title: YAP drives growth by controlling transcriptional pause release from dynamic enhancers (HuCCT1)

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary:
The Hippo/YAP signaling pathway is a crucial regulator of tissue growth and stem cell activity.YAP, a transcriptional co-activator and main effector of the pathway,   is   also   a   powerful   driver   of   tumorigenesis
However, the genetic program regulated by YAP and the mechanism by which YAP controls transcription remains to be fully elucidated. Here, we utilize global chromatin occupancy analyses to demonstrate that robust YAP binding is restricted to a relatively small number of distal regulatory elements in the genome.
YAP-occupancy defines a subset of enhancers and super-enhancers with the highest transcriptional outputs. We  find  that  YAP  modulates  transcription  from  these elements  predominantly  by regulating  promoter-proximal  Polymerase  II  (PolII) pause  release.
Mechanistically, YAP physically interacts and recruits the Mediator complex to enhancers, which then allows for recruitment of the CDK9 elongating kinase. Genetic and chemical perturbation experiments demonstrate the requirement for Mediator and CDK9 in YAP-driven phenotypes of overgrowth and tumorigenesis. Our results here uncover the molecular mechanisms employed by YAP to exert its growth and oncogenic functions, and suggest new strategies for intervention.

overall_design: A total of eight ChIP-Seq samples are available. Four directed respectively against YAP, TEAD1, TEAD4 and TAZ (WWTr1), an unrelated IgG and the INPUT material for background noise definition, a second sample directed against YAP after enrichment by HA IP (HAYAP5SA) and one sample directed against GPF after enrichment by HA IP for backgroundo noise definition of the IP procedure.

first: Giorgio

middle: G

last: Galli

first: Matteo

last: Carrara

first: Basanta

last: Gurung

first: Christian

last: Valdes-Quezada

first: Brian

last: Pepe-Mooney

first: Geert

last: Geeven

first: Wei-Chien

last: Yuan

first: Wouter

last: de Laat

first: Fernando

middle: D

last: Camargo


title: Genetic basis of transcriptome diversity in Drosophila melanogaster

status: Public on Oct 01 2015

city: East Lansing

first: Wen

last: Huang

state: MI

address: 474 S Shaw Ln, Anthony Hall 1205F

department: Animal Science

country: USA

institute: Michigan State University

type: Expression profiling by high throughput sequencing

summary: This project uses pooled poly A (+) RNA from the DGRP to derive transcript models specific to DGRP. The derived transcript models provide the basis for quantifying gene expression in the DGRP lines using genome tiling arrays.

overall_design: Pooled whole body poly A (+) RNA for females and males of the DGRP lines were barcoded, multiplexed, and sequenced on a single HiSeq 2000 lane using 100PE sequencing

first: Mary

middle: A

last: Carbone

first: Trudy

last: Mackay


title: Ribosome profiling analysis of GADD34 null cells

city: Durham

first: David

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

summary: Accumulation of misfolded proteins in the endoplasmic reticulum (ER) triggers the unfolded protein response (UPR), which results in the increased phosphorylation of the eukaryotic initiation factor, eIF2a, and widespread translational repression. Protein synthesis is subsequently restored following the stress-induced transcriptional upregulation of GADD34 (growth arrest and DNA damage transcript 34) protein, a regulator of an eIF2a phosphatase. Genome-wide ribosome foot-printing in WT and GADD34-/- MEFs established that GADD34 mRNA is translated in unstressed cells and identified numerous mRNAs, whose translation was dependent on GADD34 even in the absence of ER stress. Following UPR activation, temporal analyses showed that the translational profile in GADD34-/- MEFs was stalled, displaying a pattern that mirrors the early response to UPR in WT MEFs. Basal GADD34 expression is also required for de-repression of translation and displacement of ER-bound polysomes that occur in early UPR. Thus, the overall UPR response is delayed in the GADD34-/- MEFs, gradually recovering as CReP expression increased. These studies reveal a critical role for basal GADD34 in the propagation of UPR signals in MEFs and mice and suggest that delayed UPR signaling protects GADD34-/- mice from tunicamycin-induced renal toxicity.

overall_design: Translational and transcriptional analysis mouse embryonic fibroblasts lacking GADD34 during ER stress

middle: W

first: Angeline

middle: L

last: Tay

first: Christopher

middle: V

last: Nicchitta

first: Shirish

last: Shenolikar


title: YAP drives growth by controlling transcriptional pause release from dynamic enhancers (HuCCT1_siRNA)

first: Raffaele

last: Calogero

country: Italy

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: A total of eighteen ChIP-Seq samples are available. 8 conditions are available both in HuCCT1 cells treated with siRNA against YAP/TAZ and the siRNA control system for a total of sixteen samples: two samples directed against H3K27Ac histone mark, two samples against H3K4Me1 histone mark, two samples against Mediator 1, two samples against SMC1, two samples against Polymerase II, two samples against Phosphoserine 2 of Polymerase II tail and two samples against Phosphoserine 5  of Polymerase II tail. An exception is made for H3K4Me3 (available in this dataset for completeness regarding histone marks) and the control IgG.


title: YAP drives growth by controlling transcriptional pause release from dynamic enhancers (MSTO)

overall_design: A total of four ChIP-Seq samples are available. One directed against YAP, one directed against TEAD1, one directed against the histone mark H3K27ac and an unrelated IgG for background noise definition

first: Giorgio

last: Galli


title: Plasmodium falciparum whole-genome real-time transcription and decay

city: University Park

first: Heather

middle: J

last: Painter

state: Pennsylvania

address: Millennium Science Center

department: Molecular Biology & Biochemistry

institute: Penn State University

type:
Expression profiling by array
Other

summary: To date, total mRNA analysis throughout intraerythrocytic development of the malaria parasite, Plasmodium falciparum, has only revealed abundance profiles of each gene at a given time. Here, we reveal that biosynthetic pyrimidine labeling allows for the calculation of real-time, whole-genome analysis of transcription and stability throughout asexual development.  In turn, we are now able to determine transcriptional and decay rates at any given time during development of specific genes or subsets of genes which will drive new investigations on both transcriptional and post-transcriptional regulatory dynaimc and networks.

overall_design: A single timecourse experiment in which 48 individual cultures were highly synchronized and, at a given hour post invasion (0-47), were treated with 40um 4-TU for 10min followed immediately by Trizol total RNA extraction.  Total RNA from each timepoint was then biotinylated via a thiol-group on any transcript that incorporated a modified UTP.  Streptavidin modified transcripts were then separated from total RNA by Streptavidin magentic beads resulting in a Labeled sample.   Any mRNA that was not bound to the beads resulted in an Unlabeled sample.  A fraction of the total RNA was untreated and resulted in a Total sample.  Each hour, three samples were analyzed by microarray, Total, Unlabeled, and Labeled, resulting in 144 individual microarrays (48 for each sample type).

first: Neo

middle: C

last: Chung

first: John

last: Storey

first: Manuel

last: Llinás


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, 4L;C* and Isofagamine treated 4L;C* region specifics mouse  brain Transcriptomes (RNA-Seq)

city: Cincinnati

first: Nupur

last: dasgupta

state: OH

address: 3333, Burnet Avenue

department: human Genetics

institute: CCHMC

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived brain transcriptome profiling (RNA-seq) in neuropathic region specific Gaucher mouse brain compared with WT and Isofagamine treated mice of the same age and background and secondly to identify the DEmiRNA associated with the DEmRNA before and after treatment This will give us some insights to see if miRNA is also involved in the the regulation of the expression of the genes involved in the disease process before and after treatment.
Methods: 42-45 days old 4L;C*,  wild-type (WT)  and Isofagamine treated  4L;C* mouse brain  were generated by deep sequencing, in triplicate, using IlluminaHiseq. The sequence reads that passed quality filters were analyzed at the gene level with two methods: Burrows–Wheeler Aligner (BWA) followed and TopHat followed by DESeq. qRT–PCR validation was performed using TaqMan and SYBR Green assays

overall_design: Regional brain  mRNA profiles of ~42 -days old wild type (WT) and 4L;C* an d Isofagamine treated  mice were generated by deep sequencing, in triplicate, using IlluminaHi Seq.

last: Dasgupta

first: Youhai

last: Xu

first: Ronghua

last: Li

first: Yanyan

last: Peng

first: Manoj

last: Pandey

first: Stuart

last: Tinch

first: Benjamin

last: Liou

first: Venette

last: Inskeep

first: Wujuan

last: Zhang

first: Mehdi

last: Keddache

first: Gregory

last: Grabowski

first: Ying

last: Sun


title: sRNA profiling between the 7B-1 male-sterile tomato and its wild type in response to abiotic stress

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

type: Non-coding RNA profiling by high throughput sequencing

summary: The RNA-seq was used to identify differentially expressed miRNAs between a male sterile and wild type tomato seedlings in response to abiotic stress

overall_design: Two small RNA libraries were constructed from male-sterile and wild type tomato flower buds using the TruSeq Small RNA Sample Preparation Kit from Illumina, and were sequenced on the Illumina Hiseq2000

first: Vahid

last: Omidvar

first: Tamas

last: Dalmay

first: Martin

last: Fellner


title: Phloroglucinol functions as an intercellular chemical messenger with broad transcriptional effects in Pseudomonas protegens

city: Corvallis

first: Jeff

last: Chang

state: OR

address: 3098 Cordley Hall

department: Botany and Plant Pathology

institute: Oregon State University

summary: We demonstrate that phloroglucinol (PG), an intermediate in DAPG biosynthesis, can serve as an intercellular signal influencing the expression of pyoluteorin biosynthesis genes, the production of pyoluteorin, and inhibition of Pythium ultimum, a phytopathogenic oomycete sensitive to pyoluteorin.  In addition, we  show that phloroglucinol has broad effects on the transcriptome of Pf-5 with nanomolar versus micromolar concentrations of phloroglucinol having differential effects on the transcriptome.

overall_design: RNA sequencing of Pseudomonas protegens Pf-5 wild-type, phlAG mutant, and phlADG mutant in the presence/absence of phloroglucinol.

first: Jennifer

last: Clifford

first: Alex

last: Buchanan

first: Oliver

last: Vining

first: Teresa

last: Kidarsa

middle: H

first: Kerry

last: McPhail

first: Joyce

middle: E

last: Loper


title: Neuropathic Gaucher mouse brain

first: Nupur

last: dasgupta

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: hnRNPK is involved in mRNA processing of a significant fraction of the transcriptome

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Here, we report the first genomic-scale comprehensive characterization of mouse transcripts bound to hnRNPK. hnRNPK binding at the isoform level was evaluated via RNA-sequencing of liver samples obtained from obese and wild-type mouse models. The comparison of hnRNPK co-immunoprecipitated fractions with total RNA fractions in a given mouse model enabled quantitative evaluation of the binding affinity of hnRNPK for thousands of isoforms.

