title: Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics [MeDIP-Seq]

city: Boston

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

summary: Ten-eleven translocation (Tet) family of DNA dioxygenases converts 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5- carboxylcytosine (5caC) through iterative oxidation reactions. While 5mC and 5hmC are relatively abundant, 5fC and 5caC are at very low levels in the mammalian genome. Thymine DNA glycosylase (TDG) and base excision repair (BER) pathways can actively remove 5fC/5caC to regenerate unmethylated cytosine, but it is unclear to what extent and at which part of the genome such active demethylation processes take place. Here, we have performed high-throughput sequencing analysis of 5mC/5hmC/5fC/5caC- enriched DNA using modification-specific antibodies and generated genome-wide distribution maps of these cytosine modifications in wild-type and Tdg-deficient mouse embryonic stem cells (ESCs). We observe that the steady state 5fC and 5caC are preferentially detected at repetitive sequences in wild-type mouse ESCs. Depletion of TDG causes marked accumulation of 5fC and 5caC at a large number of distal gene regulatory elements and transcriptionally repressed/poised gene promoters, suggesting that Tet/TDG-dependent dynamic cycling of 5mC oxidation states may be involved in regulating the function of these regions. Thus, comprehensive mapping of 5mC oxidation and BER pathway activity in the mammalian genome provides a promising approach for better understanding of biological roles of DNA methylation and demethylation dynamics in development and diseases.

overall_design: In this dataset, we include the DIP-seq data of 5mC, 5hmC, 5fC and 5caC in both control and Tdg knockdown mouse embryonic stem cells.

first: Hao

last: Wu

first: Dinh

last: Diep

first: Shinpei

last: Yamaguchi

first: Ana

last: D'Alessio

first: Alan

last: Fung

first: Kun

last: Zhang

first: Yi


title: Placing the HIRA histone chaperone complex in the chromatin landscape

status: Public on Apr 18 2013

city: Glasgow

first: Peter

middle: D.

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Usf1, a Suppressor of the Circadian Clock Mutant, Reveals the Nature of the DNA-binding of the CLOCK:BMAL1 complex in mice

status: Public on Apr 21 2013

city: Dallas

first: Joseph

middle: S

last: Takahashi

state: TX

address: 5323 Harry Hines Blvd., NA4.118

department: HHMI, Neuroscience

country: USA

institute: University of Texas Southwestern Medical Center

summary: Genetic and molecular approaches have been critical for elucidating the mechanism of the mammalian circadian clock. Here, we demonstrate that the ClockΔ19 mutant behavioral phenotype is significantly modified by mouse strain genetic background. We map a suppressor of the ClockΔ19 mutation to a ∼900 kb interval on mouse chromosome 1 and identify the transcription factor, Usf1, as the responsible gene. A SNP in the promoter of Usf1 causes elevation of its transcript and protein in strains that suppress the Clock mutant phenotype. USF1 competes with the CLOCK:BMAL1 complex for binding to E-box sites in target genes. Saturation binding experiments demonstrate reduced affinity of the CLOCKΔ19:BMAL1 complex for E-box sites, thereby permitting increased USF1 occupancy on a genome-wide basis. We propose that USF1 is an important modulator of molecular and behavioral circadian rhythms in mammals. DOI:http://dx.doi.org/10.7554/eLife.00426.001.

overall_design: Examination of 3 transcriptional regulators in mouse liver at ZT8

first: Kazuhiro

last: Shimomura

first: Vivek

last: Kumar

first: Nobuya

last: Koike

first: Tae-Kyung

last: Kim


title: A Study of Small RNAs from Cerebral Neocortex of Pathology-Verified Alzheimer’s Disease, Dementia with Lewy Bodies, Hippocampal Sclerosis, Frontotemporal Lobar Dementia, and Non-Demented Human Controls

city: Lexington

last: Nelson

state: KY

address: 800 S. Limestone

department: Sanders-Brown Center on Aging

institute: University of Kentucky

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are small (20-22 nucleotides) regulatory non-coding RNAs that strongly influence gene expression. Most prior studies addressing the role of miRNAs in neurodegenerative diseases (NDs) have focused on individual controls (n = 2), AD (n = 5), dementia with Lewy bodies (n = 4), hippocampal sclerosis of aging (n = 4), and frontotemporal lobar dementia (FTLD) (n = 5) cases, together accounting for the most prevalent ND subtypes. All cases had short postmortem intervals, relatively high-quality RNA, and state-of-the-art neuropathological diagnoses. The resulting data (over 113 million reads in total, averaging 5.6 million reads per sample) and secondary expression analyses constitute an unprecedented look into the human cerebral cortical miRNome at single nucleotide resolution. While we find no apparent changes in isomiR or miRNA editing patterns in correlation with ND pathology, our results validate and extend previous miRNA profiling studies with regard to quantitative changes in NDs. In agreement with this idea, we provide independent cohort validation for changes in miR-132 expression levels in AD (n = 8) and FTLD (n = 14) cases when compared to controls (n = 8). The identification of common and ND-specific putative novel brain miRNAs and/or short-hairpin molecules is also presented. The challenge now is to better understand the impact of these and other alterations on neuronal gene expression networks and neuropathologies.

overall_design: Using RNA deep sequencing, we sought to analyze in detail the small RNAs (including miRNAs) in the temporal neocortex gray matter from non-demented controls (n = 2), AD (n = 5), dementia with Lewy bodies (n = 4), hippocampal sclerosis of aging (n = 4), and frontotemporal lobar dementia (FTLD) (n = 5) cases, together accounting for the most prevalent ND subtypes.

first: Sebastien

last: Hebert

first: Wang-Xia

last: Wang

first: Qi

last: Zhu

middle: T


title: Genome-wide maps of chromatin state for HIRA, UBN1 and ASF1a

summary: The HIRA chaperone complex, comprised of HIRA, UBN1 and CABIN1, collaborates with histone-binding protein ASF1a to incorporate histone variant H3.3 into chromatin in a DNA replication-independent manner. To better understand its function and mechanism, we integrated HIRA, UBN1, ASF1a and histone H3.3 ChIP-seq and gene expression analyses. Most HIRA-binding sites co-localize with UBN1, ASF1a and H3.3 at active promoters and active and weak/poised enhancers. At promoters, binding of HIRA/UBN1/ASF1a correlates with the level of gene expression. HIRA is required for deposition of histone H3.3 at its binding sites. There are marked differences in nucleosome and co-regulator composition at different classes of HIRA-bound regulatory site. Underscoring this, we report novel physical interactions between the HIRA complex and transcription factors, a chromatin insulator and an ATP-dependent chromatin-remodelling complex. Our results map the distribution of the HIRA chaperone across the chromatin landscape and point to different interacting partners at functionally distinct regulatory sites.

overall_design: Examination of 3 histone chaperone proteins in HeLa cells

first: Nikolay

middle: A

last: Pchelintsev

first: Tony

last: McBryan

middle: D


title: Characterization of the regulatory programs governed by ELAV-like proteins in Trypanosoma brucei

city: Montreal

first: Hamed

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

type: Expression profiling by high throughput sequencing

platform_organism:
Trypanosoma brucei
Trypanosoma brucei brucei TREU927

first: Zhiquan

last: Lu

first: Reza

last: Salavati


title: Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics

first: Li

last: Shen

type: Methylation profiling by high throughput sequencing

first: Hao

last: Wu

first: Dinh

last: Diep

first: Shinpei

last: Yamaguchi

first: Ana

middle: C

last: D'Alessio

first: Alan

last: Fung


title: Genome-wide maps of chromatin state for H3.3 tagged cells

first: Peter

last: Adams

overall_design: Examination of H3.3 histone modification in HeLA cells with accompanying FAIRE data


title: MicroRNA discovery and analysis of Dirofilaria immitis by deep sequencing.

status: Public on Apr 22 2013

city: Ya'an

first: Guangyou

last: Yang

address: Xinkang Road 46*

department: Department of Parasitology

country: China

institute: Sichuan Agricultural University

summary: To understand how microRNA are involved in the complex biology of this zoonotic parasite, we describe our initial attempts to characterize small RNA in adult Dirofilaria immitis by using Illumina/Solexa deep-sequencing technology.

overall_design: Examination of 4 different adult Dirofilaria immitis (pooled)

first: Yan

last: Fu


title: Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage

status: Public on Apr 17 2013

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: We investigated soybean seed development because (1) soybean seeds are a major source of food and fuel, (2) soybean seeds have been an excellent system for studying the basic processes controlling seed development for over three decades, and (3) new soybean genomic resources, including the sequence of the soybean genome and the gene expression profiles for all seed compartments, tissues, and cell types, can be used to gain new insights into the regulatory processes required for seed differentiation. We sequenced messenger RNA populations of specific soybean seed compartments, which will provide new insights into gene expression that are important for “making a soybean seed.”

overall_design: Seventeen compartments of the Early Maturation stage of the soybean seeds were analyzed. Three to four biological replicates were collected for each compartment.

middle: J

first: Robert

middle: B

last: Goldberg

first: Ryan

last: Kirkbride

first: Julie

last: Pelletier

first: Tina

middle: Y

first: Ssu-Wei

last: Hsu

first: Shu-Heng

last: Chang

first: Russell

middle: W

last: Baden

first: Rie

last: Uzawa

first: Alexander

last: Olson

first: Lourenz

last: Balayan

first: Erik

last: Garber

first: Meryl

last: Hashimoto

first: Uranus

last: Chau


title: The histone demethylase Jmjd3 sequentially associates with the transcription factors Tbx3 and Eomes to drive endoderm differentiation

city: Los Angeles

first: April

last: Kartikasari

address: 900 Veteran Avenue

department: Medical-Endocrinology

institute: UCLA

summary: Here we show that T-box proteins team up with chromatin modifying enzymes to drive the expression of the key lineage regulator, Eomes during endodermal differentiation of embryonic stem (ES) cells. The Eomes locus is maintained in a transcriptionally poised configuration in ES cells. During early differentiation steps, the ES cell factor Tbx3 associates with the histone demethylase Jmjd3 at the enhancer element of the Eomes locus to allow enhancer-promoter interactions. This spatial reorganization of the chromatin primes the cells to respond to Activin signaling, which promotes the binding of Jmjd3 and Eomes to its own bivalent promoter region to further stimulate Eomes expression in a positive feedback loop.

