title: MS2-affinity purification coupled with RNAseq (MAPS) revealed functional tRNA-derived RNA fragments

status: Public on Apr 16 2015

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

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

overall_design: Refer to individual Series


title: Gene transcriptional levels with or without acid treatment in Salmonella Typhimurium 14028s

city: Shanghai

first: Yu

last: Sang

address: 280 S. Chongqing Rd

department: Microbiology and Immunology

country: China

institute: Shanghai Jiao Tong University School of Medicine

type: Expression profiling by high throughput sequencing

summary:
Acetylation of lysine residues is conserved across organisms and plays important roles in various cellular functions. Maintaining intracellular pH homeostasis is crucial for the survival of enteric bacteria in acidic gastric tract. However, it remains unkown whether bacteria can utilize reversible protein acetylation system to adapt to acidic environment. Here we demonstrate that the protein acetylation/deacetylation is critical for Salmonella Typhimurium to survive in acidic environment.
We first used RNA-seq to analyze the transcriptome patterns under acid stress, and found that the transcriptional levels of genes involved in NAD+/NADH metabolism were significantly changed, leading to the increase of intracellular NAD+/NADH ratio. Moreover, acid stress down-regulated the transcriptional level of pat (encoding an acetyltranseferase) and genes encoding adenylate cyclase and cAMP-regulatory protein (CRP) which regulates pat positively. Acid signal also affects TCA cycle to promote the consumption of Ac-CoA, which reduced the donor of acetylation.
Lowered acetylation level is not only bacterial’s response to acid stress, but also positively regulates the survival rate of S. Typhimurium. The deletion mutant of pat had more stable intracellular pH, which paralleled with higher survival rate after acid treatment compared with the wild type strain and deletion mutant of cobB.
Our data suggest that bacteria can down-regulate protein acetylation level to prevent intracellular pH further falling in acid stress, and this work may provide a new perspective to understand the bacterial acid resistance mechanism.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: To use RNA-seq to analyze the transcriptome patterns under acid stress

first: Jie

last: Ren

last: Lu

first: Mingwen

last: Zhao

first: Yufeng

last: Yao


title: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RybB sRNA targetome

summary: Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RybB, a well-characterized E. coli sRNA.

overall_design: Identification of RNAs co-purified with MS2-RybB in a rne131 ΔrybB strain. RybB (without MS2) was used as control

first: David

last: Lalaouna


title: Identification of sRNA binding to ITSmetZW and ITSmetWV using MS2-affinity purification coupled with RNA sequencing (MAPS) technology

summary: During ribosomal and transfer RNA maturation, external transcribed spacer (ETS) and internal transcribed spacer (ITS) sequences are excised and, as non-functional by-products, are rapidly degraded. The 3’ETS of the glyW-cysT-leuZ polycistronic tRNA precursor was highly and specifically enriched by co-purification with at least two different small regulatory RNAs (sRNAs), RyhB and RybB. Both sRNAs were shown to base pair with the same region in the 3’ETS of leuZ (3’ETSleuZ). Disrupting the pairing by mutating 3’ETSleuZ significantly increased the activity of sRNAs, even under non-inducing conditions. Our results indicate that 3’ETSleuZ prevents sRNA-dependent remodeling of tricarboxylic acid (TCA) cycle fluxes and increases antibiotic sensitivity when sRNAs are transcriptionally repressed. This suggests that 3’ETSleuZ functions as a sponge to absorb transcriptional noise from repressed sRNAs. Finally, the fact that RybB and MicF sRNAs are co-purified with ITSmetZ-metW and ITSmetW-metV strongly suggests a much broader phenomenon.

overall_design: Identification of sRNAs co-purified with MS2-ITSmetZW and MS2-ITSmetWV. ITSmetZW and ITSmetWV (without MS2) were used as control


title: Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming

city: Montréal

first: Yoshiaki

last: Tanaka

address: 5415 boul. l'Assomption

department: Medicine

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

summary: Reprogramming of somatic cells produces induced pluripotent stem cells (iPSCs) that are invaluable resources for biomedical research. Transcriptional and epigenetic changes have been investigated to facilitate our understanding of the reprogramming process. Here, we extended the previous transcriptome studies by performing RNA-seq on cells defined by a combination of multiple cellular surface markers. We found that transcriptome changes during early reprogramming occur independently from the opening of closed chromatin by OCT4, SOX2, KLF4 and MYC (OSKM). Furthermore, our data identify multiple spliced forms of genes uniquely expressed at each progressive stage of reprogramming. In particular, we found a pluripotency-specific spliced form of CCNE1 that significantly enhances reprogramming. In addition, single nucleotide polymorphism (SNP) expression analysis reveals that monoallelic gene expression is induced in the intermediate stages of reprogramming while biallelic expression is recovered upon completion of reprogramming. Our transcriptome data provide unique opportunities in understanding human iPSC reprogramming.

overall_design: RNA samples from intermediates of hiPSC reprogramming were obtained. Gene expression of those cells were analyzed.

first: Eriona

last: Hysolli

first: In-Hyun

last: Park


title: Capture and sequence analysis of RNAs with 5'-hydroxyl termini in S. cerevisiae

status: Public on Apr 18 2015

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

country: USA

institute: University of Colorado School of Medicine

summary: Data from 5OH-seq experiments to map RNAs with 5'-hydroxyl termini in S. cerevisiae

overall_design: 17 samples of yeast RNA analyzed by 5OH-seq. 2 Replicates: +/- Xrn1,+/- Tm, +/- SAP. 1 replicate: pre-fragmented RNA

first: Sally

last: Peach


title: Sustained Efficacy and Seroconversion with the Toll-Like Receptor 7 Agonist GS-9620 in the Woodchuck Model of Chronic Hepatitis B

city: Foster City

first: Li

last: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

summary:
Background & Aims: New therapies for chronic hepatitis B (CHB) are urgently needed since current treatments rarely lead to cure. We evaluated whether the oral small molecule toll-like receptor (TLR7) agonist GS-9620 could induce durable anti-viral efficacy in woodchucks chronically infected with woodchuck hepatitis virus (WHV), a hepadnavirus closely related to human hepatitis B virus (HBV).

Methods: After evaluating the pharmacokinetics, pharmacodynamics and tolerability of oral GS-9620 in uninfected woodchucks, adult woodchucks chronically infected with WHV (n=7 per group) were dosed with GS-9620 or placebo for 4 or 8 weeks with different treatment schedules.

