title: Gene expression in the epidermis including guard cells of phot1 phot2 and pGC1::SOC1-GFP/phot1 phot2

city: Nagoya

first: Norihito

last: Nakamichi

address: Furo-cho, Chikusa

department: Institute of Transformative Bio-Molecules

institute: Nagoya University

summary: Stomata pores are surrounded by a pair of guard cells in the epidermis in plants. Stomata apature is controlled by environmental factors. Stomata opening is also enhanced by introduction of SOC1-GFP driven by GC1 promoter in phot1 phot2 double mutants (pGC1::SOC1-GFP/ phot1 phot2). Epidermis including guard cells were isolated from phot1 phot2 and pGC1::SOC1-GFP/phot1 phot2 and gene expression were analyzed.

overall_design: phot1-5 phot2-1 in gl1 background (phot1 phot2) and pGC1::SOC1-GFP/phot1 phot2 were grown under 16 h light / 8h dark, constant 22˚C conditions for 4 to 5 weeks. Epidermis including guard cells were isolated from leaves of these plants. Three biological replicates were used.

first: Toshinori

last: Kinoshita

first: Saya

last: Aoki


title: Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis

status: Public on Feb 04 2015

city: Ann Arbor

first: Lihong

last: Shi

address: 3608 BSRB, 109 Zina Pitcher Place

country: USA

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide hsa-miR-503, hsa-miR-103, and hsa-miR-494 target profiles

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin


title: Nascent transcription defined by RNA polymerase IV in Zea mays

city: Columbus

first: Jay

last: Hollick

state: OH

address: 318 West 12th Avenue

department: Molecular Genetics

institute: The Ohio State University

summary: Maize RNA Polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, repression of transposable elements (TEs), and for the regulation of specific alleles associated with TEs.  Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based transcriptional regulation.  Surprisingly, although TE-like sequences comprise >85% of the maize genome, most TEs are not transcribed at the seedling stage, even in rpd1 mutants.  Profile comparisons identify the global set of genes and TEs whose transcription is altered in the absence of RPD1, in some cases in antisense orientation.  These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for certain regions of the maize genome.

overall_design: Nuclei isolated from 10 wild-type and 10 rpd1 mutant seedlings were pooled and used to make two global run-on sequencing libraries.

first: Karl

middle: F

last: Erhard

middle: B

first: Joy-El

middle: R

last: Talbot

first: Natalie

middle: C

last: Deans

first: Allison

middle: E

last: McClish


title: Enhancer-bound LDB1 Regulates a Corticotrope Promoter Pausing Repression Program

status: Public on Feb 03 2015

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

state: CA

address: 9500 Gilman Drive

institute: HHMI/UCSD


title: Modeling the early phenotype at the neuromuscular junction of spinal muscular atrophy using patient-derived iPSCs (RNA-Seq)

city: Kyoto

first: Megumu

last: Saito

address: 53, Shogoin-Kawahara

country: Japan

institute: Kyoto University

summary: Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by mutations of the survival of motor neuron 1 (SMN1) gene. In the pathogenesis of SMA, pathological changes of the neuromuscular junction (NMJ) precede the motor neuronal loss. Therefore, it is critical to evaluate the NMJ formed by SMA patients’ motor neurons (MNs), and to identify drugs that can restore the normal condition. We generated NMJ-like structures using motor neurons (MNs) derived from SMA patient-specific induced pluripotent stem cells (iPSCs), and found that the clustering of the acetylcholine receptor (AChR) is significantly impaired. Valproic acid and  antisense oligonucleotide treatment ameliorated the AChR clustering defects, leading to an increase in the level of full-length SMN transcripts. Thus, the current in vitro model of AChR clustering using SMA patient-derived iPSCs is useful to dissect the pathophysiological mechanisms underlying the development of SMA, and to evaluate the efficacy of new therapeutic approaches.

overall_design: to evaluate the effects of VPA on the expression profiles of the MNs

first: Michiko

last: Yoshida

first: Akira

last: Watanabe


title: Enhancer-bound LDB1 Regulates a Corticotrope Promoter Pausing Repression Program [ChIP-seq]

summary: Substantial evidence supports the hypothesis that enhancers are critical regulators of cell type determination, orchestrating both positive and negative transcriptional programs; however, the basic mechanisms by which enhancers orchestrate interactions with cognate promoters during activation and repression events remain incompletely understood. Here we report the required actions of the LIM domain binding protein, LDB1/CLIM2/NLI, interacting with the enhancer binding protein, ASCL1, to mediate looping to target gene promoters and target gene regulation in corticotrope cells. LDB1-mediated enhancer:promoter looping appears to be required for both activation and repression of these target target gene promoter genes. While LDB1-dependend activated genes are regulated at the level of transcriptional initiation, the LDB1-dependent repressed transcription units appear to be regulated primarily at the level of promoter pausing, with LDB1 regulating recruitment of MTA2, a component of the NuRD complex, on these negative enhancers, required for the repressive enhancer function. These results indicate that LDB1-dependent looping events can deliver repressive cargo to cognate promoters to mediate promoter pausing events in a pituitary cell type.

overall_design: ChIP assay followed by high throughput sequencing (ChIP-seq)

first: Feng

last: Zhang

first: Bogdan

last: Tanasa

first: Daria

last: Merkurjev

first: Chijen

last: Lin

first: Xiaoyuan

last: Song

first: Wenbo

last: Li

first: Yuliang

last: Tan

first: Zhijie

last: Liu

first: Jie

first: Kenneth

middle: A

last: Ohgi

first: Anna

last: Krones

first: Dorota

last: Skowronska-Krawczyk

first: Michael

last: Rosenfeld


title: Enhancer-bound LDB1 Regulates a Corticotrope Promoter Pausing Repression Program [GRO-seq]

first: MICHAEL

overall_design: Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq)


title: Genome-wide profiling  of H3K4me3, H3K27me3 H3K27me1 and 5mC enrichment and mRNA levels in young leaves of Arabis alpina

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

type: Methylation profiling by high throughput sequencing

summary: Chromatin, DNA and RNA were extracted from young A. alpina Pajares primary stem leaves. Chromatin and DNA methylation immunoprecipitation experiments were performed using commercially available antibodies and analyzed by Illumina sequencing (ChIP-seq and MeDIP-seq). Transcriptome data were generated by RNA-seq.

overall_design: ChIP-seq analysis of H3K4me3, H3K27me3 and H3K27me1 enrichment profiles and MeDIP-seq analysis of 5mC enrichment profiles in 2 biological replicates. RNA-seq analysis of mRNA levels in 1 biological replicate.

first: Claudia

last: Chica

first: Bogna

last: Szarzynska

last: Roudier

first: Vincent

last: Colot


title: Genome-wide map of Gata6 DNA binding in mouse pancreas

city: Madrid

first: Francesc

last: Madriles

state: Madrid

address: c/ Melchor Fernandez Almagro, 3

department: Cancer Cell Biology

country: Spain

institute: CNIO

summary: We have previously described in mouse models that pancreas-specific deletion of Gata6 results in pancreas alterations by rendering pancreatic acinar cells in a non-fully differentiation state, and furthermore it accelerates tumor initiation and progression in  a pro-tumorigenic context (KrasG12V expression). We aim to determine the sites where Gata6 binds at the genome-wide level in the pancreas to unveil why its loss leads to altered pancreatic function and enhanced tumor formation when coexpressed with KrasG12V.

overall_design: Gata6 ChIP-Seq in the mouse pancreas

first: Paola

last: Martinelli

first: Enrique

last: Carrillo

first: Francisco

last: Real


title: Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

sample_organism:
Arabidopsis thaliana
Arabis alpina
Arabidopsis lyrata


title: Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis [RNA-seq]

first: Lihong

last: Shi

summary: We knocked down TR4 expression by 2 lentiviral mediated vectors at day 11 of erythroid differentiation in order to identify TR4 downstream targets.

overall_design: Two lentiviruses and one empty control were used to knockdown TR4 expression. The cells were harvested at day 11 during erythroid differentiation.

first: M

last: Sierant

first: Katherine

last: Gurdziel

first: Kim

last: Lim

first: Shuaiying

last: Cu

first: Fan

last: Zhu

first: Yuanfang

last: Guan

first: Osamu

last: Tanabe

first: James

middle: D

last: Engel


title: Genome-wide profiling  of H3K4me3, H3K27me3 H3K27me1 and 5mC enrichment and mRNA levels in young leaves of Arabidopsis lyrata

first: François

last: ROUDIER

last: Chica


title: 5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [seq]

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

summary: The discovery of cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behavior in colon cancer. 5-hmC is globally reduced in proliferating cells such as colon tumors and the gut crypt progenitors, from which tumors can arise. Here, we show that colorectal tumors and cancer cells express Ten-Eleven Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5-hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5-hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. Together our results indicate that promoters that acquire 5-hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5-hmC in tumors. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.

overall_design:
5 normal colon samples and 4 matching tumor samples were profiled for 5-hydroxymethylcytosine content genomewide using hmeDIP-seq.
The colorectal cancer cell line HCT116 was profiled for binding of TET2 genomewide by chromatin immunoprecipitation sequencing (ChIP-seq).

first: Santiago

last: Uribe-Lewis

first: Rory

last: Stark

first: Thomas

last: Carroll

first: Mark

last: Dunning

first: Silvia

last: Halim

first: Sarah

last: Vowler


title: Gata6

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: P

last: Martinelli

first: E

first: FX

last: Real


title: Genome-wide map of GATA6 DNA binding in human PDAC cells

summary: By studying a mouse model, as well as human tumors samples and cell lines, we have revealed a tumor suppressive role for Gata6 in the pathogenesis of pancreatic ductal adenocarcinoma (PDAC). In order to understand the mechanism underlying such tumor suppressive function, we analyzed the genome-wide DNA-binding of GATA6 in a human PDAC cell line (PaTu8988S). GATA6 is found to bind the promoter of genes involved in the epithelial differentiation programme, as well as of genes involved in the mesenchymal programme. With this we describe a novel GATA6-dependent mechanism of regulation of EMT.

