title: Whole-genome GR binding sites and histone acetylation status in pediatric acute lymphoblastic leukemia patient-derived xenografts following dexamethasone treatment in vivo

city: Sydney

first: Dominik

last: Beck

state: NSW

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

country: Australia

institute: University of Technology Sydney

summary: Glucocorticoids are critical components of combination chemotherapy regimens in pediatric acute lymphoblastic leukemia (ALL). However, the signaling pathways regulating apoptosis in glucocorticoid-treated lymphoid cells remain unclear. In this study, pediatric ALL patient-derived xenograft inherently sensitive to glucocorticoids were exposed to dexamethasone in vivo. Whole-genome GR binding sites and histone acetylation status were detected using chromatin immunoprecipitation sequencing analyses. This provided a global understanding of dexamethasone-induced DNA modulations in ALL cells in vivo, which is likely to be important in the understanding of mechanisms of glucocorticoid response in lymphoid malignancies.

overall_design: One xenograft (ALL-54) was derived from a patient of dexamethasone-good responder. The xenograft was innoculated into 2 NOD/SCID mice, and treated with dexamethasone (15 mg/kg) or vehicle control. Binding of glucocorticoid receptor (GR), histone acetylation and IgG control in spleen-harvest xenograft samples were detected using ChIP-seq.

first: Duohui

last: Jing

first: Jason

last: Wong

first: John

middle: E

last: Pimanda

first: Richard

middle: B

last: Lock


title: Evaluation of methyl-binding domain based enrichment approaches revisited

status: Public on Dec 20 2014

city: Richmond

first: Karolina

middle: A

last: Aberg

state: VA

address: 1112 East Clay Street

department: Center for Biomarker Resarch & Personalized Medicine

country: USA

institute: Virginia Commonwealth University

type: Methylation profiling by high throughput sequencing

summary: A comparison of methylMiner and MethylCap, two methylation enrichment kits

overall_design: The main analysis include two individuals (mice) in technical duplicates from various lab/technical conditions. The results are compared with previous studies of two human samples from a number of lab/technical conditions (human data available at dbGaP: record number phs000608.v1.p1).  In addition a DNA from a third mouse is used for investigations of specific alterations of the protocol.

first: Linying

last: Xie

first: Robin

middle: F

last: Chan

first: Min

last: Zhao

first: Ashutosh

middle: K

last: Pandey

first: Gaurav

last: Kumar

first: Shaunna

last: Clark

first: Edwin

middle: J

last: van den Oord


title: Differentially-expressed miRNAs in MDBK cells infected with bovine viral diarrhea virus compared to MDBK cells

status: Public on Dec 16 2014

city: Shihezi

first: Qiang

last: Fu

state: Xinjiang

address: Bei 4 Road

country: China

institute: Shihezi University

type: Non-coding RNA profiling by high throughput sequencing

summary: Non-canonical microRNAs (miRNAs) are a class of short endogenous RNA molecules with the ability to control development, autophagy, apoptosis and the stress response in eukaryotes by pairing with partially complementary sites in the 3' untranslated regions (UTRs) of targeted genes. Recent studies have demonstrated that miRNAs serve as critical effectors in intricate networks of host-pathogen interactions. Thereforce, the differential expression of miRNAs were evaluated in Madin-Darby bovine kidney (MDBK) cells infected with bovine viral diarrhea virus (BVDV) NADL (100 TCID50/ 0.1 ml) for 6 h compared to normal MDBK cells using Solexa high-throughput sequencing technology (BGI, China).

overall_design: Examination of small RNA populations in BVDV infected MDBK cells compared to MDBK cells

first: Chuangfu

last: Chen


title: RNF17 referees ping-pong in mouse testes [smallRNAseq]

status: Public on Dec 17 2014

city: Cold Spring Harbor

first: Vasily

last: Vagin

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor

summary: In mammals, piRNA populations are dynamic throughout male germ cell development. Embryonic piRNAs consist of both primary and secondary species and are mainly directed toward transposons. In meiotic cells, however, the piRNA population is transposon-poor and restricted to primary piRNAs derived from pachytene piRNA clusters. The mechanism controlling which piRNAs are present at each developmental stage is poorly understood. Here we show that RNF17 shapes adult meiotic piRNA content by suppressing the production of secondary piRNAs. In the absence of RNF17, ping-pong (secondary amplification) occurs inappropriately in meiotic cells – aberrantly targeting protein-coding genes and lncRNAs. Our data indicate that RNF17 comprises one component of a “refereeing” mechanism that prevents deleterious activity of the meiotic piRNA pathway by ensuring the selective loading of PIWI proteins with products of meiotic piRNA clusters.

overall_design: Examination of small RNA profile in heterozygous and homozygous RNF17 adult testes, pachytene or round spermatid sorted cells

first: Kaja

last: Wasik

first: Oliver

last: Tam

first: Yuan

last: Hao

first: Ilaria

last: Falciatori

first: Molly

last: Hammell

middle: V

first: Gregory

last: Hannon


title: Ribonuclease L Targets Discrete Sites in Influenza Virus RNA

city: Aurora

first: Daphne

middle: A.

last: Cooper

state: CO

department: Department of Microbiology

institute: University of Colorado

summary: We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and quantify ribonuclease L cleavage sites in host and viral RNAs.

overall_design: To make cDNA libraries, we exploited the 2’, 3’-cyclic phosphate at the end of RNA fragments produced by RNase L and other metal-ion-independent endoribonucleases. Using Arabidopsis thaliana tRNA ligase, RNA fragments with 2’, 3’-cyclic phosphates were covalently attached to defined RNA linkers containing an 8-base long unique molecular identifier (UMI) sequence. Libraries prepared in this manner contain cDNA derived exclusively from RNA fragments with 2', 3'-cyclic phosphates. The UMI sequence allows for detailed quantitation. We applied these methods to total RNA from A549 cells infected by influenza A virus unable to express NS1. NS1 inhibits the activation of RNase L.

first: Shuvojit

last: Banerjee

first: Arindam

last: Chakrabarti

first: Adolfo

last: García-Sastre

first: Andrew

last: Firth

first: Jay

middle: R

last: Hesselberth

first: Robert

middle: H

last: Silverman

first: David

last: Barton


title: Gene expression profiling of melanoma cell lines by high throughput sequencing

city: Los Angeles

first: Jennifer

last: Tsoi

state: CA

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: A panel of 29 melanoma cell lines were gene expression profiled by RNA-Seq.

overall_design: mRNA profiles of 29 melanoma cell lines

first: Lidia

last: Robert

first: Deborah

last: Wong

first: Mohammed

middle: S

last: Atefi

first: Antoni

last: Ribas

first: Thomas

middle: G

last: Graeber


title: RNF17 referees ping-pong in mouse testes [RNAseq]

first: Vasily

last: Vagin

overall_design: Examination of transcriptom in heterozygous and homozygous RNF17 adult testes and RNF17 immunoprecipitates

first: Kaja

last: Wasik

first: Oliver

last: Tam

first: Yuan

last: Hao

first: Ilaria

last: Falciatori


title: Next Generation Sequencing (NGS) of zebrafish larvae transcriptome by 2,2',4,4'-tetrabromodiphenyl ether (BDE47) treatment

city: Shanghai

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

summary:
Purpose: We report the application of NGS for profiling the impacts of BDE47 exposure on the transcriptome of zebrafish larvae.
Methods: mRNA profiles of 6-day-old BDE47-treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Results: Compared BDE47 treatments with solvent control, 2235 transcripts were affected after 500 μg/l exposure, in which 1338 were up-regulated and 897 were down-regulated, and 552 transcripts were affected after 5 μg/l exposure, in which 155 were up-regulated and 397 were down-regulated. High concentration of BDE47 exposure resulted in more up-regulated genes.
Conclusions: This study provides a framework for the application of high-throughput RNA sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval transcriptome.

overall_design: Examination of zebrafish larvae transcriptomes with vehicle and 2 different concentrations of BDE47 treatments.

first: Jing

last: Zhao


title: Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature

status: Public on Dec 18 2014

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mouse ES-derived motor neurons (ES-MN) exposed to SOD1 mutant mouse astrocyte conditioned media

city: New York

first: Mariano

middle: Javier

last: Alvarez

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

summary:
This datased was used to obtain a genome-wide expression signature for the early response of mouse motor neurons to mutant SOD1 astrocytes conditioned media.
Neurons, far from living in isolation, are surrounded by a host of other neuronal and non-neuronal cells, such as astrocytes. The latter entertain complex functional interactions with neighboring neurons, which, under normal conditions, are important for the their well-being. In pathological situations, however, altered astrocyte behavior may contribute to the demise of neighboring neurons. Such non-cell autonomous pathogenic scenario is increasingly considered in a variety of disorders, including amyotrophic lateral sclerosis (ALS), the most frequent adult-onset paralytic disorder. Assembly and interrogation of gene regulatory models has helped elucidate causal mechanisms responsible for the presentation of several tumor-related phenotypes. To systematically elucidate the effectors of neurodegeneration in a model of ALS, we first developed techniques for the efficient purification of motor neurons (MNs), the primary target of ALS neurodegenerative process. We then generated gene expression profiles to fully characterize the critical timepoints associated with initiation and commitment of MN degenerative progression in an in vitro murine mutant SOD1 (mSOD1) model of ALS.