Results: GS‑9620 treatment induced rapid, marked and sustained reduction in serum viral DNA (mean maximal 6.2 log10 reduction), and hepatic WHV DNA replicative intermediates, WHV cccDNA and WHV RNA, as well as loss of detectable serum WHV surface antigen (WHsAg). GS-9620 treatment also induced a sustained antibody response against WHsAg in a subset of animals. Strikingly, treatment reduced the incidence of hepatocellular carcinoma (HCC) from 71% in the placebo group to 8% in GS-9620-treated woodchucks with sustained viral load reduction. GS-9620 treatment was associated with reversible increases in serum liver enzymes and thrombocytopenia, and induced intrahepatic CD8+ T cell, NK cell, B cell and interferon (IFN) response transcriptional signatures.

Conclusions: The data demonstrate that short duration, finite treatment with the oral TLR7 agonist GS-9620 can induce a sustained antiviral response in the woodchuck model of CHB, and support investigation of this compound as a therapeutic approach to attain a functional cure in CHB patients.

overall_design: Liver biopsies were taken at various time points pre-treatment, during treatment and post-treatment from placebo-treated group and GS9620-treated group (5mg/kg QW). Total RNAs were extracted and analyzed by RNA-Seq. The number of animals analyzed at each time-point for each group was as follows: group 1 (placebo) day -14, n=7; day 43, n=7; day 71, n=7; day 120, n=7; day 250, n=7; group 5 (5 mg/kg QW) day -14, n=7; day 23, n=6; day 57, n=5; day 78, n=4; day 250, n=5.

first: Stephan

last: Menne

first: Daniel

middle: B

last: Tumas

first: Katherine

middle: H

last: Liu

first: Linta

last: Thampi

first: Dalal

last: Al Deghaither

first: Betty

last: Baldwin

first: Christine

middle: A

last: Bellezza

first: Paul

middle: J

last: Cote

first: Jim

last: Zheng

first: Randall

last: Halcomb

first: Abigail

last: Fosdick

first: Simon

middle: P

last: Fletcher

first: Stephane

last: Daffis

first: Peng

last: Yue

first: Grushenka

last: Wolfgang

first: Bud

middle: C

last: Tennant


title: Diatom acclimation to elevated CO2 via novel gene clusters and cAMP-signaling

status: Public on Apr 17 2015

city: Seattle

first: Gwenn

middle: M M

last: Hennon

state: WA

address: 616 NE Northlake

department: Oceanography

institute: University of Washington

summary: Diatoms are responsible for ~40% of marine primary productivity1, fueling the oceanic carbon cycle and contributing to natural carbon sequestration in the deep ocean2. Diatoms rely on energetically expensive carbon concentrating mechanisms (CCMs) to fix carbon efficiently at modern levels of CO23–5. How diatoms may respond over the short and long-term to rising atmospheric CO2 remains an open question. Here we use nitrate-limited chemostats to show that the model diatom Thalassiosira pseudonana rapidly responds to increasing CO2 by differentially expressing gene clusters that regulate transcription and chromosome folding and subsequently reduces transcription of photosynthesis and respiration gene clusters under steady-state elevated CO2. These results suggest that exposure to elevated CO2 first causes a shift in regulation and then a metabolic rearrangement. Genes in one CO2-responsive cluster included CCM and photorespiration genes that share a putative cyclic-AMP responsive cis-regulatory sequence, implying these genes are co-regulated in response to CO2 with cAMP as an intermediate messenger. We verified cAMP-induced down-regulation of CCM gene δ-CA3 in nutrient-replete diatom cultures by inhibiting the hydrolysis of cAMP. These results indicate an important role for cAMP in down-regulating CCM and photorespiration genes under elevated CO2 and provide insights into mechanisms of diatom acclimation in response to climate change.

overall_design: In steady-state experiments: axenic T. pseudonana cells in four biological replicates (duplicate chemostats x 2 experimental runs) were acclimated to nitrate-limitation at 70% (1.5 day-1) of max growth rate for >10 days (>15 generations) under continuous light of 80 µmol photons·m−2·s−1. Cell biomass was maintained at ~2 x 105 cells·mL−1 by 10 μM nitrate and carbonate chemistry stabilized to 300, 475 or 800 μatm CO2, verified by pH and DIC measurements. Transition samples and carbonate chemistry were collected daily from chemostat cultures as CO2 levels were increased from ~300-800 μatm at a rate ≤ 0.2 μatm·min−1 over four consecutive days (6 generations) after pre-acclimation to 300 μatm CO2 and nitrate-limitation.

middle: M

first: Justin

last: Ashworth

first: Ryan

middle: D

last: Groussman

first: Chris

last: Berthiaume

first: Rhonda

middle: L

last: Morales

first: Nitin

middle: S

last: Baliga

first: Monica

middle: v

last: Orellana

first: E

middle: V

last: Armbrust


title: The N-terminal Tail of CENP-A Confers Epigenetic Stability to Centromeres via the CENP-T Branch of the CCAN in Fission Yeast

city: La Jolla

first: Arshad

last: Desai

state: CA

address: 9500 Gilman Dr

department: Cellular & Molecular Medicine

institute: UCSD/LICR

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We employ the well-studied fission yeast centromere to investigate the function of the CENP-A (Cnp1) N-tail. We show that alteration of the N-tail did not affect Cnp1 loading at centromeres, outer kinetochore formation, or spindle checkpoint signaling, but nevertheless elevated chromosome loss. N-Tail mutants exhibited synthetic lethality with an altered centromeric DNA sequence, with rare survivors harboring chromosomal fusions in which the altered centromere was epigenetically inactivated. Elevated centromere inactivation was also observed for N-tail mutants with unaltered centromeric DNA sequences. N-tail mutants specifically reduced localization of the CCAN proteins Cnp20/CENP-T and Mis6/CENP-I, but not Cnp3/CENP-C. Overexpression of Cnp20/CENP-T suppressed defects in an N-tail mutant, suggesting a causal link between reduced CENP-T recruitment and the observed centromere inactivation phenotype. Thus, the Cnp1 N-tail promotes epigenetic stability of centromeres via recruitment of the CENP-T branch of the CCAN.

overall_design: Genome-wide localization of GFP-tagged N-tail Cnp1 variant tailswap versus wt control in cnp1 deletion background

first: Hernan

last: Folco

first: Celso

last: Espinoza


title: BCAA catabolic mutants in prolonged darkness

city: East Lansing

first: Cheng

last: Peng

state: MI

address: 603 Wilson Rd

institute: Michigan State University

summary: We used RNA-Seq to ask whether the transcripts for the proposed BCKDH subunits are upregulated in wild-type plants subjected to prolonged darkness. These experiments were performed using rosette leaves from 5-week-old, short-day-grown (8h light/16h dark) Col-0 wild-type plants moved to constant darkness for 6h, 24h, 48h and 72h, and grown in short day for 72h as control. The transcripts of eight BCAA catabolism genes were increased nine- to 400-fold within the first 6h of prolonged darkness, and remained high until the last time point. These results are consistent with the hypothesis that BCAA catabolic enzymes - including BCKDH subunits E1A1, E1B1, E1B2 and E2 - have one or more physiological roles in the dark.