overall_design: Examination of GATA6 binding to the DNA in a human PDAC cell line

first: F

middle: X


title: Global gene expression in the adult Gata6 null mouse pancreas

summary: We report the global gene expression of mouse pancreatic cells in a pancreas-specific conditional knock-out mouse for Gata6, as compared with age-matched controls. Total RNA was extracted from the pancreas of 6-8 -week old mice of the two genotypes and analyzed. at this age, Gata6P-/- pancreata are histologically normal, but the acinar differentiation programme is already altered. we observe that loss of Gata6 causes the de-repression of ectopic non-pancreatic genes, as well as some genes involved in the mesenchymal programme.

overall_design: mRNA extracted from the pancreas of 4 controls and 4 Gata6P-/- mice was sequenced.


title: Expression profiling of mouse T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia ALL211) cells following Ikaros restoration

status: Public on Feb 02 2015

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: To examine Ikaros tumor suppressor mechanisms, we have utilized inducible RNAi to dynamically restore endogenous Ikaros expression in T-ALL driven by its knockdown. This causes rapid transcriptional repression of Notch1 and associated targets including Myc, even in leukemias harboring spontaneous activating Notch1 mutations (producing aberrant ICN1) similar to those found in 60% of human T-ALL. Ikaros restoration results in sustained regression of Notch1-wild type leukemias while endogenous or engineered ICN1 expression promotes rapid disease relapse, indicating that ICN1 functionally antagonizes Ikaros in T-ALL.

overall_design: RNA-seq was performed on T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia ALL211) cells isolated from two untreated and two 3-day Dox-treated mice.

first: Matthew

middle: T

last: Witkowski

first: Yifang

last: Hu

first: Ross

last: Dickins


title: Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis [ChIP-seq]

first: Lihong

last: Shi

summary: In this study, we resolved the genome-wide binding of TR4 in differentiating human erythroid cells by performing chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). We found that TR4 preferentially binds to DR1 elements in the promoters of its target genes, and that the majority of these genes encode proteins that participate in fundamental biological functions such as mRNA processing, translation, RNA splicing and primary metabolic process. Interestingly, we also found an increased occurrence of other repeat element motifs (such as DR4, IR1 and ER6) at TR4-bound distal sites that are located more than 10 Kbp away from the nearest gene. This raises the tantalizing possibility that TR4 may heterodimerize with unique partners, including other nuclear receptors such as RXR, thus allowing TR4 to elicit unique transcriptional responses when acting at proximal (promoter) and distal (enhancer and silencer) regulatory sites during human erythropoiesis.

overall_design: Examination of TR4 genome wild binding in human erythroid cells, which are harvested at day 8, 11 and 14 during in vitro differentiation. Two replicates were included for each differentiation stage.

first: M

last: Sierant

first: Katherine

last: Gurdziel

first: Kim

last: Lim

first: Shuaiying

last: Cu

first: Fan

last: Zhu

first: Yuanfang

last: Guan

first: Osamu

last: Tanabe

first: James

last: Engel


title: Genome-wide profiling of H3K27me1 and 5mC enrichment in young leaves of Arabidopsis thaliana

first: François

last: ROUDIER

summary: Chromatin, DNA and RNA were extracted from young A. thaliana primary stem leaves. Chromatin and DNA methylation immunoprecipitation experiments were performed using commercially available antibodies and analyzed by Illumina sequencing (ChIP-seq and MeDIP-seq).

overall_design: ChIP-seq analysis of H3K27me1 enrichment profiles and MeDIP-seq analysis of 5mC enrichment profiles in 2 biological replicates.

first: Claudia

last: Chica

first: Bogna

last: Szarzynska

last: Roudier

first: Vincent

last: Colot


title: Next Generation Sequencing Comparison of C57BL/6J and BC027072 -/- Eye Transcriptomes

city: Cleveland

first: Brian

middle: Michael

last: Kevany

address: 10900 Euclid Ave.

department: Pharmacology

institute: Case Western Reserve University

summary: We report the single base pair analysis of the ocular transcriptome from wild type and BC027072 knockout animals. Comparison was analyzed to understand gene expression changes in a mouse model for early onset retinal degeneration which phenocopies a human form of autosomal recessive retinitis pigmentosa

overall_design: Eye mRNA profiles were generated from 3 week-old C57BL/6J and BC027072 -/- in triplicate and sequenced using the Illumina HiSeq 2500

middle: M

first: Krzysztof

last: Palczewski


title: Expression profiling of mouse T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia ALL65) cells following Ikaros restoration

first: Gordon

last: Smyth

overall_design: RNA-seq was performed on T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia ALL65) cells isolated from three untreated and three 3-day Dox-treated mice. There were two sequencing runs of each RNA sample.

first: Matthew

last: Witkowski

first: Yifang

last: Hu

last: Dickins


title: A global profile of replication polymerase usage

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary: We have established a novel sequencing approach to characterise usage of replicative DNA polymerases in S. pombe. This approach allows us to determine  the roles of DNA polymerase delta and epsilon in lagging strand and leading strand DNA synthesis, respectively in genome-wide scale. Utilising the dataset of usage of these polymerases, we also successfully identified DNA replication initiation sites at high resolution. Furthermore, our informatics analysis establishes genome-wide datasets of fork direction rates, replication timing and the probability of replication termination.

overall_design: We mapped ribonucleotide-incorporation by the mutated DNA polymerase delta and epsilon at single-nucleotide resolution and subsequent informatics analysis was performed to generate datasets listed here.

first: Yasukazu

last: Daigaku

first: Andrea

last: Keszthelyi

first: Carolin

last: Muller

first: Izumi

last: Miyabe

first: Tony

last: Brooks

first: Renata

last: Retkute

first: Mike

last: Hubank

first: Antony

last: Carr


title: A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation (RNA-seq)

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

summary: The transcriptional activator MyoD serves as a master controller of myogenesis. Often in partnership with Mef2, MyoD binds to the promoters of hundreds of muscle genes in proliferating myoblasts, yet activates these targets only upon receiving cues that launch differentiation. What regulates this off/on switch of MyoD function has been incompletely understood, although known to reflect the action of chromatin modifiers. Here, we identify KAP1/TRIM28 as a key regulator of MyoD function. In myoblasts, KAP1 is present with MyoD and Mef2 at many muscle genes, where it acts as a scaffold to recruit not only co-activators such as p300 and LSD1, but also co-repressors such as G9a and HDAC1, with promoter silencing as net outcome. Upon differentiation, MSK1-mediated phosphorylation of KAP1 releases the co-repressors from the scaffold, unleashing transcriptional activation by MyoD/Mef2 and their positive cofactors. Thus, our results reveal KAP1 as a previously unappreciated interpreter of cell signaling, which modulates the ability of MyoD to drive myogenesis.

overall_design: Transcriptome profiling of control and Kap1KD in C2C12 during proliferation or at 48hours differentiation stage

first: Marco

last: Cassano


title: ChIP-seq analysis of LSD2/DNA interaction in HepG2 cells in normal condition

city: Kumamoto

first: Shinjiro

last: Hino

address: 2-2-1 Honjo

institute: Kumamoto University

summary: ChIP-seq analysis of HepG2 cells revealed that many of the target genes of LSD2 were related to lipid metabolism. We found that LSD2 is an important epigenetic regulator of hepatic lipid metabolism.

overall_design: Examination of LSD2/DNA interaction in HepG2 cells in normal condition.

first: Katsuya

last: Nagaoka

first: Mitsuyoshi

last: Nakao


title: 5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer

first: Chandra

last: Chilamakuri

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

overall_design: Refer to individual Series


title: ChIP-seq analysis of LSD2/H3K4me1 interaction in control and LSD2-knockdowned HepG2 cells

summary: ChIP-seq analysis of LSD2-depleted HepG2 cells revealed that many of the target genes were related to lipid metabolism. We found that LSD2 is an important epigenetic regulator of hepatic lipid metabolism.

overall_design: Examination of LSD2/H3K4me1 interaction in control and LSD2-knockdowned HepG2 cells.


title: RNA-seq characterization of an infection of Mycobacterium smegmatis by a cluster A4 mycobacteriophage

city: Williamsburg

first: Margaret

last: Saha

state: VA

address: 540 Landrum Drive

institute: College of William and Mary

summary: We present transcriptomic analysis of an infection by a cluster A4 mycobacteriophage of its host, Mycobacterium smegmatis, at six time points (n = 2). Viral transcription is detectable 5 minutes into infection, and viral mRNA makes up the vast majority of all transcription by 30 minutes. Kampy, like many phages, has a genome organized into two arms bearing early- and late-phase genes. We identify two transcriptional start sites (TSS’s) consistent with an early promoter driving expression of half of the genome, along with a second, late-stage promoter that becomes active around 30 minutes after the start of infection.

sample_organism:
Mycolicibacterium smegmatis
Mycobacterium phage Kampy

overall_design: One timepoint before and five timepoints during infection were analyzed using an Ion Torrent PGM. Two biological replicates were sequenced for each timepoint.

first: Andrew

last: Halleran

first: Samuel

last: Clamons


title: Expression profiling of mouse T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia ALL101) cells following Ikaros restoration [RNA-Seq]

first: Gordon

last: Smyth

overall_design: RNA-seq was performed on T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia ALL101) cells isolated from three untreated and three 3-day Dox-treated mice. There were two sequencing runs of each RNA sample.

first: Matthew

last: Witkowski

first: Yifang

last: Hu

first: Ross

last: Dickins


title: RNA sequencing of allelic series of miR-17~92 mutant embryos.