overall_design: Total RNA, cytoplasmic fraction and nuclear fraction was isolated from liver of three mouse strains (wild type-normal diet, wild type-high fat diet, leptin defficient-normal diet). Cytoplasmic and nuclear fractions were subjected to immunoprecipitation with anti-hnRNPK antibody (and IgG as control). Comparison of immunoprecipitated and total fraction allowed for estimation of extent of hnRNPK-mediated translational regulation.

first: Michal

last: Mikula

first: Agnieszka

last: Paziewska

first: Maria

last: Kulecka

first: Michalina

last: Dabrowska

first: Jerzy

last: Ostrowski


title: Transcriptome analysis of mouse embryonic fibroblasts of NIPBL-haploinsufficient mice

city: Kansas City

last: Gerton

state: Missouri

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary: Cohesinopathies are characterized by mutations in the cohesin complex. Mutations in NIPBL, a cohesin loader, result in Cornelia de Lange syndrome (CdLS). CdLS is a congenital genetic disorder distinguished by craniofacial dysmorphism, abnormal upper limb development, delayed growth, severe cognitive retardation, and multiple organ malformations.It has been suggested that CdLS is caused by defects in the cohesin network that alter gene expression and genome organization. However, the precise molecular etiology of CdLS is largely unclear. To gain insights, we sequenced mRNAs isolated from mouse embryonic fibroblasts of both WT and NIPBL-haploinsufficient mice and compared their transcriptomes.

overall_design: Examination of gene expression of WT and NIPBL+/- mice by RNA-seq

first: Kobe

last: Yuen


title: Global Transcriptional Repression: Initial and Essential Step for Plasmodium Sexual Development

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university


title: Alterations to hormone regulated defense and stress response networks contribute to the greater growth of Arabidopsis F1 hybrids

city: Acton

first: Michael

last: Groszmann

state: ACT

address: Clunies Ross St

department: Agriculture

country: Australia

institute: CSIRO

summary: Heterosis, or hybrid vigor, has been exploited in agriculture to deliver increases in crop yields for over a century, yet the molecular basis is not well understood  We have studied the transcriptomes of 15 day old seedlings from intraspecific Arabidopsis hybrids with varying levels of heterosis and their parental lines in order to identify drivers of heterosis.  The patterns of altered gene expression in the hybrids point to a reduction in basal defense levels that could reflect the antagonism between plant immunity and plant growth.  Associated with this theme are changes to the salicylic acid and auxin regulated networks which are known to control abiotic and biotic defense responses as well as being important regulators of plant growth.  Increased auxin response correlates with the heterotic phenotype of greater leaf cell numbers, whereas reduced salicylic acid levels and response promotes increased leaf cell size in hybrids involving C24.  By manipulating salicylic acid levels in each of our hybrid systems, we can alter levels of heterosis, promote additional growth in the hybrids, and generate increased growth in the parents, especially C24.

overall_design: Aerial tissues of 15 days after sowing seedlings from C24, Ler, Col and their reciprocal hybrid offspring.  In total 7 biological replicates for both the C24 and Ler parents, 2 biological replicates for Col, 10 biological replicates for C24/Ler and 4 biological replicates for both C24/Col and Col/Ler were sequenced and analysed.  Each replicated consisted of a pools of 5-15 seedlings (see publication for more details)

first: Rebeca

last: Gonzalez-Bayon

first: Rebecca

last: Lyons

first: Ian

middle: K

last: Greaves

first: Kemal

last: Kazan

first: William

last: Peacock

first: Elizabeth

middle: S

last: Dennis


title: Transcriptome profiling of isolated mammalian myotube cultures that ectopically overexpress msx2

city: Boston

first: Simona

last: Cristea

state: Massachusetts

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

summary: In contrast to urodele amphibians and teleost fish, mammals lack the regenerative responses to replace large body parts. Amphibian and fish regeneration uses dedifferentiation, i.e. reversal of differentiated state, as a means to produce progenitor cells to eventually replace damaged tissues.  Therefore, activation of dedifferentiation response in mammalian tissues holds an immense promise for human regenerative medicine. msx2 expression has been shown to peak at the early time points of amphibian limb regeneration. Despite this temporal importance in the heterogenous regenerating limb tissues, the potential role of msx2 in dedifferentiation was previously not addressed in salamander or mammalian muscle cells. In order to test this, we ectopically overexpressed msx2 in mammalian myotubes and profiled their transcriptomes using next generation sequencing. We identified 4964 up-regulated and 4464 down-regulated transcripts in myotubes compared to myoblasts (uninduced GFP control cells; ≥ 1.5 fold; FDR corrected p-values < 0.01). Upon ectopic msx2 expression in myotubes, 923 transcripts were downregulated, whereas 1283 transcripts were upregulated. Based on msx2’s potential role in dedifferentiation, we reasoned that the transcripts, which are normally upregulated in myotubes in comparison to myoblasts, should go down upon msx2-expression. In accord with this idea, 575 myotube-enriched transcripts were downregulated after one day of ectopic msx2 expression. Similarly, 331 myoblast-enriched transcripts were upregulated upon msx2 expression.

overall_design: To extensively analyze transcriptome-wide changes upon ectopic msx2 expression in mammalian myotubes, we performed next generation RNA-sequencing (RNA-seq) on uninduced and induced isolated myotubes that have msx2 and GFP or GFP alone transgenes. As a reference for the undifferentiated state, we also sequenced the transcriptomes of uninduced myoblast cultures of these two transgenic constructs. Deep sequencing was performed using Illumina HiSeq.

first: Atilgan

last: Yilmaz

last: Constantinescu


title: Expression divergence of chemosensory genes between Drosophila sechellia and its sibling species and its implications for host shift [Dsec TW]

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

summary: Drosophila sechellia relies exclusively on the fruits of Morinda citrifolia, which are toxic to most insects, including its sibling species D. melanogaster and D. simulans.  Although several odorant binding protein (Obp) genes and olfactory receptor (Or) genes were suggested to be associated with the D. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking.  We therefore studied the antennal transcriptomes, the main organ responsible for detecting food resource and oviposition, of D. sechellia and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. sechellia and its two sibling species.  Using a very stringent definition of differential gene expression, we found 147 genes (including 11 chemosensory genes) were up-regulated while only 81 genes (including 5 chemosensory genes) were down-regulated in D. sechellia.  Interestingly, Obp50a exhibited the highest up-regulation, a ~100 fold increase, and Or85c – previously reported to be a larva-specific gene– showed ~20 fold up-regulation in D. sechellia.  Furthermore, Ir84a, proposed to be associated with male courtship behavior, is significantly up-regulated in D. sechellia.  We also found expression divergence in most of the receptor gene families between D. sechellia and the two sibling species.  Our observations suggest that the host shift of D. sechellia is associated with expression profile divergence in all chemosensory gene families and is achieved mostly by up-regulation of chemosensory genes.

overall_design: RNAseq experiments in wild type drosophila antennaes. The strain is D. sechellia (Tuson, #14021-0248-25).

first: Meng-Shin

last: Shiao

first: Wen-Lang

last: Fan

first: Mei-Yeh

last: Lu

first: Cedric

last: Notredame

first: Shu

last: Fang

first: Rumi

last: Kondo

first: Wen-Hsiung

last: Li


title: Acyl-CoA synthetase 1 in differentiated adipocytes from small for gestational age neonates: Putative association with fetal programming of cellular insulin sensitivity and lipid content

city: Singapore

first: Jeremie

last: Poschmann

state: Singapore

address: 60 Biopolis street

country: Singapore

institute: Genome Institute Singapore


title: Breaking the lineage barrier: Direct induction of trophoblast stem cells from murine fibroblasts

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Trophoblast stem cells represent the stem cell population of the extraembryonic lineage and arise as result of the first cell fate decision. From the blastocyst stage onwards, the extraembryonic lineage is strictly separated from the embryonic lineage by a distinct epigenetic lineage barrier. Recently, it has been shown, that this epigenetic barrier cannot be fully overcome as the expression of TS-determining factors in embryonic stem cells lead to incomplete trans-differentiation. Here we demonstrate that transient expression of Tfap2c, Gata3, Eomes and Ets2 in fibroblasts suffices to generate cells, which are almost equivalent to trophoblast stem cells based on morphology, expression and methylation patterns. Further, these induced trophoblast stem cells display self-renewal without exogenous factor expression, differentiate along the extraembryonic lineage and chimerize the placenta upon blastocyst injection. Our findings provide insights into transcription factor networks governing TSC identity and offer a new tool for studying the hierarchy of those factors.

overall_design: analysis of methylation by MeDIP-seq of contol trophoblast stem cells, mouse embryonic fibroblasts and five iTSC clones which are mouse embryonic fibroblasts reprogrammed to trophoblast stem cell-like cells

first: Caroline

last: Kubaczka

first: Claire

last: Senner

first: Monika

last: Cierlitza

first: Marcos

last: Arauzo-Bravo

first: Peter

last: Kuckenberg

first: Michael

last: Peitz

first: Myriam

last: Hemberger

first: Hubert

last: Schorle


title: Small RNA profiling during anther development in 7B-1 male-sterile tomato mutant and its wild type

first: Irina

last: Mohorianu

summary: The RNA-seq was used to identify differentially regulated miRNAs between a male sterile and wild type tomato during anther development.

first: Vahid

last: Omidvar

first: Tamas

last: Dalmay

first: Martin

last: Fellner


title: Monocytic myeloid-derived suppressor cells accumulate in the lungs of influenza A virus-infected mice

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Influenza A virus (IAV) infection causes an acute respiratory disease characterized by a strong inflammatory immune response and severe immunopathology. Pro-inflammatory mechanisms are well described in the murine IAV infection model, but less is known about the mechanisms leading to the resolution of inflammation. Here, we analyzed the contribution of monocytic myeloid-derived suppressor cells (mono-MDSC) to this process. An accumulation of mono-MDSC within the lungs was observed during the course of IAV infection and phenotypic characterization of these mono-MDSC by flow cytometry and RNA-Seq revealed an activated phenotype showing both pro- and anti-inflammatory features, including the expression of iNOS by a fraction of cells in an IFN-g-dependent manner. Mono-MDSC isolated from lungs of IAV-infected animals displayed suppressive activity when tested in vitro, and iNOS inhibitors could abrogate this suppressive activity. Collectively, our data suggest that during IAV infection monocytes can differentiate into mono-MDSC, which might contribute to the prevention of immunopathology during this life-threatening disease.

overall_design: Analysis of changes in the expression of mRNAs in three different groups

first: P

last: Milanez-Almeida

first: T

last: Ulas

first: S

last: Glage

first: K

last: Schughart

first: M

middle: B

last: Lutz

first: J

last: Huehn


title: miRNA sequencing of Trim71 conditional ("WT") and Trim71 KO mES cells

summary: We report that Trim71 mutation induces significant changes in the global expression profile of miRNAs in undifferentiated mES cells, rendering the cells prone to differentiation.