overall_design: Rosette leaf mRNA profiles of 5-week old Col wild type (WT, CS60000) and BCAA catabolic mutants ivd1-2 and hml1-2 were generated byRNA sequencing, in duplicate, using Illumina HiSeq2500.

first: Robert

last: Last


title: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RyhB sRNA targetome

first: Eric

last: Massé

summary: Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RyhB, a well-characterized E. coli sRNA.

overall_design: Identification of RNAs co-purified with MS2-RyhB in a rne131 ΔryhB strain. RyhB (without MS2) was used as control

first: Jing

last: Wang

first: David

last: Lalaouna

first: Joseph

middle: T

last: Wade


title: Identification of RNAs associated with telomeres by enChIP-RNA-Seq

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Accumulating evidence suggests important roles of RNAs interacting with genomic regions in the regulation of genome functions including X chromosome inactivation and gene expression. However, no method to identify RNAs interacting with a given genomic region in a non-biased manner has been reported. Here, we used engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) combined with the RNA-Seq analysis (enChIP-RNA-Seq) to perform non-biased search of RNAs interacting with telomeres. In enChIP-RNA-Seq, the target genomic regions are captured with an engineered DNA-binding molecule such as a TAL protein. Subsequently, RNAs are purified and subjected to the RNA-Seq analysis. The detected RNAs contained known telomere-binding RNAs including telomerase RNA and Cajal body-specific RNAs. In addition, we detected many novel telomere-binding RNAs. We confirmed binding of candidate RNAs to telomeres by the enChIP-RT-PCR analysis. Identified novel telomere-binding RNAs may play important roles in telomere functions. In addition, our results suggest that enChIP-RNA-Seq analysis would be useful for identification of RNAs interacting with specific genomic regions.

overall_design:
RNAs associated with telomeres were identified by using the enChIP technology combined with deep sequencing using Illumina Miseq. Briefly, to isolate telomeres, a TAL protein, Telomere-TAL (Tel-TAL), recognizing a 19-bp sequence containing an array of TTAGGG (telomere repeats) was fused with 3xFLAG tag and NLS (3xFN-Tel-TAL) and LexA protein (3xFNLDD)11 were expressed in a mouse hematopoietic cell line, Ba/F3, respectively. The cells were crosslinked with formaldehyde, and crosslinked chromatin was fragmented by sonication. Subsequently, chromatin complexes containing 3xFN-Tel-TAL or 3xFNLDD were immunoprepicitated with anti-FLAG M2 Ab.
Supplementary URL: http://www.nature.com/srep/2013/131108/srep03171/full/srep03171.html

first: Toshitsugu

last: Fujita

first: Hodaka

last: Fujii


title: Dynamic epigenetic regulation by menin during pancreatic islet tumor formation

city: Boston

first: Wenchu

last: Lin

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: loss of Men1 in mouse pancreatic islet cells alters the epigenetic landscape of a subset of target genes.

overall_design: H3K4me3 ChIP-seq from either mouse pancreatic islets or mouse pancreatic islet tumors harvested at different stages.

first: Hideo

last: Watanabe

first: Matthew

last: Meyerson


title: Genome-wide ChIP seq of H3.3 in WT and ATRX KO mouse ES cells

city: oxford

first: Jim

last: Hughes

address: Weatherall Institute Of Molecular Me

department: MHU

country: United Kingdom

institute: University of Oxford

summary: Regions of H3.3 binding in WT and ATRX KO mouse ES cells were identified by ChIP seq

overall_design: Chip-seq experiements were performed in WT and ATRX KO E14 mouse ES cells

first: Hsiao

last: Voon


title: WT and ATRX KO


title: WTX interacts with the transcriptional regulator TRIM28 to mediate cellular differentiation

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: WTX encodes a tumor suppressor implicated in Wilms tumor and in mesenchymal differentiation, with distinct functions in the cytoplasm, at the plasma membrane and in the nucleus. Here we report that the transcriptional corepressor TRIM28 is the major binding partner for nuclear WTX. The WTX-TRIM28 interaction supports chromatin binding by TRIM28, enhancing transcriptional silencing of some TRIM28 target sequences. In mouse ES cells, where TRIM28-mediated silencing of repetitive sequences is best characterized, Wtx knockdown similarly derepresses endogenous retroviruses and LINE elements.

overall_design: We performed digital gene expression (DGE) profiling using Helicos RNA sequencing. Helicos sequencing does not involve an amplification step, hence it has less bias, especially in sequencing of repetitive elements. We sequenced RNA extracted from mouse ESCs harboring GFP, Wtx or Trim28 hairpins. The resulting sequence reads were aligned with the RefSeq database as well as Repbase, which is a database for the repetitive sequences.

first: Woo

last: Kim

first: Arnaud

last: Amzallag

first: Brian

middle: W

last: Brannigan

last: Ting

first: Sridhar

last: Ramaswamy

first: Daniel

last: Haber


title: Brain transcriptome of Larimichthys crocea (Large yellow croaker) under hypoxia

city: Shenzhen

first: Yabing

last: Zhu

state: Guangdong

address: Main Building,Beishan Industrial Zone,Beishan Road,Yantian District

institute: BGI-tech

summary: Brain transcriptome at 0h, 1h, 3h, 6h, 12h, 24h, 48h after hypoxia stress

overall_design: Large yellow croakers (body weight at 90-100 g) were purchased from the mariculture farm in Ningde, Fuzhou, China. The fish were maintained at 25 °C in aerated water tanks (dissolved oxygen concentration: 7.8±0.5 mg per liter) with a flow through seawater supply. After 7 days of acclimation, these fish were used for the following experiments. Hypoxic time-course experiments were conducted at 25 °C using published method 30, by bubbling nitrogen gas into an aquarium. The desired pO2 was controlled by using dissolved oxygen meter (, Canada). At the onset of the time course, the oxygen content of the tank was lowered from an aerated pO2 of 100% (7.8 mg per liter) down to 20% (1.6±0.2 mg per liter) over a 30-min period. At the 1-, 3-, 6-, 12-, 24-, and 48-h time points, fish were sampled and sequenced.