city: New York

first: Andrea

last: Ventura

state: NY

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: We report the generation of an allelic series of miR-17~92 mutant mice, each carrying the targeted deletion of specific miRNA families encoded by the cluster. We integrate the phenotypic characterization of these strains with RNA-seq analysis showing the consequences of selective miRNA inactivation on gene expression in the developing embryo.

overall_design: We generated and analyzed RNA-seq data from 8 different miR-17~92 alleles, in three different microdissected tissues collected from E9.5 mouse embryos. Datasets contain biological triplicates (except for duplicates in one case, Delta_17_18_92) for a total of 71 samples.

first: Doron

last: Betel

first: Yoon-Chi

last: Han

first: Joana

last: Vidigal

first: Irtisha

last: Singh

first: Alvaro

last: Gonzalez

first: Christina

last: Leslie


title: CceR and AkgR regulate of central carbon and energy metabolism in α-Proteobacteria

city: Madison

first: Timothy

middle: J

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

platform_organism:
Cereibacter sphaeroides
Cereibacter sphaeroides 2.4.1


title: Genome-wide protein-DNA interaction analysis of CceR and AkgR transcription factors

summary: To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 2 transcription factors: CceR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of of central carbon and energy metabolism.

overall_design: Genome-wide protein-DNA interaction analysis of 2 transcription factors predicted to be involved in regulation of central carbon metabolism CceR and AkgR

first: Saheed

last: Imam


title: Ectopic CENP-A nucleosomes localize to transcription factor hotspots and subtelomeric sites in human cancer cells

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: Comparison of histone variant CENP-A in different cell lines vs. DHS profiles from same cell lines. Mock IPs included.

overall_design: Profiles of ectopic CENP-A IP after pre-clearing with CENP-B IPs, or profiles of DHS regions from mid-log culture SW480 colorectal cancer cell lines, HeLa cervical cancer cell lines, and EpiCo normal colon cell line were generated using deep sequencing after Mnase-based ChIP, in replicates, on the Illumina platform.

first: Yamini

last: Dalal

first: Rajbir

last: Athwal

first: Marcin

last: Walkiewicz

first: Song

last: Fu

first: Minh

last: Bui

first: Jordi

last: Camps

first: Mia

last: Sung

first: Thomas

last: Ried


title: A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation (ChIP-seq)

first: Evarist

last: Planet

overall_design: Kap1 and H3K9me3 ChIPseq in proliferating C2C12 cells

first: Marco

last: Cassano


title: Effect of Nbr on the length of piRNAs and endo-siRNAs in Drosophila

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

type: Non-coding RNA profiling by high throughput sequencing

summary:
nbr/CG9247 gene regulates the length of a subset of miRNAs.
It is not clear whether Nbr affects the length of other classes of small RNAs, such as piRNAs and endo-siRNAs.
To address this, we compared small RNA population in wild-type, Df(2L)BSC312/+, nbr null (nbrf02257/Df(2L)BSC312), (nbr null; pCaSper-nbr (WT)), and (nbr null; pCaSper-nbr (D435A,E437A)).
This approach revealed that, in addition to miRNAs, piRNAs and endo-siRNAs were also affected in their length in nbr null and nbr null; pCaSper-nbr (D435A,E437A).

overall_design:
4-7d ovaries were dissected in PBS, and 40ug total RNA was prepared from wild-type, Df(2L)BSC312/+, nbr null (nbrf02257/Df(2L)BSC312), (nbr null; pCaSper-nbr (WT)), and (nbr null; pCaSper-nbr (D435A,E437A)), using Trizol Reagent (#15596-018, Life Technologies, Carlsbad, CA) following the manufacturer's protocol.
The small RNAs between ~16 to ~29 nt in size were purified from 15% TBE-urea gel (#EC6885BOX, Life Technologies, Carlsbad, CA).
Small RNA libraries were prepared using Illumina's TruSeq small RNA sample preparation kit (#RS-200-0012, Illumina, Inc. San Diego, CA), following the manufacturer's protocol
The libraries were sequenced on HiSeq2000 platform (Illumina).

first: Masashi

last: Abe

first: Nancy

last: Bonini

first: Mugdha

last: Khaladkar

first: Virzhiniya

middle: L

last: Feltzin

first: Michael

last: Parisi

first: Gert

last: Hendriks


title: Pseudomonas aeruginosa PA14 differential gene expression in bqsR (PA14_29730) mutants

status: Public on Feb 01 2015

city: Pasadena

first: Dianne

last: Newman

address: 1200 E California Blvd

department: BBE and GPS

institute: Caltech

summary:
Before and after anaerobic Fe(II) shocked WT and ∆bqsR of late stationary phase P. aeruginosa PA14 strains
Associated publication: Kreamer NN, Costa F, Newman DK. 2015. The ferrous iron-responsive BqsRS two-component system activates genes that promote cationic stress tolerance. mBio 6(1):e02549-14. doi:10.1128/mBio.02549-14.

overall_design: Expression profiles of rRNA-depleted total RNA from WT and ∆bqsR Fe(II)-shocked (before and after 30 min incubation with 200 µM ferrous ammonium sulfate ) cultures grown anaerobically to deep stationary phase (A500 = 0.8) in Fe-limited (1 µM ferrous ammonium sulfate) MOPS minimal medium containing succinate as the carbon source, in triplicate

first: Naomi

middle: N

last: Kreamer


title: Predictive Value of MicroRNAs in the Progression of Oral Leukoplakias

first: Elizabeth

last: Philipone

address: 630 West 168th Street

department: Oral & Maxillofacial Pathology

institute: Columbia University

overall_design: Comparison of 10 samples from non-progressive leukoplakias (did not turn into oral squamous cell carcinoma), with 10 samples from progressive leukoplakias (turned into oral squamous cell carcinoma w/in 5 yrs)

first: Nicolas

last: Robine


title: Small RNA sequencing study of the nematode phylum

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

summary: Comparison of small RNA profiles across nematode evolution

sample_organism:
Caenorhabditis elegans
Brugia malayi
Trichinella spiralis
Romanomermis culicivorax
Nippostrongylus brasiliensis
Globodera pallida
Pristionchus pacificus
Enoplus brevis
Paragordius varius
Hypsibius dujardini
Odontophora rectangula

overall_design: Sequencing of small RNAs (15-33nt)


title: Huntington’s disease biomarker progression profile identified by transcriptome sequencing in peripheral blood

city: Leiden

first: Anastasios

last: Mastrokolias

address: LUMC, Building 2 Einthovenweg 20 2333 ZC Leiden

country: Netherlands

institute: Leiden University Medical Center

summary: In this study we investigated the suitability of blood to identify HD transcriptomic biomarkers, validated the outcome in an independent cohort and derived a first empiric panel of biomarkers capable of predicting HD motor scores. Finally we examined whether patient gene expression profiles could provide information about HD affected biological pathways.

overall_design: Examination of differentially expressed genes in peripheral whole blood using linear modelling of  gene expression data (3' DGE) against UHDRS total motor scores of Huntington's Disease mutation carriers and controls.


title: Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq

city: Copenhagen N

first: Janus

middle: Schou

last: Jakobsen

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: ChIP-seq is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libraries has impeded ChIP-seq on in vivo tissues of low cell numbers. We describe a robust, simple and scalable methodology for ChIP-seq of low-abundant cell populations, reliably amplifying 50 pg of ChIP DNA, corresponding to ~30,000 input cells for transcription factor ChIP (CEBPA) and 3,000 cells for histone mark ChIP (H3K27me3). This represents a significant advance compared to existing technologies, which involve complex and time-consuming steps of pre-amplification, making them susceptible to experimental biases.

overall_design: ChIP-seq of histone modifications H3K27me3 (2 biological replicates (I+II) , 2 ng input), H3K4me3 (2 biological replicates (II+III), 2 ng input), transcription factor CEBPA (2 biological replicates (I+II), 300 pg input), 4 diluted CEBPA libraries (pool of ChIP from 3 biol. replicates (I+II+III) 3x 100 pg input, 1x 50 pg). Additonal ChIP-seq using 10,000 cells, 1 biological replicate of each H3K4me3 and CEBPA.

middle: S

first: Marie

last: Hasemann

first: Frederik

middle: O

last: Bagger

first: Mikkel

last: Schuster

first: Anne

last: Frank

first: Johannes

last: Waage

first: Kristoffer

last: Vitting-Seerup

first: Bo

last: Porse


title: Genome-wide transcriptional analysis of PE-2 strain of Saccharomyces cerevisiae

city: campinas

first: Osmar

last: Netto

address: UNICAMP

country: Brazil

institute: Genomic and Expression Laboratory

summary: In this study we investigate the molecular physiology of the main S. cerevisiae commercial strain (PE-2) used on Brazilian bioethanol process under two distinct conditions: typical (TF) and flocculated (co-aggregated - FL) fermentation. Transcriptional machinery of PE-2 was assessed by high throughput sequencing-based methods (RNA-seq) during industrial fed-batch fermentations. Data from comparative analysis revealed distinct transcriptional profiles among conditions, characterized mainly by a deep gene repression on FL process.