overall_design: Analysis of changes in the expression of miRNAs in two different genotypes

first: Sibylle

last: Mitschka

first: Tobias

last: Goller

first: Karin

last: Schneider

first: Waldemar

last: Kolanus

first: Angela

last: Egert

first: Thomas

first: Patrick

last: Günther

first: Kevin

last: Bassler

first: Kathrin

last: Klee

first: Jia

last: Xue


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, 4L;C* and Isofagamine treated 4L;C* region specifics mouse brain miRNA profile (miRNA-Seq)

first: Nupur

last: dasgupta

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived brain transcriptome profiling (RNA-seq) in neuropathic region specific Gaucher mouse brain compared with WT and Isofagamine treated mice of the same age and background and secondly to identify the DEmiRNA associated with the DEmRNA before and after treatment This will give us some insights to see if miRNA is also involved in the the regulation of the expression of the genes involved in the disease process before and after treatment.
Methods: 42-45 days old 4L;C*,  wild-type (WT)  and Isofagamine treated  4L;C* mouse brain  were generated by deep sequencing, in triplicate, using IlluminaHiseq. The sequence reads that passed quality filters were analyzedwith two methods: Burrows–Wheeler Aligner (BWA) followed and TopHat followed by DESeq. qRT–PCR validation was performed using TaqMan and SYBR Green assays

overall_design: Regional brain  miRNA profiles of ~42 -days old wild type (WT) and 4L;C* an d Isofagamine treated  mice were generated by deep sequencing, in triplicate, using IlluminaHi Seq.

last: Dasgupta

first: Youhai

last: Xu

first: Ronghua

last: Li

first: Yanyan

last: Peng

first: Manoj

last: Pandey

first: Stuart

last: Tinch

first: Benjamin

last: Liou

first: Venette

last: Inskeep

first: Wujuan

last: Zhang

first: Mehdi

last: Keddache

first: Gregory

last: Grabowski

first: Ying

last: Sun


title: Unveil coffee molecular response mechanisms to drought through the expression of the homeobox-leucine zipper I CAHB12

city: Paterna

first: Regis

middle: Lopes

last: Correa

state: Valencia

address: CL. Catedrático Agustín Escardino 9

country: Spain

summary: Functional characterization of transgenic Arabidopsis plants constitutively expressing CAHB12 resulted in increased tolerance to drought stress, during distinct developmental stages, and increased tolerance to salt stress during seed germination. An insight into the gene set modulated by the ectopic expression of CAHB12 ectopic expression was provided by parallel sequencing (RNA-Seq) of high molecular weight and small RNA fractions. Classical drought responsive genes were mostly repressed, suggesting that other mechanisms are likely contributing to the tolerant phenotype exhibited by CAHB12-ectopically expressing plants, such as the pathway signaled by heat shock proteins and heat shock transcription factors.

overall_design: The study includes three samples in total: one wild type Arabidopsis thaliana and two transgenic lines of Arabidopsis thaliana expressing the coffee homeobox gene CaHB12. Four RNA-seq libraries were constructed and sequenced: two biological replicates for wild type and two for transgenic plants. Four libraries are also prepared for sRNA-seq from the same plants, but two extra technical replicates were sequenced (one for the wild type and one for the transgenic plants).

first: Fernanda

middle: P

last: Cruz

first: Roberta

last: Loh

first: Carlos

last: Dezar

first: Elisson

last: Romanel

first: Ighor

last: Arantes

first: Adriana

last: Arongaus

first: Eduardo

last: Romano

first: Dorothea

last: Bartels

first: Raquel

last: Chan

first: Régis

last: Corrêa

first: Bruna

last: Matta

first: Márcio

last: Ferreira


title: Effect of castration, bicalutamide, and enzalutamide on androgen receptor binding in Hi-Myc mouse prostate tumors

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

overall_design: Androgen receptor ChIP-seq was performed on Hi-Myc mice tumors 3 days after surgical castration or treatment with bicalutamide or enzalutamide

first: Charles

last: Sawyers

first: Deyou

last: Zheng

first: Brett

last: Carver


title: Acyl-CoA synthetase 1 in differentiated adipocytes from small for gestational age neonates: Putative association with fetal programming of cellular insulin sensitivity and lipid content [ChIP-Seq]

first: Jeremie

last: Poschmann

summary: We hypothesised that SGA as a proxy for intrauterine growth restriction promotes specific epigenetic marks and pathways, whose physiological implications may become apparent only in the fully differentiated state.

overall_design:
We established primary UC-MSC lines isolated from SGA and normal neonates and differentiated them into mature adipocytes.
Samples were collected from umbilical cord derived mesenchymal stem cells (UC-MSC). A sample from each SGA and control group.

first: Walter

last: Stunkel


title: The epigenetic processes of meiosis in male mice are broadly affected by the widely used herbicide atrazine

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

country: France

institute: Université de Rennes 1


title: The epigenetic processes of meiosis in male mice are broadly affected by the widely used herbicide atrazine [ChIP-Seq]

summary: Environmental factors such as pesticides are widely used in the agriculture of many countries and their negative impact on human health and fertility are largely unknown. There is a rapidly growing body of evidence that human reproductive health is negatively affected by various environmental factors, including life style and exposure to chemical compounds such as certain drugs and pesticides. Sexually reproducing organisms produce haploid gametes via a process called meiosis. Meiosis is dependent on androgen action within the testis. Pesticides and herbicides interfere with natural hormones system and are considered to be endocrine disruptors. We hypothesize that atrazine (ATZ), a herbicide used globally, adversely affects meiosis. To test this idea we used the mouse as a model organism.  Mice were treated for a three weeks with atrazine at a concentration of 100 mg/l in drinking water nearly corresponding to 25mg/kg/day. To access the extent of the toxic effect of atrazine on the epigenetic modifications on genome wide level we performed Chromatin immunoprecipitation (ChIP) using antibody against H3K4me3 followed by high throughput sequencing. Analysis of H3K4me3 marks revealed that 823 genomic loci were affected.  H3K4me3 marks are increased occupancy in highly overexpressed Speer and Trim45 genes and decreased in Entd4, Slc25a37 and LoxL2 genes. Changes in H3K4me3 occupancy in these genes may reflect answers to DNA damages in ATZ treated testis tissue. Eighty seven of differential H3K4me3 peaks are associated with meiosis specific Double Strand  Breaks (DSB) sites, showing that ATZ treatment affect DSBs repair in meiosis. Together, our data demonstrate the negative effect of atrazine on meiosis in mice.

overall_design: Genome wide analyze H3K4me3 marks distribution in testes tissue from ATZ treated animals and control.

last: Hao

first: Fatima

last: Smagulova

first: Aurore

last: Gely-Pernot


title: Androgen receptor DNA binding in response to different ligands across three prostate cancer cell lines

summary: We performed AR ChIP-seq in LNCaP-AR, VCaP and CWR22PC cells in the presence of vehicle, androgen, or androgen plus antiandrogen. These three cell lines showed variable sensitivity to these drugs.

overall_design: To determine the effects of AR agonist (R1881 vs DHT) and antagonists (Bicalutamide vs MDV3100) on the AR cistrome across a panel of prostate cancer cell lines.

first: Ling

last: Cai


title: mRNA sequencing of Trim71 conditional ("WT") and Trim71 KO mES cells

first: Joachim

last: Schultze

summary: We report that Trim71 mutation does not lead to significant changes within the core regulatory network of mES cells, however, there is an upregulation of specific genes involved in neural differentiation. We thus conclude that Trim71 KO mES cells are poised for differentiation.

overall_design: Analysis of changes in the expression of mRNAs in two different genotypes

first: Sibylle

last: Mitschka

first: Tobias

last: Goller

first: Karin

last: Schneider

first: Waldemar

last: Kolanus

first: Angela

last: Egert

first: Hubert

last: Schorle

first: Thomas

last: Ulas

first: Patrick

last: Günther

first: Kevin

last: Bassler

first: Jia

last: Xue


title: Cell context specific effect of AR antagonists on AR DNA binding and target gene expression

first: Yu

last: Chen

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (MB)

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

type: Methylation profiling by high throughput sequencing

summary: Unraveling complexity of DNA methylome is essential to decipher DNA methylation mechanism in life. However, this has been subjected to technological constraints to balance between cost and accurate measurement of the DNA methylation level. In this study, by innovatively introducing C-hydroxylmethylated adapters, we have developed MeDIP-Bisulfite sequencing (MB-seq), which could obtain DNA methylome of repertoire CpGs at single-base resolution. We found MB-seq only costs 10% of MethylC-seq, but covers 85% of total CpGs in human genome. Unlike absolute methylation levels determined by MethylC-seq and RRBS, MB-seq presented relative methylation levels that are linearly inflated. This has enlightened us to develop a MB-seq corresponding correction method for methylation level based on ridge regression, which integrates the data of MB-seq and RRBS to predict the methylation level of total 28.2 million CpGs on human genome with high accuracy (Pearson correlation coefficient, PCC=0.90). Moreover, by employing MB-seq, we generated the DNA methylome of an ovarian epithelial cell line (T29) and its oncogenic counterpart (T29H), respectively. After ridge regression, we identified 131,790 differential methylation regions (DMRs) with high accuracy between T29 and T29H, far more than 7,567 obtained from RRBS. Taken together, our result demonstrated that the MB-seq combined with ridge regression is a wide applicable approach for profiling of DNA methylome.

overall_design: Genomic DNA from T29 cell line with the input amount of 1 μg, 500 ng, 200 ng, 50 ng, respectively, was fragmented to ~100-500 bp using Covaris E210 sonicator (Covaris Inc. USA). Fragmented DNA was end-repaired, A-tailed, and ligated to C-hydroxylmethylated Illumina Multiplexing adapters following the standard Illumina protocol.MB-seq library construction for genomic DNA from T29H exactly followed the protocol mentioned above.

first: Wanshi

first: Zhong

last: Sun


title: Global Transcriptional Repression: Initial and Essential Step for Plasmodium Sexual Development [ChIP-seq]

first: masao

last: yuda

summary: Gametocytes are nonreplicative sexual forms that mediate malaria transmission to a mosquito vector. They are generated from asexual blood stage parasites, which proliferate in the circulation. However, it remains largely unknown as to how this transition is genetically regulated. Here, we report that an Apetala2 (AP2) family transcription factor, AP2-G2, regulates the transition as a transcriptional repressor. Disruption of AP2-G2 in the rodent malaria parasites, Plasmodium berghei, did not prevent commitment to the sexual stage but halted their development before manifesting sex-specific morphologies. ChIP-seq analysis revealed that AP2-G2 targets approximately 1,500 genes and recognizes a five-base motif on their promoters. Most of these target genes are required for asexual proliferation in the blood by the parasites, thereby suggesting that AP2-G2 blocks the program for asexual replication of parasites in the blood. DNA microarray analysis showed that the identified targets constituted approximately 70% of the upregulated genes in AP2-G2-depleted parasites, and a promoter assay using a centromere plasmid demonstrated that the binding motif functions as a cis-acting negative regulatory element. These results suggest that global transcriptional repression, which occurs during the initial phase of gametocytogenesis, is an essential step to promote conversion to the sexual stage.