first: Xinhua

last: Chen

first: Dingding

last: Fan

first: Yinnan

last: Mu

first: Mingji

last: Feng


title: Histone architecture of stem-cell memory T cells reveals progressive remodeling of epigenetic landscape in antigen-experienced CD8 T cells

status: Public on Apr 15 2015

city: Bethesda

first: Nicholas

last: Restifo

state: MD

address: 9000 Rockville pike

institute: NIH

summary: We investigated the genomic landscape of histone modifications in antigen-experienced CD8+ T cells. Using a ChIP-Seq approach coupled with global gene expression profiling [GSE67825], we generated genome-wide histone H3 lysine 4 (H3K4me3) and H3 lysine 27 (H3K27me3) trimethylation maps in distinct subsets of CD8+ T cells - naïve, stem cell memory, central memory, and effector memory.

overall_design: To gain insight into how histone architecture is remodeled during the differentiation of activated T cells

first: Joseph

middle: G

last: Crompton

first: Manikandan

last: Narayanan


title: Transcriptome analysis of WT and ATRX KO Cast x 129 mouse ES cells

last: Hughes

summary: Analysis of gene expression in WT and ATRX KO Cast x 129 Mouse ES cells

overall_design: Paired end RNA-seq analysis of PolyA selected RNA and PolyA depeleted RNA from  in both wildtype nd ATRX knocked out Castx129 Mouse ES Cells

first: Richard

last: Gibbons

first: Douglas

middle: R

last: Higgs


title: Myc and SAGA Rewire an Alternative Splicing Network During Early Somatic Cell Reprogramming [Reprogramming_RNASEQ]

city: Smithville

first: Sharon

last: Dent

state: Texas

address: 1800 Park Road 1C Unit Number: 0116 Smithville, TX 78957  Room Number: SRC1.104

department: Dept. of Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Pluripotent-specific transcriptional networks are sequentially reactivated as somatic cells reprogram to achieve pluripotency. How epigenetic regulators modulate this process and contribute to somatic cell reprogramming is not clear. Here we perform a functional RNAi screen to identify the earliest epigenetic regulators required for reprogramming. We identify components of the SAGA histone acetyltransferase complex, in particular Gcn5, as critical regulators of reprogramming initiation. Furthermore, we show in mouse pluripotent stem cells that Gcn5 strongly associates with Myc and that upon initiation of somatic reprogramming, Gcn5 and Myc form a positive feed forward loop that activates a distinct alternative splicing network and the early acquisition of pluripotency-associated splicing events. These studies expose a Myc-SAGA pathway that drives expression of an essential alternative splicing regulatory network during somatic cell reprogramming.

overall_design: Examination of expression level changes at D0 and D2 MEFs

first: Calley

last: Hirsch

first: Zeynep

middle: H

last: Coban Akdemir


title: Myc and SAGA Rewire an Alternative Splicing Network During Early Somatic Cell Reprogramming [mESCs_ChIPSEQ]

overall_design: Examination of 2 Gcn5-chromatin interactions in mouse embryonic stem cells


title: Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

city: Pretoria

first: Steven

middle: Grant

last: Hussey

state: Gauteng

address: Lynnwood Road, Hatfield

department: Genetics

country: South Africa

institute: University of Pretoria

summary: Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. In this first genome-wide analysis of a modified histone in a woody tissue, we developed optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation.

overall_design: Examination of H3K4me3 in developing secondary xylem tissue from two clonal individuals of E. grandis growing in the field

first: Alexander

middle: A

last: Myburg


title: Myc and SAGA Rewire an Alternative Splicing Network During Early Somatic Cell Reprogramming [Reprogramming_ChIPSEQ]

overall_design: Examination of Myc-chromatin interactions in reprogramming cells


title: Myc and SAGA Rewire an Alternative Splicing Network During Early Somatic Cell Reprogramming

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

overall_design: Refer to individual Series


title: Myc and SAGA Rewire an Alternative Splicing Network During Early Somatic Cell Reprogramming [mESCs_RNASEQ]

overall_design: Examination of expression level changes in Gcn5 KO vs WT mESCs


title: MeCP2 binds to mCH as neurons mature, influencing transcription and onset of Rett syndrome [mRNA-Seq]

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

summary: The postnatal neurodevelopmental disorder Rett syndrome (RTT) is caused by mutations in the gene encoding Methyl-CpG-binding Protein 2 (MeCP2). Despite decades of research, it remains unclear how MeCP2 actually regulates transcription or why RTT features appear only 6-18 months after birth. We examined MeCP2 binding to methylated cytosine in the CH context (mCH, where H = A, C, or T) in the adult mouse brain and found that MeCP2 binds these mCH sites, influencing nucleosome positioning and transcription. Strikingly, this pattern is unique to the mature nervous system, as it requires the increase in mCH after birth to reveal differences in MeCP2 binding to mCG, mCH, and non-methylated DNA elements. This study provides insight into the molecular mechanism governing MeCP2 targeting and how this targeting might contribute to the delayed onset of RTT symptoms.

overall_design: mRNA-Seq were conducted from 7-week-old hypothalamus from MeCP2 knockout mice and their age and genetic background matched wild types control mice. Additonal mRNA-Seq were conducted from 7-week-old hypothalamus from MeCP2 transgenic mice and their age and genetic background matched wild types control mice.

first: Wei

last: Li

first: Huda

middle: Y

last: Zoghbi


title: Genome-wide localization maps of JMJD1A, SWI/SNF components, and PPARγ in brown adipocytes treated with isoproterenol

city: meguro-ku

first: Takeshi

last: Inagaki

state: Tokyo

address: 4-6-1 Komaba

institute: Univ of Tokyo

summary: We analyzed ChIP-seq profiles for H3K4me3, H3K27ac, BRG1, ARID1A, PPARγ and JMJD1A and FAIRE-seq open chromatin profile in immortalized brown adipocytes (iBATs) treated with 1 μM isporoterenol (ISO) or vehicle for 2 hr

overall_design: ChIP-seq profiles for H3K4me3, H3K27ac, BRG1, ARID1A, PPARγ and JMJD1A and FAIRE-seq open chromatin profile in iBATs at Day 8 of differentiation treated with 1 μM isporoterenol (ISO) or vehicle for 2 hr

first: Yohei

last: Abe

first: Ryhan

last: Rozqie

first: Yoshihiro

last: Matsumura

first: Yuya

last: Tsurutani

first: Akira

last: Shiono

first: Ryo

last: Nakaki

first: Juro

last: Sakai


title: MeCP2 binds to mCH as neurons mature, influencing transcription and onset of Rett syndrome [ChIP-Seq]

overall_design: MeCP2 ChIP-Seq were conducted from ~ 7-week-old hypothalamus tissues from Mecp2-/y; MECP2-EGFP mice.