overall_design: We investigated the transcriptional changes in S. cerevisiae PE-2 strain under industrial fermentation conditions using RNA-seq protocols. We analyzed 13 fermentation time-points where 6 time-points on typical fermentation conditions (TF) and 7 time-points on flocculate conditions(FL). The raw data have been submitted to SRA as SRP014755

middle: V

last: Carvalho-Netto

first: Marcelo

middle: F

last: Carazzolle

first: Luciana

last: Mofatto

first: Paulo

last: Teixeira

first: Melline

last: Noronha

first: Luige

last: Calderón

first: Piotr

last: Mieczkowski

first: Juan

last: Argueso

first: Gonçalo

last: Pereira


title: HITS-CLIP analysis uncovers a link between the Kaposi's sarcoma associated herpesvirus ORF57 protein and host pre-mRNA metabolism

city: Dallas

first: Tao

last: Wang

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

summary: The Kaposi's sarcoma associated herpesvirus (KSHV) is an oncogenic virus that causes Kaposi's sarcoma, primary effusion lymphoma (PEL), and some forms of multicentric Castleman's disease. The KSHV ORF57 protein is a conserved posttranscriptional regulator of gene expression that is essential for virus replication. ORF57 is multifunctional, but most of its activities are directly linked to its ability to bind RNA. We globally identified virus and host RNAs bound by ORF57 during lytic reactivation in PEL cells using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). As expected, ORF57-bound RNA fragments mapped throughout the KSHV genome, including the known ORF57 ligand PAN RNA. In agreement with previously published ChIP results, we observed that ORF57 bound RNAs near the oriLyt regions of the genome. Examination of the host RNA fragments revealed that a subset of the ORF57-bound RNAs was derived from transcript 5´ ends. The position of these 5´-bound fragments correlated closely with the 5´-most exonintron junction of the pre-mRNA. We selected four candidates (BTG1, EGR1, ZFP36, and TNFSF9) and analyzed their pre-mRNA and mRNA levels during lytic phase. Analysis of both steady-state and newly made RNAs revealed that these candidate ORF57-bound pre-mRNAs persisted for longer periods of time throughout infection than control RNAs, consistent with a role for ORF57 in pre-mRNA metabolism. In addition, exogenous expression of ORF57 was sufficient to increase the pre-mRNA levels and, in one case, the mRNA levels of the putative ORF57 targets. These results demonstrate that ORF57 interacts with specific host pre-mRNAs during lytic reactivation and alters their processing, likely by stabilizing pre-mRNAs. These data suggest that ORF57 is involved in modulating host gene expression in addition to KSHV gene expression during lytic reactivation.

overall_design: HITS-CLIP was performed on TREx BCBL-Rta cells 20 hpi using antibodies against ORF57. Three biological replicates were performed.

first: Emi

last: Sei

first: Olga

last: Volovnik Hunter

first: Yang

last: Xie

first: Nicholas

last: Conrad


title: Transcriptomic characterizations associated with autopolyploidization of Chinese woad (Isatis indigotica Fort.)

city: wuhan

first: Zhou

last: Yingying

address: shizishan street 1#

country: China

institute: huazhong agriculture university

summary: The study was to obtain transcriptional data and examine gene expression of different ploidy based on RNA-Seq and bioinformatic analysis. Differentially expressed genes including both up- and down-regulated were received by pairwise contrasts of diploid, triploid and tetraploid.

overall_design: RNA from young plant leaves were isolated and gene expressions of different autoploidy via RNA-Seq and bioinformatic analysis were conducted

first: Yingying

last: Zhou

first: Zaiyun

last: Li


title: Expression profiling of mouse T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia) cells following Ikaros restoration

city: Parkville

first: Gordon

last: Smyth

address: 1G Royal Pde

institute: Walter and Eliza Hall Institute of Medical Research

overall_design: Refer to individual Series


title: Pathway Profiling of Replicative and Induced Senescence

city: Detroit

first: Maggie

last: Purcell

address: 110 E Warren

institute: Wayne State University

summary: RNA-seq was performed on LFS MDAH041 cells that were young (PD10-12), aging (PD17-19) and replicatively senescent (PD28-30), as well as spontaneously immortal cells and cells that were induced into senescence or quiescence,  in order to profile the pathways common in all 4 types of sensecence and the pathways affected as a cell approaches senescence.

overall_design: RNA was sequenced in biological triplicates of each sample using the Illumina HiSeq2000

first: Michael

last: Tainsky

first: Adele

last: Kruger


title: BAFF engages distinct NFkappaB effectors in maturing and proliferating B cells

city: San Diego

first: Harry

middle: Aaron

last: Birnbaum

state: California

address: 4406 Dawes Street

institute: UCSD Chem and Biochem

summary: Identify genes which are induced in wild type B cells under antigenic stimuli, anti-IgM vs pro-survival stimuli, BAFF. Also find the differential expressed genes which are distinct from in co-stimulated conditions.

overall_design: RNAseq analysis of wild type primary B cells stimulated with anti-IgM alone, BAFF alone, or co-stimulated with both anti-IgM and BAFF for 8 and 30 hours

first: Jonathan

last: Almaden

first: Jeremy

last: Davis-Turak

first: Alexander

last: Hoffmann


title: Functional consequences of DNA-methylation in response to regular exercise

city: Nuthetal

first: Timo

last: Kanzleiter

address: Arthur-Scheunert-Alle 114

department: Experimental Diabetology

country: Germany

institute: DIfE


title: Genome-wide changes in DNA methylation in response to physical exercise

summary: Here we describe a genome-wide analysis of DNA-methylation in muscle of trained mice. In comparison to sedentary controls 2762 genes exhibited differentially methylated CpGs in their putative promoter regions.  The majority of these genes were related to muscle growth and differentiation and a minor fraction involved in metabolic regulation. These findings suggest that DNA-methylation is involved in the regulation of muscle adaptation to regular exercise training.

overall_design: Reduced representation bisulfite sequencing of murine quadriceps muscle

first: Markus

last: Jaehnert

first: Annette

last: Schuermann


title: Genome-wide analysis reveals CLF-regulated transcripts in Arabidopsis

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: CURLY LEAF (CLF), the major histone methyltransferase of Polycomb Repressive Complex 2 (PRC2), modifies trimethylation of histone H3 lysine 27 (H3K27me3) and mediates dynamical chromatin repression in Arabidopsis. Here we profiled Arabidopsis transcriptomes obtained from roots, leaves, flowers and siliques of Col-0 and clf-28 plants using RNA-seq. Our analysis uncovered 3835 transcription units were up-regulated in clf-28. Compared with H3K27me3 ChIP-CHIP data, we found  at least 42% of them were associated with H3K27me3.

overall_design: Transcriptom profiling in roots, leaves, flowers and siliques of clf-28 plants.

first: Shulin

last: Deng

first: Huan

last: Wang

first: Jian

last: Ye

first: Nam-Hai

last: Chua


title: Extensive crosstalk between lncRNAs and mRNAs in mouse stem cells

status: Public on Jan 31 2015

city: Lausanne

first: Ana

last: Marques

address: Rue du Bugnon 27

department: Department of Computational Biology

institute: University of Lausanne

summary: To determine the temporal variation of mRNA levels, we collected and sequenced poly-adenylated RNA from all cell extracts, cytoplasmic and nuclear fractions of a conditional Dicer mutant [DTCM23/49 XY (Nesterova et al. 2008)] mouse Embryonic Stem Cells before induction of Dicer excision (day 0) and at days 4, 8, 10 and 12 following Dicer loss of function. coverage.

overall_design: RNA from whole cell extracts was collected at days 0, 4, 8, 10 and 12 following loss of Dicer function and from the cytoplasmic and nuclear fractions of cell at day 0 and 12. Three biological replicates were obtained for all samples. Poly-adenylated directional 100 base paired-end sequencing libraries were prepared for all extracts and sequenced by BGI solutions (Hong Kong).

middle: C


title: Transcription factor Msn2 dependent gene expression in two entomopathogen fungi, Beauveria bassiana and Metarhizium robertsii under thermal and oxidaitve stresses

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

institute: TIB CAS

summary: Transcription factor Msn2 played crucial roles in mediating fungal stress tolerance, a determinant to the biocontrol potential of fungal entomopathogens. We characterized for the first time the functions of Beauveria bassiana Msn2 (BbMsn2) and Metarhizium robertsii (MrMsn2) by analyzing multi-phenotypic changes in Msn2-deletion and investigating transcription patterns of WT versus ΔMsn2 of B. bassiana and M. robertsii under thermal and oxidative stresses by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in transportation, detoxification, signal transduction, and energy metabolism, were significantly repressed in expression level.

sample_organism:
Beauveria bassiana
Metarhizium robertsii

overall_design: Total RNA obtained from Bbmsn2 and MrMsn2 disruption mutant subjected to 2 mM menadione and 40 °C for 3-h response compared to the wild type strain under the same stress treatment.

first: Qian

first: Ming-Guang

last: Feng


title: Sequencing of reaction products from protospacer integration by Cas1-Cas2

status: Public on Jan 30 2015

city: Berkeley

first: James

last: Nunez

address: 731 Stanley Hall

institute: University of California, Berkeley

summary: We report the sites of protospacer integration into plasmids by Cas1-Cas2. The goal of this study is to determine the role of sequence elements on protospacer integration.

overall_design: Methods: Cas1-Cas2 integration products were fragmented, end-repaired, adapter ligated, PCR amplified, and analyzed by Illumina sequencing. Protospacer-containing reads were selected by Cutadapt and mapped to the plasmid with Bowtie.

last: Nuñez

first: Amy

last: Lee

first: Alan

last: Engelman

first: Jennifer

middle: A

last: Doudna


title: Apple russeting as seen through the RNA-seq lens: strong alterations in the exocarp cell wall

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

summary: Russeting is a commercially important defect in apple (Malus x domestica) fruit production. Apple russeting is mainly characterized by the accumulation of suberin on the inner part of the cell wall. However, knowledge on the underlying genetic components triggering this trait remains sketchy. A bulk transcriptomic profiling was performed on the exocarps of three russeted and three waxy apple varieties using RNA sequencing. This experimental design was chosen to lower the specificities of each genotype. A qPCR validation was carried out on representative genes and additional contrasting varieties. Gene ontology enrichment revealed a repression of the lignin and cuticle biosynthesis genes in the russeted exocarps, concomitantly with an enhanced expression of suberin deposition, stress responsive, primary sensing, NAC and MYB-family transcription factors, and specific triterpene biosynthetic genes. Notably, a strong correlation (R2=0.976) between the expression of a MYB93-like transcription factor and key suberin biosynthetic genes was found. Our results suggest that russeting is induced by a decreased expression of the cuticle layer biosynthetic genes, leading to a stress response which not only affects suberin deposition, but also the entire structure of the cell wall. In addition, the large number of candidate genes highlighted in this study provides a solid platform for further functional investigations.