overall_design: Balb/c mice were infected with P. berghei expressing GFP-fused AP2-G2. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Chromatins associated with GFP-tagged AP2-G2 was IPed with anti-GFP antibody, and.target genes of this transcription factor were predicted.

first: Masao

last: Yuda

first: izumi

last: kaneko

first: shiroh

last: iwanaga

first: tomomi

last: kato


title: Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression

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

overall_design: Refer to individual Series


title: Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (MethyC + MeDIP)

overall_design: For the same batch of genomic DNA extracted from T29 cell line as the MB-seq library used, MethylC-seq  and MeDIP-seq  libraries were prepared as standard procedures

last: Cai


title: YAP drives proliferation and tumorigenesis by recruiting Mediator to super- enhancer elements (CClp1)

city: Torino

first: Raffaele

last: Calogero

address: Via Nizza 52

institute: University of Torino

summary:
The Hippo/YAP signaling pathway is a crucial regulator of tissue growth and stem cell activity. YAP is also a powerful driver of tumor growth and its nuclear accumulation is frequently observed in human cancer.
However, the molecular mechanism employed by YAP to orchestrate transcriptional outputs are undefined. Here, we utilize genomic technologies to demonstrate that YAP occupancy is restricted to a small number of distal regulatory elements highly enriched for superenhancers.
Target genes associated with these elements are selectively sensitive to the loss of YAP in cancer cells. YAP directs recruitment of the Mediator complex to activate transcriptional regulation from these enhancers without affecting chromatin organization
We also provide in vivo genetic evidence that loss of Mediator rescues YAP-driven cancer cell proliferation and organ overgrowth. Our data provide a molecular mechanism behind YAP-driven tumorigenesis, and highlights transcriptional control as a potential therapeutic strategy for YAP-driven cancers.

overall_design: A total of eight ChIP-Seq samples are available. Three directed against YAP using two different antibodies (Santa Cruz, Avruch and a replicate of the Avruch run), one directed against a tagged version of YAP (C25) and its own specific control (BirA), one directed against TEAD1, the whole genomic input DNA, an unrelated IgG for background noise definition

first: Giorgio

last: Galli

first: Matteo

last: Carrara

first: Christian

last: Valdes-Quezada

first: Basanta

last: Gurung

first: Brian

last: Pepe-Mooney

first: Geert

last: Geeven

first: Wei-Chien

last: Yuan

first: Wouter

last: de Laat

first: Fernando

last: Camargo


title: Genome-wide maps of PARP-1-bound nucleosomes (human)

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

summary: PARP-1 binds to specific nucleosomes to regulate gene activity. While PARP-1's role in transcription inititaion is known, a surprising finding here was that PARP-1 is highly enriched at exon-intron and intron-exon boundaries, sort of demarcting exons. Thius indicating a role in alternative splicing.

overall_design: ChIP-seq of PARP-1-bound nucleosomes

first: Narasimharao

last: Nalabothula

first: Taha

last: Al-jumaily

first: Shao

last: Xiaorong

first: Abdallah

middle: M

last: Eteleeb

last: Xiarong

first: Robert

last: Flight

first: Hunter

last: Moseley

first: Eric

last: Rouchka

middle: N


title: YAP drives proliferation and tumorigenesis by recruiting Mediator to super- enhancer elements

first: Raffaele

last: Calogero


title: HOTAIR or shHOTAIR lentiviral infected prostate cancer cells

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University


title: Ileal immune maturation in Pediatric Crohn's Disease

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We report the global pattern of ileal gene expression in a cohort of 310 treatment-naïve pediatric Crohn Disease patients and controls.  We focus on genes with consistent altered expression in the ileum of younger (Paris age A1a) vs older (Paris age A1b) patients.

overall_design: Ileal biopsies were obtained during diagnostic colonoscopies of children and adolescents aged less than 17 years, who presented with IBD-like symptoms.  All patients underwent baseline colonoscopy and histological characterization; non-IBD controls were those with suspected IBD, but with normal radiographic, endoscopic, and histologic findings.  Biopsies were stored at -80 degrees.

first: Yael

last: Haberman

first: Lee

last: Denson


title: Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: Alterations of chromatin modifiers are frequent in cancer but their functional consequences remain often unclear. Focusing on the Polycomb protein EZH2 that deposits H3K27me3 mark, we showed that its high expression in solid tumors is a consequence, and not a cause, of tumorigenesis. In mouse and human models, EZH2 is dispensable for prostate cancer development and restrains breast tumorigenesis. High EZH2 expression in tumors results from a tight coupling to proliferation to ensure H3K27me3 homeostasis. However, this process is malfunctioning in breast cancer. Low EZH2 expression relative to proliferation and mutations in Polycomb genes are actually of poor prognosis and occur in metastases. We show that while altered EZH2 activity consistently modulates a subset of its target genes, it promotes a wider transcriptional instability. Importantly, transcriptional changes consequent to EZH2 loss are predominantly irreversible. Our study provides an unexpected understanding of EZH2's contribution to solid tumors with important therapeutic implications.


title: Transcriptome analysis of Culex cells after West Nile virus infection

city: Geelong

first: Prasad

last: Paradkar

state: Victoria

address: 5 Portarlington Road

institute: CSIRO-AAHL

summary: High throughput sequencing was performed using Illumina HiSeq to identify differentially regulated genes in Culex mosquitoes after West Nile virus infection.

overall_design: Culex quinquefasciatus mosquito cell line (Hsu) was infected with West Nile virus for 48 hours, paired-end sequencing was performed on the transcriptome. The experiment was conducted in duplicate. Sequence reads were mapped to Culex quin transcripts in Vectorbase by using Tophat2 and abundaces of specific transcripts were compared between control and West Nile virus infected samples using Cufflinks.

first: Julio

last: Rodriguez-Andres

last: Trinidad

first: Jean-Bernard

last: Duchemin

first: Peter

last: Walker


title: Broad existence of pluripotent factor regulated transcript isoforms with stage-specific alternative first exon (SAFE) in mouse embryonic stem cells

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

country: China

institute: Institute of Zoology,CAS

summary: Alternative first exon isoforms are frequently observed among transcriptomes derived from different developmental stages of eukaryotes. Stage-specific alternative first exon (SAFE) transcripts are usually involved in the regulation of cell development in spatiotemporal manners. The transcriptome analysis for RNA-seq data make it possible to identify specifically used first exons in mouse embryonic stem cells (mESCs) compared to somatic cells, just like tail tip fibroblasts (TTFs). In this study, we identify 128 genes producing SAFE isoforms in mESCs.

overall_design: mRNA profiles of mouse ESCs and TTFs were generated by deep sequencing using Illumina HiSeq 2000.

first: Guihai

last: Feng

first: Man

last: Tong

first: Xiu-jie

last: Wang


title: IL-1β and SERPINA3 are markers of an aggressive Barrett’s Oesophagus phenotype identified using mRNA sequencing

city: Dublin

first: Finbar

middle: Patrick

last: MacCarthy

address: St. James's Hospital, James's Street,

department: Clinical Medicine

country: Ireland

institute: Institute of Molecular medicine,Trinity Centre for Health Sciences,

summary:
Introduction: The identification of biomarkers in Barrett’s oesophagus (BO) that stratify groups at risk of progressing to oesophageal adenocarcinoma (OAC) would allow tailored surveillance strategies. We have applied a novel high throughput RNA sequencing analysis characterizing the BO mRNA transcriptome across the metaplasia-dysplasia sequence to identify potential markers of progression in an unbiased fashion and functionally validated these at the protein level.
Methods: Matched biopsy samples for histology and RNA extraction were taken from BO patients of known histological grade. RNA was extracted from matched samples and sequenced to 60bp length (paired-end).21 samples were sequenced (HGD,7; LGD, 7 and SIM, 7). Reads obtained were mapped to NCBI build37.2 using TopHat. Read count generation, normalisation and differential expression (DE) analysis was performed using the HTSeq-DESeq pipeline. Significantly DE genes (>2 fold change in expression with B-H adjusted p-value <0.1) were further assessed for network and biological relevance using Ingenuity Pathway analysis. Candidate genes were selected and validated in a larger cohort (n=64) using RT-PCR.  Targets were further validated (by ELISA and immunohistochemistry) in independent cohorts of patients using serum and tissue microarrays.
Results: DE analysis was performed in 3 groups with 2 conditions at a time using the lower grade cohort as control and the higher grade as comparator: SIM vs. LGD (demonstrated 218 DE genes, 131 up-regulated in LGD, 87 down-regulated compared to SIM), SIM vs. HGD (49 DE, 27 up, 22 down) and LGD vs. HGD (317 DE, 81 up, 216 down). Six network-central candidate genes (FOSB, IL-1B, SERPINA3, KLK7, GSTM5 &SCUBE2) were selected for RT-PCR validation following network and functional analysis. Circulating IL-1β and SERPINA-3 demonstrated progressive significant increases in expression across the dysplasia sequence to OAC (p<0.005)). This was confirmed at the tissue level showing significant differences between SIM and dysplastic BO (p<0.05).
Conclusion: The use of RNA-sequencing as a detailed and unbiased analysis method identifies IL-1β and SERPINA-3 as novel candidates differentially expressed along the metaplasia-dysplasia-cancer sequence in BO.

overall_design: RNA sequencing was performed on mRNA extracted from oesophgeal biopsies from patients with non dysplstic Barrett's esophagus, low grade dysplasia and high grade dysplasia using Illumina GAIIx

first: Shane

last: Duggan

first: Emma

last: Quinn

first: James

last: Phelan

first: Ronan

last: Feighery

first: Jacintha

last: O’Sullivan

first: Dermot

last: Kelleher

first: John

last: Reynolds

last: O’Toole


title: Genome-wide analysis of H3K27me3 in Ezh2-conditional iMEFs

first: Nicolas

last: Servant

summary: We analyzed the genomic distribution of H3K27me3 in a clone of c-Myc iMEFs (clone C2) either i) wild-type for Ezh2, ii) in the presence of overexpressed exogenous Ezh2, iii) Ezh2-mutant, and iv) Ezh1/Ezh2 pre-deletion (Ezh1/Ezh2 introduced before deletion of endogenous Ezh2) and Ezh2 post-deletion rescue (Ezh2 re-introduced in Ezh2-mutant cells).

