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis, storage, and dispersal of lipids. These key physiological responses to a high-fat meal all stem from the endoplasmic reticulum (ER), where lipids are formed and assigned to their fates.

overall_design: A feeding time course was undertaken with 6.5-dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high-fat or low-fat food. 5% egg yolk emulsion (high-fat) feeds and 10% egg white (low-fat) feeds were prepared. At the appropriate time points, digestive organs (intestine, liver, pancreas) were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.

first: Erin

last: Zeituni

first: Xiaobin

first: Steven

last: Farber


title: Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers is Suppressed by a MicroRNA [RNA-Seq]

first: Timothy

last: McKinsey

summary: BRD4 governs pathological cardiac gene expression by binding acetylated chromatin, resulting in enhanced RNA polymerase II (Pol II) phosphorylation and transcription elongation. Here, we describe a signal-dependent mechanism for regulation of BRD4 in cardiomyocytes. BRD4 expression is suppressed by microRNA-9 (miR-9), which targets the 3’ untranslated region of the Brd4 transcript. In response to stress stimuli, miR-9 is downregulated, leading to derepression of BRD4 and enrichment of BRD4 at long-range super-enhancers (SEs) associated with pathological cardiac genes. A miR-9 mimic represses stimulus-dependent targeting of BRD4 to SEs and blunts Pol II phosphorylation at proximal transcription start sites, without affecting BRD4 binding to SEs that control constitutively expressed cardiac genes. These findings suggest that dynamic enrichment of BRD4 at SEs genome-wide serves a crucial role in the control of stress-induced cardiac gene expression, and define a miR-dependent signaling mechanism for the regulation of chromatin state and Pol II phosphorylation.

overall_design: RNA-seq in neonatal rat ventricular myocytes

first: Mathew

middle: S

last: Stratton

first: S

last: Halder

first: Charles

last: Lin

first: Jay

middle: E

last: Bradner


title: Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers is Suppressed by a MicroRNA [ChIP-Seq]

overall_design: ChIP-Seq in neonatal rat ventricular myocytes

first: Matthew

middle: Y

first: Saptarsi

last: Haldar

first: James


title: Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) (4C-seq)

first: Daniel

last: Ibrahim

overall_design: Circular Chromosome Conformation Capture (4C seq) and Capture Hi-C experimetns at the Sox9/Kcnj locus in developing distal limbs of mutants and WT animals at E12.5 as well as from patient fibroblasts

first: Martin

last: Franke

first: Robert

last: Schöpflin

first: Verena

last: Heinrich

first: Guillaume

last: Andrey

first: Stefan

last: Mundlos


title: Bromodomain-containing Protein 4 (BRD4) is Required for the Maintenance of a Mammary Epithelial Phenotype [RNA-Seq]

last: Johnsen

state: Niedersachsen

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

institute: University Medical Center Göttingen

summary: Bromodomain-containing protein 4 (BRD4) is an important epigenetic reader which promotes gene transcription to modulate cell-specific functions and is under intensive investigation for its potential as an anti-tumor therapeutic target. However, the role of BRD4 in non-transformed cells remains unclear. Here we demonstrate that BRD4 is required for the expression of epithelial-specific genes and suppression of stem cell-like properties by binding to the distal regions of epithelial-related genes. Moreover, BRD4 occupancy correlates with enhancer activity and enhancer RNA (eRNA) transcription of epithelial differentiation-specific genes. Interestingly, we show that BRD4 perturbation regulates the expression of Grainy Head-like transcription factor, GRHL3, whose depletion partially mimics BRD4 inhibition and blocks differentiated phenotype. By binding to the distal regions of GRHL3, BRD4 promotes RNA polymerase-II occupancy and thus affects eRNA transcription. Altogether, these findings provide evidence that BRD4 promotes a differentiated epithelial phenotype in non-transformed mammary cells at least in part through the activation of GRHL3 expression.

overall_design: mRNA expression profiles of MCF10A cells under negative control siRNA, BRD4 siRNA or JQ1 treatment, in duplicates.

first: Sankari

last: Nagarajan

first: Upasana

last: Bedi


title: HU treatment of Sulfolobus solfataricus P2

status: Public on Oct 05 2016

city: Bloomington

first: Stephen

middle: D

last: Bell

state: IN

address: Simon Hall MSB

department: MCB

institute: Indiana University

summary: Hydroxyurea (HU) is toxic to Sulfolobus cells. To address the basis of the HU toxicity, we performed transcriptome analyses on untreated cells and cells following exposure to 5 mM HU for 4 hours.

overall_design: RNA-seq of S. solfataricus grown for 4 hours +/- 5 mM HU. Three biological replicates pooled per sample.