overall_design: In order to draw a consistent picture of the gene expression profiles specific to both russeted and waxy apples and at the same time to highlight and interpret the mechanism leading to the russeted phenotype, a bulk RNA-sequencing was performed on the exocarp of a group of three distinct fully-russeted apple varieties ('Patte de loup', 'Reinette Parmentier', 'St Edmund's Pippin') and a second one including 3 fully waxy varieties ('Gala', 'CRAW/Ma/AF42', and 'CRAW/Ma/AG94').

first: S

first: G

last: Guerriero

first: A

last: Deleruelle

first: M

last: Lateur

first: D

last: Evers

first: C

last: André

first: J

last: Hausman


title: Role of histone lysine demethylase LSD2 in hepatic metabolism

city: Kumamoto

first: Shinjiro

last: Hino

address: 2-2-1 Honjo

institute: Kumamoto University

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


title: A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation

first: Evarist

last: Planet

address: Route Cantonale

institute: EPFL


title: An improved protocol for small RNA library construction by using High-Definition adapters [cell line]

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

institute: University of Oxford

summary: Most of small RNA library construction methods are based on RNA ligases, which prefer to join the molecules (small RNAs and adapters) that can anneal to each other and form a ligase favoured structure. Different platforms for next generation sequencing use different adapter sequences, causing the cloning bias. Adapters with degenerated nucleotides at the ligating ends (High Definition, HD adapters) were developed to reduce the cloning bias. However, above 90% of the cloning products is adapter dimer when the current available commercial kits and their corresponding protocols are used.  Here we adopted and further improved a method demonstrated in a publically available patent (http://www.google.com/patents/WO2011056866A2?cl=en). Using the improved method, we constructed the small RNA libraries by using the total RNA of chondrosarcoma cell line. The adapter dimer was significantly reduced. The small RNA sequences were also analysed.

overall_design: The small RNA libraries of cultured chondrosarcoma cell line were constructed by using an improved protocol where high-definition (HD) adapters were used.

first: Ping

last: Xu

first: Martina

last: Billmeier

first: Darrell

last: Green

first: William

middle: D

last: Fraser

first: Tamas

last: Dalmay


title: An improved protocol for small RNA library construction by using High-Definition adapters

summary: Most of small RNA library construction methods are based on RNA ligases, which prefer to join the molecules (small RNAs and adapters) that can anneal to each other and form a ligase favoured structure. Different platforms for next generation sequencing use different adapter sequences, causing the cloning bias. Adapters with degenerated nucleotides at the ligating ends (High Definition, HD adapters) were developed to reduce the cloning bias. However, above 90% of the cloning products is adapter dimer when the current available commercial kits and their corresponding protocols are used.  Here we adopted and further improved a method demonstrated in a publically available patent (http://www.google.com/patents/WO2011056866A2?cl=en). Using the improved method, we constructed the small RNA libraries by using the total RNA of Medicago truncatula leaf tissue. The adapter dimer was significantly reduced. The small RNA sequences were also analysed.

overall_design: The small RNA libraries of medicago truncatula leaves were constructed by using an improved protocol where high-definition (HD) adapters were used.


title: Doxorubicin induces double-strand breaks at CpG island promoters

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Doxorubicin is a widely used chemotherapeutic drug that intercalates between DNA base-pairs and posions Topoisomerase II, although the mechanistic basis for cell killing remains speculative. Here we show that both anthracyclines and Topoisomerase II poison cause enhanced DNA double-strand breaks around CpG island promoters of active genes genome-wide. We propose that torsion-based enhancement of nucleosome turnover exposes promoter DNA, ultimately causing DNA breaks around promoters that contributes to cell killing.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: We have analyzed mouse squamous cell carcinoma cells treated with doxorubicin, aclarubicin and etoposide. The direct in situ Breaks Labeling, Enrichment on Streptavidin (BLESS, PMID 23503052) method was used for mapping DNA double-strand breaks genome-wide.

first: Fan

last: Yang

first: Christopher

last: Kemp

first: Steven


title: Proteasome Function is Required for Platelet Production

city: Salt Lake City

first: Jesse

middle: Worth

last: Rowley

state: Ut

department: Medicine

institute: University of Utah

summary: RNA-seq expression analysis of transcripts encoding proteasome subunits in human CD34+ cord blood cell-derived megakaryocytes and mouse bone marrow-derived megakaryocytes.

overall_design: Analysis of transcript expression in human CD34+ cord blood cell-derived megakaryocytes and mouse bone marrow-derived megakaryocytes.

first: Dallas

last: Shi

first: Robert

last: Campbell

first: Joseph

middle: E

last: Italiano

middle: W

first: Andrew

last: Weyrich


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cardiac-specific Bmi1 deletion

city: Madrid

first: Manuel

last: Gomez

address: Melchor Fernández Almagro, 3

institute: CNIC


title: Exon-Intron circular RNAs regulate transcription in the nucleus

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: We report the high-throughput sequencing of Pol II

overall_design: One sample of IgG and Pol II

first: Lin

last: Mei


title: RNA-seq analysis of withdrawal of miR-155 hyperexpression in miR-155-addicted tumors

city: New Haven

last: Cheng

state: CT

address: 55 Prospect St

institute: Yale University

summary: Overexpression of miR-155 in hematological tissue leads to the onset of lymphoma, and Tet-off shutdown of this overexpression reverses the disease phenotype in mir-155LSLtTA mice. This study compares the gene expression profiles of tumors with miR-155 overexpression and withdrawal.

overall_design: Examination of mRNA from 2 conditions: miR-155 overexpressing tumors and miR-155 overexpressing tumors from mice exposed to doxycycline (DOX) for 16hrs prior to harvest; samples in triplicate; tumors generated in flanks of nude mice by subcutaneous injection of splenic cells from diseased mir-155LSLtTA mice.

first: Frank

last: Slack


title: Characterization of microRNA-offset RNAs in human embryonic stem cells (hESCs)

city: Stockholm

first: Suvi

middle: Tuulia

last: Asikainen

state: Huddinge

address: Karolinska University Hospital

department: CLINTEC

country: Sweden

institute: Karolinska Institutet

summary: Small RNA molecules, including microRNAs (miRNAs), play critical roles in regulating pluripotency, proliferation and differentiation of embryonic stem cells. miRNA-offset RNAs (moRNAs) are similar in length to miRNAs, align to miRNA precursor (pre-miRNA) loci and are therefore believed to derive from processing of the pre-miRNA hairpin sequence. Recent next generation sequencing (NGS) studies have reported the presence of moRNAs in human neurons and cancer cells and in several tissues in mouse, including pluripotent stem cells. In order to gain additional knowledge about human moRNAs and their putative development-related expression, we applied NGS of small RNAs in human embryonic stem cells (hESCs) and fibroblasts. We found that certain moRNA isoforms are notably expressed in hESCs from loci coding for stem cell-selective or cancer-related miRNA clusters. In contrast, we observed only sparse moRNAs in fibroblasts. Consistent with earlier findings, most of the observed moRNAs derived from conserved loci and their expression did not appear to correlate with the expression of the adjacent miRNAs. We provide here the first report of moRNAs in hESCs, and their expression profile in in comparison to fibroblasts. Moreover, we expand the repertoire of hESC miRNAs. These findings provide an expansion on the known repertoire of small non-coding RNA contents in hESCs.

overall_design: We performed small RNA-seq analysis from three samples: one from hESC line HS401, one from hESC line HS181 and one from human foreskin fibroblast line HFF-1

first: Liisa

last: Heikkinen

first: Outi

last: Hovatta

first: Garry

last: Wong


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cardiac-specific Bmi1 deletion [human]

summary: To explore the primary cause of Dilated Cardiomyopathy in heart samples from DCM-diagnosed patients who had undergone heart transplant (hDCM), we set out to identify differentially expressed genes by massively parallel sequencing of heart samples.

overall_design: Methods: Heart mRNA profiles from DCM-diagnosed patients who had undergone heart transplant (hDCM) were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Susana

last: Gonzalez

first: Ileana

last: Gonzalez-Valdez


title: Top2a identifies and provides epigenetic rationale for novel combination therapeutic strategies for aggressive prostate cancer

city: Buffalo

first: Qiang

last: Hu

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: We perform RNA-seq on matched orthotopic murine primary and metastatic prostate cancer samples to identify differential gene expressions

overall_design: RNA-seq was performed on orthotopic murine primary and metastatic tumor samples using Illumina Hi-Seq 2000 platform

first: Leigh

last: Ellis

first: Jianmin

last: Wang


title: Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy

city: west Haven

first: Mauris

middle: Chukwudebelu

last: Nnamani

address: 300 heffernan drive B31-ABC/rm269

department: Systems Biology institute, EEB

summary: A major challenge in biology is to determine how evolutionarily novel characters originate, however, mechanistic explanations for the origin of novelties are almost completely unknown. The evolution of mammalian pregnancy is an excellent system in which to study the origin of novelties because extant mammals preserve major stages in the transition from egg-laying to live-birth. To determine the molecular bases of this transition we characterized the pregnant/gravid uterine transcriptome from tetrapods, including species in the three major mammalian lineages, and used ancestral transcriptome reconstruction to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved endometrial expression during the origins of mammalian pregnancy, including numerous genes that mediate maternal-fetal communication and immunotolerance.Furthermore we show that thousands of regulatory elements active in decidualized human endometrial stromal cells are derived from ancient mammalian transposable elements which provided binding sites for transcription factors that mediate decidualization and endometrial cell-type identity. Our results indicate that one of the defining mammalian novelties evolved via domestication of ancient mammalian transposable elements into hormone-responsive regulatory elements throughout the genome.