overall_design: Examination of the binding of pluripotency factors to mouse embryonic stem cells and embryoid bodies

first: A

middle: E

first: J

middle: X

last: Zhou

first: M

last: Kanji

first: D

middle: N

last: Chan

last: Sinha

last: Grapin-Botton

last: Magnuson

first: W

last: Lowry

last: Bhushan


title: Genome-wide profiling of 5-Formylcytosine reveals it roles in epigenetic priming

city: Atlanta

first: Keith

last: Szulwach

state: GA

address: 615 Michael Street, Whitehead Suite 301

institute: Emory University

summary: TET proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are excised by mammalian DNA glycosylase TDG, implicating 5mC oxidation in DNA demethylation. Here we show that the genomic locations of 5fC can be determined by coupling chemical reduction with biotin tagging. Genome-wide mapping of 5fC in mouse embryonic stem cells (mESCs) reveals that 5fC preferentially occurs at poised enhancers among other gene regulatory elements. Application to Tdg null mESCs further suggests that 5fC production coordinates with p300 in remodeling epigenetic states of enhancers. This process, which is not influenced by 5hmC, appears to be associated with further oxidation of 5hmC and commitment to demethylation through 5fC. Finally, we resolved 5fC at base-resolution by hydroxylamine-based protection from bisulfite-mediated deamination, thereby confirming sites of 5fC accumulation. Our results reveal roles of active 5mC/5hmC oxidation and TDG-mediated demethylation in epigenetic tuning at regulatory elements.

overall_design: We report here a chemical labeling method that effectively differentiates 5fC from 5mC, 5hmC, and 5caC in genomic DNA. First, we quantitatively protect endogenous 5hmC with a regular glucose using b-glucosytransferase-catalyzed 5hmC glucosylation. Then, we selectively reduce 5fC with NaBH4 to 5hmC, and chemically label the resulting 5hmC (from 5fC) with an azide-modified glucose. Biotin can be installed subsequently for specific enrichment of 5fC. Our method thereby provides an effective tool of general utility for the genomic localization of 5fC. Here we provide genome-wide profiles of 5hmC, 5fC, and p300 in Tdg fl/fl and Tdg-/- mESCs as well as a 5fC control (Non-NaBH4) and polyA RNA-Seq expression data. Genome-wide profiles of 5hmC and 5fC in mESCs differentiated to embryoid bodies are also included. We also report the development and application of a single-base resolution method for the detection of 5fC in genomic DNA by hydroylamine mediated protection of 5fC from deamination during bisulfite treatment, or 5fC Chemical Assisted Bisulfite Sequencing (fCAB-Seq). We applied this method in parallel with conventional ChIP-Methyl-Seq to H3K4me1 ChIP enriched DNA from Tdg fl/fl and Tdg-/- mice.


title: C/EBP Maintains Chromatin Accessibility in Liver and Facilitates Glucocorticoid Receptor Recruitment to Steroid Response Elements

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: DNase-seq and ChIP-seq determine that C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements

overall_design: DNase-seq and ChIP-seq (GR, C/EBPb and RNAPII) in intact liver from adrenalectomized mice injected with dex (1h)

first: Lars

last: Grontved

first: Gordon

last: Hager


title: Species- and condition-specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

summary: Although Candida albicans and Candida dubliniensis are most closely related, both species significantly behave differently with respect to morphogenesis and virulence. In order to gain further insight into the divergent routes for morphogenetic adaptation in both species, we investigated qualitative along with quantitative differences in the transcriptomes of both organisms by cDNA deep sequencing. Following genome-associated assembly of sequence reads we were able to generate experimentally verified databases containing 6016 and 5972 genes for C. albicans and C. dubliniensis, respectively. About 95% of the transcriptionally active regions (TARs) contain open reading frames while the remaining TARs most likely represent non-coding RNAs. Comparison of our annotations with publically available gene models for C. albicans and C. dubliniensis confirmed approximately 95% of already predicted genes, but also revealed so far unknown novel TARs in both species. Qualitative cross-species analysis of these databases revealed in addition to 5802 orthologs also 399 and 49 species-specific protein coding genes for C. albicans and C. dubliniensis, respectively. Furthermore, quantitative transcriptional profiling using RNA-Seq revealed significant differences in the expression of orthologs across both species. We defined a core subset of 84 hyphal-specific genes required for both species, as well as a set of 42 genes that seem to be specifically induced during hyphal morphogenesis in C. albicans. Species specific adaptation in C. albicans and C. dubliniensis is governed by individual genetic repertoires but also by altered regulation of conserved orthologs on the transcriptional level.

sample_organism:
Candida albicans
Candida dubliniensis

platform_organism:
Candida albicans
Candida dubliniensis

overall_design: We investigated qualitative along with quantitative differences in the transcriptomes of both organisms by cDNA deep sequencing. In a first step, we reevaluated the in silico predicted gene models by collecting experimental data using FLX - technology for sequencing strand-specific and normalized cDNA libraries derived from blastospores and hyphae. In the second step, quantitative RNA-Seq (GAIIX) was applied to C. albicans hyphal cells and C. dubliniensis blastospore and hyphal cells to complement reevaluation of the gene models with FLX data as well as to measure differential gene expression across the species with two biological replicates.

first: Stefan

last: Lorenz

first: Philip

last: Stevens

first: Elena

last: Lindemann

first: Ulrike

last: Schoeck

first: Julia

last: Retey

first: Steffen

last: Rupp


title: Genome-wide non-polyadenylated transcription in differentiating mouse embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation

city: Jerusalem

first: Ilana

last: Livyatan

address: Silberman Bldg. Room 2-542 Givat Ram

department: Genetics

country: Israel

institute: Hebrew University

summary: The transcriptional landscape in embryonic stem cells (ESCs) and during ESC differentiation has received considerable attention in recent years, but reports have so far been confined to the polyadenylated fraction of RNA, while the non-polyadenylated (NPA) fraction remained largely unexplored. Notwithstanding, the NPA RNA super-family, which is mainly comprised of fundamental components of the RNA translational machinery, the RNA splicing machinery, and RNA-RNA or RNA-DNA interacting complexes, has every potential to participate in the regulation of pluripotency and stem cell fate. We conducted a comprehensive analysis of NPA RNA in murine ESCs and ESC-derived Neural Progenitor Cells (NPCs) using a combination of whole genome tiling arrays and Next Generation Sequencing technologies. This strategy allowed for the transcriptional characterization of already well-defined NPA RNA subclasses in this unique biological context as well as the identification of many new members of these functional ncRNA classes. In addition, we describe a group of novel, conserved RNAs (snacRNAs: small, non-polyadenylated conserved), some of which are differentially expressed between ESC and NPCs, providing the first evidence of a novel group of potentially functional ncRNAs involved in the regulation of pluripotency and stem cell fate. We further show that minor spliceosomal snRNAs, which are non-polyadenylated, are almost completely absent in ESCs and are upregulated in differentiation. Finally, we show differential processing of the minor intron of the polycomb group gene Eed. Our data suggest that non-polyadenylated RNA, both known and novel, play important roles in embryonic stem cells.

overall_design:
We extracted total RNA from undifferentiated ESCs and 7 day NPCs. Total RNA was divided into poly(A+) and poly(A-) enriched fractions using a modified version of Oligotex extraction (Qiagen). Briefly, after the hybridization of the total RNA to oligo(dT) beads, supernatants were saved rather than discarded and then subjected to isopropanol-ethanol extraction to obtain the Poly(A-) fraction.

This submission represents RNA-Seq component of study.

first: Malka

last: Nissim-Rafinia

first: Radha

last: Duttagupta

first: Thomas

middle: R

last: Gingeras

first: Eran

last: Meshorer


title: DDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary: Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from the most heterochromatic transposons to euchromatic genes determines the requirement of DDM1 for methylation maintenance in all sequence contexts. We also show that small RNA-directed DNA methylation (RdDM) is inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. DDM1 and RdDM independently mediate nearly all transposon methylation, which is catalyzed by the methyltransferases MET1 (CG), CMT3 (CHG), DRM2 (CHH) and CMT2 (CHH), and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that the Arabidopsis genome is defined by a heterochromatic continuum that governs the access of DNA methyltransferases and potentially all DNA binding proteins.

overall_design: Examination of DNA methylation, transcription and nucleosomes in Arabidopsis wild-type and/or ddm1, RdDM and DNA methylase mutants.

first: Assaf

last: Zemach

first: Ping-Hung

last: Hsieh

first: Devin

last: Coleman-Derr

first: Ka

last: Thao

first: Stacey

middle: L

last: Harmer

first: Daniel

last: Zilberman


title: Identification of RVE8 target genes

status: Public on Apr 15 2013

city: Durham

first: Polly

middle: Yingshan

last: Hsu

state: NC

address: Duke University

department: Biology

institute: Duke University

summary: The goal of this study is to identify the targets of RVE8, a MYB-like transcription factor involved in the circadian clock in Arabidopsis. Analysis of 7 days old rve8-1 RVE8::RVE8:GR and rve8-1 seedlings treated with dexamethasone or mock identified genes responsive to RVE8 induction.The RVE8 up-regulated genes are enriched for evening-phased genes while the down-regulated genes are enriched for a morning phase. This study reveals that RVE8 is a master regulator of circadian gene expression in Arabidopsis.

overall_design: Transgenic line rve8-1 RVE8::RVE8:GR and rve8-1 treated with DEX or mock with three biological replicates each, 12 samples in total.


title: Comparison of MicroRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues

city: Columbus

first: wei

last: meng

state: Ohio

address: 400 W12 street

department: Radiation Oncology

institute: The Ohio State University

summary: MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (3-9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (Pearson’s r=0.71-0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified.

overall_design: we analyzed eight matched frozen and FFPE tissues of different histologies for which detailed processing and storage information.