overall_design:
ES cells were derived from transgenic Hlxb9-GFP1Tmj mice expressing eGFP and CD2 driven by the mouse HB9 promoter. These cells were then differentiated into motor neurons (ES-MN) as described previously [PMID 12176325]
ES-MN were exposed to non-transgenic (NTg), G93A mutant SOD1 (mSOD1) or wtSOD1 over-expression astrocytes conditioned media for 0 days (time zero control), 1 day, and 3 days. Total RNA was extracted and profiled by RNAseq.

first: Serge

last: Przedborski

first: Andrea

last: Califano

first: Burcin

last: Ikiz


title: Global analysis of non-coding small RNAs in Arabidopsis in response to jasmonate treatment by deep sequencing technology

city: Beijing

first: Zhiping

last: Jin

address: Chaoyang District, Beichenxilu

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

summary: In plants, non-coding small RNAs play a vital role for plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate (JA) pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. 30 new miRNAs and 27 new miRNA candidates were identified through a bioinformatics approach. 49 known miRNAs (belonging to 24 families), 15 new miRNAs and new miRNA candidates (belonging to 11 families) and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs (belonging to 9 families) were repressed by JA.

overall_design: 2 samples were examined: wild type treated with JA, and the JA-deficient aos mutant.

first: Bosen

last: Zhang

first: Daoxin

last: Xie


title: Maternal microRNAs in Drosophila melanogaster

city: Colchester

first: Antonio

last: Marco

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

summary: MicroRNAs detected in Drosophila melanogaster unfertilized eggs

overall_design: Bloomington w[1118] flies were kept at 25ºC on cornmeal based media, with 12 hours light/dark cycles. Virgin females were sorted at the pupae stage to avoid any unwanted fertilization. In a population cage I let 80-100 females to lay eggs in apple juice agar plates for 8 hours, collecting 1 hour after dawn. Eggs were collected with a sieve and washed with saline solution. Small RNA was size selected and sequenced.


title: RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis

status: Public on Dec 15 2014

city: Santiago de Compostela

first: Diego

last: Robledo

address: Rúa Lope Gómez de Marzoa s/n CIBUS building

department: Genetics

institute: University of Santiago de Compostela

summary:
Background: Enteromyxosis caused by the intestinal myxozoan parasite Enteromyxum scophthalmi is a serious threat for turbot (Scophthalmus maximus, L.) aquaculture, causing severe catarrhal enteritis leading to a cachectic syndrome, with no therapeutic options available. There are still many aspects of host-parasite interaction and disease pathogenesis that are yet to be elucidated, and to date, no analysis of the transcriptomic changes induced by E. scophthalmi in turbot organs has been conducted. In this study, RNA-seq technology was applied to head kidney, spleen and pyloric caeca of severely infected turbot with the aim of furthering our understanding of the pathogenetic mechanisms and turbot immune response against enteromyxosis.
Results: A huge amount of information was generated with more than 23,000 identified genes in the three organs, amongst which 4,762 were differently expressed (DE) between infected and control fish. Associate gene functions were studied based on gene ontology terms and available literature, and the most interesting DE genes were classified into five categories: 1) immune and defence response; 2) apoptosis and cell proliferation; 3) iron metabolism and erythropoiesis; 4) cytoskeleton and extracellular matrix and 5) metabolism and digestive function. The analysis of down-regulated genes of the first category revealed evidences of a connexion failure between innate and adaptive immune response, especially represented by a high number of DE interferon-related genes in the three organs. Furthermore, we found an intense activation of local immune response at intestinal level that appeared exacerbated, whereas in kidney and spleen genes involved in adaptive immune response were mainly down-regulated. The apoptotic machinery was only clearly activated in pyloric caeca, while kidney and spleen showed a marked depression of genes related to erythropoiesis, probably related to disorders in iron homeostasis. The genetic signature of the causes and consequences of cachexia was also demonstrated by the down-regulation of the genes encoding structural proteins and those involved in the digestive metabolism.
Conclusions: This transcriptomic study has enabled us to gain a better understanding of the pathogenesis of enteromyxosis and identify a large number of DE target genes that bring us closer to the development of strategies designed to effectively combat this pathogen.

overall_design: Four samples per organ (kidney, spleen and pyloric caeca) were sequenced by Illumina HiSeq 2000 as 100bp paired-end reads. For each organ, three samples were taken from Enteromyxum severely infected turbot and the remaining one was a pool of three control turbot.

first: Paolo

last: Ronza

first: Peter

middle: W

last: Harrison

first: Ana-Paula

last: Losada

first: Roberdo

last: Bermúdez

first: Belén

last: Pardo

first: María-José

last: Redondo

first: Ariadna

last: Sitjà-Bobadilla

first: María-Isabel

last: Quiroga

first: Paulino

last: Martínez


title: Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Super-enhancers and stretch enhancers (SEs) drive expression of genes that play prominent roles in normal and disease cells, but the functional importance of these clustered enhancer elements is poorly understood, so it is not clear why genes key to cell identity have evolved regulation by such elements. Here we show that super-enhancers consist of functional constituent units that concentrate multiple developmental signaling pathways at key pluripotency genes in embryonic stem cells and confer responsiveness to signaling of their associated genes. Cancer cells frequently acquire SEs at genes that promote tumorigenesis, and we show that these genes are especially sensitive to perturbation of oncogenic signaling pathways. Super-enhancers thus provide a platform for signaling pathways to regulate genes that control cell identity during development and tumorigenesis.

overall_design: ChIP-Seq for H3K27ac and RNA Pol II in mouse embryonic stem cells with CRISPR-deleted enhancers

first: Denes

last: Hnisz

first: Jurian

last: Schuijers

first: Charles

middle: Y

last: Lin

first: Abraham

last: Weintraub

first: Brian

last: Abraham

first: Tong

middle: I

last: Lee

first: James

last: Bradner


title: Defective removal of ribonucleotides from DNA promotes systemic autoimmunity

city: Dresden

first: Min Ae

last: Lee-Kirsch

address: Fetscherstraße 74

department: Universitätsklinikum Carl Gustav Carus

country: Germany

institute: TU Dresden

summary: Constitutive low level DNA damage in RNASEH2 deficiency is linked to innate immune activation. Hierarchical clustering of over 16000 transcripts revealed remarkably similar profiles in patients with lupus erythematosus and patients with AGS with up-regulation of genes involved in DNA damage signaling and type I-IFN signaling.

overall_design: Comparison of transcriptional profiles of native RNASEH2-deficient patient fibroblasts with wild type cells.

first: Claudia

last: Günther

first: Barbara

last: Kind

first: Martin

last: Reijns

first: Nicole

last: Berndt

first: Manuel

last: Martinez-Bueno

first: Christine

last: Wolf

first: Victoria

last: Tüngler

first: Osvaldo

last: Chara

first: Young

first: Norbert

last: Hübner

first: Louise

last: Bicknell

first: Sophia

last: Blum

last: Krug

first: Franziska

last: Schmidt

first: Stefanie

last: Kretschmer

first: Sarah

last: Koss

first: Katy

last: Astell

first: Georgia

last: Ramantani

first: Anja

last: Bauernfeind

first: David

last: Morris

first: Deborah

middle: C

last: Graham

first: Doryen

last: Bubeck

first: Andrea

last: Leitch

first: Stuart

last: Ralston

first: Elizabeth

last: Blackburn

first: Manfred

last: Gahr

first: Torsten

last: Witte

first: Timothy

last: Vyse

first: Inga

last: Melchers

first: Elisabeth

last: Mangold

first: Markus

last: Nöthen

last: Aringer

first: Annegret

last: Kuhn

first: Kirsten

last: Lüthke

first: Leonore

last: Unger

first: Annette

last: Bley

first: Alice

last: Lorenzi

first: John

last: Isaacs

first: Dimitra

last: Alexopoulou

first: Karsten

last: Conrad

first: Andreas

last: Dahl

first: Axel

last: Roers

first: Marta

last: Alarcon-Riquelme

first: Andrew

last: Jackson

first: Min


title: RNA-SEQ analysis of E14.5 pooled dorsal root ganglia control samples

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: A comparative RNA-SEQ analysis of control total RNA preparations from pooled E14.5 dorsal root ganglia was carried out to determine the performance of the RNAseq reactions at differing concentrations (3ng, 10ng & 30ng in high or low volumes) and concordance among different institutions using the same source of RNA.

overall_design: RNA was extracted from E14.5 dorsal root ganglia dissected from wild type C57BL/6J embryos and sequenced using Illumina Hiseq 2500 platform.

first: E

middle: M

last: Southard-Smith

first: Masato

last: Hoshi

first: Mike

last: Heinz

first: Eric

last: Tycksen

first: Sanjay

last: Jain


title: Global analysis of photosynthesis transcriptional regulatory networks [ChIP-seq]

city: Madison

first: Timothy

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

summary: To gain a deeper understanding of the transcription factors that regulate photosynthesis in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 4 transcription factors (FnrL, PrrA, CrpK and RSP_2888) known or predicted to be involved in the regulation of photosynthesis.

overall_design: Genome-wide protein-DNA interaction analysis of 4 transcription factors known or predicted to be involved in the regulation of photosynthesis in Rhodobacter sphaeroides, using ChIP-seq and complementary assays.

first: Saheed

last: Imam


title: A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

summary: To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).