overall_design: Examination of histone modification and DNAse hypersensitivity in decidualized dESC

first: Vincent

last: Lynch

first: Aurelie

last: Kapusta

first: Kathryn

last: Brayer

first: Silvia

last: Plaza

first: Erik

last: Mazur

first: Deena

last: Emera

first: Shehzad

middle: Z

last: Sheikh

last: Grutzner

first: Stefan

last: Bauersachs

first: Alexander

last: Graf

first: Steven

last: Young

first: Jason

last: Lieb

first: Francesco

last: DeMayo

first: Cedric

last: Feschotte

first: Gunter

middle: P

last: Wagner


title: ChIP-seq of WT(with 35S-SUC2 transgene) and proMBD7::gMBD7:4xMYC transgenic plants

status: Public on Jan 29 2015

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary:
In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3) as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation

Using ChIP-seq to study the genomic targeting principle of MBD7 protein

overall_design: Examination of MBD7 protein binding principle using ChIP-Seq. WT and proMBD7::gMBD7::4xMYC transgenic plants were used for ChIP-seq.

first: Zhaobo

last: Lang

first: Mingguang

last: Lei

first: Xingang

last: Wang

first: Kai

last: Tang

first: Daisuke

last: Miki


title: A dual cis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages.

city: Rozzano

first: Alberto

last: Termanini

state: MI

address: Via Manzoni, 113

country: Italy

institute: Istituto Clinico Humanitas

summary: The transcription factor (TF) interferon regulatory factor 8 (IRF8) controls both developmental and inflammatory stimulus-inducible genes in macrophages, but the mechanisms underlying these two different functions are largely unknown. One possibility is that these different roles are linked to the ability of IRF8 to bind alternative DNA sequences. We found that IRF8 is recruited to distinct sets of DNA consensus sequences before and after lipopolysaccharide (LPS) stimulation. In resting cells, IRF8 was mainly bound to composite sites together with the master regulator of myeloid development PU.1. Basal IRF8–PU.1 binding maintained the expression of a broad panel of genes essential for macrophage functions (such as microbial recognition and response to purines) and contributed to basal expression of many LPS-inducible genes. After LPS stimulation, increased expression of IRF8, other IRFs, and AP-1 family TFs enabled IRF8 binding to thousands of additional regions containing low-affinity multimerized IRF sites and composite IRF–AP-1 sites, which were not premarked by PU.1 and did not contribute to the basal IRF8 cistrome. While constitutively expressed IRF8-dependent genes contained only sites mediating basal IRF8/PU.1 recruitment, inducible IRF8-dependent genes contained variable combinations of constitutive and inducible sites. Overall, these data show at the genome scale how the same TF can be linked to constitutive and inducible gene regulation via distinct combinations of alternative DNA-binding sites.

overall_design: Chromatin immuno-precipitations of transcription factors IRF8, IRF1, PU.1, STAT1, STAT2 and of H3 lysine 27 acetylated followed by multiparallel sequencing, performed in bone marrow-derived macrophages from wild type (WT) and BXH2/TyJ mice. Cells were treated with lipopolysaccharide (LPS) for 2 or 4 hours, or interferon b (IFNb) for 30 or 60 minutes, 2 or 4 hours, or left unstimulated.

first: Alessandra

last: Mancino

first: Iros

last: Barozzi

first: Serena

last: Ghisletti

first: Renato

last: Ostuni

first: Elena

last: Prosperini

first: Keiko

last: Ozato

first: Gioacchino

last: Natoli


title: A Ribonuclease Coordinates siRNA Amplification and mRNA Cleavage during RNAi

city: Taipei

first: Hsin-yue

last: Tsai

address: 128 academia road sec 2, nankang

department: Institute of biological chemistry

country: Taiwan

institute: Sinica academia

summary: Effective silencing by RNA-interference (RNAi) depends on mechanisms that amplify and propagate the silencing signal. In some organisms, small-interfering (si) RNAs are amplified from target mRNAs by RNA-dependent RNA polymerase (RdRP). Both RdRP recruitment and mRNA silencing require Argonaute proteins, which are generally thought to degrade RNAi targets by directly cleaving them. However in C. elegans, the enzymatic activity of the primary Argonaute, RDE-1, is not required for silencing activity.   We show that RDE-1 can instead recruit an endoribonuclease, RDE-8, to target RNA. RDE-8 can cleave RNA in vitro and is needed for the production of 3′ uridylated fragments of target mRNA in vivo.  We also find that RDE-8 promotes RdRP activity, thereby ensuring amplification of siRNAs.  Together, our findings suggest a model in which RDE-8 cleaves target mRNAs to mediate silencing, while generating 3’ uridylated mRNA fragments to serve as templates for the RdRP-directed amplification of the silencing signal.

overall_design: We examined the role of rde-8 in C. elegans small RNA biogenesis pathways, including endogenous and exogenous RNAi pathways. We performed 3' RACE seq from the sel-1 target mRNA and correlate with small RNAs from wild type, rde-8 and rde-8 transgenic strains after sel-1(RNAi) for different lengths of time.

first: Hsin-Yue

first: C

last: Mello


overall_design: Refer to individual Series


title: Epigenetic targeting of activation-induced cytidine deaminase

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Precisely how AID is recruited to these off-target sites is not entirely understood. To gain further insight into how AID selects its targets we compared AID-mediated translocations in two different cell types, B cells and mouse embryonic fibroblasts (MEFs). AID targets a distinct set of hotspots in the two cell types. In both cases, hotspots are concentrated in highly transcribed but stalled genes. However, transcription alone is insufficient to recruit AID activity. Comparison of genes similarly transcribed in B cells and MEFs but targeted in only one of the two cell types reveals a common set of epigenetic features associated with AID recruitment in both cell types. AID target genes are enriched in chromatin modifications associated with active enhancers (such as H3K27Ac) and marks of active transcription (such as H3K36me3) in both fibroblasts and B cells, indicating that these features are universal mediators of AID recruitmen

overall_design: Analysis of total mRNA and PolII loading in activated B lymphocytes and Mouse Embryonic Fibroblasts (MEFs)

first: Qiao

first: Mila

last: Jankovic

first: Israel

middle: T

last: Silva

first: Ofir

last: Hakim

first: Kaihui

last: Yao

first: Anna

last: Gazumyan

first: Christian

last: Mayer

first: Rushad

last: Pavri

first: Rafael

last: Casellas

first: Davide

last: Robbiani

first: Michel

last: Nussenzweig


title: The catalytically inactive Domains Rearranged Methyltransferase3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis

first: Christopher

middle: Joel

last: Hale

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

summary: DNA methylation is a mechanism of epigenetic gene regulation and genome defense conserved in many eukaryotic organisms. In Arabidopsis, the DNA methyltransferase DRM2 controls RNA-directed DNA methylation in a pathway that also involves the plant specific RNA Polymerase V (Pol V). The Arabidopsis genome also encodes an evolutionarily conserved but catalytically inactive DNA methyltransferase DRM3. Here, we show that DRM3 has moderate effects on global RNA-directed DNA methylation and small RNA abundance throughout the genome, and DRM3 protein physically interacts with Pol V.  In drm3 mutants, we observe a lower level of Pol V-dependent transcripts, even though Pol V chromatin occupancy is increased at many sites in the genome. These findings suggest that DRM3 acts to promote Pol V transcriptional elongation or assist in the stabilization of Pol V transcripts, and shed further light on the mechanism of RNA-directed DNA methylation.

overall_design:
For wildtype plants as well as drm3, drm2, and nrpe1 mutants ChIP-seq was carried out using an endogenous NRPE1 antibody given to us by the Craig Pikaard lab. Two biological replicates of ChIP-seq were also carried out using anti-Flag resin on wildtype and drm3 plants carrying a Flag epitope tagged version of NRPE1. Small RNA sequencing was carried out on Col, drm3, drm2, and nrpe1 plants. Finally, whole-genome bisulfite sequencing analysis was carried out on previously published datasets (as detailed below) which were realigned using a newer genome version and mapping protocol. As such the updated processed files are part of this submission.
Please note that the drm2, drm3, and nrpe1 mutant libraries used in this study were previously published (GSE39901), as were the 2 other Col replicates used (GSE36129) as below and thus duplicated sample records were created for the convenient retrieval of the complete raw data from SRA;

Bisulfite_seq-Col_1 - GSM881756
Bisulfite_seq-Col_2 - GSM1193638
Bisulfite_seq-drm3 - GSM981017
Bisulfite_seq-drm2 - GSM981015
Bisulfite_seq-nrpe1- GSM981040

middle: J


title: The NAD+-Dependent SIRT1 Deacetylase Translates a Metabolic Switch into Regulatory Epigenetics in Skeletal Muscle Stem Cells

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

summary: Selective genetic ablation of the SIRT1 deacetylase domain in skeletal muscle results in increased H4K16 acetylation and deregulated activation of the myogenic program in satellite cells

overall_design: To establish the role of the deacetylase SIRT1 in skeletal muscle we examined the genome wide distribution of H4K16ac  in quiescent (FI) and proliferating (Cul) satellite cells isolated from WT mice (C57Bl/6 background) and SIRT1mKO (generated via breeding of Pax7cre/+ knock-in mice with mice containing the floxed exon 4 SIRT1 allele). We also analyzed the distribution of SIRT1 in quiescent and proliferating FACS isolated WT satellite cells (two replicates).   We generated the mRNA profiles (at least two replicate for each experiment) of FACS isolated quiescent, proliferating and differentiating (1 day in differentiation medium) satellite cells of WT mice and SIRT1mKO. The selective genetic ablation of the SIRT1 deacetylase domain in skeletal muscle results in increased H4K16 acetylation and deregulated activation of the myogenic program.

first: James

middle: G

last: Ryall

first: Stefania

last: Dell’Orso

first: Assia

last: Derfoul

first: Aster

last: Juan

first: Xuesong

last: Feng

first: Daphney

last: Clermont

first: Miroslav

last: Koulnis

first: Gustavo

last: Gutierrez-Cruz

first: Marcella

last: Fulco

first: Vittorio

last: Sartorelli


title: Gene expression profiling in the endometrium of pregnant mammals

city: Chicago

first: Vincent

middle: J.