title: LncRNA  Sequencing Analysis of Mouse spermatogonial stem cells during Glial cell-derived neurotrophic factor（GDNF）treatment

city: Nan Jing

first: wang

last: Min

state: Jiang Su

address: Hanzhong Road 140,

department: State key laboratory of reproductive medicine

institute: Nan Jing Medical Univerity

type: Non-coding RNA profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides and have little or no potential for translation. More and more studies have domenstrated mammalian lncRNAs are intrinsically functional and growing data indicate lncRNAs are determinants of stem cell fate by regulating potency, self-renewal and differentiation. There is no report of lncRNAs in spermatogonial stem cells（SSCs）, and importance of lncRNAs in germline linage stem cell has not been investigated yet. here, we presents a large –scale profiling of all lncRNAs in SSCs as well as those lncRNAs regulated by SSC dependent growth factor GDNF through high throughput sequencing.

overall_design: Spermatogonial stem cells were first suffered from an 18 hr GDNF withdrawal followed by refreshment with GDNF for 8 hrs and RNA samples were collected from normal culture wells (N), GDNF 18hr withdrawal wells (0hr), and GDNF 8 hr refreshed cells (8hr). After all GDNF treatment, cultured germ cell clumps were gently blowed with a 200μl pipette, and followed by Total RNA isolation and sequencing by Illumina HiSeqTM 2000

first: M

last: Wang

first: L

first: X

last: Wu


title: RNA sequencing of heart samples of myotonic dystrophic (DM1) patients

status: Public on Apr 14 2015

city: ILLKIRCH

first: nicolas

last: charlet

address: 1 Rue laurent Fries

country: France

institute: IGBMC

summary: Analysis of alternative splicing in  heart (left ventricles) samples of 3 adult DM1 patients versus 3 adult controls

overall_design: PolyA RNA from left ventricles (heart) of 3 controls and 3 DM1 patients were analysed by massive parrallel sequencing

first: Nicolas

last: CHARLET-BERGUERAND

first: Masanori

last: TAKAHASHI

first: Bernard

last: JOST


title: Self-organization of polarized cerebellar plate neuroepithelium in three-dimensional culture of human pluripotent stem cells

city: Chuo-ku

first: Keiko

last: Muguruma

state: Kobe

address: 2-2-3 Minatojima-minamimachi

institute: RIKEN:Center for Developmental Biology

summary: During cerebellar development, the main portion of the cerebellar plate neuroepithelium (NE) gives birth to Purkinje cells and interneurons, while the germinal zone at its dorsal edge, called the rhombic lip (RL), generates granule cells and cerebellar nuclei neurons. However, it remains elusive how these components work together to generate the intricate structure of the cerebellar anlage. In this study, we found that a polarized cerebellar anlage structure self-organizes in three-dimensional (3D) human ES cell (hESC) culture. This NE is capable of differentiating into electrophysiologically functional Purkinje cells. The addition of FGF19 promotes spontaneous generation of dorsoventrally polarized NE structures containing cerebellar and basal plates. Furthermore, further addition of SDF1 promoted the generation of stratified cerebellar plate NE with RL-like germinal zones self-forming at the edge. Thus, hESC-derived cerebellar progenitors exhibit substantial self-organizing potential for generating a polarized structure reminiscent of the early human cerebellar anlage at the first trimester.

overall_design: Examination of mRNA profile in two different treated human ES cells .

first: Ayaka

last: Nishiyama

first: Hideshi

last: Kawakami

first: Kouichi

last: Hashimoto

first: Yoshiki

last: Sasai


title: MeCP2 binds to mCH as neurons mature, influencing transcription and onset of Rett syndrome [Mnase-Seq]

first: kaifu

last: chen

overall_design: Mnase-Seq were conducted from 7-week-old hypothalamus from MeCP2 knockout mice and their age and genetic background matched wild types control mice.

first: Wei

last: Li

first: Huda

last: Zoghbi


title: Analysis of gut microbiota by pyrosequencing of 16S rRNA gene in F344 rats

city: Seongnam-si

first: Nayoung

last: Kim

state: Gyeonggi-do

address: 173-82, Gumi-ro, Bundang-gu

department: Internal Medicine

country: South Korea

institute: Seoul National University Bundang Hospital

summary: Chronic acid suppression by proton pump inhibitor (PPI) has been hypothesized to alter the gut microbiota via a change in intestinal pH. To evaluate the changes in gut microbiota composition by long-term PPI treatment.

overall_design: Twenty-four week old F344 rats were fed with (n = 5) or without (n = 6) lansoprazole (PPI) for 50 weeks. Then, profiles of luminal microbiota in the terminal ileum were analyzed. Pyrosequencing for 16S rRNA gene was performed by genome sequencer FLX (454 Life Sciences/Roche) and analyzed by metagenomic bioinformatics.

first: Cheol

last: Shin


title: Expression data from liver, PFC and amygdala of mice treated with PPAR agonists

city: Austin

first: Laura

last: Ferguson

state: TX

address: 1601 Trinity St Bldg. B, Rm 5.222

department: Waggoner Center for Alcohol and Addiction Research

institute: Dell Medical School, University of Texas at Austin

summary: Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that act as ligand-activated transcription factors. Although prescribed for dyslipidemia and type-II diabetes, PPAR agonists have demonstrated therapeutic properties for several brain disorders, including alcohol dependence. PPAR agonists decrease ethanol consumption and reduce withdrawal severity and susceptibility to stress-induced relapse in rodents. However, the cellular and molecular mechanisms facilitating these properties have yet to be investigated and little is known about their effects in the brain. We tested three PPAR agonists in a continuous access two-bottle choice (2BC) drinking paradigm and found that tesaglitazar and fenofibrate decreased ethanol consumption in male C57BL/6J mice while bezafibrate did not. Hypothesizing that fenofibrate and tesaglitazar are causing brain gene expression changes that precipitate the reduction in ethanol drinking, we gave daily oral injections of fenofibrate, tesaglitazar and bezafibrate to mice for eight consecutive days and collected liver, prefrontal cortex and amygdala 24 hours after last injection. RNA was isolated and purified using MagMAX-96 Total RNA Isolation Kit. Biotinylated, amplified cRNA was generated using Illumina TotalPrep RNA Amplification Kit and hybridized to Illumina MouseWG-6 v2.0 Expression microarrays.

overall_design: Mice were divided into four groups (N=10 per group): fenofibrate, tesaglitazar, bezafibrate and saline. See summary and protocols for details.