first: Aviv

last: Regev

first: Andrea

last: Pauli

first: Alexander

last: Schier


title: Global analysis of photosynthesis transcriptional regulatory networks

platform_organism:
Cereibacter sphaeroides
Cereibacter sphaeroides 2.4.1


title: Enhancer Analysis in Peripheral Nerve Injury

first: John

last: Svaren

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: ChIP-seq of H3K27acetylation in sham and injured nerve. Schwann cells play an important role in the response of peripheral nerve to injury. This study was designed to identify enhancers that are altered in sciatic nerve at 3 days post-injury to help identify pathways that mediate the gene expression reprogramming that occurs in Schwann cells after nerve injury. We employed ChIP-seq analysis of H3K27 acetylation as a mark of actively engaged enhancers, and compared enhancers in the distal stump of transected sciatic nerve compared to contralateral (sham) condition.

overall_design: 2 independent ChIP samples each for Sham and Injury conditions, with respective inputs

first: Holly

last: Hung

first: Guannan

last: Sun

first: Sunduz

last: Keles


title: Whole-transcriptome analysis of endothelial-to-hematopoietic stem cell transition

status: Public on Dec 14 2014

first: Elaine

last: Dzierzak

address: 47 Little France Crescent

department: MRC Centre for Inflammation Research

institute: University of Edinburgh

summary: Hematopoietic stem cells (HSCs) are generated via a natural transdifferentiation process known as endothelial-to-hematopoietic cell transition (EHT). Due to small numbers of embryonal arterial cells undergoing EHT and the paucity of markers to enrich for hemogenic endothelial cells, the genetic program driving HSC emergence is largely unknown. Here, we use a highly sensitive RNAseq method to examine the whole transcriptome of small numbers of enriched aortic HSCs (CD31+cKit+Ly6aGFP+), hemogenic endothelial cells (CD31+cKit-Ly6aGFP+) and endothelial cells (CD31+cKit-Ly6aGFP-).

overall_design: Comparison of mRNA profiles of endothelial cells, hemogenic endothelial cells, and hematopoietic stem cells generated by deep-sequencing of sorted populations from pool of embryos, in triplicate.


title: A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (ATAC-Seq)

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into distinct cell fates are not fully understood. Here, we identify chromatin-regulating and cell-fate-determining transcription factors (TF) governing dendritic cell (DC) development by annotating the enhancer and promoter landscapes of the DC lineage. Combining these analyses with detailed over-expression, knockdown and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC  epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, differential activity of TF can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes.

overall_design: Here we profiled accessible chromatin of moDC and pDC using ATAC-seq assay, developed by Buenrostro et al. (2013)


title: Senescence leads to epigenomic disruption invoking hallmarks of reprogramming and pluripotency

city: Philadelphia

first: Shelley

middle: L

last: Berger

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Departments of Cell & Developmental Biology; Biology; Genetics

institute: University of Pennsylvania


title: A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (RNA-Seq)

overall_design: Here analyzed 2 experiments, each one contains samples of moDC and pDC ex vivo cultured cells. The first experiment contains 32 samples of moDC and pDC following stimulation with various TLR stimulators. The second experiment contains 8 samples of moDC and pDC following perturbations; Cebpb and Irf8 knock down or over expression.


title: 7q11.23 dosage-dependent dysregulation in the human pluripotent state primes aberrant transcriptional programs in disease-relevant lineages (RNAseq)

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology & University of Milano, Italy

summary: We apply the cellular reprogramming experimental paradigm to two disorders caused by symmetrical copy number variations (CNV) of 7q11.23 and displaying a striking combination of shared as well as symmetrically opposite phenotypes: Williams Beuren syndrome (WBS) and 7q microduplication syndrome (7dupASD). Through a uniquely large and informative cohort of transgene-free patient-derived induced pluripotent stem cells (iPSC), along with their differentiated derivatives, we find that 7q11.23 CNV disrupt transcriptional circuits in disease-relevant pathways already at the pluripotent state. These alterations are then selectively amplified upon differentiation into disease-relevant lineages, thereby establishing the value of large iPSC cohorts in the elucidation of disease-relevant developmental pathways. In addition, we functionally define the quota of transcriptional dysregulation specifically caused by dosage imbalances in GTF2I (also known as TFII-I), a transcription factor in 7q11.23 thought to play a critical role in the two conditions, which we found associated to key repressive chromatin modifiers. Finally, we created an open-access web-based platform (accessible at http://bio.ieo.eu/wbs/ ) to make accessible our multi-layered datasets and integrate contributions by the entire community working on the molecular dissection of the 7q11.23 syndromes.

overall_design: We reprogrammed skin fibroblasts from patients harbouring a 7q11.23 hemi-deletion (WBS, 4 patients; +1 atypical deletion, AtWBS) or microduplication (7dupASD; 2 patients), as well as from one unaffected relative and two unrelated controls, using integration-free mRNA-reprogramming, leading to the establishment of a total of 27 characterized iPSC clones. We profiled these by RNAseq (either polyA or ribo-zero). To isolate the contribution of GTF2I to the transcriptional dysregulation, we created stable lines expressing a short hairpin against GTF2I from a representative subset of these iPSC clones, and profiled by RNAseq 7 such lines along with their respective scramble controls. Finally, we also profiled by RNAseq mesenchymal stem cells (MSC) derived from a representative subset of the lines.

first: Antonio

last: Adamo

first: Sina

last: Atashpaz

first: Pierre-Luc

last: Germain

first: Matteo

last: Zanella

last: D'Agostino

first: Veronica

last: Albertin

first: Josh

last: Chenoweth

first: Lucia

last: Micale

first: Carmela

last: Fusco

first: Christian

last: Unger

first: Bartolomeo

last: Augello

first: Orazio

last: Palumbo

first: Brad

last: Hamilton

first: Massimo

last: Carella

first: Emilio

last: Donti

first: Giancarlo

last: Pruneri

first: Angelo

last: Selicorni

first: Elisa

last: Biamino

first: Paolo

last: Prontera

first: Ronald

last: McKay

last: Merla


title: 7q11.23 dosage-dependent dysregulation in the human pluripotent state primes aberrant transcriptional programs in disease-relevant lineages (ChIP-Seq)

first: Giuseppe

last: Testa

overall_design: We tested three antibodies against GTF2I for ChIP-seq application, and selected the one showing the best enrichment to profile GTF2I bindings across a panel of 12 iPSC lines established from patients harbouring a 7q11.23 hemi-deletion (WBS; 5 patients) or microduplication (7dupASD; 2 patients), as well as from two independent controls individuals.

first: Antonio

last: Adamo

first: Sina

last: Atashpaz

first: Pierre-Luc

last: Germain

last: Zanella

last: D'Agostino


title: Deterministic direct reprogramming of somatic cells to pluripotency [RRBS]

status: Public on Dec 13 2014

first: Asaf

last: Zviran

address: 234 Herzl Street

department: Molecular Genetics

summary: Somatic cells can be directly reprogrammed to pluripotency by exogenous expression of transcription factors, classically Oct4, Sox2, Klf4 and c-Myc. While distinct types of somatic cells can be reprogramed with varying efficiencies and by different modified reprogramming protocols, induced pluripotent stem cell (iPSC) induction remains inefficient and stochastic where a fraction of the cells converts into iPSCs. The nature of rate limiting barrier(s) preventing majority of cells to convert into iPSCs remains elusive. Here we show that neutralizing Mbd3, a core member of the Mbd3/NURD co-repressor and chromatin-remodeling complex, results in deterministic and synchronized reprogramming of multiple differentiated cell types to pluripotency. 100% of Mbd3 depleted mouse and human somatic cells convert into iPSCs after seven days of reprogramming factor induction. Our findings delineate a critical pathway blocking the reestablishment of pluripotency, and offer a novel platform for future dissection of epigenetic dynamics leading to iPSC formation at high resolution.

overall_design: Reduced representation bisulfite sequencing (RRBS) was applied to mouse iPS cells and mouse embryonic fibroblast (MEF) before and after DOX induction (initiating reprogramming by OSKM factors) from randomly selected Mbd3+/+ and Mbd3flox/- clonal cell line series. Polyclonal donor cell cultures were harvested at days 0,4 and 8 after DOX reprogramming without selection or sorting for any marker or passaging, and mapped for similarity to subcloned iPSC lines.

first: Y

last: Rais

first: E

last: Chomsky

first: S

last: Shipony

last: Mukamel

first: J

last: Hanna


title: Human cells contain natural double-stranded RNAs with potential regulatory capacity

city: Illkirch-Graffenstaden

first: Maximiliano

middle: M.

last: Portal

state: Alsace

address: 1 rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: IGBMC

summary: Although recent evidence suggests that overlapping sense/antisense transcription is a common feature in higher eukaryotes, the possibility that overlapping transcripts could interact to each other and bear a specific biological function has not been explored. Here we show that a plethora of sense/antisense transcript pairs are co-expressed from 8q24.21 within the same cell and acquire a stable double-stranded RNA conformation. Interestingly, these molecules display predominantly nuclear localization and establish specific interactions with nuclear components. A detailed characterization of a particular sense/antisense pair (ndsRNA-2a) revealed that this molecule displays differential localization throughout the cell cycle, interacts with RCC1 and RAN and through the latter with the mitotic RANGAP1-SUMO1/RANBP2 complex. Notably, an increased number of bi/multi-nucleated cells and chromatin bridges were observed upon ndsRNA-2a overexpression, whereas strand-specific ndsRNA-2a knockdown leads to mitotic catastrophe and cell death. This suggests a functional role of ndsRNA-2a in cell cycle progression that critically requires its double stranded nature. Finally, the identification of hundreds of sense/antisense transcripts pairs harboring ndsRNA profile signatures and their regulation by cellular cues suggests that ndsRNAs constitute a novel class of regulatory molecules that are likely to be involved in a plethora of biological processes.