last: Lynch

address: 920 E. 58th Street

department: Human Genetics

institute: The University of Chicago

summary: A major challenge in biology is to determine how evolutionarily novel characters originate, however, mechanistic explanations for the origin of novelties are almost completely unknown. The evolution of mammalian pregnancy is an excellent system in which to study the origin of novelties because extant mammals preserve major stages in the transition from egg-laying to live-birth. To determine the molecular bases of this transition, we characterized the pregnant/gravid uterine transcriptome from tetrapods, including species in the three major mammalian lineages, and used ancestral transcriptome reconstruction to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved or lost uterine expression during the origins of mammalian pregnancy, including the loss of genes responsible for the mineralization of the eggshell in the Mammalian and Therian stem-lineages, and the recruitment of genes into uterine expression that mediate maternal-fetal communication and maternal immunotolerance of the fetal allograft in the Therian and Eutherian stem-lineages. Our results indicate that one of the defining mammalian novelties evolved through a step-wise process that dramatically changed uterine gene expression, generating a suite of evolutionary innovations that support prolonged gestations.

sample_organism:
Ornithorhynchus anatinus
Dasypus novemcinctus
Canis lupus familiaris

overall_design: We report genome-wide gene expression generated by mRNA-Seq from the pregnant endometrium of dog, armadillo, and the platypus.

first: Deena

last: Emera


title: Bioinformatics approaches for viral metagenomics in plants using short RNAs : model case of study and application to a Cicer arietinum population

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

institute: Institute for Sustainable Plant Protection

summary: Size fractionated small RNA from total RNA extracts of Cicer arietinum leaves and from Nicotiana benthamiana infected by Cymbidium ringspot virus were mixed in a ratio of 1000 to 1 in amount, respectively.  The RNA was  ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit Please see www.illumina.com for details of the sequencing technology.

overall_design: Short RNA fractionation and characterization


title: MethlyC-Seq of Col-0 WT, idm3-3 and mbd7-2 (CS876032) mutant

first: Jian-Kang

last: Zhu

summary: In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3)  as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation.  MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation  and physically associates with other anti-silencing factors, including the histone acetyltransferase  IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation  by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA,  which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation.

overall_design: Whole genome methylation maps of idm3-3, mbd7-2(CS876032) and Col-0 WT were generated using BS-seq

first: Zhaobo

last: Lang

first: Mingguang

last: Lei

first: Xingang

last: Wang

first: Kai

last: Tang

first: Daisuke

last: Miki


title: Structure and Thermodynamics of N6-methyladenosine in RNA: a Spring-Loaded Base Modification

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: We determine m6A modification sites in GM12878 cells.

overall_design: Examination of m6A modification sites on the transcriptome of GM12878 cells, using a m6A-specific antibody.

first: Caroline

last: Roost

first: Stephen

middle: R

first: Pedro

last: Batista

first: Howard

last: Chang

first: Eric

last: Kool


title: MethlyC-Seq of wild type (with 35S-SUC2 transgene) and idm3-1, mbd7-1 mutants (same 35S-SUC2 background)

summary:
In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3) as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation

Using MethylC-Seq to provide single-base resolution of DNA methylation status in WT and idm3-1, mbd7-1 mutants

overall_design: Whole genome methylation maps of mbd7-1, idm3-1 and WT (all three are from 35S-SUC transgene background) were generated using BS-seq


title: Ribosome profiling data obtained from HEK293T cells 30 minutes after treatment with arsenite to a final concentration of 40 µM

status: Public on Jan 27 2015

city: Cork

first: Pavel

middle: V

last: Baranov

state: Co. Cork

address: Western Gateway Building, UCC

department: Biochemistry and Cell Biology

country: Ireland

institute: University College Cork

summary: Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eIF2. However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. Although this led to a ~4.5-fold general translational repression, the protein coding ORFs of certain individual mRNAs exhibited resistance to the inhibition. Nearly all resistant transcripts possess at least one efficiently translated uORF that repress translation of the main coding ORF under normal conditions. Site specific mutagenesis of two identified stress resistant mRNAs (PPP1R15B and IFRD1) demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases. Phylogenetic analysis suggests that at least two regulatory uORFs (namely in SLC35A4 and MIEF1) encode functional protein products.

overall_design: Ribosome profiling of sodium arsenite treated cells for examination of translational response to induction of eIF2 phosphoylation

first: Dmitry

last: Andreev

first: Patrick

middle: B

last: O’Connor

first: Ciara

last: Fahey

first: Elaine

middle: M

last: Kenny

first: Ilya

last: Terenin

first: Sergey

last: Dmitriev

first: Paul

last: Cormican

first: Derek

last: Morris

first: Ivan

middle: N

last: Shatsky


title: RNA profiling in Drosophila virilis and Drosophila yakuba

first: Christos

last: Samakovlis

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

institute: Stockholm University

summary: Gene annoation and determination of gene expression levels in Drosophila virilis and Drosophila yakuba by deep sequencing.

sample_organism:
Drosophila virilis
Drosophila yakuba

platform_organism:
Drosophila virilis
Drosophila yakuba

overall_design: Total RNA-seq data from heads of 2-5 day old mated D virilis and D yakuba females, 1 sample from each species.

middle: C

last: Lai

first: Jakub

middle: O

last: Westholm


title: Loss of EZH2 results in enhanced recruitment of EZH1, Pol II and Stat5 and precocious mammary gland development (SuperSeries)

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

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


title: The naked endosperm genes encode duplicate ID domain transcription factors required for maize endosperm differentiation

status: Public on Jan 28 2015

city: Ames

first: Philip

middle: W

last: Becraft

state: IA

address: Molecular Biology Building

department: Genetics, Development and Cell Biology

country: USA

institute: Iowa State University

summary: The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm developent. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology.

overall_design: We performed RNA seq analysis of mid-mature (15DAP) endosperm in two cell types [aleurone (A) and starchy endosperm (S)] of wild type B73 (B) and nkd mutant (N) kernels with three independent biological replicates.

first: Anjanasree

middle: K

last: Neelakandan

first: Bryan

last: Gontarek

first: Gibum

last: Yi

first: Erik

last: Vollbrecht


first: Alberto

last: Termanini

summary: IThe transcription factor (TF) interferon regulatory factor 8 (IRF8) controls both developmental and inflammatory stimulus-inducible genes in macrophages, but the mechanisms underlying these two different functions are largely unknown. One possibility is that these different roles are linked to the ability of IRF8 to bind alternative DNA sequences. We found that IRF8 is recruited to distinct sets of DNA consensus sequences before and after lipopolysaccharide (LPS) stimulation. In resting cells, IRF8 was mainly bound to composite sites together with the master regulator of myeloid development PU.1. Basal IRF8–PU.1 binding maintained the expression of a broad panel of genes essential for macrophage functions (such as microbial recognition and response to purines) and contributed to basal expression of many LPS-inducible genes. After LPS stimulation, increased expression of IRF8, other IRFs, and AP-1 family TFs enabled IRF8 binding to thousands of additional regions containing low-affinity multimerized IRF sites and composite IRF–AP-1 sites, which were not premarked by PU.1 and did not contribute to the basal IRF8 cistrome. While constitutively expressed IRF8-dependent genes contained only sites mediating basal IRF8/PU.1 recruitment, inducible IRF8-dependent genes contained variable combinations of constitutive and inducible sites. Overall, these data show at the genome scale how the same TF can be linked to constitutive and inducible gene regulation via distinct combinations of alternative DNA-binding sites.

overall_design: Bone marrow cells isolated from C57BL/6 or BXH2/TyJ mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days. Macrophages were subjected to different treatment (see individual samples for details). Total RNA was extracted from 5x106 cells using RNAeasy kit (Qiagen). Libraries were prepared from 1-2 µg of RNA, after oligo-dT selection, using the TruSeq RNA sample preparation kit (Illumina).

first: Alessandra

last: Mancino

first: Iros

last: Barozzi

first: Serena

last: Ghisletti

first: Renato

last: Ostuni

first: Elena

last: Prosperini

first: Keiko

last: Ozato

first: Gioacchino

last: Natoli


title: RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease

city: St Louis

first: Winnie

last: Pong

state: MO

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

summary: Expression profiling of distinct central nervous system (CNS) cell populations has been employed to facilitate disease classification and to provide insights into the molecular basis of brain pathology. One important cell type implicated in a wide variety of CNS disease states is the resident brain macrophage (microglia). In these studies, microglia are often isolated from dissociated brain tissue by flow sorting procedures [fluorescence-activated cell sorting (FACS)] or from postnatal glial cultures by mechanic isolation. Given the highly dynamic and state-dependent functions of these cells, the use of FACS or short-term culture methods may not accurately capture the biology of brain microglia. In the current study, we performed RNA-sequencing using Cx3cr1+/GFP labeled microglia isolated from the brainstem of 6-week-old mice to compare the transcriptomes of FACS-sorted versus laser capture microdissection (LCM). While both isolation techniques resulted in a large number of shared (common) transcripts, we identified transcripts unique to FACS-isolated and LCM-captured microglia. In particular, ∼50% of these LCM-isolated microglial transcripts represented genes typically associated with neurons and glia. While these transcripts clearly localized to microglia using complementary methods, they were not translated into protein. Following the induction of murine experimental autoimmune encephalomyelitis, increased oligodendrocyte and neuronal transcripts were detected in microglia, while only the myelin basic protein oligodendrocyte transcript was increased in microglia after traumatic brain injury. Collectively, these findings have implications for the design and interpretation of microglia transcriptome-based investigations.

overall_design: Wildtype and GFP expressing microglia from mouse brainstems were flow sorted or captured by laser microdissection.  Differences between the two isolation methods were verified and further examined in neurodegenerative disease models.