first: Wei

last: Meng

first: Joseph

middle: P

last: McElroy

first: Stefano

last: Volinia

first: Jeff

last: Palatini

first: Sarah

last: Warner

first: Leona

last: Ayers

first: Kamalakannan

last: Palanichamy

first: Arnab

last: Chakravarti

first: Tim

last: Lautenschlaeger


title: RNA-seq expression analysis to determine expression profile similarities between fibroblasts, induced endothelial cells from fibroblasts, and human dermal microvascular endothelial cells

status: Public on Apr 14 2013

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: The goal of this study was to determine the similarity between human dermal microvascular endothelial cells, induced endothelial cells from fibroblasts, and fibroblasts through RNA-seq expression analysis.  RNA samples from independently induced cultures, plus fibroblast and human dermal microvascular endothelial cultures were converted into individual cDNA libraries using Illumina TruSeq methods and subjected to single-end 50 base-sequence analysis at 20-30 million read depths.

overall_design: Examination of one fibroblast culture, one human dermal mibrovascular endothelial cell culture, and two induced endothelial cell cultures.

first: Bruce

last: Aronow

first: John

last: Cooke


title: Transcriptomics of Bacillus thuringiensis Strain CT-43.

city: Wuhan

first: Wang

last: Jieping

address: Shizishan Street No. 1

institute: State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University

summary: We investigated the gene expression and metabolic regulatory mechanisms associated with the high-level accumulation of ICPs by performing the transcriptomics analysis of B. thuringiensis strain CT-43, using Illumina high throughout sequencing (RNA-seq) technique.

overall_design: The bacterial cells were collected at the time points of 7 h, 9 h, 13 h and 22 h for the whole-genome transcriptomics, respectively.

first: Jieping

last: Wang

first: Han

last: Mei

first: Jin

last: He


title: Regulatory role of glycerol in Candida albicans biofilm formation

status: Public on Apr 12 2013

city: Pittsburgh

first: Jigar

middle: V

last: Desai

state: PA

address: 4400 Fifth Avenue

institute: Carnegie Mellon University

summary: Biofilm formation on medically implanted devices by Candida albicans poses a significant clinical challenge. Here we compared biofilm-associated gene expression in two clinical C. albicans isolates, SC5314 and WO-1, to identify shared gene regulatory responses that may be functionally relevant. Among the 50 genes most highly expressed in biofilms relative to planktonic (suspension-grown) cells, we were able to recover insertion mutations in 25 genes. We observed that 20 of the 25 mutants have altered biofilm-related properties, including cell-substrate adherence, cell-cell signaling, and azole susceptibility. We focused on the most highly up-regulated gene in biofilms, RHR2, which specifies the glycerol biosynthetic enzyme glycerol-3-phosphate phosphatase. Glycerol is 5-fold more abundant in biofilm cells than planktonic cells, and an rhr2D/D strain accumulates 2-fold less biofilm glycerol than the wild type. Under in vitro growth conditions, the rhr2D/D mutant has reduced biofilm biomass and reduced adherence to silicone. The rhr2D/D mutant is severely defective in biofilm formation in vivo, in a rat catheter infection model. Expression profiling of the rhr2D/D mutant indicates that it has reduced expression of cell surface adhesin genes ALS1, ALS3, and HWP1, as well as a large fraction of all other biofilm up-regulated genes. Reduced adhesin expression is the cause of the rhr2D/D mutant biofilm defect, because overexpression of ALS1, ALS3, or HWP1 restores biofilm formation ability to the mutant in vitro and in vivo. Our findings indicate that internal glycerol has a regulatory role in biofilm gene expression, and that adhesin genes are among the main functional Rhr2-regulated genes.

overall_design: Gene expression profiles, in duplicate; (1) for biofilm vs. planktonic growth conditions for the two wild-type clinical isolates of Candida albicans (SC5314 and WO1-white/WO1-opaque), and (2) for rhr2Δ/Δ mutant and complemented strain, via RNA-deep sequencing using Illumina GA2 and HiSeq2000 platforms, respectively

first: Vincent

middle: M

last: Bruno

first: Shantanu

last: Ganguly

first: Ronald

last: Stamper

first: Kaitlin

middle: F

last: Mitchell

first: Norma

last: Solis

first: Elizabeth

last: Hill

first: Wenjie

last: Xu

first: Scott

middle: G

last: Filler

first: David

last: Andes

first: Saranna

last: Fanning

first: Frederick

last: Lanni

first: Aaron


title: Weight loss after gastric bypass surgery in human obesity induces promoter methylation

status: Public on Apr 11 2013

city: Copenhagen N

first: Morten

last: Rasmussen

address: Panum Building 6.6 Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

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

overall_design: Refer to individual Series


title: MBD-seq of GBP Muscle samples

summary: MBD-Seq in Vastus Lateralis from male Subjects before and after GBP surgery

overall_design: Skeletal muscle samples were obtained from subjects immediately before and 6 months after Gastric Bypass surgery

first: Henriette

last: Kirchner

first: Jie

last: Yan

first: Francisc

last: Kantor

first: Anna

last: Krook

first: Erik

last: Näslund

first: Juleen

last: Zierath


title: Inactive or moderately active human promoters are enriched for inter-individual epialleles

city: Cambridge

first: Thomas

middle: A

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

institute: University of Cambridge


title: Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA CaptureSeq]

city: San Francisco

first: Abhinav

last: Nellore

address: 513 Parnassus Avenue

institute: UCSF

summary: Long noncoding RNAs (lncRNAs) have been described in cell lines and various whole tissues, but lncRNA analysis of development in vivo is limited. Here, we comprehensively analyze lncRNA expression for the adult mouse subventricular zone neural stem cell lineage. We utilize complementary genome-wide techniques including RNA-seq, RNA CaptureSeq, and ChIP-seq to associate specific lncRNAs with neural cell types, developmental processes, and human disease states. By integrating data from chromatin state maps, custom microarrays, and FACS purification of the subventricular zone lineage, we stringently identify lncRNAs with potential roles in adult neurogenesis. shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells. Our data and workflow thus provide a uniquely coherent in vivo lncRNA analysis and form the foundation of a user-friendly online resource for the study of lncRNAs in development and disease.

overall_design: RNA CaptureSeq was perfomed on RNA extracted from adult mouse subventricular zone to better characterize rare lncRNA isoforms. Genomic regions used to design capture array are included in the raw file target_regions.bed.

first: Alexander

last: Ramos


title: Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA-seq]

overall_design: RNA-seq (both paired end and single) from the adult neurogenic niches- subventricular zone (SVZ), olfactory bulb (OB), dentate gyrus (DG) and control non-neurogenic tissue, striatum (STR). Reads were used to assemble a lncRNA catalogue and determine expression values for both protein-coding and noncoding genes


title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [ChIP-seq_nr6a1]

status: Public on Apr 10 2013

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

summary: MicroRNAs (miRNAs) are critical to proliferation, differentiation, and development. Here, we characterize gene expression in murine Dicer-null adult mesenchymal stem cell lines, a fibroblast cell type.  Loss of Dicer leads to de-repression of let-7 targets at levels that exceed 10-100 fold with increases in transcription.  Direct and indirect targets of this miRNA belong to a mid-gestation embryonic program that encompasses known oncofetal genes as well as oncogenes not previously associated with an embryonic state.  Surprisingly, this mid-gestation program represents a distinct period that occurs between the pluripotent state of the inner cell mass at embryonic day 3.5 and the induction of let-7, upon differentiation, at embryonic day 10.5.  Within this mid-gestation program, we characterize the let-7 target Nr6a1, an embryonic transcriptional repressor that regulates gene expression in adult fibroblasts following miRNA loss.  In total, let-7 is required for the continual suppression of embryonic gene expression in adult cells, a mechanism that may underlie its tumor suppressive function.

overall_design: Examination of genes directly bound by Flag-HA-NR6A1 in Dicer WT (Dicer f/f) adult mesenchymal stem cells (immortalized monoclonal lines of murine MSCs).

first: Allan

last: Gurtan

first: Arvind

last: Ravi

first: Peter

last: Rahl

first: Andrew

middle: D

last: Bosson

first: Courtney

middle: K

last: JnBaptiste

first: Arjun

first: Charles

last: Whittaker

first: Richard

last: Young

first: Phillip

last: Sharp


title: Arabidopsis small RNAs associated with RDR6-dependent RNA-directed DNA Methylation

middle: Keith

last: Slotkin

address: 318 West 12th Ave.

department: Molecular Genetics

summary:
Background: The majority of plant transposable elements (TEs) are found in a silenced state that is epigenetically propagated by the maintenance of symmetrical DNA methylation. TE methylation is established and reinforced by a mechanism of RNA-dependent DNA methylation, which is dependent on transcription of the PolIV RNA polymerase. Recently, a pathway has been described that initiates de novo DNA methylation dependent on components of the RNAi post-transcriptional silencing pathway, independent of PolIV. To define the function of this new pathway, we have focused on the RDR6 protein, which plays a central role in the pathway we refer to as RDR6-dependent RNA-directed DNA Methylation (RDR6-RdDM).
Methods: We have sequenced total small RNAs from wild-type and three mutant genotypes: ddm1, ddm1/rdr6, and rdr6.
Conclusions: We demonstrate that RDR6-RdDM utilizes 21 and 22 nucleotide siRNAs to de novo methylate actively transcribing TEs. In addition, we find that the RDR6-RdDM pathway functions in the efficient initiation and re-establishment of TE transcriptional silencing, while it is not necessary to maintain trans-generational epigenetic silencing.

overall_design: Examination of flower bud small RNAs from wild-type and 3 mutant genotypes

first: R

first: Kaushik

last: Panda


title: Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo


title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [CLIP-Seq]

overall_design: Adult mesenchymal stem cells (immortalized monoclonal lines of murine MSCs) with Dicer (WT: Dicer f/f), were infected with dox-inducible Flag-HA-hAgo2 or untagged hAgo2 and then UV cross-linked.  An immunoprecipitation was carried out with anti-Flag and anti-HA antibodies, and associated RNAs were sequenced.