overall_design: PLB985 long (3x datasets) and small (3x datasets) strand specific RNA-Seq for captured RNAs. Global PLB985 for long (2x datasets) and small RNAs (2x datasets). Global libraries for EtOH (vehicle) treated (1x dataset) or retinoic acid induced differentiated PLB985 cells (1x dataset).

first: Hinrich

last: Gronemeyer


title: 7q11.23 dosage-dependent dysregulation in the human pluripotent state primes aberrant transcriptional programs in disease-relevant lineages

overall_design: Refer to individual Series


title: RNAseq Replicate experiments from PD38 and PD79 IMR90s

first: Shelley

last: Berger

summary: RNAseq replicate in Proliferating and Senescent IMR90s

overall_design: We used RNAseq to examine RNA levels in human IMR90 replicative senescence (RS)

first: Gabriel

last: Otte

first: Brian

last: Capell


title: Genome-Wide Mapping of 5-mC and 5-hmC in severely Preeclamptic Placentas.

first: Li

last: Xiaotian

state: Shanghai

address: Fangxie Road 419 in Huangpu District

department: Obstetrics Department

institute: Obstetrics and Gynecology Hospital of Fudan University

summary: Preeclampsia (PE) is a major contributor of maternal mortality with uncertain etiology. Recent studies suggested that epigenetic modifications, including DNA methylation, play a vital role in the development of PE. In this study, we have mapped genome-wide distribution of 5-methylcytosin (5-mC) and 5-hydroxymethylcytosine (5-hmC) using MeDIP and (h)MeDIP in the placentas from severely preeclamptic patients and normal controls. A total 194485 pooled 5-mC peaks and 138133 pooled 5-hmC peaks were identified, of which 714 5-mC peaks and 119 5-hmC peaks showed significant difference between patients and controls (>2-fold, p<0.05).To our knowledge, this is the first report of DHMRs (Differentially Hydroxy-Methylated Regions) in preeclamptic placenta. We not only confirmed the aberrant DNA methylated regions in the process of preeclampsia reported previously, but also identified unreported regions. A total of 4 selected DMRs (Differentially Methylated Regions) were also confirmed by MassARRAY EppiTYPER. Of these, PTPRN2, which had low level of 5-mC and high level of 5-hmC at gene body, was further verified to have lower methylation level at promoter regions in case group compared with controls. In conclusion, our study provided genome-wide distribution of 5-mC and 5-hmC in severe PE and normal controls, which have further clinical value for the identification of diagnostic and therapeutic markers for severe PE.

overall_design: Examination of 5-mC and 5-hmC pattern in 4 control cases' tissue and 4 severely Preeclamptic Placentas cases' tissue.

first: Lan

last: Fei

first: Zhu

last: Lisha

first: Lv

last: Ruitu


title: Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection

status: Public on Dec 12 2014

city: Uppsala

first: Anna

last: Åsman

address: PO Box 7080

department: Molecular Sciences

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

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


title: Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection [host plant infection]

summary: Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. Results: To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Conclusions: Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans.

overall_design: Small RNA sequence data from Phytophthora infestans-infected potato leaf tissue and P. infestans mycelium tissue. Three infection stage time-points. Two P. infestans lines: 88089 (wild-type) and PiDcl1 (transformant PiDcl1 knock-down). No replicates. Total number of samples: 8.

first: Ramesh

last: Vetukuri

first: Sultana

middle: N

last: Jahan

first: Johan

last: Fogelqvist

first: Pádraic

last: Corcoran

middle: O

last: Avrova

first: Stephen

last: Whisson

first: Christina

last: Dixelius


title: H3K9me3 ChIPseq experiments from PD IMR90s

summary: H3K9me3 ChIPseq in Proliferating and Senescent IMR90s

overall_design: We used ChIP-seq to examine the global binding of H3K9me3 in human IMR90 replicative senescence (RS) and oncogene-induced (OIS)


title: Lamin B1 ChIPseq experiments from ER:RAS IMR90s

summary: Lamin B1 from OIS IMR90s

overall_design: We used ChIP-seq to examine the global binding of Lamin B1 in human IMR90 oncogene-induced senescence

first: Zhixun

last: Dou


title: Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection [life cycle]

summary: Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. Results: In order to identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Conclusions: Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs whose levels are elevated during infection of P. infestans on potato.

overall_design: Small RNA sequence data from two Phytophthora infestans isolates. Four life-cycle stages from each isolate. No replicates. Total number of samples: 8.

middle: K


title: MORC1 represses transposable elements in the mouse male germ line

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA methylated and silent genes. MORC1 deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homolog DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites.  Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation.

overall_design: This data includes: 47 RNA-seq, 4 smRNA-seq, 6 BS-seq, and 2 ChIP-seq datasets

first: William

middle: A

last: Pastor


title: Gene expression levels in three Neurospora species reveal genes crucial for sexual reproduction in Neurospora crassa

city: New Haven

first: Jeffrey

middle: P

last: Townsend

state: CT

address: 135 College street

department: Biostatistics

institute: Yale School of Public Health

summary: Many fungi form complex three-dimensional fruiting bodies, within which the meiotic machinery for sexual spore production has been considered to be largely conserved over evolutionary time.  Indeed, much of what we know about meiosis in plant and animal taxa has been deeply informed by studies of meiosis in Saccharomyces and Neurospora.  Nevertheless, the genetic basis of fruiting body development and its regulation in relation to meiosis in fungi is barely known, even within the best studied multicellular fungal model Neurospora crassa. We characterized morphological development and genome-wide transcriptomics in the closely related species Neurospora crassa, Neurospora tetrasperma, and Neurospora discreta, across eight stages of sexual development. Despite diverse life histories within the genus, all three species produce vase-shaped perithecia. Transcriptome sequencing provided gene expression levels of 2479 orthologous genes among all three species. Expression of key meiosis genes and sporulation genes, corresponded to developmental differences among these Neurospora species during sexual development. Screening N. crassa knockout crosses of genes selected for their expression differences across species, eight genes, whose functions were previously unknown, are found to be critical for the successful formation of perithecia. The absence of these genes in mutant crosses resulted in either no perithecium formation or in arrested development at an early stage. Our results provide insight into the genetic basis of Neurospora sexual reproduction, which is also of great importance with regard to other multicelluar ascomycetes, including fungal pathogens closely related to Neurospora in the Sordariomycetes, such as Fusarium spp, Magnaporthe oryzae, and Nectria haematococca

overall_design: mRNA were sampled and compared from eight time points across sexual reproduction in three Neurospora species

first: Zheng

last: Wang


title: Gene expression levels in three Neurospora species reveal genes crucial for sexual reproduction in Neurospora

sample_organism:
Neurospora discreta
Neurospora tetrasperma


title: Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma

city: Illkirch

first: Patrick

last: Laurette

address: 1 Rue Laurent Fries

summary: Malignant melanoma is an aggressive cancer known for its notorious resistance to most current therapies. The basic helix-loop-helix microphthalmia transcription factor (MITF) is the master regulator determining the identity and properties of the melanocyte lineage, and is regarded as a lineage-specific ‘oncogene’ that has a critical role in the pathogenesis of melanoma. MITF promotes melanoma cell proliferation, whereas sustained supression of MITF expression leads to senescence. By combining chromatin immunoprecipitation coupled to high throughput sequencing (ChIP-seq) and RNA sequen- cing analyses, we show that MITF directly regulates a set of genes required for DNA replication, repair and mitosis. Our results reveal how loss of MITF regulates mitotic fidelity, and through defective replication and repair induces DNA damage, ultimately ending in cellular senescence. These findings reveal a lineage-specific control of DNA replication and mitosis by MITF, providing new avenues for therapeutic intervention in melanoma. The identification of MITF-binding sites and gene- regulatory networks establish a framework for under- standing oncogenic basic helix-loop-helix factors such as N-myc or TFE3 in other cancers.

overall_design: 4 samples corresponding to genomic occupancy profiling of MITF (Cl8), PolII (501Mel), H3K4me3 501Mel). Anti-HA ChIP-seq on untagged cell line (501Mel) was used as a control.

first: Thomas

last: Strub

first: Stephanie

last: LeGras

first: Irwin

last: Davidson


title: Integrated genome and transcriptome sequencing from the same cell

status: Public on Dec 11 2014

city: Utrecht

first: Lennart

last: Kester

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

type: Genome variation profiling by high throughput sequencing

summary: Single-cell genomics and single-cell transcriptomics have recently emerged as powerful tools to study the biology of single cells at a genome-wide scale. Here we describe a method that allows the integration of genomic DNA and mRNA sequencing from the same cell. We use this method to correlate DNA copy number variation to transcriptome variability among individual cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: First, hand-picked single cells are lysed and reverse transcribed using a poly-A primer including cell-specific barcodes, a 5' Illumina adapter and a T7 promoter overhang to convert mRNA to single stranded cDNA (ss cDNA). The gDNA and single stranded cDNA are then subjected to quasilinear whole genome amplification, as previously described, using an adapter with a defined 27 nucleotide sequence at the 5’ end followed by 8 random nucleotides. After 7 rounds of amplification, the gDNA and cDNA are copied to generate a variety of different short amplicon (0.5–2.5 kb) species, with a majority of amplicons containing adapter Ad-2 at both ends and a small fraction of cDNA derived amplicons containing Ad-2 at one end and Ad-1x at the other. Next, the sample is split into two tubes to further amplify gDNA and cDNA. The tube used to sequence gDNA is amplified using PCR. Following sonication, adapter Ad-2 removal, and cell-specific indexed Illumina library preparation, this half is used to sequence gDNA. The tube used to sequence cDNA is converted to double-stranded cDNA and amplified using in vitro transcription such that the amplified RNA (aRNA) is uniquely produced from cDNA but not gDNA. 3’ Illumina adapters are then ligated to the aRNA followed by reverse transcription and PCR, allowing quantification of mRNA.