first: Li

last: Liew


title: RBYP stimulates PRC1 to shape chromatin-based communication between polycomb repressive complexes [ChIP-seq]

city: London

first: Hamish

last: King

address: 4 Newark St

department: Blizard Institute

institute: Queen Mary University of London

summary: Polycomb Repressive Complexes (PRC), and their chromatin-modifying activities, are essential for the correct regulation of gene expression during cellular differentiation and development. Although their role in transcriptional repression is well described, a detailed molecular understanding of their complex assembly and enzymatic activity has been lacking. We therefore set out to characterize the relationship between PRC1 complex composition and its ability to catalyse H2AK119ub1 for one of the most abundant PRC1 complexes in embryonic stem cells, PCGF1-PRC1. Biochemical reconstitution of the PCGF1-PRC1 complex revealed that RYBP/YAF2 was essential for robust enzymatic activity of the complex. Using calibrated ChIP-seq for H2AK119ub1, we identify that RYBP-dependent PRC1 activity has a widespread role in shaping H2AK119ub1 levels genome-wide in mouse embryonic stem cells. Furthermore, these H2AK119ub1 levels stimulate PRC2 activity as part of an activity-based feedback loop, which we demonstrate is required for maintenance of transcriptional repression. Together, these observations uncover complex-based principles for PRC1 assembly and activity, and further our understanding of Polycomb domain function.

overall_design: RYBPfl/fl;YAF2-/- ES cells were treated with tamoxifen (OHT) for 96 hours prior to ChIP-seq for RYBP, RING and SUZ12.

first: Nathan

middle: R

last: Rose

first: Neil

last: Blackledge

first: Rob

last: Klose


title: RBYP stimulates PRC1 to shape chromatin-based communication between polycomb repressive complexes

summary:
 	Polycomb Repressive Complexes (PRC), and their chromatin-modifying activities, are essential for the correct regulation of gene expression during cellular differentiation and development. Although their role in transcriptional repression is well described, a detailed molecular understanding of their complex assembly and enzymatic activity has been lacking. We therefore set out to characterize the relationship between PRC1 complex composition and its ability to catalyse H2AK119ub1 for one of the most abundant PRC1 complexes in embryonic stem cells, PCGF1-PRC1. Biochemical reconstitution of the PCGF1-PRC1 complex revealed that RYBP/YAF2 was essential for robust enzymatic activity of the complex. Using calibrated ChIP-seq for H2AK119ub1, we identify that RYBP-dependent PRC1 activity has a widespread role in shaping H2AK119ub1 levels genome-wide in mouse embryonic stem cells. Furthermore, these H2AK119ub1 levels stimulate PRC2 activity as part of an activity-based feedback loop, which we demonstrate is required for maintenance of transcriptional repression. Together, these observations uncover complex-based principles for PRC1 assembly and activity, and further our understanding of Polycomb domain function.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: EPRS is a Critical Regulator of Cell Proliferation and Estrogen Signaling in ER+ Breast Cancer

city: New York

first: XIANXIAO

last: ZHOU

state: NY

address: 1470 Madison AVE

department: Department of Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

summary: Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functions in cellular translation.  Recent evidence suggests that ARS genes may participate in a wide array of cellular processes, and may contribute to the pathology of autoimmune disease, cancer, and other diseases.  Several studies have suggested a role for the glutamyl prolyl tRNA synthetase (EPRS) in breast cancers, although none has demonstrated any underlying mechanism about how EPRS contributes to carcinogenesis.  In this study, we identified EPRS as upregulated in estrogen receptor positive (ER+) human breast tumors in the TCGA and METABRIC cohorts, with copy number gains in nearly 50% of samples in both datasets.  EPRS expression is associated with reduced overall survival in patients with ER+ tumors in TCGA and METABRIC datasets.  EPRS expression was also associated with reduced distant relapse-free survival in patients treated with adjuvant tamoxifen monotherapy for five years, and EPRS-correlated genes were highly enriched for genes predictive of a poor response to tamoxifen.  We demonstrated the necessity of EPRS for proliferation of tamoxifen-resistant ER+ breast cancer, but not ER- breast cancer cells.  Transcriptomic profiling showed that EPRS regulated cell cycle and estrogen response genes.  Finally, we constructed a causal gene network based on over 2500 ER+ breast tumor samples to build up an EPRS-estrogen signaling pathway.  EPRS and its regulated estrogenic gene network may offer a promising alternative approach to target ER+ breast cancers that are refractory to current anti-estrogens.

overall_design: Validation of EPRS Regulated Downstream Signature

first: Igor

last: Katsyv

first: Minghui

last: Wang

first: Won-min

last: Song

first: Xianxiao

last: Zhou

first: Yongzhong

last: Zhao

first: Sun

last: Park

first: Jun

last: Zhu

first: Bin

last: Zhang

first: Hanna

last: Irie


title: RNA-seq Based Transcriptomic Map Reveals New Insights Into Mouse Salivary Gland Development and Maturation

city: Buffalo

first: Satrajit

last: Sinha

address: 701 Ellicott Street

department: Department of Biochemistry

institute: State University of New York at Buffalo

summary: Analysis of gene expression changes during mouse salivary gland development using RNA-Seq

overall_design: RNA was collected and analyzed for at least two biological replicates each from six developmental timepoints (E14.5, E16.5, E18.5, P5, 4 weeks, 12 weeks)

first: Christian

last: Gluck

first: Akinsola

last: Oyelakin

first: Sangwon

last: Min

first: Kirsten

last: Smalley

first: Rose-Anne

last: Romano


title: RBYP stimulates PRC1 to shape chromatin-based communication between polycomb repressive complexes [calChIP-seq]

first: Hamish

last: King

overall_design: RYBPfl/fl;YAF2-/- ES cells were treated with tamoxifen (OHT) for 96 hours prior to calChIP-seq for H2AK119ub1 and H3K27me3.