overall_design: Experiment 1: H3K27me3 ChIP-seq in C2 iMEFs either Ezh2 WT, Ezh2-mutant or Ezh2 post-rescue condition. Experiment 2: H3K27me3 ChIP-seq in C2 iMEFs either Ezh2 WT, Ezh2-mutant, in the presence of overexpressed Ezh2, in Ezh1 pre-rescue condition and in Ezh2 pre-rescue condition.

first: Aurélie

last: Teissandier

first: Raphaël

last: Margueron

first: Michel

last: Wassef


title: HOTAIR or shHOTAIR lentiviral infected prostate cancer cells [ChIP-Seq]

first: Jindan

last: Yu

summary: LNCaP prostate cancer cells were infected by lentivirus expressing either ctrl or HOTAIR, and the cells were cultured in hormone-deprived condition (Ethl) or in the presence of androgen (R1881). C4-2B prostate cancer cells were infected by lentivirus expressing either shCtrl or shHOTAIR, and the cells were cultured in hormone-deprived condition (Ethl) or in the presence of androgen (R1881).

overall_design: ChIP-Seq examination of AR binding sites in LNCaP and C4-2B cells following HOTAIR de-regulation.

first: Ali

last: Zhang

first: Jonathan

last: Zhao


title: Serial RNA-seq of a single human

city: Austin

first: Russell

last: Poldrack

state: TX

address: 100 East 24th Street, R9975

institute: University of Texas at Austin

summary:
Psychiatric disorders are characterized by major fluctuations in psychological function over the course of weeks and months, but the dynamic characteristics of human brain function over this timescale in healthy individuals are unknown.  Over a period of 18 months, we performed intensive phenome-wide assessment of a single human, including brain connectivity using resting fMRI, measurements of psychological and physical health, and transcriptomic and metabolomic profiling.
Brain connectivity varied across sessions in relation to behavioral variables including mood, fatigue, and food/caffeine intake, as well as variables related to inflammation and gut health.   Pathway-based analysis of gene expression in peripheral lymphocytes identified associations with physical health and brain connectivity, including associations between specific brain networks and a broad set of immune-related pathways. Metabolomic measures were strongly associated with dietary variance.
 This study integrates dense neuroimaging and -omics profiling to provide a detailed picture of the joint dynamics of human brain and metabolic function over time, an approach that is critical for the understanding of brain disorders characterized by increased variability of brain function.

overall_design:
Repeated measures on a single individual;
RNA was extracted from PBMCs from a single human repeatedly over the course of 18 months, under fasted conditions at a consistent time of day.  This was collected along side a large number of other variables including brain imaging.
More information is available at http://www.myconnectome.org


title: Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (RNA)

first: Fengbiao

last: Mao

overall_design: Total RNAs were extracted from T29 and T29H with RNeasy Mini Kit (QIAGEN, Germany). RNA quality was quality-controlled by Bioanalyser 2100 (RNA nano kits, Agilent). mRNA-Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA), and then subjected to transcriptome sequencing on the Illumina Hiseq 2000

first: Wanshi

last: Cai

first: Zhong

last: Sun


title: Genome-wide ChIP-Seq analysis of genomic Stat3 binding sites in murine gastric tumors following stimulation with IL6 or IL11

city: Heidelberg - Melbourne

first: Stefan

last: Thiem

address: 145 Studley Road

department: Cancer Research

institute: Olivia Newton-John Cancer Research Institute


title: High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila

city: Freiburg

first: Fidel

last: Ramirez

address: Stübeweg 51

department: Bioinformatics Unit

institute: Max Planck Institute for Immunobiology and Epigenetics

summary: Hi-C analysis of two Drosophila male cell lines, combined with 4C-seq of frequent long-range contacts between HAS.

overall_design: We carried out Hi-C experiments in the male Drosophila melanogaster cell lines S2 and clone8, both in biological duplicates. Analyses were complemented by 4C-seq and S2 and female Kc cells and with DNA FISH.

last: Ramírez

first: Thomas

last: Lingg

first: Sarah

last: Toscano

first: Kin

last: Lam

first: Georgiev

last: Plamen

first: Chung

last: Ho-Ryung

first: Bryan

last: Lajoie

first: Elzo

last: de Wit

first: Ye

first: Wouter

last: de Laat

first: Job

last: Dekker

last: Manke

first: Asifa

last: Akhtar


title: Genome-wide ChIP-Seq analysis of genomic Stat3 binding sites in murine gastric tumors following stimulation with IL6 or IL11 (CisGenome)

summary: The latent transcription factor STAT3 is a point of convergence for numerous oncogenic signaling pathways and is excessively activated in the majority of human epithelial cancers. STAT3 promotes many hallmarks of cancer including enhanced proliferation, increased survival, sustained angiogenesis, immune evasion and tumor-promoting inflammation. We performed chromatin immunoprecipitations (ChIP) followed by next-generation sequencing (ChIP-Seq) to identify genomic Stat3 binding sites in established gastric tumors of gp130F/F mutant mice (Tebbutt et al., 2002) following administration of recombinant human interleukin (IL)-6 or IL11. The study was designed to assess differences in Stat3 recruitment in response to IL6 and IL11, two cytokines which both activate Stat3 through the shared IL6 cytokine family receptor subunit gp130. In gp130F/F mice, a robust model for inflammation-associated intestinal-type gastric tumorigenesis, the Y757F knock-in mutation in the gp130 receptor triggers spontaneous gastric tumor formation in a strictly IL11-dependent manner, but independent of IL6 signaling (Ernst et al., 2008). Therefore, the study aimed to identify IL6- and IL11-specific Stat3 target genes. In total, we identified 948 or 961 significant Stat3-DNA interactions in gp130F/F tumors following IL6 or IL11 administration, respectively. These interactions were validated by binding motif analysis which showed that at least 30% of all Stat3-associated genomic regions comprise a Stat3 consensus binding sequence.

overall_design: Chromatin was extracted from gastric tumor tissue of gp130F/F mice collected 60 min after a single systemic (intraperitoneal) administration of PBS (vehicle control), recombinant human IL6 or IL11 (5 ug). ChIP reactions were carried out using a Stat3-specific antibody (Santa Cruz SC-482X) and the SIGMA Imprint ChIP Kit. The ChIP DNA was sequenced with Illumina's Genome Analyzer II. Following short read alignment, significantly enriched genomic regions in each of the three samples were identified using CisGenome software (Ji et al., 2008 and 2011), resulting in three lists of genomic Stat3 binding sites and associated genes or microRNAs.

first: Matthias

last: Ernst

first: Roberto

last: Barrero


title: An epigenetic role for disrupted paternal gene expression in postzygotic seed abortion in Arabidopsis interspecific hybrids

first: Z Jeffrey

middle: Jeffrey

last: Chen

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: Interspecific hybrids in Arabidopsis result in seed abortion that causes reproductive barrier. To investigate the allelic expression pattern at transcriptome level during early seed abortion stage, we performed RNA-seq analysis in F1 interspecific hybrids with three different ecotypes in A. thaliana as maternal and A. arenosa as paternal and identified MEGs and PEGs. Interestingly, PEGs showed distinct expression pattern in several aspects, compared to MEGs: PEGs showed ecotype-specific expression pattern, suggesting a role for PEGs in ecotype-dependent seed lethality. 35% of previously known MEGs in non-lethal hybrids were found as PEGs in our lethal interspecific hybrids, implying the presence of abnormal paternal allelic upregulation. The correlation test between the upregulation of PEGs and previously reported paternal-excess interploidy cross (2X6) which exhibited seed abortion showed that dosage disruption by abnormal paternal upregulation is correlated with seed abortion. Moreover, epigenetic disruption appears to cause some of abnormal upregulation of paternal alleles in PEGs via mis-regulation of MEA-mediated PcG2 and MET1-mediated DNA methylation. The results provide clue on the critical role of PEGs in seed abortion via disruption of dosage balance and epigenetic regulation.

sample_organism: Arabidopsis thaliana x Arabidopsis arenosa

overall_design: RNAsequensing of 3 F1 interspecific hybrids and 1 F8 allotetraploid from 4 DAP silique tissues in Arabidopsis

first: Ryan

last: Kirkbride

first: Helen

last: Yu

first: Gyoungju

last: Nah

first: Changqing

last: Zhang

first: Xiaoli

last: Shi

first: Z


title: Genome-wide ChIP-Seq analysis of genomic Stat3 binding sites in murine gastric tumors following stimulation with IL6 or IL11 (MACS)

first: Stefan

last: Thiem

overall_design: Chromatin was extracted from gastric tumor tissue of gp130F/F mice collected 60 min after a single systemic (intraperitoneal) administration of PBS (vehicle control), recombinant human IL6 or IL11 (5 ug). ChIP reactions were carried out using a Stat3-specific antibody (Santa Cruz SC-482X) and the SIGMA Imprint ChIP Kit. The ChIP DNA was sequenced with Illumina's Genome Analyzer II. Following short read alignment, significantly enriched genomic regions in each of the three samples were identified using MACS software (Zheng et al., 2008), resulting in three lists of genomic Stat3 binding sites and associated genes or microRNAs.

first: Ulrich

last: Wagner

first: Bing

last: Ren


title: Epigenetic Control of Skeletal Development by the Histone Methyltransferase Ezh2

status: Public on Sep 30 2015

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Inhibition of H3K27 methyltransferase EZH2 enhances osteogenic commitment of human mesenchymal progenitors and Ezh2 inactivation in mouse calvarial cells induces a post-proliferative state concomitant with increased production of a bone-related mineralizing extra-cellular matrix.

overall_design: Expression of genes of interest, including Ezh2, was assessed during osteogenic differentiation of human adipose-derived mesenchymal (AMSCs) on plastic (2D) and on porous-sintered titanium discs (3D). We also assessed gene expression when AMSCs were differentiated into the adipogenic lineage. In addition, the effect of GSK126 on osteogenic differentiation of AMSCs was also evaluated. Finally, we compared gene expression in calvarial bones obtained from wild type mice and mice lacking functional Ezh2 in the mesenchymal lineage (Prrx1-Cre, 3 day old female mice).