first: Siddharth

last: Dey

first: Bastiaan

last: Spanjaard

first: Magda

last: Bienko

first: Alexander

last: van Oudenaarden


title: The Hydra magnipapillata head regeneration transcriptome

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2300 Biological Sciences III

department: Developmental & Cell Biology

institute: University of California Irvine

summary: Hydra has long been studied for its remarkable ability to regenerate its head. Previous studies focusing on molecular mechanisms of axial patterning and head regeneration using a candidate gene approach have revealed a central role for the canonical Wnt pathway. We performed a global gene expression analysis during Hydra magnipapillata head regeneration using RNA-seq to identify additional genes that are transcriptionally regulated during the regeneration of the head organizer in hydra. Differential expression analysis revealed a set of 4,978 genes with significant changes during a 48-hour head regeneration time-course that includes many key genes in the Wnt, TGF-β/BMP and MAP kinase pathways. We observed the differential regulation of several genes that are part of the epithelial-to-mesenchymal transition in bilaterians such as Snail. We assembled 806 novel putative lincRNAs with 176 of these are differentially expressed during the time course. We observed the coordinated transcriptional regulation of several factors that regulate the effective pool of free β-catenin that together synergize to increase the amount of β-catenin available for transcriptional regulation of downstream genes. The differential expression of Snail and some of its interacting regulators and downstream targets suggests that a partial-EMT-like response is involved in hydra head regeneration. This time-course is a valuable resource for the study of the transcriptional dynamics of head regeneration in hydra.

overall_design: mRNA profiling of regenerating head from 6 time points post bisection of Hydra head (H. magnipapillata), generated by deep sequencing, in duplicates, using Illumina HiSeq2500.

first: Rabi

last: Murad

first: Lydia

last: Gee

first: Hans

middle: R

last: Bode


title: Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus

first: Sager

middle: Jayesh

last: Gosai

state: Pennsylvania

address: 433 S University Ave.

department: Biology

institute: Universiry of Pennsylvania

summary: Post-transcriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure, and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of RNAs in the nucleus has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP binding site mapping approach on Arabidopsis seedling nuclei in vivo to globally profile these features within the nuclear compartment. We reveal opposing patterns of secondary structure and RBP binding levels throughout native messenger RNAs that demarcate alternative splicing and polyadenylation. We also uncover a collection of protein bound sequence motifs, and identify their structural contexts, co-occurrences in transcripts encoding functionally related proteins, and interactions with putative RBPs. Finally, we identify a nuclear role for the chloroplast RBP, CP29A. In total, we provide the first simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus.

overall_design: Protein interaction profile sequencing (PIP-seq) in Arabidopsis seedling nuclei.  These are crosslinked with formaldehyde and treated with two RNases (ssRNase and dsRNase) with two replicates

middle: J

first: Shawn

last: Foley

first: Brian

middle: D

last: Gregory


title: Gene expression levels in three Neurospora species reveal genes crucial for sexual reproduction in Neurospora tetrasperma

first: Jeffrey

last: Townsend

first: Zheng

last: Wang


title: A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (ChIP-Seq)

first: Ido

last: Amit

overall_design: Here analyzed 2 experiments, each one contains samples of moDC and pDC ex vivo cultured cells. The first experiment contains 32 samples of moDC and pDC following stimulation with various TLR stimulators. The second experiment contains 8 samples of moDC and pDC following perturbations; Cebpb and Irf8 knock down or over expression.


title: IRF4/BATF and interleukin-33 orchestrate development and maintenance of adipose tissue resident regulatory T cells

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: To understand the differentiation of effector Tregs in more detail, we have performed transcriptional profiling of central Tregs and effector Tregs, based on Blimp1 expression. We performed RNA-sequencing of Foxp3+ regulatory T cells, comparing Blimp1/GFP+ and Blimp1/GFP- cells

overall_design: Three biologically independent samples for each condition were sequenced (condition 1: CD4+ CD25high Blimp1/GFP+; condition 2: CD4+ CD25high Blimp1/GFP-); cells were sorted from pooled spleens and lymphnodes of Blimp1/GFP reporter mice

first: Axel

last: Kallies

first: Yang

last: Liao

first: Gordon

last: Smyth


title: Genes regulated by the winged helix transcription factor Rfx6 in adult beta cell in the mouse

first: Tao

last: YE

institute: IGBMC (CNRS/INSERM/UDS)

summary: The goal of this study was to identify genes which are differentiatlly expresesd upon induced inactivation of Rfx6 in beta cell in adult  mice

overall_design: Rfx6fl/fl; Ins1-CreERT2 (mut) and Rfx6fl/fl (ctrl) 8 weeks old mice were injected subcutaneously with tamoxifen  daily during 3 days. Pancreatic islets were isolated 5 days after the first injection and RNA purified.

first: Julie

last: Piccand

first: Céline

last: Keime

first: Gérard

last: Gradwohl


title: Rfx6 target genes in the Min6b1 cell line, a pancreatic beta cell model

summary: Increasing evidence suggests that loss of beta cell characteristics may cause insulin secretory deficiency in diabetes but the underlying mechanisms remain unclear. Here we show that Rfx6, whose mutation leads to neonatal diabetes in man, is essential to maintain key features of functionally mature beta cells in mice. Rfx6 loss in adult beta cells leads to glucose intolerance, impaired beta cell glucose sensing and to defective insulin secretion. This is associated with reduced expression of core components of the insulin secretion pathway including GLucokinase, the Abcc8/SUR1 subunit of  KATP channels and voltage-gated Ca2 channels, which are direct targets of Rfx6. Moreover, Rfx6 contributes to the silencing of the vast majority of “disallowed” genes, a group usually specifically repressed in adult beta cells, and thus to the maintenance of beta cell maturity. These findings raise the possibility that changes in Rfx6 expression or activity may contribute to beta cell failure in man.

overall_design: Two ChIP-Seq experiments have been performed : 1) anti-HA ChIP-Seq on 3HA-Rfx6 transfected Min6b1 cells and 2) anti-HA ChIP-Seq on Min6b1 cells

first: Perrine

last: Strasser


title: Gene expression profiling of zebrafish embryos at 5 days post fertilization

city: Leiden

first: Wouter

last: Veneman

state: Zuid-Holland

address: Einsteinweg 55

department: Institute Biology Leiden

institute: Leiden University

summary: We use the zebrafish embryo model to study the innate immune response against Mycobacterium marinum. Therefore, we injected M. marinum  into the yolk at the 64 cell stage and took samples at 5 days post injection.

overall_design: This deep sequence study was designed to determine the gene expression profile by  Mycobacterium marinum  infection. RNA was isolated from embryos at 5 days post injection. Wildtypes zebrafish embryos were micro-injected into the yolk (64 cell stage) with 40 CFU of Mycobacterium marinum E11 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), or Non-injected as a control. After injections embryos were transferred into fresh egg water and incubated at 28°C. At 5 days post injection 50 embryos per group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

first: W

first: A

last: Ordas

first: H

last: Spaink


title: Enhanced MyoD-Induced Transdifferentiation to a Myogenic Lineage by Fusion to a Potent Transactivation Domain

city: Durham

first: Charles

middle: A.

last: Gersbach

state: NC

address: 101 Science Dr

department: Biomedical Engineering

institute: Duke University

summary: Synthetic transcription factors can be applied to many areas of biotechnology, medicine, and basic research.  Currently, the most common method for engineering synthetic transcription factors has been based on programmable DNA-binding domains of zinc finger proteins, Transcription Activator-Like Effectors (TALEs), and most recently the CRISPR/Cas9 system. These transcription factor platforms consist of the DNA-binding domain fused to potent transcriptional activation domains, most commonly the tetramer of the minimal transactivation domain of the VP16 protein from herpes simplex virus, referred to as VP64. Although many applications are well-suited for the targeted activation of a single gene, genetic reprogramming requires the coordinated regulation of many nodes of natural gene networks as is typically performed by naturally occurring reprogramming factors. Thus we sought to combine principles from each of these approaches by attaching potent transcriptional activation domains to a natural reprogramming factor to increase the efficiency and/or rate of cell fate conversion. In this study, we evaluated the effects of fusing potent activation domains to the transcription factor MyoD, the master regulator of the skeletal myoblast lineage. In certain non-myogenic lineages, MyoD overexpression causes upregulation of the myogenic gene network and conversion to a myoblast phenotype including cell fusion into multinucleated myotubes. Compared to wild-type MyoD, the VP64-MyoD fusion protein induced greater overall reprogramming of global gene expression. This simple approach for increasing the potency of natural reprogramming factors circumvents the need for screening engineered proteins and leads to a more robust cellular reprogramming compared to treatment with the wild type transcription factor.

overall_design: Human dermal fibroblasts were transduced with a single tet inducible lentivirus that expresses either WT-MyoD or VP64-MyoD in response to treatment with doxycycline. Untreated human dermal fibroblast served as the negative control. Gene expression was measured using mRNA-seq, and differential expression was calculated using DESeq. All experiments were performed in biological duplicates.