first: Nathan

last: Rose

first: Neil

last: Blackledge

first: Rob

last: Klose


title: Identification of cell cycle regulated, DHT induced AR binding events

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

summary: The androgen receptor (AR) is required throughout all stages of disease progression.  Despite this, little is known about the function of AR in the mitotic cell cycle.  Here, we report novel AR binding as a result of examining the AR cistrome in actively cycling cells.

overall_design: AR binding was assessed in LNCaP prostate cancer cells arrested in various cell cycle phases and stimulated with DHT in order to identify novel, cell cycle regulated binding.

first: Karen

last: Knudsen


title: RBYP stimulates PRC1 to shape chromatin-based communication between polycomb repressive complexes [RNA-seq]

overall_design: RYBPfl/fl;YAF2-/- ES cells were treated with tamoxifen (OHT) for 96 hours prior to nuclear RNA-seq.


title: Identification of avirulence genes in the barley powdery mildew fungus (Bgh) by RNA-sequencing and transcriptome-wide association analysis on a set of Bgh isolates

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

summary: Disease resistance (R) genes encoding intracellular nucleotide-binding domain and Leucine-rich repeat proteins (NLRs) are key components of the plant innate immune system and typically detect the presence of isolate-specific avirulence (AVR) effectors from pathogens. NLRs define the fastest evolving gene family of flowering plants and are often arranged in gene clusters containing multiple paralogs, contributing to extensive copy number and allele-specific NLR variation within a host species. Barley mildew resistance gene locus A (MLA) represents one of only few R genes that have been subject to extreme functional diversification, resulting in allelic resistance specificities each recognizing a cognate but largely unidentified AVRA gene of the powdery mildew fungus, Blumeria graminis f sp hordei (Bgh). We performed RNA-sequencing of Bgh-infected barley leaves at two different time-points to obtain transcriptome data for 16 Bgh isolates, containing different AVRA genes. Subsequently, we analyzed the expression levels in the different isolates with a specific focus on previously described candidate secreted effectors (CSEPs) and additionally performed a transcriptome-wide association analysis including these 16 isolates and the previously published reference isolate DH14. These analyses identified AVRA1 and AVRA13, encoding two CSEPs that are recognized by MLA1 and MLA13 alleles, respectively. The avirulence function of both candidates could be verified by transient expression of the effector genes in barley leaves or protoplasts that was sufficient to trigger an MLA1 or MLA13 allele-specific cell death response. AVRA1 recognition by MLA1 is also retained in transgenic Arabidopsis lines.

overall_design: Detached leaves of the barley cultivar Pallas or Manchuria were infected with 16 different Bgh isolates, each containing different AVRA effectors. For each isolate, samples were collected at 18 and 48 hours post inoculation (hpi), resulting in a total of 32 RNA-seq samples that were analyzed.

first: Xunli

last: Lu

first: Takaki

last: Maekawa

first: Paul

last: Schulze-Lefert


title: Identification of DHT induced cell cycle dependent trascriptome and AR binding events

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


title: Function of deubiquitinase USP21 in mouse embryonic stem cell

city: Shanghai

first: Liu

last: Zhenping

address: 1239 Si Ping Road

institute: Tongji University


title: Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

country: South Korea

institute: Chonnam National University Medical School

summary:
Background: The expression of microRNAs (miRNAs) is primarily regulated during their transcription. However, the transcriptional regulation of miRNA genes has not been studied extensively owing to the lack of sufficient information about the promoters and transcription start sites of most miRNAs.

Results: In this study, we identified the transcription start sites of human primary miRNAs (pri-miRNAs) using DROSHA knockout cells. DROSHA knockout resulted in increased accumulation of pri-miRNAs and facilitated the precise mapping of their 5′ end nucleotides using the rapid amplification of cDNA ends (RACE) technique. By analyzing the promoter region encompassing the transcription start sites of miRNAs, we found that the unrelated miRNAs in their sequences have many common elements in their promoters for binding the same transcription factors. Moreover, by analyzing intronic miRNAs, we also obtained comprehensive evidence that miRNA-harboring introns are spliced more slowly than other introns.

Conclusions: The precisely mapped transcription start sites of pri-miRNAs, and the list of transcription factors for pri-miRNAs regulation, will be valuable resources for future studies to understand the regulatory network of miRNAs.

overall_design: The poly(A) enriched RNAs from wild type and DROSHA knockout cells were applied for RNA-seq.


title: Function of deubiquitinase USP21 in mouse embryonic stem cell [ChIP-Seq]

summary: Nanog is a master pluripotency factor of embryonic stem cells (ESCs). Stable expression of Nanog is required to maintain the stemness of ESCs, although Nanog is a short-lived protein and quickly degraded by the ubiquitin-dependent proteasome system (UPS). Here, we report that the deubiquitinase USP21 interacts with, deubiquitinates and stabilizes Nanog and therefore maintains the protein level of Nanog in mouse-ESCs (mESCs). Loss of USP21 results in Nanog destruction, mESCs differentiation and reduced the somatic cell reprogramming efficiency. USP21 is a transcriptional target of the LIF/STAT3 pathway and is downregulated upon differentiation. Moreover, differentiation cues promote ERK-mediated phosphorylation and dissociation of USP21 from Nanog, thus leading to Nanog degradation. Additionally, USP21 is recruited to gene promoters by Nanog to deubiquitinate histone H2A at K119 and thus facilitates Nanog-mediated gene expression. Together, our findings provide a regulatory mechanism by which extrinsic signals regulate mESC fate via deubiquitinating Nanog.