first: Dana

last: Most

first: Yuri

last: Blednov

first: R

last: Harris


title: Analysis of the RDR6-dependent ein5 ski2 profile in Arabidopsis

city: West Lafayette

first: Damon

last: Lisch

state: IN

address: 915 West State Street

institute: Purdue University


title: MeCP2 binds to mCH as neurons mature, influencing transcription and onset of Rett syndrome


title: Small RNA mediated immune responses: insights from analyses of nine soybean R-gene near-isogenic lines and their susceptible parent

first: Meixia

last: Zhao

address: 915 W State Steet

department: Agronomy

summary: Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are negative regulators to target endogenous genes and repetitive sequences in plants. Although miRNAs and trans-acting or phased siRNAs (tasiRNAs or phasiRNAs) were found to target hundreds of disease related genes in Medicago, their role in plant-pathogen interactions in the legumes, particularly the R genes mediated interaction of soybean and the pathogen Phytophthora sojae is poorly understood. A deep sequencing was performed on nine soybean near isogenic lines (NILs) each carrying an Rps (Resistance to Phytophthora sojae) gene and their recurrent parent “Williams”, with sampling performed both pre- and post-inoculation with P. sojae. From these data, 44 known MIRNA loci with new miRNA variants, 78 novel miRNAs corresponding to 108 precursors, and 208 phasiRNA-producing (PHAS) loci were identified. Our data showed that overall the expression levels of miRNAs, phasiRNAs and siRNAs were extensively down-regulated after pathogen-inoculation. Moreover, the down-regulation levels in the nine resistant NILs were significantly higher than that detected in the susceptible Williams, and variations of small RNA expression within the resistant NILs were also observed, suggesting the molecular responses of different Rps lines are distinct. Surprisingly, the expression level changes of 21-nt phasiRNAs were significantly positively correlated with that of the corresponding mRNA level of the PHAS genes, suggesting the cascade effects of miRNA triggers on the downstream PHAS genes and phasiRNAs. Our data provided a comprehensive picture regarding small RNA based regulation of target genes, particularly NB-LRRs, involved in the responses to the pathogen.

overall_design: 20 samples were sequenced, 10 inoculated with P. sojae, the other 10 were mock-inoculated

first: Jixian

last: Zhai

first: Feng

last: Lin

first: Jacob

last: Shreve

first: Jyothi

last: Thimmapuram

first: Teresa

middle: J

last: Hughes

first: Blake

middle: C

last: Meyers

first: Jianxin

last: Ma


title: Transcript profiles of juvenile female brown trout exposed to glyphosate and Roundup herbicides.

city: Swansea

first: Tamsyn

last: Uren Webster

address: Wallace Building

institute: Swansea University

summary: This study aimed to investigate the hepatic transcriptional response of brown trout to glyphosate, and its formulated product, Roundup. We exposed juvenile female brown trout to three concentrations of glyphosate (0.01, 0.5 and 10 mg/L) and Roundup (0.01, 0.5 and 10 mg/L glyphosate acid equivalent) for 14 days and sequenced the hepatic transcriptome of 6 individual females per treatment group in order to determine the global mechanisms of toxicity of this widely used herbicide. We assembled the brown trout transcriptome using an optimised de novo approach, and subsequent differential expression analysis identified a total of 1020 differentially-regulated transcripts across all treatments. Differentially-expressed transcripts included those encoding components of the antioxidant system, a number of stress-response proteins and pro-apoptotic signalling molecules. Functional analysis also revealed over-representation of pathways involved in regulation of cell-proliferation and turnover, and up-regulation of energy metabolism and other metabolic processes. Together, these transcriptional changes are consistent with generation of oxidative stress and the widespread induction of compensatory cellular stress response pathways. The mechanisms of toxicity identified were similar across both glyphosate and Roundup treatments, including for environmentally relevant concentrations. The significant alterations in transcript expression observed at the lowest concentrations tested raises concerns for the toxicity of this herbicide to fish populations inhabiting contaminated rivers.

overall_design: Fish were exposed to 3 concentrations of glyphosate (0.01, 0.1 and 10 mg/L), 3 concentrations of Roundup (0.01, 0.5 and 10 mg/L glyphosate acid equivalent) and water controls for 14 days. Liver mRNA from 6 replicate individuals per treatment was sequenced in an Illumina HiSeq 2500 platform. Two control groups (n=6 fish per group) were included. Using a de novo approach, we assembled the hepatic transcriptome for brown trout. Sequence reads were re-mapped to the assembled transcriptome using Bowtie2 and transcript expression profiling was conducted using EdgeR. ERCC spike controls were added to all individual samples, allowing for the assessment of the reproducibility and dynamic range for transcript expression quantification in our experiments. For the group exposed to 0.1 mg/L glyphosate, only 3 females were available to sequence and the variability between individuals was very high with 1 female identified as an outlier. For this reason, data from this treatment group was deemed unreliable and excluded from the analysis.

middle: M

first: Eduarda

last: Santos


title: Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of miRNA-mRNA Target Pairs in KSHV-Infected Cells [mRNA-Seq]

first: Coralie

last: Viollet

address: 10 Center Dr

institute: NIH/NCI

summary:
This SuperSeries is composed of the SubSeries listed below.
Purpose: Kaposi’s sarcoma (KS)-associated herpesvirus (KSHV) causes several lymphoproliferative disorders, including KS, a common AIDS-associated malignancy. Cellular and viral microRNAs (miRNAs) have been shown to play important roles in regulating the expression of genes in oncogenesis. Herpesviruses, including KSHV, encode for miRNAs that are involved in angiogenesis, inflammation and apoptosis. A better knowledge of the miRNA-mediated pathways that regulate KSHV infection is therefore essential for an improved understanding of viral infection and pathogenesis.
Methods: In this study, we used deep sequencing to analyze miRNA, both viral and human, and mRNA expression in KS tumor-derived human cells.
Results: This approach revealed 153 differentially expressed human miRNAs between KSHV-positive and -negative cells. Differential expression of eight miRNAs was independently confirmed by qRT-PCR. We additionally showed that a majority (~73%) of KSHV-regulated miRNAs are down-regulated, including most members of the 14q32 miRNA cluster. Specifically, human miR-409-3p, which is known to target the pro-angiogenic growth factor angiogenin and the inflammation marker fibrinogen-beta, was significantly down-regulated in KSHV-infected cells based on deep sequencing and qRT-PCR. Despite this substantial down-regulation of cellular miRNAs, hsa-miR-708-5p was significantly up-regulated by KSHV and has been shown to directly inhibit pro-apoptotic protease Caspase-2. Finally, we evaluated to what extent there was an inverse correlation between miRNA and mRNA expression levels. Using filtered datasets, we identified relevant canonical pathways that were significantly enriched.
Conclusion: Taken together, our data demonstrate that most human miRNAs affected by KSHV are repressed and our findings highlight the relevance of studying the post-transcriptional gene regulation of miRNAs for KSHV-associated malignancies.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design: Refer to individual Series. 6 samples analyzed (one cell type). Two experimental conditions: uninfected vs. chronically KSHV-infected cells (n=3). Two sequencing platforms: microRNA-Seq and mRNA-Seq.