first: Ami

last: Kabadi

first: Pratiksha

last: Thakore

first: Christopher

last: Vockley

first: David

middle: G

last: Ousterout

first: Tyler

last: Gibson

first: Farshid

last: Guilak

first: Timothy

middle: E

last: Reddy


title: Genome-wide analysis of WT1-controlled gene expression in podocytes

city: Boston

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: We identified binding sites of the Wilms' tumor suppressor protein WT1 in the mouse podocyte genome in vivo by ChIP-seq. Furthermore, we provide a podocyte transcriptome derived from primary podocytes that were isolated by FACS on mouse glomeruli. In short, we show that WT1 activates a highly specific podocyte transcriptome by binding to putative podocyte-specific enhancers and TSS of target genes. Genes bound by WT1 in podocytes include the majority of genes mutated in hereditary podocytopathies as well as components of the slit diaphragm, actin cytoskeleton, extracellular matrix, and within endocytosis pathways. Furthermore, we infer a podocyte TF network from DNA-binding motifs enriched at WT1-bound loci that includes Tead, Lmx1b, Mafb, Tcf21, and Fox-class transcription factors.

overall_design: Examination of transcription factor binding sites for WT1 by ChIP-seq. Transcriptome analysis of podocytes by RNA-seq.

first: Jordan

last: Kreidberg

first: Thomas

last: Benzing

first: Martin

last: Kann


title: Transcriptional response of Saccharomyces cerevisiae to potassium starvation

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

summary: In this study we investigated the transcriptional response of the yeast Saccharomyces cerevisiae to potassium starvation. To this end yeast cells were grown for 60 min in media without potassium or in media with a standard potassium concnetration (50 mM KCl).   Using Serial Analysis of Gene Expression (SAGE)-tag sequencing the effect of potassium starvation on the transcriptome was determined.

overall_design: 4 samples of cells grown in media without potassium and 4 samples of cells grown in the presence of potassium were analyzed.

first: I

last: Anemaet

first: G


title: RNA-SEQ analysis of the developing lower urogenital region

status: Public on Dec 10 2014

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: We will use micro-dissection and FACS techniques to isolate cell types from the developing lower urogenital region and perform a transcriptional analysis using RNA-SEQ.  This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs.  In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database.

overall_design: Total RNA was obtained from FACS isolated embryonic day 17.5 bladders using Tg(Upk2-cre)6Xrw x Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo transgenic mice.  The long term goal is to generate a transcriptional atlas of developing lower urogenital region.

first: Kerry

last: Schneider

first: Eric

middle: W

last: Brunskill

first: Cathy

last: Mendelsohn


title: Spatiotemporal embryonic transcriptomics reveals the evolutionary history of the endoderm germ layer

city: Haifa

first: Itai

last: Yanai

address: Technion City

institute: Technion - Israel Institute of Technology

summary: The concept of germ layers has been one of the foremost organizing principles in developmental biology, classification, systematics and evolution for 150 years. Of the three germ layers, the mesoderm is found in bilaterian animals but is absent in species in the phyla Cnidaria and Ctenophora, which has been taken as evidence that the mesoderm was the final germ layer to evolve. The origin of the ectoderm and endoderm germ layers, however, remains unclear, with models supporting the antecedence of each as well as a simultaneous origin. Here we determine the temporal and spatial components of gene expression spanning embryonic development for all Caenorhabditis elegans genes and use it to determine the evolutionary ages of the germ layers. The gene expression program of the mesoderm is induced after those of the ectoderm and endoderm, thus making it the last germ layer both to evolve and to develop. Strikingly, the C. elegans endoderm and ectoderm expression programs do not co-induce; rather the endoderm activates earlier, and this is also observed in the expression of endoderm orthologues during the embryology of the frog Xenopus tropicalis, the sea anemone Nematostella vectensis and the sponge Amphimedon queenslandica. Querying the phylogenetic ages of specifically expressed genes reveals that the endoderm comprises older genes. Taken together, we propose that the endoderm program dates back to the origin of multicellularity, whereas the ectoderm originated as a secondary germ layer freed from ancestral feeding functions.

overall_design: Two temporal assays of Caenorhabditis elegans embryonic development, starting at the zygote: (a) Embryos collected at fixed (~10 minute) time intervals. (b) Embryo segregates, up to five lines of blastomeres, isolated in reference to mitotic events. There were 184 samples in total, representing 100 distinct data points (50 in each assay).

first: Tamar

last: Hashimshony

last: Feder

first: Michal

last: Levin

first: Brian

last: Hall


title: RNA-seq studies reveal new insights into p63 and the transcriptomic landscape of the mouse skin

city: BUFFALO

first: SATRAJIT

last: SINHA

address: 701 ELLICOTT STREET

institute: SUNY AT BUFFALO

summary: Analysis of gene-probe expression data (FPKM) for mouse skin using single-end read RNA-seq

overall_design: RNA was collected and analyzed for 2 biological replicates each from 3 developmental stages (E18.5, P3, 10 weeks)

first: Jason

last: Rizzo

first: Rose-Anne

last: Romano

first: Jonathan

last: Bard

first: Satrajit

last: Sinha


title: The Gac regulon in Pseudomonas chlororaphis 30-84

city: College station

first: Dongping

last: Wang

address: Wellborn

institute: TAMU

summary: The GacS/GacA two component regulatory system globally activates the production of secondary metabolites including phenazines in Pseudomonas chlororaphis 30-84. To better understand the regulatory role of the Gac system, we conducted RNA-seq analyses to determine the regulon of the response regulator GacA. Transcriptome analyses identified over 700 genes differentially regulated by GacA. Consistent with our previous findings, phenazine biosynthetic genes were significantly down-regulated in a gacA mutant. The expression levels of phenazine regulatory genes such as phzI, phzR, iopA, iopB, rpoS and pip were also decreased. Moreover, the expression of three none-coding RNAs (ncRNAs) including rsmX, rsmY and rsmZ was significantly decreased by gacA mutation consistent with the presence of GacA binding sites in their promoters. Our results also demonstrated that over-expression of rsmZ from a non-gac regulated promoter resulted in the restoration of AHL and phenazine production as well as the expression of other secondary metabolites in gac mutants. The role of RsmA and RsmE in phenazine production was also investigated.  Over-expression of rsmE, but not rsmA, resulted in decreased AHL production and phenazine gene expression in P. chlororaphis. Consistently, a mutation in rsmE bypassed the requirement of GacA in phenazine gene expression. On the contrary, constitutive expression of the phzI/phzR quorum sensing system was not able to rescue phenazine production in the gacA mutant indicating the direct impact of Gac system on the transcript stability of phenazine biosynthetic genes. Together, these results indicate that the Gac system regulates phenazine production at multiple levels and exerts its positive effect on AHL and phenazine biosynthesis via RsmZ and RsmE. A model is proposed to illustrate the GacA regulon in P. chlororaphis 30-84.

sample_organism: Pseudomonas chlororaphis subsp. aureofaciens 30-84

overall_design: A total of 6 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas chlororaphis wild type strain (3 replicates);  Pseudomonas chlororaphis gacA mutant (3 replicates).

first: Elizabeth

last: Pierson


title: Genes regulated in mouse liver by expressing ectopically hURI in hepatocytes

city: Madrid

first: Nabil

last: Djouder

address: C/Melchor Fernandez Almagro, 3

institute: CNIO

summary: RNA-seq was performed using the RNA extracted from the bottom half of right lobe of mouse livers. Mice fall into two groups, mutant group which express ectopic hURI and their control littermates which do not express hURI. Two time points were considered in the study, 1-week-old mice, expressing hURI since 1 week (n =3, 4 for control and mutant, respectively) and 8-week-old mice expressing hURI since 8 week (n= 4, 3 for control and mutant, respectively), as hURI is expressed since conception.

overall_design: Determination of differentially expressed transcripts over two time points (1 week and 8 weeks) in mouse livers expressing hURI (1 week and 8 weeks).

first: Krishna

middle: S

last: Tummala

first: Osvaldo

last: Graña

first: David

last: González-Pisano


title: Lysine-Specific Demethylase 1 Has Dual Functions as a Major Regulator of Androgen Receptor Transcriptional Activity

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

country: Canada

institute: UNIVERSITY HEALTH NETWORK

summary: Lysine Specific Demethylase 1 (LSD1, KDM1A) functions as a transcriptional corepressor through demethylation of histone 3 lysine 4 (H3K4), but has coactivator function on some genes through unclear mechanisms. We show that LSD1, interacting with CoREST, associates with and coactivates androgen receptor (AR) on a large fraction of androgen-stimulated genes. A subset of these AR/LSD1-associated enhancer sites have histone 3 threonine 6 phosphorylation (H3T6ph), and these sites are further enriched for androgen-stimulated genes. Significantly, despite its coactivator activity, LSD1 still mediates H3K4me2 demethylation at these androgen-stimulated enhancers. FOXA1 is also associated with LSD1 at AR regulated enhancer sites, and a FOXA1 interaction with LSD1 enhances binding of both proteins at these sites. These findings show LSD1 functions broadly as a regulator of AR function, that it maintains a transcriptional repression function at AR-regulated enhancers through H3K4 demethylation, and has a distinct AR-linked coactivator function mediated by demethylation of other substrates.

overall_design: Determine the role of LSD1 in androgen signaling.