first: Amel

last: Dudakovic

first: Andre

last: van Wijnen


title: Illumina Human Polycystic Liver Disease and Normal Biliary Stem Cell RNAseq

city: The Hague

first: Edgar

last: Wills

address: Andrej Sacharowstraat 37

department: Gastroenterology & Hepatology

country: Netherlands

institute: RadboudUMC

summary:
Background & aims: Polycystic liver disease (PLD) is an autosomal dominantly inherited disorder caused by mutations in genes such as PRKCSH and SEC63. It has been thought that cysts develop from biliary progenitor cells due to loss-of-heterozygosity (LOH), leading to aberrant proliferation or defects in differentiation. Cyst expansion can be suppressed by somatostatin analogues such as lanreotide. There is no human in vitro model available that truly recapitulates polycystic liver disease. We hypothesize that PLD progenitors can form bipotent liver organoids that carry key features of cyst development. To find gene expression differences between Human Polycystic Liver Disease and Normal Biliary Stem Cells.
Methods: Cells from normal biliary duct (n=6), cyst biliary epithelium (n=60) and cyst fluid (n=31) were isolated and placed under conditions suitable for expansion of human adult liver stem cells. We analyzed genetic LOH, gene expression, differentiation capacity, response to lanreotide and cilium formation of these organoids.
Results:  Cholangiocytes from cyst biliary epithelium (47/60) and cyst fluid (9/31) proved capable of expanding as bipotent liver organoids. Multiple cyst organoids displayed LOH surrounding PRKCSH or SEC63 regions. Organoids formed cilia when proliferation was inhibited. Neither hepatocyte nor biliary differentiation of PLD organoids was impaired. RNAseq revealed no significantly dysregulated pathway in PLD organoids. Lanreotide significantly decreased expansion of liver organoids in comparison to negative control (197% ± 46% versus 547% ± 28%; p: 0.038).
Conclusion & discussion: Biliary progenitor cells from patient cyst epithelium and fluid can expand into liver organoids. They recapitulate key characteristics of PLD, and are a promising human in vitro model for research, diagnostics and treatment of polycystic liver diseases and cholangiociliopathies.

overall_design:
8 polycystic liver disease samples versus 4 control samples
RADBOUDUMC

first: Joost

last: Drenth


title: RNA-seq Profiles in Preferential Iron Trafficking Characterizes Glioblastoma Stem-like Cells

city: Cleveland

first: Tyler

last: Miller

state: Ohio

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic Lerner Research Institute

summary: Glioblastomas display hierarchies with self-renewing cancer stem-like cells (CSCs). RNA sequencing and enhancer mapping revealed regulatory programs unique to CSCs causing upregulation of the iron transporter transferrin, the top differentially expressed gene compared to tissue-specific progenitors. Direct interrogation of iron uptake demonstrated CSCs potently extract iron from the microenvironment more effectively than other tumor cells. Systematic interrogation of iron flux determined that CSCs preferentially require transferrin receptor and ferritin - two core iron regulators - to propagate and form tumors in vivo.  Depleting ferritin disrupted CSC mitotic progression, through the STAT3-FoxM1 regulatory axis, revealing an iron-regulated CSC pathway. Iron is a unique, primordial metal fundamental for earliest life forms, and on which CSCs have an epigenetically programmed, targetable dependence.

overall_design: RNA-seq of primary patient-derived GBM cancer stem cells and normal human neural progenitor cells

first: David

last: Schonberg

first: Robert

middle: T

last: Karl

first: Paul

last: Tesar

first: Jeremy

last: Rich


title: Epigenetic Profile in Preferential Iron Trafficking Characterizes Glioblastoma Stem-like Cells

overall_design: H3K4me1 histone modifications were mapped by ChIP-seq in Glioblastoma Stem Cells directly from a subcutaneous xenograft tumor

middle: L


title: Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense.

city: College Station

first: Claudia

middle: Marcela

last: Castillo-González

state: Texas

department: Biochemistry & Biophysics

institute: Texas A&M University

summary: Transcriptional gene silencing (TGS) can serve as an innate immunity against invading DNA viruses throughout Eukaryotes. Geminivirus code for TrAP protein to suppress the TGS pathway. Here we identified an Arabidopsis H3K9me2 histone methyltransferase, Su(var)3-9 homolog 4 (SUVH4/KYP), as a bona fide cellular target of TrAP. TrAP interacts with the catalytic domain of KYP and inhibits its activity in vitro. TrAP elicits developmental anomalies phenocopying several TGS mutants, reduces the repressive H3K9me2 mark and CHH DNA methylation, and reactivates numerous endogenous KYP-repressed loci in vivo. Moreover, KYP binds to the viral chromatin, and controls its methylation to combat virus infection. Notably, kyp mutants support systemic infection of TrAP-deficient Geminivirus. We conclude that TrAP attenuates the TGS of the viral chromatin by inhibiting KYP activity to evade host surveillance. These findings provide new insight on the molecular arms race between host antiviral defense and virus counter defense at an epigenetic level.

overall_design: Examination of DNA methylation using bisulfite conversion of unmethylated cytosines in three genetic backgrounds of Arabidopsis thaliana.

first: Xiuren

first: Xiuying

last: Liu

first: Xiu-Jie

last: Wang


title: Preferential Iron Trafficking Characterizes Glioblastoma Stem-like Cells

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

overall_design: Refer to individual Series


title: Binding of STAT5 upon IL-2 treatment to genomic sites in mouse CD8 T cells costimulated in vivo through CD134 plus CD137

city: Farmington

first: Anthony

last: Vella

state: CT

address: 263 Farmington Avenue

department: Immunology

institute: University of Connecticut Health Center

summary: OT-I CD8 T cells primed with cognate SIINFEKL peptide and agonists to the costimulatory receptors CD134 and CD137 were stimulated with and without IL-2, and then STAT5 ChIP-seq was performed.

overall_design: Examination of IL-2-induced STAT5 binding to genomic sites in effector CD8 T cells

first: Naomi

last: Tsurutani


title: Comparative “-omics” in Mycoplasma pneumoniae Clinical Isolates Reveals Key Virulence Factors

city: Barcelona

first: Luca

last: Cozzuto

state: Barcelona

address: Carrer Dr. Aiguader 88

department: CRG core facilities

institute: Centre for genomic regulation (CRG)

summary: The human respiratory tract pathogen M. pneumoniae is one of the best characterized minimal bacterium. Until now, two main groups of clinical isolates of this bacterium have been described (types 1 and 2), differing in the sequence of the P1 adhesin gene. Here, we have sequenced the genomes of 23 clinical isolates of M. pneumoniae. Studying SNPs, non-synonymous mutations, indels and genome rearrangements of these 23 strains and 4 previously sequenced ones, has revealed new subclasses in the two main groups, some of them being associated with the country of isolation. Integrative analysis of in vitro gene essentiality and mutation rates enabled the identification of several putative virulence factors and antigenic proteins; revealing recombination machinery, glycerol metabolism and peroxide production as possible factors in the genetics and physiology of these pathogenic strains. Additionally, the transcriptomes and proteomes of two representative strains, one from each of the two main groups, have been characterized to evaluate the impact of mutations on RNA and proteins levels. This study has revealed that type 2 strains show higher expression levels of CARDS toxin, a protein recently shown to be one of the major factors of inflammation. Thus, we propose that type 2 strains could be more toxigenic than type 1 strains of M. pneumoniae.

overall_design: 4 strains (6009, 2882, 5817, 5954) were analyzed, with two biological replicates

first: Maria

last: Lluch Senar


title: Sugar responsive regulatory network that controls organismal carbohydrate, amino acid and lipid homeostasis [set 2]

city: Helsinki

first: Ville

last: Hietakangas

address: Viikinkaari 9

country: Finland

institute: University of Helsinki

summary: Maintaining metabolic homeostasis in response to fluctuating nutrient intake requires intricate coordination between tissues of multicellular animals. The insulin/glucagon axis is well known to hormonally coordinate organism-wide carbohydrate metabolism. The ChREBP/Mondo-Mlx transcription factors regulate glycolytic and lipogenic genes locally in hepatocytes and adipocytes, but its role in systemic metabolic homeostasis has remained poorly understood. We demonstrate that Mondo-Mlx controls gene activity in several peripheral tissues of Drosophila melanogaster, where it regulates nutrient digestion and transport as well as carbohydrate, amino acid and lipid metabolism. In addition to directly regulating metabolic genes Mondo-Mlx controls a regulatory network composed of the Activin ligand Dawdle and GLI similar transcription factor Sugarbabe. Dawdle and Sugarbabe contribute to the regulation of a subset of Mondo-Mlx-dependent processes, including sugar-induced de novo synthesis of serine and fatty acids. In summary, our study establishes Mondo-Mlx sugar sensor as a master regulator of organismal metabolic homeostasis upon sugar feeding.

overall_design: Control (sug17d/+) and sugarbabe null mutant (sug17d/sug def) third instar larvae were fed control low sugar or high sugar diet and total RNA was extracted from the whole larvae.

first: Havula

last: Essi

first: Mattila

last: Jaakko

first: Suominen

last: Erja

first: Hietakangas

last: Ville


title: Sugar responsive regulatory network that controls organismal carbohydrate, amino acid and lipid homeostasis


title: Identification and profiling of microRNAs associated with white and black plumage pigmentation in the white and black feather bulbs of ducks by RNA-Sequencing

city: Wuhan

first: Sheila

middle: Nabwire

last: Apopo

state: Hubei

address: No.1,Shizishan Street · Hongshan District

department: Animal Science

institute: Huazhong Agricultural University

summary: Purpose: MicroRNAs (miRNAs) play important roles in many biological processes by regulating gene expression at the post-transcriptional level. However, the mechanism by which specific miRNAs may regulate plumage pigmentation has remained largely elusive. In this study, we sequenced miRNAs using Solexa sequencing and then performed a detailed analysis of their expression profiles between the black and white feather bulbs of ducks. This study provides the foundation for subsequent studies on the prospective practical role for such miRNAs in post-transcriptional gene regulation linked to plumage pigmentation.

overall_design: Methods: Black and white feather bulbs profiles of four ducks namely, Cui Hei, Kaiya, Liancheng pure breeds and Kaiya-Liancheng F2, were generated by illumina solexa sequencing . Three feather bulbs from the same individual duck were pooled as one samples. Samples from the same breed were pooled as one and sent to Beijing Genomics Institute (BGI, China) for small RNA library construction and sequencing. The libraries were prepared with NEBNext® UltraTM RNA Library Prep Kit. Sequencing was performed using Illumina sequencing technology (Illumina HiSeq 2000). The sequence quality was assessed with FastQC software . Clean sequence reads were analysed by miRDeep2 software version 2.1.2 .  We compared the miRNA expression profiles between black and white feather libraries of ducks using the DEGseq software  and our own perl script. miRNAs that adhered to the criteria log2-fold change ≥1 or ≤ -1 and p-value ≤0.05 were considered to be differentially expressed. The Student's t-test was used to compute the value. Validation of 10 conserved miRNAs sequencing data was performed using the SYBR Green assay.