overall_design: Examination of the function of USP21 in mouse embryonic stem cells E14 cell line.

first: Ping

last: Wang

first: Xin

last: Xie

first: Cizhong

last: Jiang


title: Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver [oxBS-Seq and BS-Seq]

city: Guangzhou

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

institute: Sun Yat-sen University

summary: DNA methylation at the 5-postion of cytosine (5mC) is a well-established epigenetic modification which regulates gene expression and cellular plasticity in development and disease. The ten-eleven translocation (TET) gene family is able to oxidize 5mC to 5-hydroxmethylcytosine (5hmC), providing an active mechanism for DNA demethylation, and may also provide its own regulatory function. Here we applied oxidative bisulfite sequencing to generate whole-genome DNA methylation and hydroxymethylation maps at single-base resolution in paired human liver and lung normal and cancer. We found that 5hmC is significantly enriched in CpG island (CGI) shores while depleted in CGS themselves, in particular at active genes, resulting in a 5hmC but not 5mC bimodal distribution around CGI corresponding to H3K4me1 marks. Hydroxymethylation on promoters, gene bodies, and transcription termination regions showed strong positive correlation with gene expression within and across tissues, suggesting that 5hmC is a mark of active genes and could play a role gene expression mediated by DNA demethylation. Comparative analysis of methylomes and hydroxymethylomes at differentially methylated regions (DMRs) revealed that 5hmC is significantly enriched in both tissue specific DMRs (t-DMRs) and cancer specific DMRs (c-DMRs), and 5hmC is negatively correlated with methylation changes, particularly  in non-CGI associated DMRs. Analysis of differentially methylated regions (DMRs) in normal and tumor tissues revealed that gain or loss of 5hmC negatively correlated with changes in 5mC, especially on non-CGI associated DMRs, suggesting a profound role for hydroxymethylation in regulation of dynamic DNA demethylation. Together these findings indicate that changes in 5mC as well as in 5hmC and coupled to H3K4me1 correspond to differential gene expression in tissues and matching tumors, revealing an intricate gene expression regulation through interplay of methylome, hydroxymethylome, and histone modifications.

overall_design: To explore 5-hydroxymethylation landscape between human normal and tumor tissues

first: Yun

last: Liu

first: Andrew

last: Feinberg


title: Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver


title: Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver [RNA-Seq]

overall_design: RNA-Seq analysis of human normal and tumor tissues


title: A single-cell transcriptome atlas of the human pancreas [CEL-seq2]

status: Public on Oct 04 2016

city: Utrecht

first: Mauro

last: Muraro

state: Utrecht

address: Uppsalalaan, 8

institute: Single Cell Discoveries

summary: To understand organ function it is important to have an inventory of the cell types present in the tissue and of the corresponding markers that identify them. This is a particularly challenging task for human tissues like the pancreas, since reliable markers are limited.  Transcriptome-wide studies are typically done on pooled islets of Langerhans, which obscures contributions from rare cell types and/or potential subpopulations. To overcome this challenge, we developed an automated single-cell sequencing platform to sequence the transcriptome of thousands of single pancreatic cells from deceased organ donors, allowing in silico purification of all main pancreatic cell types. We identify cell type-specific transcription factors, a subpopulation of REG3A-positive acinar cells, and cell surface markers that allow sorting of live alpha and beta cells with high purity. This resource will be useful for developing a deeper understanding of pancreatic biology and pathophysiology of diabetes mellitus.

overall_design: Islets of Langerhans were extracted from human cadaveric pancreata and kept in culture until single-cell dispersion and FACS sorting. Single-cell transcriptomics was performed on live cells from this mixture using an automated version of CEL-seq2 on live, FACS sorted cells. The StemID algorithm was used to identify clusters of cells corresponding to the major pancreatic cell types and to mine for novel cell type-specific genes as well as subpopulations within the known pancreatic cell types.

first: Gitanjali

last: Dharmadhikari

first: Eelco

last: de Koning

first: Alexander

last: van Oudenaarden


title: ATAC-Se1 to investigate the spatial choreography of the accessible genome

city: Palo Alto

first: Xingqi

last: Chen

state: CA

address: 269 Campus Drive

institute: Stanford University

summary: In order to completely understand the spatial choreography of the accessible genome in the 3D intact nucleus, we had developed a new technique termed assay of transposase accessible chromatin by visualization (ATAC-see). In brief, we had labeled the adaptor in hypersensitive Tn5 transposase with fluorophore dye and performed the Tn5 tagmentation on the fixed culture cells slide. We had performed ATAC-see in different types of cells and found out there are cell types specific spatial choreography of the accessible genome in the 3D intact nucleus, which is tightly linked to cell types specific function. Importantly, we could images the open chromatin distribution and do the sequencing on the exactly same sample, which offer a powerful tool to understand how the open chromatin organize in the 3D nucleus and how the open chromatin regulate gene expression.