middle: H

first: Changmeng

last: Cai

first: Steven

last: Balk

first: Myles

last: Brown


title: Transcriptome changes associated with cold acclimation in two species of the Drosophila virilis group

status: Public on Dec 27 2014

city: St Andrews,

first: Darren

middle: James

last: Parker

state: Fife

address: Dyers Brae House

department: Centre for Biological Diversity

institute: University of St. Andrews

summary: For many organisms the ability to cold acclimate with the onset of seasonal cold has major implications for their fitness. In insects, where this ability is widespread, the physiological changes associated with increased cold tolerance have been well studied. Despite this, little work has been done to trace changes in gene expression during cold acclimation that lead to an increase in cold tolerance. We used an RNA-Seq approach to investigate this in two species of the Drosophila virilis group. We found that the majority of genes that are differentially expressed during cold acclimation differ between the two species. Despite this, the biological processes associated with the differentially expressed genes were broadly similar in the two species. These included: metabolism, cell membrane composition, and circadian rhythms, which are largely consistent with previous work on cold acclimation / cold tolerance. In addition, we also found evidence of the involvement of the rhodopsin pathway in cold acclimation, a pathway that has been recently linked to thermotaxis. Interestingly, we found no evidence of differential expression of stress genes implying that long-term cold acclimation and short-term stress response may have a different physiological basis.

sample_organism:
Drosophila virilis
Drosophila montana

platform_organism:
Drosophila virilis
Drosophila montana

overall_design: Whole fly mRNA-seq using the SOLiD 5500 XL and SOLiD V4 of two speices of fly (drosophila montana and drosophila virilis) cold acclimated or kept at ambient temperature

first: D

first: L

last: Vesala

first: M

last: Ritchie

first: A

last: Laiho

last: Hoikkala

last: Kankare


title: A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Adipose stem cells (ASCs) and adipocytes play a crucial role in maintaining energy balance. We aim to examine the temporal relationship between gene expression and histone modification transitions during in vitro differentiation of human ASCs into adipocytes. Here, we examine by RNAseq proliferating ASCs (Day -2 prior to adipogenic induction), confluent ASCs (Day 0, adipogenic induction), pre-adipocytes (Day 3) and maturing adipocytes (Day 9). We find 1060, 5452 and 2216 genes differentially expressed between D-2/D0, D0/D3 and D3/D9 respectively. We identify gene clusters with distinct and dynamic expression patterns. In particular, adipogenic induction is marked by temporal waves of gene induction and downregulation. We report two types of transcriptional waves: (i) those showing transient induction or inactivation at D0, D3 or D9, and involved in sensory perception and immune response functions; and (ii) those showing long-lived induction or repression at these time points. Our data reveal a dynamic network of gene regulation during adipogenesis, involving signaling, immune and developmental processes. We identify 15 unique epigenetic states using Hidden Markov Modeling which reflects an epigenetically highly organised genome showing enhancer states are commonly consecutive. A heatmap for the abundance of epigenetic states for the expression clusters reveals a link between expression and epigenetic marking of the state suggesting an increase in the number of number of chromatin states with increase in expression. Our data point to a model of increased epigenetic complexity associated with gene expression.

overall_design: Examination of expression of profiles of ASCs across differentiation

first: Akshay

last: Shah

first: Anja

last: Oldenburg


title: The genome of the grape powdery mildew pathogen

city: Berkeley

first: Abraham

last: Morales-Cruz

address: 1 Cyclotron Road

institute: Joint Genome Institute

summary: Powdery mildew (Erysiphe necator) is a widespread and economically important disease of grapevines. Large quantities of fungicides are used for its control, accelerating the incidence of fungicide-resistance. A shotgun approach was applied to sequence and assemble the E. necator genome of five isolates, and RNA-seq and comparative genomics were used to predict and annotate protein-coding genes. In addition, a collection of 98 E. necator isolates collected from diverse locations was used for SSR profiling and was screened for copy number variation and presence/absence of a single point mutation (Y136F) in the CYP51 gene, a key target for DMI fungicides. Our results show that the E. necator genome is exceptionally large and repetitive and suggests that transposable elements are responsible for genome expansion. Frequent structural variations were found between isolates and included copy number variant (CNV) in CYP51. We show that CYP51 copy number correlates with expression level and that an increase in copy number is detected in isolates collected from fungicide-treated vineyards. This copy number variation was usually detected with the CYP51 mutant allele (Y136F), suggesting that an increase in copy number becomes advantageous only when the allele is mutated. We also show that CYP51 copy number correlates with fungal growth in the presence of DMI fungicide in vitro. These results suggest that copy number variation can be adaptive in the development of resistance to DMI fungicides in E. necator.

overall_design: Detach Carignan leaves were sprayed with a Erysiphe necator C-strain conida suspension, leaves were collected in 4 time points (12 hours, 24 hours, 3 days, and 6 days) post inoculation. For each time point, two leaves from the same seedling were pooled and frozen in liquid nitrogen, and each time point was performed in triplicate.

first: Laura

last: Jones

first: Katherine

middle: C

last: Amrine

first: Dario

last: Cantu


title: CRISPR reveals a distal murine-specific enhancer required for Sox2 expression in mouse embryonic stem cells

status: Public on Dec 09 2014

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

summary: The pluripotency of embryonic stem cells (ESCs) is maintained by a small group of master transcription factors including Oct4, Sox2 and Nanog. These core factors form a regulatory circuit controlling the transcription of a number of pluripotency factors including themselves. Although a lot of previous studies have identified key factors regulating this core network in trans, the contribution of cis-regulatory DNA sequences on the transcription of these key pluripotency factors remains elusive. We analyzed epigenomic data within the 1.5 Mb gene-desert regions around Sox2 gene and predicted only one 13kb-long enhancer located 100kb downstream of Sox2 in mouse ES cells. This enhancer is occupied by Oct4, Sox2, Nanog, and mediator complex and forms a long-range DNA looping to Sox2 locus. We hypothesized that this enhancer is critical for Sox2 gene expression and tested this hypothesis by deleting this entire 13-kb enhancer with a simple highly-efficient double-excision CRISPR strategy. Allele-specific of Sox2 transcripts in heterozygous enhancer-deletion clones showed that the enhancer affects expression through a cis-acting mechanism. Strikingly, although this distal enhancer is not conserved in other mammals including human, it is responsible for over 90% of Sox2 expression in mouse ESCs. Taken together, our results provide direct evidence that in mouse ESCs, Sox2 transcription is primarily driven by a species-specific distal enhancer, which may provide new perspectives explaining the physiological difference between human and mouse ES cells.

overall_design: This dataset include ChIP-seq of H3K4me3 and H3K27ac in a hybrid mouse ES cells (F123). H3K27ac in J1 mouse ES cells. And RNA-seq in F123 mESCs with complete Sox2 enhancer deletion or enhancer haploinsufficient clones.

first: Yan

last: Li

first: Chloe

last: Rivera

first: Haruhiko

last: Isshi


title: Sperm miRNA from bulls consuming toxic and non-toxic tall fescue seed

city: Clemson

first: Scott

middle: L

last: Pratt

state: SC

address: 138 Poole Ag Center

institute: Clemson University

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

platform_organism:
Bos taurus
synthetic construct

overall_design: Refer to individual Series


title: Gene profile of aged Wt, miR-155-/-, miR-146a-/- and DKO CD4+ T cells

city: Salt lake city

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr East

department: Pathology

institute: University of Utah

summary: Differential gene expression profile of CD4+ T cells from 10 months old Wt, miR-155-/-, miR-146a-/- and DKO mice spleens.

overall_design: Wt, miR-155-/-, miR-146a-/- and DKO mice were aged 10 months, CD4+ T cells were sorted from mice spleens for analyses.

first: Ruozhen

last: Hu


title: AF9 Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation

city: Houston

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: The recognition of modified histones by “reader” proteins constitutes a key mechanism regulating gene expression in the chromatin context. Compared with the great variety of readers for histone methylation, few protein modules that recognize histone acetylation are known. Here we show that the evolutionarily conserved YEATS domains constitute a novel family of acetyllysine readers. The human AF9 YEATS domain binds strongly to histone H3K9 acetylation and, to a lesser extent, H3K27 and H3K18 acetylation. Crystal structural studies revealed that AF9 YEATS adopts an eight-stranded immunoglobin fold and utilizes a serine-lined aromatic “sandwiching” cage for acetyllysine readout, representing a novel recognition mechanism that is distinct from that of known acetyllysine readers. Histone acetylation recognition by AF9 is important for the chromatin recruitment of the H3K79 methyltransferase DOT1L. Together, our studies identify the YEATS domain as a novel acetyllysine-binding module, thereby establishing the first direct link between histone acetylation and DOTL1-mediated H3K79 methylation in transcription control.

overall_design: ChIP-seq analysis of AF9, H3K79me3, H3K9ac in Hela cells and H3K79me3 in Hela AF9 knockdown and Hela Dot1L knockdown cells.

first: Hong

last: Wen

first: Wei

first: Xiaobing

last: Shi


title: Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers

city: Shanghai

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

institute: Tongji University

summary: Nucleosome organization determines chromatin state, which subsequently controls genes expression or silencing. Nucleosome remodeling occurs during somatic cell reprogramming, but it remains undetermined to what degree the re-established nucleosome organization resembles between induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs). We generated genome-wide nucleosome maps in mouse ESCs and in iPSCs reprogrammed from somatic cells belonging to three different germ layers using a secondary reprogramming system. Pairwise comparisons showed that the nucleosome organizations in the iPSCs, regardless of the iPSCs¿ tissue of origin, were nearly identical to the ESCs, but distinct to mouse embryonic fibroblasts (MEF). There is a canonical nucleosome arrangement of -1, nucleosome depletion region, +1, +2, +3, et al. nucleosomes around the transcription start sites of active genes whereas only a nucleosome occupies at silent transcriptional units. Transcription factor binding sites possessed characteristic nucleosomal architecture such that their access was governed by the rotational and translational settings of the nucleosome. Interestingly, the tissue-specific genes were highly expressed only in the parental somatic cells of the corresponding iPS cell line before reprogramming, but had a similar expression level in the all resultant iPSCs and ESCs. The re-established nucleosome landscape during nuclear reprogramming provides a conserved setting for accessibility of DNA sequences in mouse pluripotent stem cells. No persistent residual expression program or nucleosome positioning of the parental somatic cells that reflected their tissue of origin were passed onto the resulting mouse iPSCs.