first: David

last: Davis

first: Martin

last: Reczko

first: Joseph

last: Ziegelbauer

first: Francesco

last: Pezzella

first: Jiannis

last: Ragoussis

first: Robert

last: Yarchoan


title: Genome-wide chromatin binding of transcription factor E2F1 in castration resistant prostate cancer (CRPC) cells

city: San Antonio

first: Kexin

last: Xu

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

summary: Our computational approach identified E2F1 as a collaborative factor for EZH2 in transcriptional regulation of cancer-related genes. This experiment is designed to validate the interaction between E2F1 and EZH2 on the chromatin. By obtaining over 1 billion bases of sequence from chromatin immunoprecipitated DNA, we generated the genome-wide localizations of E2F1 in CRPC cell line LNCaP-abl cells, and found that Indeed, these sites are enriched near the transcription start sites of EZH2-activated genes. Further analysis of the transcription factor motifs enriched at these peaks revealed the enrichement of androgen receptor motif, suggesting a co-activator role for EZH2 in concert with AR. Our work demonstrated a novel funtion of EZH2 in transcriptional activation by directly binding to the chromatin sites that cooperate with AR.

overall_design: Study of the chromatin localizations of PRC2 complex core subunits and different histone marks in 2 cell types

first: Han

first: Chen-Hao

last: Chen


title: Glucocorticoid receptor (GR) binding in primary macrophages isolated from WT and GRdim mice

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: We report ChIP-seq data for GR in bone marrow-derived primary macrophages isolated from WT and GRdim mice.

overall_design: Examination of GR binding in WT and GRdim mice on a genome-wide scale

first: Henriette

last: Uhlenhaut


title: Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of miRNA-mRNA Target Pairs in KSHV-Infected Cells [microRNA-Seq]


title: Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

summary: Alternative splicing (AS) generates vast transcriptomic complexity in the vertebrate nervous system. However, the extent to which trans-acting splicing regulators and their target AS regulatory networks contribute to nervous system development is not completely understood. To address these questions, we have generated mice lacking the vertebrate- and neural-specific Ser/Arg-repeat related protein of 100 kDa (nSR100/SRRM4). Loss of nSR100 impairs development of the central and peripheral nervous systems, in part by disrupting neurite outgrowth, cortical layering in the forebrain, and axon guidance in the corpus callosum. Accompanying these developmental defects are widespread changes in AS that primarily result in shifts to non-neural patterns for different classes of splicing events. The main component of the altered AS program comprises 3-27 nucleotide neural microexons, an emerging class of highly conserved alternative splicing event associated with the regulation of protein interaction networks in developing neurons and neurological disorders. Remarkably, inclusion of a 6-nucleotide nSR100-activated microexon in Unc13b transcripts is sufficient to rescue a neuritogenesis defect in nSR100 mutant primary neurons. These results thus reveal critical in vivo neurodevelopmental functions of nSR100, and they further link these functions to a conserved program of neural microexon splicing.

overall_design: mRNA profiles of mouse control or nSR100/Srrm4 KO cortex or hippocampus using high-throughput sequencing data.

first: Mathieu

last: Quesnel-Vallières

first: Sabine

middle: P

last: Cordes

first: Benjamin

last: Blencowe


title: PANCR, the PITX2 adjacent noncoding RNA, is specifically expressed in human left atria and regulates PITX2c expression

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

summary:
Purpose: Common genetic variation at chromosome 4q25 lead to the strongest locus associated with atrial fibrillation (AF), the most frequent arrhythmia.  The mechanism of association is currently unknown.  We recently have identified a novel noncoding RNA expressed in the left atria.  To determine the potential functional roles of the LNCRNA adjacent to PITX2 (PANCR) via knockdown in cardiomyocytes

Methods and Results: H9 differentiated cardiomyocytes were treated with siRNA targeting PANCR and PITX2c and a scrambled control in triplicate.  RNA and small RNA extracted and sent for sequencing.  Approximately 50 million read fragments mapped to the transcriptome using STAR aligner to hg19 and fragments counted with htseq.  EdgeR was used to quantify the differences between treatment groups.   There were significant changes upon knocking down PITX2c or PANCR in the RNA sequencing with high concordance of effect sizes between the two treatments (r2 = 0.85).  Similar to the RNAseq analysis, this miRNAseq analysis shows that the effects of PANCR knockdown on miRNA expression may be largely mediated by through its effect on PITX2c expression.

Conclusion: PANCR knockdown decreased PITX2c expression in H9 differentiated cardiomyocytes, and altered the transcriptome similar to PITX2c knockdown.

overall_design: H9 derived cardiomyoctyes were treated with siRNA knockdown (scrambled control, PANCR, PITX2c) in triplicate and RNA and smallRNAs extracted for sequencing.

first: Shamone

last: Gore-Panter

first: Jeffrey


title: FLT3-ITD mutations and TET2 loss synergistically alter global DNA methylation in AML

city: New York

first: Yanwen

last: Jiang

state: NY

institute: Weill Cornell Medical College

type: Methylation profiling by high throughput sequencing

summary: Studies of AML patient samples have shown that specific combinations of AML disease alleles confer an adverse outcome, however, in vivo models do not exist for the majority of common, poor-prognosis genotypes.  Here we show that TET2/FLT3 mutations can cooperate to induce AML in vivo using a genetically engineered mouse model, and that this model has a defined stem-cell population with a characteristic transcriptional and epigenetic profile. TET2 and FLT3 mutations cooperate to induce site-specific changes in DNA methylation and gene expression, including at loci that regulate hematopoietic differentiation.  We demonstrate that re-expression of genes that are silenced in TET2/FLT3-mutant AML restores normal differentiation, demonstrating that the epigenetic program of TET2/FLT3-mutant AML cells can be reversed in vitro and in vivo.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Using ERRBS, we profiled genome-wide DNA methylation patterns of the hematopoietic stem cells (LSK) population in Wide-type, Flt3-IDT, Tet2-/-, and Tet2-/-Flt3-IDT mice, each in triplicates

first: Alan

last: Shih

first: Cem

last: Meydan

first: Chris

last: Mason

first: Ari

last: Melnick

first: Ross

middle: L

last: Levine


title: Constraint and divergence of global gene expression in the mammalian embryo

city: Stanford

first: Cheryl

last: Smith

state: CA

address: 300 Pasteur Dr.