overall_design: We had compared the ATAC-seq libraries under different conditions such as with different Tn5s (Illumina Nextera Tn5, home-made Tn5 with and without Atto labeled on the adaptors in GM12878 cells), with and without fixation (in HT1080 cells ) and the cells growing on different materials (growing HT1080 cells on slide and suspensions cells in the tubes). In addition, we had performed ATAC-seq in human neutrophil.

first: Ying

last: Shen

first: Howard

last: Chang


title: Reg4+ Deep Crypt Secretory cells function as epithelial niche for Lgr5+ stem cells in colon

first: Kay

last: Wiebrands

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Lgr5+ stem cells reside at crypt bottoms of the small and large intestine. Small intestinal Paneth cells supply Wnt3, EGF and Notch signals to neighboring Lgr5+ stem cells. While the colon lacks Paneth cells, Deep Crypt Secretory (DCS) cells are intermingled with Lgr5+ stem cells at crypt bottoms. Here, we report Reg4 as a marker of DCS cells. To investigate a niche function, we eliminated DCS cells using the diphtheria-toxin receptor gene knocked into the murine Reg4 locus. Ablation of DCS cells results in loss of stem cells from colonic crypts and disrupts gut homeostasis and colon mini-gut formation. In agreement, sorted Reg4+ DCS cells promote organoid formation of single Lgr5+ colon stem cells. Stem cells are forced to generate DCS cells in vitro by combined Notch inhibition and Wnt activation. We conclude that Reg4+ DCS cells serve as Paneth cell equivalents in the colon crypt niche.

overall_design: To define a global gene expression signature of DCS cells, we performed RNA-sequencing (RNA-seq) of sorted Reg4-dsRed+ and Lgr5-GFP+ cells from colonic epithelium. Sorting and RNA-seq library preparation was performed twice, to obtain a biological replicate.

first: Nobuo

last: Sasaki

first: Norman

last: Sachs

first: Anna

last: Lyubimova

first: Harry

last: Begthel

first: Maaike

last: van den Born

first: Johan

middle: H

last: van Es

first: Wouter

last: Karthaus

first: Vivian

first: Hans

last: Clevers


title: Bromodomain-containing Protein 4 (BRD4) is Required for the Maintenance of a Mammary Epithelial Phenotype [ChIP-Seq]

city: Göttingen

first: Steven

last: Johnsen

overall_design: ChIP-sequencing of BRD4 and H3K27ac in MCF10A cells.

first: Sankari

last: Nagarajan

first: Upasana

last: Bedi


title: Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification.

city: Corvallis

first: Brett

middle: Lewis

last: Mellbye

state: OR

address: Cordley Hall 2082

department: Botany and Plant Pathology

institute: Oregon State University

summary: Quorum sensing (QS) is a widespread process in bacteria used to coordinate gene expression with cell density, diffusion dynamics, and spatial distribution through the production of diffusible chemical signals. To date, most studies on QS have focused on model bacteria that are amenable to genetic manipulation and capable of high growth rates, but many environmentally important bacteria have been overlooked. For example, representatives of proteobacteria that participate in nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, produce QS signals called acyl-homoserine lactones (AHLs). Nitrification emits nitrogen oxide gases (NO, NO2, and N2O), which are potentially hazardous compounds that contribute to global warming. Despite considerable interest in nitrification, the purpose of QS in the physiology/ecology of nitrifying bacteria is poorly understood. Through a quorum quenching approach, we investigated the role of QS in a well-studied AHL-producing nitrite oxidizer, Nitrobacter winogradskyi.We added a recombinant AiiA lactonase to N. winogradskyi cultures to degrade AHLs to prevent their accumulation and to induce a QS-negative phenotype and then used mRNA sequencing (mRNA-Seq) to identify putative QS-controlled genes. Our transcriptome analysis showed that expression of nirK and nirK cluster genes (ncgABC) increased up to 19.9-fold under QS-proficient conditions (minus active lactonase). These data led to us to query if QS influenced nitrogen oxide gas fluxes in N. winogradskyi. Production and consumption of NOx increased and production of N2O decreased under QS-proficient conditions. Quorum quenching transcriptome approaches have broad potential to identify QS-controlled genes and phenotypes in organisms that are not genetically tractable.

overall_design:
Examination of quorum-sensing-proficient (Treatment) and quorum-sensing-deficient (Reference/control) cells through mRNA-seq. N=4.
The quorum-sensing-deficient reference treatment (A) was accomplished by addition of purified, recombinant AiiA lactonase. The quorum-sensing-proficient treatment (HK) was accomplished by addition of heat-denatured AiiA lactonase.

middle: L

first: Andrew

last: Giguere

first: Peter

last: Bottomley

first: Luis

last: Sayavedra-Soto


title: Bromodomain-containing Protein 4 (BRD4) is Required for the Maintenance of a Mammary Epithelial Phenotype


title: BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire [mRNA-Seq]

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

institute: University of Stuttgart

summary: We examined context specific function of BRD4 in promoting lineage specific gene expression and show that BRD4 is essential for osteoblast differentiation.