middle: B


title: ChIP-seq and mRNA-seq experiment to find the direct target genes of ATF4 and CHOP

city: Ann Arbor

first: Maureen

last: Sartor

state: MI

address: 2017 Palmer Commons Bldg., 100 Washtenaw Ave

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

summary: We report the direct target genes of ATF4 and CHOP in response to endoplasim reticulum stress through next generation sequencing. By obtaining genowide sequence from chromatin immunoprecipitated DNA with anti-CHOP and anit-ATF4, we identified direct binding sites of ATF4 and CHOP in promoter regions of their target genes in mouse embrynic fibroblasts (MEFs) in response to ER stress. In addition, we obtained list of genes which are differentially regulated in Atf4 or Chop-deficient MEFs compared to the wild-type MEFs in response to ER stress. We found that genes related with unfolded protein response and protein synthesis were directly regulated by ATF4 and CHOP. Through this observation, we conclude that main role of ATF4 and CHOP as transcription factors is to enhance mRNA translation in respone to ER stress. This sutdy provide new insight of genetic network of ATF4 and CHOP in response to ER stress.

overall_design: For ChIP-seq, Chop+/+ and Chop-/- MEFs were treated with Tunicamycin, N-glycosylation inhibitor, to induce ER stress for 8hr. Atf4+/+ and Atf4-/- MEFs were also treated same condition for ChIP-Seq. For mRNA-seq, wild-type, Atf4-/-, and Chop-/- MEFs were treated with tunicamycin for 8hr for experiments.

first: Randal

middle: J

last: Kaufman

first: Jaeseok

last: Han


title: A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

summary: The histone variant H2A.Z plays key roles in gene expression, DNA repair, and centromere function. H2A.Z deposition is controlled by SWR-C chromatin remodeling enzymes that catalyze the nucleosomal exchange of canonical H2A with H2A.Z. Here we report that acetylation of histone H3 lysine 56 (H3-K56Ac) alters the substrate specificity of SWR-C, leading to promiscuous dimer exchange where either H2A.Z or H2A can be exchanged from nucleosomes. This result is confirmed in vivo, where genome-wide analysis demonstrates widespread decreases in H2A.Z levels in yeast mutants with hyperacetylated H3K56.  Our work also suggests that a conserved SWR-C subunit may function as a “lock” that prevents removal of H2A.Z from nucleosomes. Our study identifies a histone modification that regulates a chromatin remodeling reaction and provides insights into how histone variants and nucleosome turnover can be controlled by chromatin regulators.

overall_design: H2A.Z ChIP seq experiments in mutants with constitutive H3K56ac

first: Shinya

last: Watanabe

first: Oliver

last: Rando

first: Craig

last: Petersen


title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [mRNA-seq_Flag-HA-NR6A1_overexpr]

first: A

last: Bhutkar

overall_design: mRNAs from Flag-HA-NR6A1-overexpressing Dicer wild-type adult mesenchymal stem cells (immortalized monoclonal lines of murine MSCs) and vector-only Dicer WT MSCs were analyzed.

first: Allan

last: Gurtan

first: Arvind


title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts

last: Ravi

first: Peter

last: Rahl

first: Andrew

first: Courtney


title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [RNA-seq_siRNA_transfection]

overall_design: mRNAs from adult mesenchymal stem cells (immortalized monoclonal lines of murine MSCs) with and without Dicer (WT: Dicer f/f, KO: Dicer -/-), were analyzed. WT and KO cells were transfected with a nontargeting control siRNA. KO cells were separately transfected with a synthetic let-7g siRNA duplex, or an siRNA targeting Nr6a1.

last: Bosson

last: JnBaptiste

first: Arjun

first: Charles

first: Richard


title: Spatial Transcriptional Profile of the Chick and Mouse Endocardial Cushions Identify Novel Regulators of Endocardial EMT in vitro

status: Public on Apr 16 2013

city: Nashville

first: Daniel

last: DeLaughter

state: TN

address: Preston Research Building Room 460

department: Cell and Developmental Biology

institute: Vanderbilt University Medical School

summary:
Objective: We developed an unbiased strategy to identify genes important in endocardial epithelial-to-mesenchymal transformation (EMT) using a spatial transcriptional profile.
Methods and Results:  Endocardial cells overlaying the cushions of the atrioventricular canal (AVC) and outflow tract (OFT) undergo an EMT to yield VICs. RNA sequencing (RNA-seq) analysis of gene expression between AVC, OFT, and ventricles (VEN) isolated from chick and mouse embryos at comparable stages of development (chick HH18; mouse E11.0) was performed. EMT occurs in the AVC and OFT cushions, but not VEN at this time. 210 genes in the chick (n=1) and 105 genes in the mouse (n=2) were enriched 2-fold in the cushions.  Gene regulatory networks (GRN) generated from cushion-enriched gene lists confirmed TGFβ as a nodal point and identified NF-κB as a potential node. To reveal previously unrecognized regulators of EMT four candidate genes, Hapln1, Id1, Foxp2, and Meis2, and a candidate pathway, NF-κB, were selected.  In vivo spatial expression of each gene was confirmed by in situ hybridization and a functional role for each in endocardial EMT was determined by siRNA knockdown in a collagen gel assay.
Conclusions: Our spatial-transcriptional profiling strategy yielded gene lists which reflected the known biology of the system. Further analysis accurately identified and validated previously unrecognized novel candidate genes and the NF-κB pathway as regulators of endocardial cell EMT in vitro.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: 3 separate regions of the developing heart tube were dissected and processed for RNA sequencing analysis in both HH18 chick and E11.0 ICR mouse (done in duplicate)

first: Danos

middle: C

last: Christodoulou

first: Jamille

middle: Y

last: Robinson

first: Christine

middle: E

last: Seidman

first: HS

last: Baldwin

first: Jon

first: Joey

last: Barnett


title: Signaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: Estrogen dependent signaling in MCF-7 cells

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: We used Global Run-on and Sequencing (GRO-seq) to measure the rate of transcription elongation by RNA polymerase II (Pol II) following gene activation.  We observed that Pol II elongation rates can vary as much as 4-fold at different genomic loci and in response to two distinct cellular signaling pathways (i.e., estrogen and TNFα).  Elongation rates are slowest near the promoter and increase during the first ~15 kb transcribed into the gene body.  Gene body elongation rates correlate with the density of Pol II, consequently resulting in systematically higher rates of transcript production at genes with higher Pol II density.  By monitoring Pol II dynamics following short inductions, we found that E2 stimulates gene expression by increasing Pol II initiation, whereas TNFα stimulates the release of Pol II from promoter proximal pause sites.  Collectively, our results identify previously uncharacterized variation in the rate of Pol II elongation and highlight elongation as an important, variable, and regulated rate limiting step in the transcription cycle.

overall_design: Using GRO-seq over a time course (0, 10, 25, and 40 min) of estrogen signaling in ER-alpha positive MCF-7 human breast cancer cells.

last: Danko

first: Nasun

last: Hah

first: Xin

last: Luo

first: Andre

last: Martins

first: Leighton

last: Core

first: John

middle: T

last: Lis

first: Adam

last: Siepel

first: W


title: Signaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: TNF-alpha dependent signaling in AC16 cells

overall_design:
Using GRO-seq over a time course (0, 10, and 30 min) of
TNFa signaling in AC16, immortalized adult human ventricular cardiomyocyte cells.

first: Charles

middle: L


title: Tfe3-bound regions in naive pluripotent mouse embryonic stem (ES) cells

first: Joerg

last: Betschinger

institute: Wellcome Trust and Medical Research Council Stem Cell Institute

summary: The bHLH transcription factor Tfe3 is a powerful regulator of pluripotency and we report a genome-wide analysis of Tfe3 occupancy in mouse ES cells. Nuclear localization of Tfe3 is inhibited by a protein complex containing the tumor-suppressor Folliculin (Flcn) and we also determine Tfe3 binding sites in ES cells expressing an shRNA targeting Flcn. Specificity is controlled for by using unspecific IgGs and ES cells expressing an shRNA targeting Tfe3.

overall_design: ChIP-Seq profiling of Tfe3 in ES cells

first: Jennifer

last: Nichols

first: Philip

last: Corrin

first: Patrick

last: Paddison

first: Austin

last: Smith


title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [small_RNA-Seq]

first: A

last: Bhutkar

overall_design: Small RNAs from adult mesenchymal stem cells (immortalized clonal lines of murine MSCs) with and without Dicer (Dicer f/f, Dicer -/-) were analyzed.

first: Allan

last: Gurtan

first: Arvind

last: Ravi

first: Peter

last: Rahl

first: Andrew

last: Bosson

first: Courtney

last: JnBaptiste

first: Arjun

last: Whittaker

first: Richard

last: Young

first: Phillip

last: Sharp


title: Transcriptomic analysis of  fungus Penicillium decumbens and brlA deletion strains in different culture medium

status: Public on Apr 09 2013

city: Jinan

first: Yuqi

last: Qin

address: 27 Shanda Nan Lu

institute: Shandong University

summary: Transcriptomic analysis of  fungus Penicillium decumbens and brlA deletion strains in liquid medium and solid medium respectivelly

overall_design: Examination of differential gene expressions by Penicillium decumbens strains 114-2 and brlA deletion stains in liquid medium and solid medium

first: Mei

last: Chen

first: Yinbo

last: Qu


title: Maternally deposited germline piRNAs silence the tirant retrotransposon in somatic cells

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

summary: Transposable elements (TEs), whose propagation can result in severe damage to the host genome, are silenced in the animal gonad by Piwi-interacting RNAs (piRNAs). piRNAs produced in the ovaries are deposited in the embryonic germline and initiate TE repression in the germline progeny. Whether the maternally transmitted piRNAs play a role in the silencing of somatic TEs is, however, unknown. Here we show that maternally transmitted piRNAs from the tirant retrotransposon in Drosophila are required for the somatic silencing of the TE and correlate with an increase in histone H3K9 trimethylation an active tirant copy.

overall_design: Comparison of tirant piRNAs in two Drosophila simulans natural populations.