first: Xiaoyong

last: Du

first: Shijun

last: Li


title: Genome-wide Analysis of Human Constitutive Androstane Receptor (CAR) Transcriptome in Wild-type and CAR-knockout HepaRG cells

city: Baltimore

first: Hongbing

address: 20 Penn Street

institute: University of Maryland, Baltimore

summary: The constitutive androstane receptor (CAR, NR1I3) modulates the transcription of numerous genes involving drug metabolism, energy homeostasis, and cell proliferation. Most functions of CAR however were defined from animal studies. Given the known species difference of CAR and the significant cross-talk between CAR and the pregnane X receptor (PXR), it is extremely difficult to decipher the exact role of human CAR (hCAR) in gene regulation, relying predominantly on pharmacological manipulations.  Here, utilizing a newly generated hCAR-knockout (KO) HepaRG cell line, we carried out RNA-seq analysis of the global transcriptomes in wild-type (WT) and hCAR-KO HepaRG cells treated with CITCO, a selective hCAR agonist, phenobarbital (PB), a dual activator of hCAR and hPXR, or vehicle control. Real-time PCR assays in separate experiments were used to validate RNA-seq findings. Our results indicate that genes encoding drug-metabolizing enzymes are among the main clusters altered by both CITCO and PB. Specifically, CITCO significantly changed the expression of 135 genes in an hCAR-dependent manner, while PB altered the expression of 227 genes in WT cells of which 94 were simultaneously modulated in both cell lines reflecting the dual effects of PB on hCAR/PXR. Notably, we found that many genes promoting cell proliferation and tumorigenesis were up-regulated in hCAR-KO cells, suggesting that hCAR may play an important role in cell growth that differs from mouse CAR. Together, our results reveal both novel and known targets of hCAR and support the role of hCAR in maintaining the homeostasis of metabolism and cell proliferation in the liver.

overall_design: Compare the mRNA profiles of HepRG WT and hCAR-KO cells after DMSO, PB and CITCO treatment, each sample was done in duplicate.

first: Daochuan

first: Mackowiak

last: Bryan


title: Sugar responsive regulatory network that controls organismal carbohydrate, amino acid and lipid homeostasis [set 1]

overall_design: Wild type and Mlx1 mutant third instar larvae were fed control low sugar or high sugar diet and the total RNA was extracted from the whole larvae.


title: Chemoresistance signature generated by genome-wide analysis of methylation, microRNAs, and gene expression in chemoresistant breast cancer cells

city: Wu Xi

first: Dong-Xu

last: He

address: Jiangnan University

department: Jiangnan University

institute: National Engineering Laboratory for Cereal Fermentation Technology

summary: We used RNA-seq and RRBS sequence to characterize the transcriptomic and methylome changes in chemoresistant and sensitive breast cancer cells

overall_design: Analysis of a transcriptome and methylome breast cancer cells

first: Fei

last: Gao

first: Feng

last: Gu

first: De-Sheng

last: Gong

first: Xiao-Ting

first: Ai-Qin

last: Mao

first: Jian

last: Jin

first: Li

last: Fu

first: Xin

last: Ma


title: Ovine rumen papillae biopsy via oral endoscopy; a rapid and repeatable method for serial sampling

city: Mosgiel

first: Kathryn

last: McRae

address: Puddle Alley

department: Animal Productivity

country: New Zealand

institute: AgResearch

summary:
AIMS: To explore and validate the utility of rumen endoscopy for collection of rumen papillae for gene expression measurement.
METHODS: Four adult Coopworth ewes were fasted for either 4 or 24 hours. Animals were sedated, placed in a dorsally recumbent position at 45 degrees with the head upright, and an endoscope inserted via a tube inserted into the mouth. Biopsies of rumen papillae were taken from the ventral surface of the rumen atrium under visual guidance. Two biopsies were collected from one of the animals that had been fasted for 4 hours, and three from one of the animals that had been fasted for 24 hours. Video of the rumen atrium and reticulum was also collected.
The animals recovered uneventfully. Biopsies were subsequently used for extraction and sequencing of mRNA.
RESULTS: The ventral surface of the rumen atrium was accessible after 4 hours off pasture, but a larger region was accessible after 24 hours of fasting. Sedation allowed access for endoscope use for around 5 to 10 minutes after which increased saliva flow was noted. Rumen papillae biopsies were easily collected, with samples from a variety of sites collected in the ∼10 minute time window. High quality RNA was obtained for stranded mRNA sequencing. Of the resulting reads, 69–70% mapped uniquely to version 3.1 of the ovine genome, and 48–49% to a known gene. The rumen mRNA profiles were consistent with a previously reported study.
CONCLUSIONS: This method for obtaining rumenal tissue was found to be rapid and resulted in no apparent short or long term effects on the animal. High quality RNA was successfully extracted and amplified from the rumen papillae biopsies, indicating that this technique could be used for future gene expression studies. The use of rumen endoscopy could be extended to collection of a variety of rumen and reticulum anatomical measurements and deposition and retrieval of small sensors from the rumen. Rumen endoscopy offers an attractive and cost effective approach to repeated rumen biopsies compared with serial slaughter or use of cannulated animals.

overall_design: Four adult Coopworth ewes were fasted for either 4 or 24 hours. Animals were sedated, placed in a dorsally recumbent position at 45 degrees head upright, and endoscope inserted via a tube inserted into the mouth. Biopsies of rumen papillae were taken from the ventral surface of the rumen atrium under visual guidance. Multiple rumen papillae biopsies were collected from several animals. Video of the rumen atrium and reticulum was also collected. The animals recovered uneventfully. Biopsies were subsequently used for extraction and sequencing of mRNA.

first: Michael

last: Shultz

first: Grant

last: Shackell

first: Colin

middle: G

last: Mackintosh

first: Marcelo

middle: F

last: Martinez

first: Kevin

middle: J

last: Knowler

first: Merrilee

last: Williams

first: Christine

last: Ho

first: Sara

last: Elmes

first: John

middle: C

last: McEwan


title: Expression data from fully engorged Haemaphysalis flava ticks (FE) midgut and partially engorged Haemaphysalis flava ticks (PE) midgut (MGs)

city: Changsha City

first: XingLI

last: Xu

address: Furong District

institute: Hunan Agricultural University

summary: To characterize the differentially expressed genes between fully engorged ticks and partially engorged ticks

overall_design: A total of 60 midguts of all collected Haemaphysalis flava ticks (30 fully engorged ticks and 30 partially engorged ticks) were dissected.

first: Tian-Yin

last: Cheng

first: Xing-Li


title: Genome-wide maps of CD14-dependent and CD14-independent bladder innate immune responses to UPEC

city: Gold Coast

first: Glen

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

institute: Griffith University

summary: We report a transcriptional response in the mouse bladder that encompasses multiple innate immune networks not previously associated with CD14. Major CD14-dependent pathways included immune cell trafficking, differential cytokine production in macrophages, and IL-17 signaling

overall_design: We used RNA-based sequencing technology for high-throughput profiling of innate immune responses in mouse bladder and the role of CD14 in these responses


title: Promoter-proximal R-loops regulate binding of chromatin regulators and pluripotency [DRIP-RNAseq]

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

institute: A*STAR

summary: Numerous chromatin-remodelling factors are regulated by interactions with RNA. However, the contexts in which chromatin-remodelling factors encounter various RNA species, as well as the molecular functions of RNA binding, are poorly understood. Here we show that R-loops, RNA:DNA hybrids consisting of nascent transcripts hybridized to template DNA strands, facilitate embryonic stem cell (ESC) differentiation by modulating the binding of two key chromatin-remodelling enzymes near gene promoters. As previously shown for polycomb repressive complex 2 (PRC2)1-5, we find that the Tip60-p400 histone acetyltransferase and nucleosome-remodelling complex binds in cis to nascent transcripts. However, whereas chromatin binding by PRC2 is broadly inhibited by transcription6, transcription is necessary for maximal Tip60-p400 binding at most target loci. Given that nascent transcripts expressed from GC-rich promoters frequently form R-loops7, we mapped the genomic locations of R-loops in mouse ESCs, observing higher average Tip60-p400 levels and lower average PRC2 levels at genes with R-loops near their transcription start sites (TSSs). Disruption of R-loops by overexpression of RNaseH1 broadly reduced Tip60-p400 and increased PRC2 enrichment, demonstrating R-loops exert both positive and negative effects on chromatin association by regulatory factors. Consistent with these findings, RNaseH1 overexpression results in widespread changes in gene expression and inhibits ESC differentiation, allowing undifferentiated cells to persist for at least two weeks after differentiation is induced. These results define a novel mechanism by which promoter-proximal R-loops modulate chromatin structure to facilitate changes in cellular identity.

overall_design: We examined the genome-wide localization of R-loop in mouse ES cells.

first: Thomas

last: Fazzio

first: Poshen


title: Promoter-proximal R-loops regulate binding of chromatin regulators and pluripotency [RNA-seq]

overall_design: We examined the transcriptional profile in control and RNaseH1 overexpression mouse ES cells during differentiation.


title: Promoter-proximal R-loops regulate binding of chromatin regulators and pluripotency [ChIP-seq]

overall_design: We exmined the genome-wide localization of Tip60 and p400 before/ after transcription inhibition in mouse ES cells, and examined genomic binding profiles of Tip60 complex and Suz12 upon overexpression of RNaseH1 by ChIP-seq.


title: Molecular characterization of diabetic heart of akita (RNA-Seq)

city: omaha

first: Paras

middle: Kumar

last: Mishra

state: Nebraska

address: DRC1 Room 5047

department: Cellular and Integrative Physiology

institute: University of Nebraska medical center

summary: To understand the molecular profile of diabetic heart in animal model of type 1 diabeties Akita, we performed RNA sequencing of heart tissue (male) at the 12 week to understand systemic changes.

overall_design: There were two groups. Wlid type and Akita (Ins2+/-). Both have same genetic background and akita has mutation in Insulin 2 gene.

first: Varun

last: Kesherwani

middle: K


title: KLF15 Establishes the Landscape of Circadian Expression in the Heart

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Road, Room 4537

department: Case Cardiovascular Research Institute

institute: Case Western Reserve University

summary: In the heart, KLF15 directs a biphasic circadian rhythm, while preventing extraneous oscillation at the transcriptomic level.

overall_design: We compared the cardiac circadian transcriptome of KLF15 KO (cK15) and control (α-MHC cre) mice using RNA sequencing analysis (RNAseq)

first: Lilei

last: Zhang


title: Analysis of the bovine monocyte-derived macrophage response to Mycobacterium avium subspecies paratuberculosis infection using RNA-seq