overall_design: We performed  mRNA sequencing from hFOB cells (undifferentiated and differentiated for 5 days into osteoblastic lineage) following BRD4 inhibition by JQ1 or siRNA mediated depletion.  The mRNA-Seq includes namely 7 conditions: undifferentiated hFOBs treated with DMSO or non-targeting control siRNA (siCNTR), differentiated hFOBs with DMSO or siCNTR treatments; differentiated hFOBs treated with JQ1 or two siRNAs against BRD4 (#3 & #4). The libraries were performed in triplicates.

first: Zeynab

last: Najafova


title: BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire

overall_design: Refer to individual Series


title: mRNA expression profile of Lymphocytes

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: Vα24 invariant natural killer T (iNKT) cells are a subset of T lymphocytes implicated in the regulation of broad immune responses. They recognize lipid antigens presented by CD1d on antigen-presenting cells and induce both innate and adaptive immune responses, which enhance effective immunity against cancer, represent promising therapeutic target. However, reduced iNKT-cell numbers and function have been observed in many patients with cancer. To overcome this obstacle, we reprogramed human iNKT cells to pluripotency and then redifferentiated into regenerated iNKT cells in vitro through IL-7/IL-15-based optimized cytokine combination. They showed proliferation and IFN-γ production in response to α-galactosylceramide, induced dendritic cell maturation and downstream activation of cancer antigen-specific cytotoxic T lymphocytes in vitro, and exhibited NKG2D- and DNAM-1-mediated natural killer celllike cytotoxicity against cancer cell lines. Their immunological features and availability in an unlimited supply from induced pluripotent stem cells offer the potential to develop effective immunotherapies against cancer.

overall_design: Expression profile of the lymphocytes (n = 17) by highthrouput sequencing

first: Shuichi

last: Kitayama

first: Yasutaka

last: Mizoro

first: Shin

last: Kaneko


title: ILC progenitor CEL-seq

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Here we identify the c-kit+ CILP population which generates all ILC subsets including NK cells, and the CD25- ILC2-restricted Sca-1+ CILP. We mapped the transcriptional changes that occur in ILC progenitor commitment identifying new regulatory factors and provide a map for early ILC differentiation. Finally, we mapped the subsequent transcriptional changes that occur in c-kit+ CILP in absence of Id2 and Tcf7, key regulators downstream of Nfil3.

overall_design: 100 cells of each population were purified from wild-type, Id2-/- or TCF7-/- mice. 64 samples were analysed in 2 different experiment. We purified Common innate lymphoid progenitor (CLP), a4b7-expressing CLP, common innate lymphoid progenitor (CILP), Sca1+ CILP, and Group 2 innate lymphoid cell progenitor (ILC2p).

first: Cyril

last: Seillet

first: Lisa

last: Mielke

first: Daniela

last: Zalcenstein

first: Jerry

last: Gao

first: Wei

last: Shi

first: Matthew

last: Ritchie

first: Shalin

last: Naik

first: Nicholas

last: Huntington

first: Sebastian

last: Carotta

first: Gabrielle

middle: T

last: Belz


title: Single Cell RNA-seq Study of Midbrain and Dopaminergic Neuron Development in Mouse, Human, and Stem Cells

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: In order to get a better molecular understanding of human midbrain development, this study defines cell types of the ventral midbrain in both human and mouse as well as stem cell-derived dopaminergic neuron preparations, and reveals the temporal dynamics of key lineages across development and the adult.

overall_design: Single cells according to Samples list consisting of: Human embryo ventral midbrain cells between 6 and 11 weeks of gestation, mouse ventral midbrain cells at six developmental stages between E11.5 to E18.5, Th+ neurons at P19-P27, and putative dopaminergic neurons at P28-P56 FACS-sorted from Slc6a3-Cre/tdTomato mice. Stem cells (iPSCs and ESCs) preparation at different stages of differentiation towards Th+ neurons.

first: Gioele

last: LaManno

first: Daniel

last: Gyllborg

first: Ernest

last: Arenas


title: BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire [ChIP-Seq]

first: Cristiana

last: Lungu

overall_design:
We performed ChIP-sequencing from hFOB cells (undifferentiated and differentiated for 5 days into osteoblastic lineage) .  We generated BRD4 and RNA POLII ChIP-Seq data from undifferentiated and differentiated cells; H3K27ac, H3K27me3 and H2Bub1 ChIP-Seq data from undifferentiated and differentiated cells with DMSO or JQ1 treatment.  Consistently, Input DNA from all the three conditions was included as well. C/EBPb, TEAD1, FOSL2, JUND and STAT3 ChIP-Seq was performed in differentiated hFOBs .
We performed ChIP-sequencing from L3.6 cells.  We generated BRD4 ChIP-Seq data.