first: Anne

last: Solga

first: Jason

last: Walker

first: Todd

last: Wylie

first: Vincent

last: Magrini

first: Anthony

last: Apicelli

first: Malachi

last: Griffith

first: Obi

middle: L

first: Shinichi

middle: F

last: Kohsaka

first: Gregory

last: Wu

first: David

last: Brody

first: Elaine

last: Mardis

middle: H

last: Gutmann


title: HIV-1 integrase variants retarget viral integration and are associated with disease progression in a chronic infection cohort.

status: Public on Jan 26 2015

city: Leuven

first: Jonas

last: Demeulemeester

state: Belgium

address: ON5 Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB – KU Leuven

summary: Distinct integration patterns of different retroviruses have puzzled virologists for over 20 years. The viral integrase (IN), as part of the intasome complex, docks onto the target DNA (tDNA) and catalyzes the insertion of the viral genome into the host chromatin. We identified retroviral IN amino acids directly contacting tDNA bases and affecting the local integration site sequence biases. These residues also determine the propensity of the virus to integrate into flexible tDNA sequences. Remarkably, natural polymorphisms INS119G and INR231G retarget viral integration away from gene dense regions, without affecting the interaction with the lentiviral tethering cofactor LEDGF/p75 (PSIP1). Precisely these variants were associated with rapid disease progression in a chronic HIV-1 subtype C infection cohort. These findings link integration site selection to virulence and viral evolution but also to the host immune response and antiretroviral therapy, since HIV-1 IN119 is under selection by HLA alleles and integrase inhibitors.

overall_design: LEDGF/p75 (PSIP1) ChIP-Seq using A300-848 antibody (recognizes p75 isoform) and input control in primary CD4+ T-cells

first: Madapura

last: Pradeepa

first: Rik

last: Gijsbers


title: Genome wide maps of replicative polymerase contributions to the fully replicated yeast genome

city: Edinburgh

first: Martin

last: Taylor

state: Midlothian

address: Crewe Road

department: MRC Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

summary: We report the application of high through-put tag sequencing to measure the location  and strand of DNA embedded ribonucleotides in the yeast genome. Mutations in the catalytic subunits of the  polymerases (pol1-L868M, pol2-M644G and pol3-L612M) lead to the increased incorporation of ribonucleotides during DNA replication, providing an in vivo label with which to track the contribution of each polymerase to the fully replicated genome. Yeast strains used in this study are deleted for rnh201, encoding the catalytic subunit of the RNase H2 gene so that embedded ribonucleotides are not rapidly removed by ribonucleotide excision repair following DNA replication. Analysis of this data demonstrates that polymerase alpha contributes to the fully replicated genome.

overall_design: Sequencing of DNA embedded ribonucleotides in S. cerevisiae strains to map the contribution of replicative polymerases to the fully replicated genome.

middle: S

middle: A

last: Reijns

first: Andrew

middle: P

last: Jackson


title: Analysis of transcriptome sequences from two flower types of C. vulgaris

city: Erfurt

last: Behrend

address: Kuehnhaeuser Strasse 101

department: Plant Propagantion

institute: Leibniz Institute of Vegetable and Ornamental Crops

summary: The production of heather (Calluna vulgaris) in Germany is highly dependent on cultivars with mutated flower morphology, the so-called diplocalyx bud bloomers. So far, this unique flower type of C. vulgaris has not been reported in any other plant species. The flowers are characterised by an extremely extended flower attractiveness, since the flower buds remain closed throughout the complete flowering season. The flowers of C. vulgaris bud bloomers are male sterile, because the stamens are missing. Furthermore, petals are converted into sepals. Therefore the diplocalyx bud bloomer flowers consist of two whorls of sepals directly followed by the gynoecium. A broad comparison of wild type and bud bloomer’s flowers was undertaken to identify genes differentially expressed in the bud flowering phenotype and in the wild type of C. vulgaris. Transcriptome sequence reads were generated using next generation 454 sequencing of two flower type specific cDNA libraries. In total, 360,000 sequence reads were obtained, assembled to 12,200 contigs, functionally mapped, and annotated. Transcript abundances in wild type and bud bloomer’s libraries were compared and 365 differentially expressed genes detected. Among these differentially genes, CvPI was identified which is the orthologue of the Arabidopsis B gene PISTILLATA (PI) and considered as the most promising candidate gene. Quantitative PCR was performed to analyse the gene expression levels of two C. vulgaris B genes CvPI and CvAP3 in both flower types. CvAP3 which is the orthologue of the Arabidopsis B gene APETALA (AP3) turned out to be ectopically expressed in sepals of wild type and bud bloomer flowers. CvPI expression was proven to be reduced in the flowers of bud blooming cultivars. Differential expression patterns of the B-class genes CvAP3 and CvPI were identified to cause characteristics of flower morphology in C. vulgaris wild type and bud blooming flowers leading to the following hypotheses: ectopic expression of CvAP3 is a convincing explanation for the formation of a completely petaloid perianth in the wild type and the “bud flowering” phenotype. In C. vulgaris, CvPI is essential for determination of petal and stamen identity. The characteristic transition of petals into sepals potentially depends on the observed deficiency of CvPI and CvAP3 expression in bud blooming flowers. However, the complete loss of stamens in bud blooming flowers remains to be explained.

overall_design: two samples were analysed, each representing a flower type

first: Thomas

last: Borchert

first: Annette

last: Hohe


title: The Transcriptional Stress Response of Candida albicans to Weak Organic Acids

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

summary: Candida albicans is the most important fungal pathogen of humans, causing severe infections especially in nosocomial and immunocompromised settings.  However, it is also the most prevalent fungus of the normal human microbiome, where it shares its habitat with hundreds of trillions of other microbial cells.  Despite weak organic acids (WOAs) being among the most abundant metabolites produced by bacterial microbiota, little is known about their effect on C. albicans.  Here we employed a sequencing-based profiling strategy to systematically investigate the transcriptional stress response of C. albicans to lactic, acetic, propionic and butyric acid at several time points after treatment.  Our data reveal a complex transcriptional response, with individual WOAs triggering unique gene expression profiles and with important differences between acute and chronic exposure.  In spite of all these dissimilarities, we found significant overlaps between the gene expression changes induced by each WOA, which lead us to uncover a core transcriptional signature that was unrelated to the general response to low pH.  Genes commonly up-regulated by WOAs were enriched in several iron transporters, which was associated with an overall decrease in intracellular iron concentrations.  Moreover, chronic exposure to any WOA lead to down-regulation of RNA synthesis and ribosome biogenesis genes, which resulted in significant reduction of total RNA levels in general and of ribosomal RNA in particular.  In conclusion, this study suggests that GI microbiota might directly influence C. albicans physiology via production of WOAs, with possible implications of how this fungus interacts with its hosts in both health and disease.

overall_design: Transcriptional profiling of wild-type Candida albicans strain SC5314 under 6 differents condition (2 controls, 4 weak acids) at 4 time points by cDNA deep-sequencing, with 4 biological replicates, on the Illumina HiSeq 2000 platform. 96 total samples were sequenced (6 x 4 x 4).

first: Fabien

last: Cottier

first: Alrina

last: Tan

first: Jinmiao

last: Chen

first: Josephine

last: Lum

first: Francesca

last: Zolezzi

first: Norman

last: Pavelka


title: RNA-SEQ analysis of various developing and adult kidney components

first: GUDMAP

last: Developers

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

summary: We used micro-dissection techniques and/or FACS to isolate cell types from the developing and adult kidney (E11.5 ureteric buds, E12.5, P1 and P4 cap mesenchyme, E15.5 collecting ducts, proximal tubules, ureter, Adult renal proximal tubules, podocytes, endothelial and mesangial cells). RNA-SEQ analysis was performed to determine the transcriptional profile of each cell type, identify component specific transcripts and 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 is obtained from micro-dissected and/or FACS isolated embryonic and adult kidney components. The long term goal is to generate a transcriptional atlas of developing kidney.

last: Potter

first: Eric

last: Brunskill

first: Steven


title: Loss of EZH2 results in enhanced recruitment of EZH1, Pol II and Stat5 and precocious mammary gland development

first: Keunsoo

last: Kang

summary: Establishment and differentiation of mammary alveoli during pregnancy are controlled by prolactin through the transcription factor STAT5. As pregnancy progresses mammary signature genes are activated in a defined temporal order, which coincides with the recruitment of STAT5 to respective regulatory sequences. This study addressed the question whether the methyltransferase and transcriptional co-activator EZH2 controls the differentiation clock of mammary epithelium. Ablation of Ezh2 from mammary stem cells resulted in precocious differentiation of alveolar epithelium and accelerated activation of mammary signature genes. This coincided with enhanced occupancy by EZH1, Pol II and STAT5 to mammary-specific loci. Notably, loss of EZH2 did not result in overt changes in genome-wide and gene-specific H3K27me3 patterns, suggesting that enhanced EZH1 recruitment can compensate for the loss of EZH2. However, differentiated mammary epithelia failed to form in the combined absence of EZH1 and EZH2. Transplantation experiments failed to demonstrate a role for EZH2 in the biology of mammary stem and progenitor cells. In summary, while EZH1 and EZH2 serve redundant functions in the establishment of H3K27me3 and formation of mammary alveoli, the presence of EZH2 is required to obtain controlled temporal differentiation of mammary epithelium.

overall_design: ChIP-seq EZH1, EZH2, PolIII; WT and E2KO mammary cells

first: KyungHyun

last: Yoo

first: Tim

last: Hensel

first: Gertraud

last: Robinson

first: Lothar

last: Hennighausen


title: Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion

status: Public on Jan 23 2015

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

summary: The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes accumulation of local H3K9me2, and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. ChIP timecourse experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly-synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion.

overall_design: Examination of transcription factor occupancy in cells with newly synthesized Oct4.

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