first: Abdou

last: Akkouche

first: Thomas

last: Grentzinger

first: Marie

last: Fablet

first: Claudia

last: Armenise

first: Nelly

last: Burlet

first: Séverine

last: Chambeyron

first: Cristina

last: Vieira


title: Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [ChIP-seq]

first: Abhinav

last: Nellore

overall_design: CHIP-seq was performed on SVZ-derived neurospheres to determine the chromatin state of lncRNA promoters in adult neural stem cells

first: Alexander

last: Ramos


title: Nkx2-1 Represses a Latent Gastric Differentiation Program in Lung Adenocarcinoma

first: Sebastian

last: Hoersch

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

summary: Tissue-specific differentiation programs become dysregulated during cancer evolution. The transcription factor Nkx2-1 is a master regulator of pulmonary differentiation that is downregulated in poorly differentiated lung adenocarcinoma.  Here we use conditional murine genetics to study the fate of lung epithelial cells upon loss of their master cell fate regulator.  Nkx2-1 deletion in normal and neoplastic lung causes not only loss of pulmonary identity but also gastric transdifferentiation.  Nkx2-1 maintains pulmonary identity by sequestering the Foxa1 transcription factor at lung-specific loci and by inhibiting Foxa1 binding to gastrointestinal targets.  Murine Nkx2-1-negative lung tumors mimic the mucinous subtype of human lung adenocarcinoma, which also exhibits gastric transdifferentiation.  Nkx2-1-negative lung adenocarcinomas are dependent on the gastrointestinal gene Hnf4a for efficient initiation.  Thus, loss of Nkx2-1 causes transdifferentiation rather than stable dedifferentiation in vivo, suggesting that inactivation of both active and latent differentiation programs are required for tumors to reach a primitive, dedifferentiated state.

overall_design: ChIP-seq data from murine lung adenocarcinomas on (i) transcription factors Nkx2-1 and Foxa in Nkx2-1-deleted tumors and Nkx2-1-positive control tumors, and (ii) four histone marks in Nkx2-1-deleted tumors and Nkx2-1-positive control tumors. (All samples in duplicate and with input controls, i.e. (2 x [(3+3) + (2+8)]) - 1  = 31 samples total - 1 input control used for transcription factor and histone mark, GSM1059357)

first: Eric

last: Snyder

first: Hideo

last: Watanabe

first: Margaret

last: Magendantz

first: Tiffany

first: Diana

last: Wang

first: Denise

last: Crowley

first: Charles

first: Matthew

last: Meyerson

first: Shioko

last: Kimura

first: Tyler

last: Jacks


title: FAIRE-seq in primary human megakaryocytes, erythroblasts and monocytes

status: Public on Apr 08 2013

city: Hinxton

first: Dirk

middle: Stefan

last: Paul

address: Wellcome Trust Genome Campus

department: Human Genetics

institute: Wellcome Trust Sanger Institute

summary: Maps of open chromatin in three primary human blood cell types of the myeloid lineage (megakaryocytes, erythroblasts and monocytes) using the formaldehyde-assisted isolation of regulatory elements method followed by next-generation sequencing (FAIRE-seq). We also generated FAIRE-seq data in the megakaryocytic cell line CHRF-288-11. In addition to our data sets, we retrieved FAIRE-seq data for the erythroblastoid cell line K562 (ENCODE Project Consortium 2012) and pancreatic islets (Gaulton et al. 2010), and reanalyzed these data sets using the same methodology.

overall_design: Genome-wide open chromatin profiles of megakaryocytes, erythroblasts and monocytes (in each 2 individuals), pancreatic islets (1 individual), CHRF 288-11 megakaryocytic cells (2 samples) and K562 erythroblastoid cells (2 samples).

middle: S

first: Panos

last: Deloukas


title: Genome-wide maps of DNA cytosine methylation state in during normal differentiation commitment in hematopoietic stem cells (HSC) and in Special AT-rich sequence-binding protein1 (Satb1) - deficient HSC

status: Public on Apr 07 2013

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: Our data show Satb1 deficiency leads to alterations in DNA cytosine methylation and a commitment-primed epigenetic state in HSCs.

overall_design: Examination of DNA cytosine methylation in wild type HSC and differentiation-committed progenitors as well as in wild type HSC and HSC lacking Satb1 (n=2 each).

first: Ulrich

last: Steidl

first: Britta

last: Will

first: Francine

last: Garrett-Bakelman

first: Ari

last: Melnick


title: Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

status: Public on Apr 05 2013

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. Here, we report global analyses of two prototypical SR proteins SRSF1 (SF2/ASF) and SRSF2 (SC35) using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts (MEFs). Unexpectedly, we find that these SR proteins promote both inclusion and skipping of exons in vivo, but their binding patterns do not explain such opposite responses. Further analyses reveal that loss of one SR protein is accompanied by coordinated loss or compensatory gain in the interaction of other SR proteins at the affected exons. Therefore, specific effects on regulated splicing by one SR protein actually depend on a complex set of relationships with multiple other SR proteins in mammalian genomes.

overall_design: SRSF1 and SRSF2 CLIP-seq

first: Shatakshi

last: Pandit

first: Yu

last: Zhou

first: Lily

last: Shiue

first: Gabriela

last: Coutinho-Mansfield

first: Hairi

last: Li

first: Jinsong

last: Qiu

first: Jie

last: Huang

first: Gene

last: Yeo

first: Manuel

last: Ares


title: p53 induces transcriptional and translational programs to supress cell proliferation and growth

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

institute: Tel Aviv University

overall_design: Refer to individual Series


title: Transcriptome Sequencing in wild and domesticated tomato species

city: Tuebingen

first: Daniel

last: Koenig

address: Spemmannstr 30

department: Molecular Biology

institute: Max Planck Institute for Developmental Biology

summary: RNA-seq of seedlings of four tomato species Solanum habrochaites, Solanum lycopersicum, Solanum pimpinelliolium, and Solanum pennellii. An additional panel of samples include many tissues from Solanum lycopersicum and Solanum pennellii in two light conditions

sample_organism:
Solanum lycopersicum
Solanum pimpinellifolium
Solanum pennellii
Solanum habrochaites

overall_design:
Tissue experiement was designed as a complete factorial and the seedling experiment includes for species with seven or eight replicates
SRA_study_accession: SRP019504

first: Julin

last: Maloof


title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [ChIP-seq_histone]

first: A

last: Bhutkar

overall_design: Examination of histone modifications in adult mesenchymal stem cells (immortalized monoclonal lines of murine MSCs) with and without Dicer (WT: Dicer f/f, KO: Dicer -/-).

first: Allan

last: Gurtan

first: Arvind

last: Ravi

first: Peter

last: Rahl

first: Andrew

last: Bosson

first: Courtney

last: JnBaptiste

first: Arjun

first: Charles

last: Whittaker

first: Richard

last: Young

first: Phillip

last: Sharp


title: ChIP-Seq for cofactors in cancer

status: Public on Apr 13 2013

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Critical drivers of cancer progression are likely controlled through the actions of transcription factors and cofactors that bind to the genome and form enhancers that stimulate gene expression.  We present ChIP-seq analysis of key transcriptional regulators, cofactors and histone modifications that indicate transcriptional activity across a range of different cancer cells.

overall_design: ChIP-seq was performed against the cofactors Med1, Brd4 and CDK7 in MM1.S multiple myeloma cells; Brd4 in Sk-MEL-5 melanoma cells; and H3K9/K14 acetylation in MV4;11 leukemia cells,

first: Anders

last: Lars

first: Ana

last: DAlessio


title: Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

city: Wageningen

first: Ruud

last: de Maagd

address: PO Box 619

country: Netherlands

institute: Plant Resarch International

summary: By using parallel analysis of RNA ends (PARE) for global identification of miRNA targets and comparing four different stages of tomato fruit development we identified a large number of target genes of miRNAs.

overall_design: PARE libraries were produced, one each, for tomato fruits at 5 days after pollination, mature green fruit, Breaker fruit, and 7 days after Breaker stge fruits

first: Rumyana

last: Karlova

first: Jan

last: van Haarst


title: microRNA profiling of root tissues and root forming explant cultures in Medicago truncatula

status: Public on Apr 03 2013

city: Canberra

first: rod

last: eyles

address: Linnaeus Way

country: Australia

institute: Australian National University

summary: To identify key miRNAs involved in root meristem formation in M. truncatula, deep sequencing was used to compare the miRNA populations dreived from four tissues. These were;  root tip tissue, containing the root apical meristem, elongation zone tissue,  root forming callus tissue  and non-root forming callus tissue. We identified 83 previously reported miRNAs, 24 new to M. truncatula, in 44 families. For the first time in M. truncatula, members of conserved miRNA families mir165, miR181 and miR397 were found. Bioinformatic analysis identified 38 potential novel miRNAs. Many miRNAs were differentially expressed between tissues, particularly RFC and NRFC.

overall_design: Examination and comparison of the microRNA population of four Medicago truncatula tissue types

first: Rodney

middle: P

last: Eyles

first: Philip

middle: H

last: Williams

first: Stephen

last: Ohms

first: Georg

last: Weiller

first: Huw

last: Ogilvie

first: Michael

last: Djordjevic

first: Nijat

last: Imin


title: Comparison of tomato fruit gene expression data obtained by microarray analysis and by treatment of degradome sequencing data as an RNAseq experiment

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


title: Promoters Active in Interphase are Bookmarked during Mitosis by Ubiquitination

status: Public on Apr 04 2013

city: Columbus

first: Jeffrey

last: Parvin

address: 904 Biomedical Research Tower

department: Biomedical Informatics

institute: the Ohio State University

summary: We analyzed genome-wide modification of chromatin by ubiquitination in human cells and whether this mark changes through the cell cycle using modified ChIP-seq technique (ChAP-seq).

overall_design: Chromatin affinity purification was based on a standard ChIP method with modification of a two-step affinity purification.

first: Mansi

last: Arora

first: Jie

last: Zhang


title: Macro histone variants preserve cell identity by preventing the gain of H3K4me2 during reprogramming

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

country: Spain

institute: ISCIII

summary: Transcription factor-induced reprogramming of somatic cells to pluripotency is a very inefficient process, probably due to the existence of important epigenetic barriers that are imposed during differentiation and that contribute to preserve cell identity. In an effort to decipher the molecular nature of these barriers, we followed a genome-wide approach, in which we identified macro histone variants (macroH2A) as highly expressed in human somatic cells but downregulated after reprogramming to pluripotency, as well as strongly induced during differentiation. Knock down of macro histone variants in human keratinocytes increased the efficiency of reprogramming to pluripotency, while overexpression had opposite effects. Genome-wide occupancy profiles show that in human keratinocytes macroH2A.1 preferentially occupies genes that are expressed at low levels and are marked with H3K27me3, including pluripotency-related genes and bivalent developmental regulators, at which its presence prevents the regain of H3K4me2 during reprogramming, over imposing an additional layer of repression that preserves cell identity.