first: Steven

last: Johnsen

first: Zeynab

last: Najafova


title: CPEB4 RNA immunoprecipitation and sequencing (RIP-seq) in SK-Mel-103 melanoma cells

city: Madrid

first: Eva

last: Pérez-Guijarro

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Centre

summary: Identification of the mRNAs bound by CPEB4 in melanoma cells

overall_design: RIP-seq analysis of the mRNAs bound by CPEB4 in SK-Mel-103 melanoma cells left non-infected (NI) vs transduced with CPEB4 shRNA and harvested at day 6 after lentiviral infection. Experiments were performed in biological in duplicates

first: E

first: O

last: Graña

first: M

last: Soengas


title: Function of deubiquitinase USP21 in mouse embryonic stem cell [RNA-Seq]

first: Liu

last: Zhenping

summary: Ubiquitination-mediated protein degradation of key transcriptional factors is important to the self-renewal of embryonic stem (ES) cells.  However, little is known about the deubiquitination in ES self-renewal and differentiation. Here, we report that deubiquitinase USP21 is an important positive regulator to keep ES cells under undifferentiation stasus by deubiquitination and stabilization of Nanog, a key transcriptional factor of ES cells. Loss of USP21 led to ES cells differentiation and defect in reprogramming.

overall_design: Gene expression profiles of mouse embryonic stem cell after USP21 knockdown were generated by deep sequencing, using Illumina HighSeq2000, respectively.

first: Ping

last: Wang

first: Xin

last: Xie

first: Cizhong

last: Jiang

first: Jiali

last: Jin

first: Zhenping

last: Liu


title: Increased response to nicotine in human dopaminergic neurons derived from iPSC carrying the risk-associated SNP rs16969968

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Many addictive drugs such as nicotine mediate reward and reinforcing mechanisms within the mesolimbic pathway involving midbrain dopaminergic (mDA) neurons via nicotinic acetylcholine receptors (nAChRs). Previously, genome-wide association analyses (GWAs) identified several nucleotide polymorphism (SNP) associated with increased risk of addictive phenotypes including the nonsynonymous rs16969968 SNP encoding D398->N398 variation in the CHRNA5 gene (Bierut et al., 2008; Saccone et al., 2007) . However, the etiology and the pathophysiology associated with the N398 allele is unknown. Previous animal studies using a knock-in of human CHRNA5 N398 revealed increased nicotine consumption.  However, given the evolutionary distance between mice and humans, identifying intrinsic factors that affect addiction may correlate poorly, limiting the conclusiveness of these studies.  In this study, induced pluripotent stem cell (iPSC) lines were derived from cryopreserved lymphocytes drawn from patients with homozygous minor alleles (N398) of rs16969968 and demonstrated nicotine addiction as well as age- and gender-matched unaffected controls carrying the major allele (D398).  Cultures of primarily mDA neurons were prepared from these iPSC lines. Gene expression analysis using RT-PCR and RNAseq revealed similar expression of mRNAs encoding subunits of nAChR in mDA neurons derived from both D398 and N398 iPSC lines, however, gene ontology (GO) analysis revealed an increased enrichment of genes associated with neuroactive ligand-receptor interactions and Ca2+ signaling pathways in N398 neurons.  Moreover, the N398 neuronal population responded more actively to application of nicotine in both electrophysiological analysis and Ca2+-imaging analysis.  Together, these results suggest that the N398 variation affects Ca2+-signaling in neurons, which may explain the predisposition of subjects carrying this mutation for addictive behavior in subjects carrying the nonsynonymous rs16969968 SNP (Sherva et al., 2008).

overall_design: Three samples of midbrain dopaminergic (mDA) cultures derived from iPSC were prepared from a human iPSC line carrying homozygous major allele for rs16969968 (D398) and three samples from iPSC line carrying the homozygous minor allele (N398) were compared.  As a control for differentiation, four samples of CD4+ T-cell-derived iPSC, reprogrammed using Sendai viral vectors, were prepared from two different cell lines at multiple passages.

first: Zhiping

last: Pang

first: Eileen

last: Oni

first: Mavis

last: Swerdel

first: Alana

last: Toro-Ramos


title: Genome-wide mapping of nucleosome positions in Saccharomyces cerevisiae in response to different nitrogen conditions

status: Public on Oct 03 2016

city: Wuxi

first: Peng

last: Zhang

address: 1800 Lihu road

institute: Jiangnan University

summary: Comparison of 3 different nucleosome ponsitions in response to 3 nitrogen conditions

first: Jingwen

last: Zhou


title: High motivation for exercise is associated with altered chromatin regulators of monoamine receptor gene expression in the striatum of selectively bred mice

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Though exercise is critical for health and wellbeing, many lack the motivation to exercise, and it is unclear how motivation might be increased. To uncover the molecular underpinnings of increased motivation for exercise, we analyzed the transcriptome of the striatum in four mouse lines selectively bred for high voluntary wheel running and four non-selected control lines. The striatum was dissected and RNA was extracted and sequenced from four individuals of each strain. We found multiple genes and gene systems with strong relationships to both selection and running history over the previous 6 days. Among these genes were Htr1b, a serotonin receptor subunit, and Slc38a2, a marker for both glutamatergic and GABAergic signaling. Systems analysis of the raw results found enrichment of transcriptional regulation and kinase genes. Further, we identified a splice variant affecting the Wnt related Golgi signaling gene Tmed5. Using coexpression network analysis, we found a cluster of interrelated coexpression modules with relationships to running behavior. From these modules, we built a network correlated with running that predicts a mechanistic relationship between transcriptional regulation by nucleosome structure, a system implicated in our previous work, and Htr1b expression, implicated in the present work. Using the Library of Integrated Cellular Signals, we found that the tyrosine kinase inhibitor Linifanib and the delta-opioid receptor antagonist 7-benzylidenenaltrexone (BNTX) produced similar patterns of gene expression in multiple cell lines as we observed in the striatum of the high-runner lines. Hence, these two drugs are predicted to increase motivation for exercise. Taken together, our findings support a neurobiological framework of exercise motivation where chromatin state leads to differences in dopamine signaling through modulation of both the primary neurotransmitters glutamate and GABA, and by neuromodulators such as serotonin.