overall_design: Gene expression profiles of 5 cell lines with or without biological replicates

first: Cizong

last: Jiang

first: Shaorong

last: Gao


title: Gene expression profile of Tfh cells and aged CD4 T cells from wild type, miR-155 knockout, miR-146a knockout and double knockout mice


title: Genome-wide identification of rat long non-coding RNAs

city: Toledo

first: Bina

last: Joe

state: Ohio

address: Block Health Science Bldg, 3000 Arlington Ave

department: Department of Physiology and Pharmacology

institute: University of Toledo, College of Medicine and Life Sciences

summary: In the current study, we have focused on a distinct group of non-coding elements, lncRNA, and profiled renal tissues from three different inbred rat strains. We chose the three strains S, SHR and R for the main purpose of cataloging lncRNA annotations from  the most widely used rat models of cardiovascular and renal disease.

overall_design: Identification of lncRNAs on the rat genome by next generation RNA sequencing (NGS)

first: Kathirvel

last: Gopalakrishnan


title: RNA sequencing based analysis of the bacterial transcriptome

city: Norman

first: James

last: Creecy

state: Oklahoma

address: 770 Van Vleet Oval

department: Microbiology

institute: University of Oklahoma

summary: To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture.

overall_design: E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media (carbon, nitrogen, or phosphate limited) and the total transcriptome of log and stationary phase samples was sequenced.

first: Tyrrell

last: Conway


title: Haemophilus parasuis gene expression the in lung

status: Public on Dec 05 2014

city: Barcelona

first: BERNARDO

last: BELLO ORTI

state: Barcelona

address: Bellaterra

department: Bacteriology

institute: CReSA

summary:
Purpose: Identify differentially expressed genes in pig lung, compared to growth on chocolate agar plate.
Methods: In order to study the gene expression at this location, we sequenced ex vivo and in vivo H. parasuis transcriptome using a metatranscriptomic approach. Gene expression was compared with conventional plate culture.
Results: down-regulation of anabolic and catabolic pathways, coupled with up-regulation of membrane-related genes involved in carbon acquisition, iron binding and pathogenesis.
Conclusions: This data sheds some light on the scarcely studied in vivo transcriptome of H. parasuis, revealing nutritional virulence as an adaptive strategy for host survival.

overall_design: To examine the gene expression during lung infection, ex vivo incubation of the bacteria in porcine lungs was carried out. To assess the validity of the ex vivo model, RNA was obtained from Nagasaki recovered from the lungs of a pig after a short in vivo infection.

first: Bernardo

last: Bello-Orti

first: Virginia

last: Aragon


title: Transcription Factors GATA4 and HNF4A Control Distinct Aspects of Intestinal Homeostasis in Conjunction With the Transcription Factor CDX2

status: Public on Dec 08 2014

city: Boston

first: Adrianna

middle: Katrina

last: San Roman

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute and Harvard Medical School

summary:
To determine whether the intestine-restricted transcription factor (TF) CDX2 functionally interacts with the endoderm-wide TF HNF4A, we crossed tissue-specific conditional Cdx2 and Hnf4a knockout mice to generate compound mutant mice.
We used RNA-sequencing to profile gene expression changes in compound mutant mice compared to control mice. The compound mutant mice had a significantly worse phenotype than either single mutant, and gene expression was significantly perturbed in compound mutants compared to control mice.

overall_design: Total RNA isolated from control and compound mutant (Hnf4a-del;Cdx2-del) jejunal mouse intestinal epithelium was prepared for sequencing using the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's instructions. 75-base-pair single-end reads were sequenced on an Illumina NextSeq 500 instrument. The data include 2 independent biological replicates per genotype.

middle: K

first: Boaz

last: Aronson

first: Stephen

last: Krasinski

first: Ramesh

last: Shivdasani

first: Michael

last: Verzi


title: The Sm protein methyltransferase PRMT5, is not required for primordial germ cell specification in mice

city: Los Angeles

first: Juehua

last: Yu

state: CA

address: 615 Charles E. Young South BSRB 457

institute: UCLA

summary: PRMT5 is a type II protein arginine methyltransferase with roles in stem cell biology, reprogramming, cancer and neurogenesis. During embryogenesis in the mouse it was hypothesized that PRMT5 functions with the master germline determinant BLIMP1 to promote primordial germ cell (PGC) specification. Using a Blimp1-Cre germline conditional knockout, we discovered that Prmt5 has no major role in murine germline specification, or the first global epigenetic reprogramming event involving depletion of cytosine methylation from DNA and histone H3 lysine 9 dimethylation from chromatin. Instead, we discovered that PRMT5 functions at the conclusion of PGC reprogramming I to promote proliferation, survival and expression of the gonadal germline program as marked by MVH. We show that PRMT5 regulates gene expression by promoting methylation of the Sm spliceosomal proteins, and significantly altering the spliced repertoire of RNAs in mammalian embryonic cells and primordial cells.

overall_design: Examination of transcriptional profile of iPHet (Control) vs. iPKO (Prmt5 knock out) 2i Embryonic Stem Cells

first: Amander

middle: T

last: Clark

first: Ziwei

last: Li


title: Transcriptome Analysis of Sexual Dimorphic Chinese White Wax Scale Reveals Key Differences in Developmental Programs and Transcription Factor Expression

city: Kunming

first: Pu

last: Yang

address: Bailongsi

institute: Insect

summary: We showed that, male E. pela, despite displaying complete metamorphosis similar to holometabolous insects, formed the sister group to hemimetabolous female E. pela and also clustered with Hemiptera. The gene expression profile and Gene Ontology (GO) analysis revealed that the two sexes engaged in distinct developmental programs. In particular, female development appeared to prioritize the expression of genes related to cellular, metabolic, developmental processes, and anatomical structure formation in nymphs. In contrast, male larval development is characterized by the significant down-regulation of genes involved in chitin, the respiratory system, and neurons. The results also suggest that pathways involved in fat metabolism and storage are differently used between the sexes.

overall_design: Retinal mRNA profiles of male prepulae and male pupae generated by deep sequencing, no replicate, using Illumina


title: Enhancer-core promoter specificity separates developmental and housekeeping regulation

city: Vienna

first: Alexander

last: Stark

address: Dr Bohr-Gasse 7

country: Austria

institute: Research Institute for Molecular Pathology (IMP), Vienna Biocenter VBC

summary: Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters – one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genes’ core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.

overall_design: STARR-seq was performed in S2 and OSC cells using two core promoters each representing housekeeping and developmental transcription programs. Data for housekeeping promoters (hkCP) are presented in this series; Data for developmental core promoters (dCP) samples are presented in GSE40739.

first: Muhammad

middle: A

last: Zabidi

first: Cosmas

last: Arnold

first: Katharina

last: Schernhuber

first: Michaela

last: Pagani

first: Martina

last: Rath

first: Olga

last: Frank


title: Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment [RNA-seq]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: Macrophages are hematopoietic cells critical for innate immune defense, but also control organ homeostasis in a tissue-specific manner. Tissue-resident macrophages, therefore, provide a well-defined model to study the impact of ontogeny and microenvironment on chromatin state. Here, we profile the dynamics of four histone modifications across seven tissue-resident macrophage populations, as well as monocytes and neutrophils. We identify 12,743 macrophage-specific enhancers and establish that tissue-resident macrophages have distinct enhancer landscapes. Our work suggests that a combination of tissue and lineage-specific transcription factors form the regulatory networks controlling chromatin specification in tissue-resident macrophages. The environment has the capacity to alter the chromatin landscape of macrophages derived from transplanted adult bone marrow in vivo and even differentiated macrophages are reprogramed when transferred into a new tissue. Altogether, these data provide a comprehensive view of macrophage regulation and highlight the importance of microenvironment along with pioneer factors in orchestrating macrophage identity and plasticity.

overall_design: 7 tissue-resident macrophage populations were isolated, as well as monocytes and neutrophils, and transcriptome analysis was performed. Experiment was done in duplicates.


title: Core and region enriched networks of behaviorally regulated genes: the singing epigenome

city: Cambridge

first: Andreas

middle: R

last: Pfenning

address: Computer Science and Artificial Intelligence Laboratory

department: CSAIL

institute: Massachusetts Institute of Technology

summary: We queried a songbird brain to discover behaviorally regulated transcriptional mechanisms relevant for speech behavior. About 10% of zebra finch genes showed regulation during singing, and most were brain-region specific. We propose that the brain-regional diversity of the singing-regulated gene networks is derived both from differential combinatorial binding of transcription factors and the epigenetic state of these genes before singing begins. To test this hypothesis, we measured H3K27ac two brain regions that participate in song production.

overall_design: The examination of H3K27ac in two brain regions of zebra finch in singing and silent conditions

first: Osceola

last: Whitney

first: Fang

last: Liu

first: Anne

last: West

first: Erich

last: Jarvis