overall_design: Gemone wide occupancy of HA:macroH2A.1 in human keratinocytes

first: Borja

last: Sese

first: Bernd

last: Klueber

first: Josipa

last: Bilic

first: Stephanie

last: Boue

first: Merce

last: Marti

first: Juan

last: Izpisua-Belmonte


title: KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy [Seq]

city: Lausanne

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

country: Switzerland

institute: EPFL

summary: A multilayered transcription regulatory system is unveiled, where protein- and RNA-based repressors are super-imposed in combinatorial fashion to govern the timely triggering of an essential step of erythropoiesis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Analyses of transcriptional profiles and chromatin state in KAP1 WT and KO (or KD)  cells

first: Isabelle

last: Barde

first: Benjamin

last: Rauwel

first: Ray

middle: M

last: Marin-Florez

first: Andrea

last: Corsinotti

first: Elisa

last: Laurenti

first: Sandra

last: Offner

first: Sonia

last: Verp

first: Julien

last: Marquis

first: Jiri

last: Vanicek

first: Didier

last: Trono


title: Quartz-Seq: a simple and highly quantitative method for single-cell RNA-Seq

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

summary: We report novel single-cell RNA-Seq, called Quartz-Seq. Quartz-Seq was simplified method compared with previous methods based on poly-A tailing reaction.

overall_design: RNA-seq by illumina TruSeq, KAPA library preparation kit, single-cell Quartz-Seq and single-cell Smart-Seq by illumina HiSeq 2000/1000

first: Yohei

last: Sasagawa

first: Hiroki

middle: R

last: Ueda


title: The effect of nicotinamide on dysregulated genes associated with frataxin deficiency in FRDA.

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

summary: To investigate the efficacy of nicotinamide treatment using our ex-vivo primary lymphocyte model, we performed high-throughput RNA sequencing on libraries generated from untreated and nicotinamide treated samples.

overall_design: PBMC isolated from FRDA affected individuals were cultured to prepare the primary lymphocyte cell lines. The primary cultured cells were either treated with 10mM nicotinamide or without the addition of drug during the 3-days treatment. RNA was extracted after the treatment and then RNA-seq libraries were generated by standard protocols.

first: Ping

last: Chan


title: Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX

city: Heidelberg

first: Lukas

last: Chavez

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

summary: Idax/Cxxc4 is the CXXC domain protein that preferentially binds unmethylated CpG sites in vitro. By performing genome-wide mapping of Idax/Cxxc4, we report here that Idax is preferentially enriched in CpG-rich regions in genome including the promoters containing CpG islands.

overall_design: ChIP-seq binding site detection of Myc-Idax and Myc-IdaxDBM over cells expressing an empty vector in stable HEK293T cell lines; two replicates per condition (2x ChIP Myc-Idax, 2x ChIP Myc-IdaxDBM, 2xChIP empty vector)

first: Tarmo

last: Aijo

first: Myunggon

last: Ko

first: Anjana

last: Rao


title: MLL-AF6 leukemia

city: Boston

first: Amit

last: Sinha

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute


title: KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy

first: Adamandia

last: Kapopoulou


title: tRNA fragment profiling in CLP1 mutant (kinase-dead) mice

city: Vienna

first: Javier

last: Martinez

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

summary: Loss of CLP1 activity results in the accumulation of novel sets of small RNA fragments derived from aberrant processing of tyrosine pre-tRNA. Such tRNA fragments sensitize cells to oxidative stress-induced p53 activation and p53-dependent cell death.

overall_design: 2 samples, Wt and Clp1(k/k), no replicates

first: Toshikatsu

last: Hanada

first: Stefan

last: Weitzer


title: Roles for Transcript Leaders in Translation and mRNA Decay Revealed by Transcript Leader Sequencing

city: Cambridge

first: Joshua

middle: A

last: Arribere

address: 31 Ames St

department: Biology

institute: MIT

summary: Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-Sequencing (TL-Seq), a technique combining enzymatic capture of m7G-capped mRNA 5'-ends with high-throughput sequencing. TL-Seq identified mRNA start sites for the majority of yeast genes and revealed many examples of intragenic TL heterogeneity. Transcription initiation sites occur in at least 5% of protein-coding regions and are concentrated near the 5'ends of ORFs. These truncated mRNAs are translated, based on ribosome density analysis. Translation Associated TL-Seq (TATL-Seq), which combines TL-Seq with polysome fractionation, revealed substantial differences in translation of alternative TL isoforms. Globally, while some TL features are associated with poor translation and nonsense-mediated mRNA decay (uAUGs, very short length), others (secondary structure, long length) have much less impact than predicted from analyses of individual genes. TL-Seq and TATL-Seq can be applied to any eukaryote to investigate TL-mediated regulation of gene expression.

overall_design: TL-Seq (+/- pyrophosphatase), TATL-Seq (TL-Seq libraries from polysome gradient)

first: Wendy

middle: V

last: Gilbert


title: Genome-wide transcriptional responses of two metal-tolerant symbiotic Mesorhizobium isolates to zinc and cadmium exposure

status: Public on Apr 02 2013

city: Montpellier

first: geraldine

last: maynaud

address: Campus International de Baillarguet TA-A82/J

institute: CIRAD

summary: Mesorhizobium metallidurans STM 2683 and Mesorhizobium sp. strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils. They tolerate unusually high zinc and cadmium concentrations as compared to other mesorhizobia. This work aims to study the gene expression profiles associated with zinc or cadmium exposure and to identify genes involved in metal tolerance in these two metallicolous Mesorhizobium strains of interest for mine phytostabilization purposes.

sample_organism:
Mesorhizobium metallidurans STM 2683
Mesorhizobium sp. STM 4661

overall_design: Mesorhizobium metallidurans STM 2683 and Mesorhizobium sp. strain STM 4661 with three treatments (control, Zn and Cd).

first: Géraldine

last: Maynaud

first: Brigitte

last: Brunel

first: Damien

last: Mornico

first: Maxime

last: Durot

first: Dany

last: Severac

first: Emeric

last: Dubois

first: Elisabeth

last: Navarro

first: Jean

last: Cleyet-Marel

first: Antoine

last: Le Quéré


title: Genome-wide analysis of mouse intestinal adenoma identifies early steps in the formation of cancer-specific DNA methylation patterns

first: Lukas

last: Chavez

summary: Aberrant CpG methylation is a universal trait of cancer cell genomes and can result in epigenetic modulation of gene activity; however, at which stages tumour-specific epigenetic patterns arise is unknown. Here, we analyse the methylome of APCM in mouse intestinal adenoma as a model of intestinal cancer initiation, and inventory a map of over 13,000 adenoma-specific recurrent differentially methylated regions (DMRs). We find that multiple genes coding for Polycomb proteins are upregulated in adenoma, and concomitantly, hypermethylated DMRs form preferentially at Polycomb target sites. We establish that DMRs are absent from proliferating intestinal epithelial cells or intestinal stem cells, and thus arise de novo after loss of APC. Importantly, a core set of DMRs is conserved in human colon cancer, defining a class of early epigenetic alterations that are distinct from known sets of epigenetically silenced tumour suppressors. The data presented suggests a sequence of events that leads to an altered methylome of colon cancer cells, and may allow more specific selection of clinical epigenetic biomarkers.

overall_design: Analysis of the methylome and RNA expression in adenoma of Apc-Min/+ mutant mice and of normal intestine in Apc-Min/+ and Apc-+/+ wild type mice.

first: Christina

last: Grimm


title: Genome wide mapping of histone 3 lysine 79 dimethylation in MLL-AF6 murine leukemias

first: Amit

last: Sinha

summary: We report the genome wide distribution of H3K79 dimethylation in mouse MLL-AF6 positive leukemias to assess whether this epigenetic mark drives MLL-target gene expression.

overall_design: Examination of H3K79 dimethylation in  bone marrow cells from sacrificed terminally ill MLL-AF6 positive leukemic mice. The retroviral MSCV-IRES-neo-MLL-AF6 construct was transduced into mouse bone marrow lineage negative Kit +, Sca + (LSK) cells and these cells were injected after G418 selection into irradiated syngenic mice to establish MLL-AF6 positive leukemias.

first: Aniruddha

last: Deshpande

first: Scott

last: Armstrong


title: Understanding transcriptional changes associated with the transition to selfing in Arabidopsis thaliana

city: Toronto

first: Stephen

last: Wright

state: Ontario

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

institute: University of Toronto

summary: RNA-seq reads from the selfing species Arabidopsis thaliana were produced from flowers to study the consequences of the transition from the ancestral state (outcrossing) to the derived state (selfing). This was done in the context of examining another species in the Arabidopsis genus (A. lyrata) and another species pair (Capsella rubella versus Capsella grandiflora, which are selfing and outcrossing, respectively). These samples were generated to complement part of this larger study. Briefly, the shift from outcrossing to selfing is common in flowering plants, but neither the genomic consequences nor the speed with which they appear are well understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self-compatible <200,000 years ago. We present a reference genome for the species, and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor C. grandiflora. There is a clear shift in the expression of genes associated with flowering phenotypes; a similar shift is seen in the related genus Arabidopsis, where self-fertilization evolved about 1 million years ago. DNA sequence polymorphisms distinguishing the two Capsella species reveal rapid genome-wide relaxation of purifying selection in C. rubella but without a concomitant change in transposable element abundance. Overall, we document that the transition to selfing may be typified by shifts in expression for genes that function in pollen and flower development, along with a measurable reduction of purifying selection.

overall_design:
As part of a cross-species comparison of gene expression, RNA-seq data was generated in biological replication (2 replicates) from Arabidopsis thaliana at the floral stage. In total, two samples (biological replicates) were used. The reference strain was used for the experments (strain Col-0). Resulting data about gene expression was used as part of a larger study.
The Capsella rubella and Capsella grandiflora data are included in GEO Series GSE45518.