overall_design: Total RNA samples from a total of 31 biological replicates (striatum samples from individual mice) were sequenced: 15 biological replicates from the four replicate randomly-bred control lines (control) and 16 samples from the replicate lines selected for high voluntary wheel running (selected). Each line included 4 biological replicates except Line 1 (L1), which only had 3 biological replicates.

middle: C

first: Petra

last: Majdak

first: Samuel

last: Perez

first: Matthew

last: Reilly

first: Theodore

last: Garland Jr

first: Justin

last: Rhodes


title: Small RNA sequencing of human milk cells reveals numerous known and novel miRNAs, with no effects of milk removal

city: Crawley

first: Mohammed

last: Alsaweed

state: WA

address: 35 stirling hwy

department: Biochemistry

institute: UWA

summary: Very little is known about miRNAs found in breastmilk cells, which also reflect the cells of the lactating mammary epithelium. Our hypothesis is that breastmilk cells are richer in miRNA compared to other milk fractions, such as skim milk. Further, the effects of milk removal by the infant on milk cell miRNA content and/or composition have not been investigated. Breastmilk cells conserved higher miRNA content than previously published lipid and skim fractions of breastmilk as well as other known sources of miRNA in humans. Specifically, 1,467 known mature miRNAs were identified and a further 1996 novel miRNAs, of which 89 were highly expressed. As previously shown, post-feed milk contained more cells than pre-feed milk, and the same was observed for miRNA content. However, no statistically significant difference was found in the expression of the total known and novel miRNAs between pre- and post-feed milk (p=0.76), although 27 known miRNAs and 1 novel miRNA were higher expressed in post-feed milk. As expected, samples richer in viable cells contained more known miRNAs (p = 0.01). Functional analysis of the top 10 most highly expressed known miRNAs showed that they may be potentially involved in crucial roles for the infant, including body fluid balance, thirst, appetite, immune responses, and development. In conclusion, breastmilk is highly rich in miRNA which may play important functions in the breastfed infant and the lactating breast. Milk removal by the infant can influence the total miRNA content of breastmilk, similar to its cell and fat content, but the miRNA composition remains constant

overall_design: Freshly expressed breastmilk samples were collected from 10 mothers on month 2 of lactation. Total RNA and miRNA content were quantified in pre- and post-feed samples from each mother. Next generation sequencing using illumina HiSeq 2000 was performed on 20 samples (one sample pre-feed and one sample post-feed from each mother) to profile mature miRNAs in the breastmilk cellular fraction. Filtered (clean) reads were aligned to the latest version of miRBase 21.0. Also, mireap software was used to predict novel miRNAs. Linear mixed effect models and ANOVA were used to compare miRNA expression levels between samples.

first: Foteini

last: Kakulas

first: Donna

last: Geddes

first: Peter

last: Hartmann

first: John

last: Newnham

first: Chin-Tat

last: Lai

last: Savigni


title: ATACseq to determine chromatin accessibility in activated or Tfr-suppressed B cells

status: Public on Oct 02 2016

city: Boston

first: Arlene

last: Sharpe

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Tfh and B cells were cultured together with or without Tfr cells.  After 4 days Tfh and B cells were sorted and prepared for ATAC-seq

overall_design: Examination of chromatin accessibility in activated or suppressed B cells

last: Sage


title: Crosstalk between androgen and proinflammatory signaling activates a distinct transcription program in prostate cancer cells

city: Kuopio

first: Einari

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

institute: University of Eastern Finland

summary: Crosstalk of androgen signaling induced with dihydrotestosterone (DHT) and proinflammatory signaling induced with tumor necrosis-factor alpha (TNFa) was analyzed in prostate cancer cells (LNCaP) by following chromatin binding of androgen receptor (AR), p65 (activating subunit of nuclear-factor kappa-B [NFkB]), FOXA1 and PIAS1+2 chromatin binding using ChIP-seq and transcriptional changes using GRO-seq.

overall_design: LNCaP cells that were cultured in charchoal stripped medium were induced with DHT (100mM, 2h), TNFa (1000 U/ml, 2h) or both (DHT+TNFa), while DMSO treatment was used as a control. Chromatin binding of AR, p65, FOXA1, and PIAS (isoforms 1 and 2) were analyzed using ChIP-seq and changes in transcription was analyzed using global run-on sequencing (GRO-seq). All samples were done as biological replicates. Role of FOXA1 in chromatin binding of p65 was analyzed in FOXA1 siRNA silenced and control siRNA transfected cells using ChIP-seq.

first: Marjo

last: Malinen

first: Minna

middle: U

last: Kaikkonen

first: Jorma

last: Palvimo