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

institute: University College Dublin

summary: Johne's disease, caused by infection with Mycobacterium avium subsp. paratuberculosis, (MAP), is a chronic intestinal disease of ruminants with serious economic consequences for cattle production in the United States and elsewhere. During infection, MAP bacilli are phagocytosed and subvert host macrophage processes, resulting in subclinical infections that can lead to immunopathology and dissemination of disease. Analysis of the host macrophage transcriptome during infection can therefore shed light on the molecular mechanisms and host-pathogen interplay associated with Johne's disease. Here, we describe results of an in vitro study of the bovine monocyte-derived macrophage (MDM) transcriptome response during MAP infection using RNA-seq. MDM were obtained from seven age- and sex-matched Holstein-Friesian cattle and were infected with MAP across a 6-h infection time course with non-infected controls. We observed 245 and 574 differentially expressed (DE) genes in MAP-infected versus non-infected control samples (adjusted P value ≤0.05) at 2 and 6 h post-infection, respectively. Functional analyses of these DE genes, including biological pathway enrichment, highlighted potential functional roles for genes that have not been previously described in the host response to infection with MAP bacilli. In addition, differential expression of pro- and anti-inflammatory cytokine genes, such as those associated with the IL-10 signaling pathway, and other immune-related genes that encode proteins involved in the bovine macrophage response to MAP infection emphasize the balance between protective host immunity and bacilli survival and proliferation. Systematic comparisons of RNA-seq gene expression results with Affymetrix® microarray data generated from the same experimental samples also demonstrated that RNA-seq represents a superior technology for studying host transcriptional responses to intracellular infection.

overall_design: Description of the bovine host transcriptomic response following infection of bovine monocyte-derived macrophages with Mycobacterium avium subspecies paratuberculosis

first: Maura

last: Casey

first: Kieran

last: Meade

first: Nicolas

last: Nalpas

first: Maria

last: Taraktsglou

middle: A

last: Browne

first: Kate

last: Killick

first: Stephen

middle: D

last: Park

first: Eamonn

last: Gormley

first: Karsten

last: Hokamp

last: Magee


title: Androgen Receptor profiling in tumor specimens yields hallmarks of prostate cancer outcome

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Molecular Pathology

institute: Netherlands Cancer Institute

summary: Prostate cancer is the most prevalent malignancy in men. Biomarkers for outcome prediction are urgently needed, since high-risk patients may benefit from additional therapy at early stages of the disease, greatly increasing the chance for cure. To identify prognostic markers and to determine causal players in prostate cancer progression, we assessed changes in chromatin state during tumor development and progression.  In addition, we identified a distinct Androgen Receptor/chromatin binding profile between primary prostate cancers and tumors with an acquired resistance to therapy. These differential Androgen Receptor/chromatin interactions dictated expression of a distinct gene signature with strong prognostic potential in another cohort of prostate cancer patients. Further refinement of the signature provided us with a concise list of nine genes that hallmark prostate cancer outcome in multiple independent validation series. In this report, we identified a novel gene expression signature for prostate cancer outcome through integration of multilevel genomic data on chromatin accessibility and transcriptional regulation with publicly available transcriptomic and clinical datastreams. With this, we present a highly innovative pipeline for biomarker discovery that is easily implementable in other fields of oncology.

overall_design: Accessible chromatin was mapped genome-wide by FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements) in 4 primary, 3 hormonal therapy-resistant and 3 metastatic prostate cancers, as well as in 4 normal prostate specimens. Androgen receptor (AR) binding to DNA was profiled by ChIP-seq (Chromatin Immunoprecipitation) genome-wide in 4 primary and 3 therapy-resistant prostate tumors.

first: Suzan

last: Stelloo

first: Ekaterina

last: Nevedomskaya

first: Andre

middle: M

last: Bergman


title: Molecular characterization of diabetic heart of akita

first: Paras

last: Mishra

overall_design: Refer to individual Series


title: A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation

city: Ashburn

first: Robert

last: Tjian

state: VA

address: 19700 Helix Dr

institute: HHMI Janelia Research Campus

summary: To study the function of E3 ligase Huwe1 knockdown on C2C12 proliferation and differentiation, we use mRNA-seq to compare gene expression profiles between control wild-type C2C12 myoblasts and two Huwe1 knockdown C2C12 cell lines generated by different shRNAs on differentiation Day 0 (proliferation medium) and Day 6 (differentiation medium for 6 days). To study the potential roles of Huwe1 in maintainance of muscle morphology, we use mRNA-seq to compare gene expression profiles between control and Huwe1 knockdown myotubes. To study whether downregulation of USP10 deubiquitinase is of functional significance during muscle differentiation, we compare gene expression profiles between control wildtype and USP10 overexpressing C2C12 cells on differentiation Day 6.

overall_design: Control and Huwe1 knockdown C2C12 cells were collected on differentiation day 0, day 6 and day 8. Control and USP10 overexpressed C2C12 cells were collected on differentiation day 6. Subsequently, directional mRNA-seq expriments were performed with mRNAs purified from the collected cells.

first: Li

last: Li


title: Glucocorticoid receptor and nuclear factor kappa-b affect 3D chromatin organization

city: Nijmegen

first: Shuang-Yin

last: Wang

address: Geert Grooteplein 28

department: Molecular Biology

institute: RIMLS

summary:
The impact of signal dependent transcription factors, such as glucocorticoid receptor (GR) and NFκB on the three-dimensional organization of chromatin remains a topic of discussion. The possible scenarios range from remodeling of higher order chromatin architecture by activated transcription factors to recruitment of activated transcription factors to pre-established long-range interactions.
Using 4C-seq and high-resolution ChIA-PET analysis of P300 we observed agonist-induced changes in long-range chromatin interactions, and uncovered interconnected enhancer-enhancer hubs spanning up to one megabase. The vast majority of activated GR and NFκB appears to join pre-existing P300 enhancer hubs without affecting the chromatin conformation. In contrast, binding of the activated transcription factors to loci with their consensus response elements leads to increased formation of an active epigenetic state of enhancers and a significant increase in long-range interactions within pre-existing enhancer networks. De novo enhancers or ligand-responsive enhancer hubs preferentially interact with ligand-induced genes.
We demonstrate that, at a subset of genomic loci, ligand-mediated induction leads to active enhancer formation and an increase in long-range interactions, facilitating efficient regulation of target genes. Therefore, our data suggest an active role of signal dependent transcription factors in chromatin and long-range interaction remodeling.

overall_design: Using DNaseI-seq and ChIP-seq for P300, H3K4me1, H3K4me3 and H3K27ac, we systematically characterized the GR and NFκB binding sites and their chromatin state in well-synchronized HeLa cells. The vast majority of binding sites (90%) is at distal regulatory regions that displayed the epigenetic marks of active enhancers (‘pre-programmed’) whereas at a small fraction, TF binding is concomitant with de novo establishment of an active chromatin state. Next, we mapped the distal chromatin interactions made by the GR and NFκB bound regulatory elements by generating high-resolution chromatin interaction profiles using the ChIA-PET method. For the ChIA-PET analysis we used antibodies against enhancer-associated P300 and against RNA-Polymerase II (POLII). P300 is a co-factor shared by GR and NFκB and its genomic occupancy in general is considered a hallmark of active enhancers. We specifically scrutinized the local chromatin interaction networks at genomic loci that are de novo programmed and compared them to those of pre-programmed loci. Subsequently, we extended our analysis using high-resolution 4C technology on a subset of 10 genomic viewpoint harboring de novo programmed regulatory elements. Our comprehensive analysis using ChIA-PET and 4C technologies provide compelling evidence for the active roles GR and NFκB in setting up the regulatory interaction networks de novo. In addition, such agonist induced de novo interaction networks preferentially make direct long-range contacts with the agonist responsive genes. Collectively, our study reveals a previously unappreciated signal dependent TF induced dynamic changes in chromatin regulatory networks and its impact on gene regulation.

first: Nagesha

last: Rao

first: Tatyana

last: Kuznetsova


title: Phospho-HLXB9 binding sites in mouse insulinoma cells

city: Bethesda

first: Sunita

last: Agarwal

state: MD

address: 10 Center Drive,

department: NIDDK,MDB

institute: NIH

summary: We have shown that increased β-cell proliferation in functioning pancreatic neuroendocrine tumors (insulinomas) correlated with expression of phosphorylated isoform of the transcription factor HLXB9 which is an embryonic beta-cell differentiation factor (HLXB9 is also known as HB9, MNR2, and MNX1). To investigate  the  target genes of phospho-HLXB9 we did  ChIP-seq using anti-HB9-PO4. This would help us better understand how phospho-HLXB9 regulates its targets and affects β-cell proliferation in insulinoma cells.

overall_design: Chromatin was prepared from 10 million cells of a mouse pancreatic islet β-cell line overexpressing HLXB9.  ChIPs with rabbit anti-HB9-PO4 were done using the Millipore ChIP-assay kit. ChIP-Seq libraries (input and anti-HB9-PO4-ChIP) were prepared with the Illumina ChIP-Seq DNA sample prep kit (catalog #: IP-102-1001). ChIP-Seq libraries were sequenced for 36 bp, and sequences were analyzed (Illumina, NIDDK genomics core facility).

first: Shruti

last: Desai


title: Transcriptome of Frankia in nitrogen-fixing root-nodule symbiosis with Datisca glomerata

city: Davis

first: Alison

last: Berry

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California

summary: A transcriptome of Cluster II Frankia in nitrogen-fixing root-nodule symbiosis with the host plant, Datisca glomerata, was obtained by Illumina sequencing and mapping to the corresponding published genome (NCBI Bioproject PRJNA46257).  Major metabolic pathways detected in Cluster II Frankia in symbiosis with Datisca glomerata were comparable to those described as up-regulated in the Frankia alni-Alnus glutinosa symbiosis (N Alloisio et al, MPMI 23(5):593-607, 2010):  nitrogenase biosynthesis, tricarboxylic acid cycle, respiratory-chain related functions, oxidation protection, and terpenoid biosynthesis.  These functions are consistent with the primary activities of Frankia in root nodules, e.g. to carry out the energetically-demanding fixation of atmospheric dinitrogen to ammonium, and to maintain internal reducing conditions.  Expression of genes coding for amino-acid biosynthetic pathways, including arginine as reported previously (AM Berry et al. Funct Plant Biol 38, 645–652, 2011) was detected.  A striking difference from other Frankia strains, revealed in the transcriptome of the Cluster II Frankia in symbiosis, was the expression of homologs of rhizobial nodulation genes, nodA, nodB and nodC.

overall_design: Total RNA was extracted from indeterminate root nodules of Datisca glomerata, in early nitrogen-fixation stage, to catalog the gene-expression patterns of Frankia, the microsymbiont, integrated over different stages of symbiotic development.

first: Elizabeth

last: Wilbanks

first: Marc

last: Facciotti


title: R loops regulate promoter-proximal chromatin architecture and cellular differentiation

first: Benson

last: Chen

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


title: Promoter-proximal R-loops regulate binding of chromatin regulators and pluripotency [RIP-seq]

overall_design: We examined the interacting RNAs in Tip60-p400 complex by RIP-seq in mouse ES cells.

first: Thomas

last: Fazzio

first: Poshen

middle: B