first: Richard

last: Clark

first: Joshua

middle: G

last: Steffen

first: Khaled

last: Hazzouri

middle: I


title: Transcriptome sequencing of human hepatocellular carcinoma

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: Deep high-throughput transcriptome sequencing (RNA-seq) performed on 3 pairs of matched tumor and adjacent non-tumorours (NT) tissues from HCC patients of Chinese origin generated 183.6-million reads that could be aligned. We discovered a number of differentially expressed genes and multiple types of somatic single nucleotide variations (SNVs) in expressed genes.  After the removal of the error alignments, high-quality reads were mapped to the human reference sequence (GRCh37/hg19) using three different softwares TopHat, Burrows-Wheeler Aligner (BWA) and CLC Genomics Workbench (CLC).  The high-quality variants were identified using VarScan with the following parameters: minimum coverage depth of 10, variation frequency of more than 30% and base quality of more than 15.  A total of 568, 545 and 494 potential somatic single nucleotide variants (SNVs), including 94, 89 and 101 coding somatic SNVs (cSNVs), were identified in 3 tumor samples HCC448T, HCC473T and HCC510T, respectively. Validation analysis was carried out for 10 of the intersected cSNVs (all are non-synonymous substitutions) within selected genes of interests with the majority confirmed.

overall_design: Examination of 3 paired human hepatocellular carcinoma and matched non-tumor tissues

first: Chi

first: Si

last: Lok


title: Understanding transcriptional changes associated with the transition to selfing in Arabidopsis thaliana by using outgroup data

summary: RNA-seq reads from the outcrossing species Arabidopsis lyrata were produced from flowers to study the consequences of the transition from the ancestral state (outcrossing) to the derived state (selfing) that is observed in the sister species Arabidopsis thaliana. This was done in the context of examining another species pair (Capsella rubella versus Capsella grandiflora, which are selfing and outcrossing, respectively). These samples were generated to complement part of this larger study. Briefly, the shift from outcrossing to selfing is common in flowering plants, but neither the genomic consequences nor the speed with which they appear are well understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self-compatible <200,000 years ago. We present a reference genome for the species, and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor C. grandiflora. There is a clear shift in the expression of genes associated with flowering phenotypes; a similar shift is seen in the related genus Arabidopsis, where self-fertilization evolved about 1 million years ago. DNA sequence polymorphisms distinguishing the two Capsella species reveal rapid genome-wide relaxation of purifying selection in C. rubella but without a concomitant change in transposable element abundance. Overall, we document that the transition to selfing may be typified by shifts in expression for genes that function in pollen and flower development, along with a measurable reduction of purifying selection.

overall_design:
As part of a cross-species comparison of gene expression, RNA-seq data was generated in biological replication (2 replicates) from Arabidopsis lyrata at the floral stage. In total, two samples (biological replicates) were used. The reference strain was used for the experments (strain MN47). Resulting data about gene expression was used as part of a larger study.
The  Capsella rubella and Capsella grandiflora data are included in GEO Series GSE45518.


title: Transcriptomic analyses of Myc-induced zebrafish liver cancer

city: Singapore

first: Weiling

last: Zheng

address: 21 Lower Kent Ridge Road

country: Singapore

institute: National University of Singapore

summary: To study the characteristics and mechanisms of Myc-induced zebrafish liver tumor, next-generation sequencing-based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up-regulated in the Myc-induced liver tumors. Cross-species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc-induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma (HCC). Thus, our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species.

overall_design: Transcriptome profiling of tumor samples (M+D+) and control samples (M-D-, M+D-, M-D+) were generated by deep sequencing, each in duplicates, using 3' RNA-SAGE on the SOLiD system.

first: Zhen

last: Li

first: Zhiyuan

last: Gong


title: Genetic, functional and molecular features of glucocorticoid receptor binding (sequencing)

status: Public on Apr 01 2013

city: Chicago

first: Joseph

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

summary: Glucocorticoids (GCs) are key mediators of stress response and are widely used as pharmacological agents to treat immune diseases, such as asthma and inflammatory bowel disease, and certain types of cancer. GCs act mainly by activating the GC receptor (GR), which interacts with other transcription factors to regulate gene expression.   Here, we combined different functional genomics approaches to gain molecular insights into the mechanisms of action of GC. By profiling the transcriptional response to GC over time in 4 Yoruba (YRI) and 4 Tuscans (TSI) lymphoblastoid cell lines (LCLs), we suggest that the transcriptional response to GC is variable not only in time, but also in direction (positive or negative) depending on the presence of specific interacting TFs.  Accordingly, when we performed ChIP-seq for GR and NF-kB in two YRI LCLs treated with GC or with vehicle control, we observed that features of GR binding sites differ for up- and down-regulated genes. Finally, we show that eQTLs that affect expression patterns only in the presence of GC are 1.9-fold more likely to occur in GR binding sites, compared to eQTLs that affect expression only in its absence.   Our results indicate that genetic variation at GR and interacting transcription factors binding sites influences variability in gene expression, and attest to the power of combining different functional genomic approaches.

overall_design: GR and NFkB ChIP-seq in lymphoblastoid cell lines treated with either dexamethasone or EtOH (vehicle for dexamethasone) for 1 hour.

first: Francesca

last: Luca

first: Allison

last: Richards

first: David

middle: B

last: Witonsky

first: Matthew

last: Stephens

first: Anna

last: Di Rienzo


title: Genome-wide transcriptional response of the filamentous fungus Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger

city: Nottingham

first: Laure

last: Ries

address: School of Biology, University Park

institute: University of Nottingham

summary: The induction of genes in response to exposure of T. reesei to wheat straw was explored using genome-wide RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to the lignocellulose. After 24 h of exposure to straw, transcript levels of known and predicted lignocellulose-degrading enzymes increased to around 8% of total cellular mRNA in T. reesei, which was much less when compared to A. niger. The bulk of enzymes used to deconstruct wheat straw is similar in both fungi. Other, non-plant cell wall-degrading enzymes which may aid in lignocellulose degradation were also uncovered in T. reesei and similar to those described in A. niger. Antisense transcripts were also shown to be present in T. reesei and their expession can be regulated by the respective growth condition.

overall_design: Triplicate samples of T. reesei cultivated in each of the three following conditions were taken: 1) After 48 h growth in glucose-based minimal media; 2) After transfer of mycelia from glucose-based media into media containing wheat straw as a sole carbon source and 3) 5 h after addition of glucose to straw cultures.

first: Steven

last: Pullan

first: Stephane

last: Delmas

first: Sunir

last: Malla

first: Martin

middle: J

last: Blythe

last: Archer


title: The Capsella rubella genome and the genomic consequences of rapid mating system evolution

first: Stephen

last: Wright

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

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata
Capsella rubella
Capsella grandiflora

overall_design: Refer to individual Series


title: Genetic regulation of human adipose microRNA expression and its consequences for metabolic traits

city: Los Angeles

first: Mete

last: Civelek

address: 675 Charles E. Young Dr. S. MRL 3220

department: Medicine

institute: University of California Los Angeles

summary: The genetics of messenger RNA expression has been extensively studied in humans and other organisms, but little is known about genetic factors contributing to microRNA (miRNA) expression. We examined natural variation of miRNA expression in adipose tissue in a population of 200 men who have been carefully characterized for metabolic syndrome phenotypes as part of the METSIM study. We genotyped the subjects using high-density SNP microarrays and quantified the mRNA abundance using genome-wide expression arrays and miRNA abundance using next generation sequencing. We reliably quantified 356 miRNA species that were expressed in human adipose tissue, a limited number of which made up most of the expressed miRNAs. We mapped the miRNA abundance as an expression quantitative trait and determined cis regulation of expression for 9 of the miRNAs and of the processing of one miRNA (miR-28). The degree of genetic variation of miRNA expression was substantially less than that of mRNAs. For the majority of the miRNAs, genetic regulation of expression was independent of the host mRNA transcript expression. We also showed that for 108 miRNAs, mapped reads displayed widespread variation from the canonical sequence. We found a total of 24 miRNAs to be significantly associated with metabolic syndrome traits. We suggest a regulatory role for miR-204-5p which was predicted to inhibit ACACB, a key fatty acid oxidation enzyme that has been shown to play a role in regulating body fat and insulin resistance in adipose tissue.

overall_design: miRNA expression profiling of adipose tissue isolated from 200 humans

first: M

first: R

last: Hagopian

first: A

last: Lusis

last: Laakso


title: White-Opaque Switching in Natural MTLa/alpha Isolates of Candida albicans: Evolutionary Implications for Roles in Host Adaptation, Pathogenesis and Sex

city: beijing

first: Jing

last: Xie

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute Of Microbiology Chinese Academy of Sciences

summary: The discovery of white-opaque switching in natural MTLa/alpha isolates of Candida albicans sheds new light on the evolution of phenotypic plasticity and host adaptation.

overall_design: Comparing gene expression of white and opaque cells of a MTL a/alpha strain

first: Li

last: Tao

first: Clarissa

last: Nobile

first: Yaojun

last: Tong

first: Guobo

last: Guan

first: Yuan

last: Sun

first: Chengjun

last: Cao

first: Aaron

middle: D

last: Hernday

first: Alexander

last: Johnson

first: Lixin

last: Zhang

first: Feng-yan

last: Bai

first: Guanghua

last: Huang


title: Next Generation Annotation of prokarotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011

city: Castanet Tolosan

first: Erika

last: Sallet

address: 24 Chemin de Borde Rouge, CS 52627

department: Plant Health and the Environment

institute: INRA/CNRS

summary: With a view to re-annotate the genome sequence of the nitrogen fixing bacterium Sinorhizobium meliloti, we generated oriented sequences of transcripts. To cover a large number of expressed genes we prepared RNA from bacteria grown in three very different physiological conditions including bacteria grown in liquid cultures (in both exponential and stationary growth phases) and from 10-day-old nodules in which bacteria were differentiated in nitrogen fixing bacteroids. The transcripts sequences were then integrated into EuGene-P, a new prokaryotic genome annotation tool able to integrate high throughput data including oriented RNA-Seq data directly into the prediction process, which led to the production of an accurate and complete annotation of the genome of S. meliloti strain 2011.

sample_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: 18 samples corresponding to bacteria in 3 different conditions. For each condition, both short and long RNA fractions were analyzed, and three replicates per condition and per RNA fraction were performed.

first: Brice

last: Roux

first: Laurent

last: Sauviac

first: Françoise

last: Jardinaud

first: Sébastien

last: Carrère

first: Thomas

last: Faraut

first: Fernanda

last: de Carvalho-Niebel

first: Jérôme

last: Gouzy

first: Pascal

last: Gamas

first: Delphine

last: Capela

first: Claude

last: Bruand

last: Schiex


title: Genetic, functional and molecular features of glucocorticoid receptor binding

first: Joseph

middle: C

last: Maranville


title: The histone chaperone Spt6 coordinates histone H3K27 demethylation to regulate gene expression and myogenesis

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

summary: Histone chaperones affect chromatin structure and gene expression through interaction with histones and RNA polymerase II (PolII). Here, we report that the histone chaperone Spt6 counteracts H3K27me3, an epigenetic mark deposited by the Polycomb Repressive Complex 2 (PRC2) and associated with transcriptional repression. We found that Spt6 is required for proper engagement and function of the H3K27 demethylase KDM6A (UTX) on muscle genes and regulates muscle gene expression and cell differentiation. ChIP-Seq experiments revealed an extensive genome-wide overlap of Spt6, PolII and KDM6A at transcribed regions that are devoid of H3K27me3. Mammalian cells and zebrafish embryos with reduced Spt6 display increased H3K27me3 and diminished expression of the master regulator MyoD, resulting in myogenic differentiation defects. As a confirmation for an antagonistic relationship between Spt6 and H3K27me3, inhibition of PRC2 permits MyoD re-expression in myogenic cells with reduced Spt6. Our data indicate that, through cooperation with PolII and KDM6A, Spt6 orchestrates removal of H3K27me3, thus effectively controlling developmental gene expression and cell differentiation.

overall_design: Examination of Spt6 and KDM6A levels in a skeletal muscle cells at various developmental stages

first: A

last: Wang

first: Kambiz

last: Mousavi

first: Vittorio

last: Sartorelli


title: Stress-associated H3K4 methylation accumulates during postnatal development and aging of Rhesus macaque brain

first: Dali

last: Han

address: 5801 South Ellis Avenue

department: Department of Chemisty

institute: University of Chicago

summary: We examined the histone modification H3K4 dimethylation (H3K4me2) in the prefrontal cortex of individual Rhesus macaques at different ages by chromatin immunoprecipitation, followed by deep sequencing (ChIP-seq) at the whole genome level

overall_design: Four Rhesus macaque prefrontal cortex samples with 0.4, 9,22 and 26 years old were used for H3K4me2 ChIP-Seq

first: Yixing

first: Jackie


title: Methylation-dependent and -independent genomic targeting principles of the MBD protein family

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

summary: In order to gain insight into DNA methylation readout, we have established a controlled strategy for profiling genomic targeting of chromatin-interacting factors in vivo. With this approach we determined binding preferences for the methyl-CpG binding domain (MBD) family of proteins, including disease relevant mutants, deletions and isoforms. In vivo binding of MBD proteins occurs as a linear function of local methylation density, and is dependent on functional MBD domain – methyl-CpG interactions. This directs specificity of MBD proteins to methylated, CpG dense and inactive regulatory regions. In contrast, binding to unmethylated sites is MBD protein specific and mediated via alternative domains or protein-protein interactions. The latter is observed for NuRD complex-mediated MBD2 tethering to a subset of unmethylated, tissue-specific regulatory regions, similar to MBD3. These functional binding maps reveal methylation-dependent and -independent binding modes determined by distinct protein domains and revise current models of DNA methylation readout through MBD proteins.

overall_design: Comparative binding analysis for the MBD family of proteins utilizing recombinase-assisted mapping of biotin-tagged proteins (RAMBiO). This set contains maps for 29 samples including wild type MBD proteins, mutants and domain variants in mouse ES cells, derived neurons (NP and TN) and Dnmt1/3a/3b triple-KO ES cells (TKO).

first: Tuncay

last: Baubec

first: Robert

last: Ivanek

first: Florian

last: Lienert

last: Schübeler


title: Marker gene discovery for Staphylococcus epidermidis infection in zebrafish embryos

city: Leiden

first: Wouter

last: Veneman

state: Zuid-Holland

address: Einsteinweg 55

department: Institute Biology Leiden

institute: Leiden University


title: Marker gene discovery for Staphylococcus epidermidis infection in zebrafish embryos (RNA-Seq)

summary: We use the zebrafish embryo model to study the innate immune response against Staphylococcus epidermidis. Therefore, we injected S. epidermidis  into the yolk at 2 hpf and took samples at 5 days post injection.

overall_design: This deep sequence study was designed to determine the gene expression profile by  Staphylococcus epidermidis infection. RNA was isolated from embryos at 5 days post injection. Wildtypes zebrafish embryos were micro-injected into the yolk (2hpf) with 20 CFU of S. epidermdis O-47 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), or Non-injected as a control. After injections embryos were transferred into fresh egg water and incubated at 28°C. At 5 days post injection 100-200 embryos per group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

first: W

first: H

last: Spaink

last: Meijer


title: The Kdm5c histone demethylase controls enhancer and promoter function.

city: Utrecht

first: Richard

last: van Schaik

address: Universiteitsweg 100

department: Molecular Cancer Research

institute: UMCUtrecht

summary: Here, we show that the Kdm5c/Smcx member of the Jarid1 family of H3K4 demethylases is recruited to both enhancer and core promoter elements in ES and neuronal progenitor cells (NPC). Knockdown of Kdm5c deregulates transcription via a local increase in H3K4me3. While at core promoters the function of Kdm5c is to restrict transcription, loss of Kdm5c impairs enhancer function. Remarkably, an impaired enhancer function activates promoter activity from Kdm5c-bound intergenic regions. Our results demonstrate that the Kdm5c demethylase plays a crucial role in the functional identity and discrimination of enhancers and core promoters. We speculate that this is related to recruitment of H3K4me3 binders like the TFIID and NURF complexes6-8. Providing functional identity to genomic regions through balancing enzymes that deposit and remove histone modifications may prove to be a general epigenetic mechanism for the functional indexing of eukaryotic genomes.

overall_design: Examination of the KDM5C binding sites in mouse embryonic stem cells and in neuronal progenitor cells. Effect of KDM5C knock down on H3K4me3 and H3K4me1 levels and gene expression.

first: Nikolay

last: Outchkourov

middle: T

last: Timmers


title: Gene expression analysis of murine SAMHD1 deficient peritoneal macrophages (S1056 to S1075)

status: Public on Mar 31 2013

city: Dresden

first: Tina

last: Schumann

address: Fetscherstraße 74

department: Medical Faculty "Carl Gustav Carus"

institute: Institute of Immunology

summary: To elucidate responses of myeloid cells to SAMHD1 deficiency in the absence of exogenous viral infection, we performed global gene expression analysis of SAMHD1 deficient macrophages.

overall_design: Peritoneal macrophages from 10 mutants and 10 controls were FACS sorted. Isolated RNA was subjected to next generation mRNA sequencing.

first: Rayk

last: Behrendt

first: Andreas

last: Dahl

first: Dimitra

last: Alexopoulou


title: Expression and FoxA1 binding in asynchronous and mitotic HUH7 cells

city: Philadelphia

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania


title: TALE transcription factors binding and transcriptional effect

city: Madrid

first: Daniel

last: Mateos San Martín

address: Melchor Fernández Almagro 3

department: DBDC

institute: Fundación CNIC


title: High-throughput pyrosequencing of forum domains termini (FT) isolated and amplified from human HEK293T cells

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary:
Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed.
We performed a genome-wide mapping of forum domains termini in human HEK293T cells  cultured cells using deep sequencing of the termini. We found that forum domains termini correspond to the fragile sites in human chromosomes and forum domains contain clusters of several or many genes inside. The largest forum domains correspond to the coordinately expressed main clusters of HOX genes genes.  Our results indicate that forum domains correspond to big multi-gene chromosomal units some of which could be co-coordinately activated or repressed.

overall_design: 2 sample examined: forum termini from HEK293T cells in two independent experiments

first: Yurii

last: Kravatsky


title: TALE transcription factors binding and transcriptional effect [RNA-Seq]

summary: Meis, Prep and Pbx1 TALE homeoproteins interactions with Hox proteins are essential for development and disease. Although Meis and Prep behave similarly in vitro, their in vivo activities remain largely unexplored. We show that Prep and Meis interact with largely independent sets of genomic sites and select different DNA binding sequences, with Prep associating mostly with promoters and house-keeping genes and Meis with promoter-remote regions and developmental genes. Hox target sequences associate strongly with Meis but not with Prep binding sites, while Pbx1 cooperates with both Prep and Meis. Accordingly, Meis1 shows strong genetic interaction with Pbx1 but not with Prep1. Meis1 and Prep1 nonetheless co-regulate a subset of genes, predominantly through opposing effects. Notably, the TALE homeoprotein binding profile subdivides Hox clusters into two domains differentially regulated by Meis1 and Prep1. After duplication of the ancestral gene, Meis and Prep thus specialized their interactions but maintained significant regulatory coordination.

overall_design: RNA-seq of 2 Meis1 and Prep1 loss of function mutants in E11.5 C57BL/6 embryonic mice


title: Aspergillus fumigatus transcriptome under normoxia and hypoxia conditions

city: rockville

first: suchitra

last: pakala

state: maryland

address: 9704 medical center dr

institute: JCVI

summary: To better understand the effect of hypoxia, RNA-Seq technology was used to profile the Aspergillus fumigatus during adaptation to hypoxia at 12, 24 and 36 h time points.

overall_design: Four samples examined: from the fungus grown under normoxia and hypoxia conditions

last: Cramer

first: Natalie

last: Fedorova

first: Suchitra

last: Pakala

first: Suman

first: Vinita

last: Joadar

first: Bridget

last: Barker

first: William

last: Nierman