department: Pathology

institute: Stanford University

summary: We profiled genome-wide gene expression of 170 individual mid-gestation (embryonic day 11.5) whole mouse embryos derived from a 2-generation interspecies mouse cross and asked to what extent genetic variation drives four important parameters of regulatory architecture: allele-specific expression (ASE), imprinting, trans-regulatory effects, and maternal effect. The inbred strain C57BL/6J and wild-derived inbred strain CAST/EiJ were used in reciprocal crosses to generate F1 embryos. F1 progeny were backcrossed to C57BL/6J in reciprocal crosses to generate 154 N2 embryos. We employed a backcross design, in which N2 offspring have genotypically distinct parents, to enable comparison of gene expression for offspring from each side of the reciprocal cross. Our findings demonstrate that genetic variation contributes to widespread gene expression differences during mammalian embryogenesis.

overall_design: Transcriptome analysis of E11.5 mouse embryos: 16 F1 embryos from reciprocally crossed C57BL/6J and CastEi/J parents; and 154 N2 embryos from reciprocal backcross of F1s to the C57BL/6J parent.

first: Noah

last: Spies

first: Jesse

last: Rodriguez

first: Julie

last: Baker

first: Serafim

last: Batzoglou

first: Arend

last: Sidow


title: Transcription factor binding in liver tissue isolated from WT and GRdim mice

first: Hee-Woong

last: Lim

summary: We report ChIP-seq and ChIP-exo data for GR in liver tissue isolated from WT and GRdim mice. Comparison of the mouse models reveals that GR interacts with the genome as both a monomer and dimer.

overall_design: Examination of GR, RNAPII and CEBPb binding in WT and GRdim mice on a genome-wide scale

first: David

last: Steger


title: RRBS profiling of mouse ESCs (wild type and DNMT KOs)

status: Public on Apr 13 2015

city: Cambridge

first: Rahul

last: Karnik

address: 419 Broadway

summary: DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Somatic patterns of DNA methylation are largely static, apart from focal dynamics at gene regulatory elements. To further advance our understanding of the role of DNA methylation in human development and disease, we inactivated all three catalytically active DNA methyltransferases in human embryonic stem cells (ESCs) using CRISPR/Cas9 genome editing. Disruption of DNMT3A or DNMT3B individually, as well as of both enzymes in tandem, creates viable, pluripotent cell lines with distinct effects on their DNA methylation landscape as assessed by whole-genome bisulfite sequencing. Surprisingly, in contrast to mouse, deletion of DNMT1 resulted in rapid cell death in human ESCs. To overcome the immediate lethality, we generated a doxycycline (DOX) responsive tTA-DNMT1* rescue line and readily obtained homozygous DNMT1 mutant lines. However, DOX-mediated repression of the exogenous DNMT1* initiates rapid, global loss of DNA methylation, followed by extensive cell death, demonstrating that DNA methylation is essential for human ESCs cultured in standard conditions. In summary, our data provide a comprehensive characterization of DNMT mutant ESCs, including single base genome-wide maps of their targets.

first: Alex

last: Meissner


title: EZH2 inhibitor efficacy in non-Hodgkin lymphoma does not require suppression of H3K27 mono-methylation

first: Barbara

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

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

overall_design: Refer to individual Series


title: Functional Antagonism Between CELF and Mbnl Proteins in Cytoplasm and Nucleus [RNA Bind-N-Seq]

city: Gainesville

first: Eric

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: The CUG-BP and ETR-3-like factor 1 (Celf1) RNA binding protein plays an important role in heart and muscle development, and is over-expressed in the disease myotonic dystrophy.  Celf1 has known roles in regulation of RNA splicing, RNA stability, and protein translation.  To identify transcriptome-wide targets of the Celf1 protein, we performed CLIP-seq against Celf1 using the 3B1 antibody, in myoblasts, heart tissue, and muscle tissue.

overall_design: RNA Bind-N-Seq was performed using recombinant CELF1 protein in the presence of competing amounts of recombinant MBNL1 protein.

first: Amanda

last: Ward

first: Jennifer

last: Cherone

first: Jimena

last: Giudice

first: Thomas

first: Daniel

last: Treacy

first: Peter

last: Freese

first: Nicole

last: Lambert

first: Tanvi

last: Saxena

first: Tom

last: Cooper

first: Christopher

last: Burge


title: EZH2 inhibitor efficacy in non-Hodgkin lymphoma does not require suppression of H3K27 mono-methylation [ChIP-Seq]

state: MA

summary: Here we report the discovery of highly potent and selective EZH2 small molecule inhibitors, their validation by a cellular thermal shift assay, their application across a large lymphoma cell panel and their efficacy in GCBDLBCL xenograft models.

overall_design: Baseline ChIP-seq measurement of KARPAS-422 cell line H3K27me3 levels, without treatment. Two samples -- H3K27me3 and Input included as control.

first: William

middle: D

last: Bradley

first: Charlie

last: Hatton

first: Feng

last: Zhao

first: Shivani

last: Garapaty-Rao

first: Patrick

last: Trojer


title: Epigenomic Evolution of Diffuse Large B-cell Relapse

first: Yanwen

last: Jiang

summary: Here we characterize an association between disease progression and DNA methylation in Diffuse Large B cell Lymphoma (DLBCL). By profiling genome-wide DNA methylation at single base-pair resolution in thirteen DLBCL diagnosis-relapse sample pairs, we show DLBCL patients exhibit heterogeneous evolution of tumor methylomes during relapse. We identify differentially methylated regulatory elements and determine a relapse–associated methylation signature converging on key pathways such as transforming growth factor beta (TGF-beta) receptor activity.  We also observe decreased intra-tumor methylation heterogeneity from diagnosis to relapsed tumor samples. Relapse-free patients display lower intra-tumor methylation heterogeneity at diagnosis compared to relapsed patients in an independent validation cohort. Furthermore, intra-tumor methylation heterogeneity is predictive of time to relapse.  Therefore, we propose that epigenomic heterogeneity may support or drive the relapse phenotype and can be used to predict DLBCL relapse.

overall_design: Using ERRBS, we profiled genome-wide DNA methylation patterns of non-relapse DLBCL tumor samples at diagnosis, relaspe DLBCL patient samples at diagnosis and relaspe.

first: Heng

last: Pan

first: Giorgio

last: Inghirami

first: Wayne

last: Tam

first: Olivier

last: Elemento


title: Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis with biological replications and increased sequencing depth

first: Damon

last: Lisch

summary: Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3   -5    mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5   -3    exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5   -3    and 3   -5    cytoplasmic mRNA decay pathways. In this experiment, we did three replicates in sequencing that help increase the power in identify the differentially represented genes.The sequencing depth was also increased. Therefore we identified more siRNA-generating loci than that in previous study (GSE52408) (441 vs. 200 loci).

overall_design: Examination of small RNA profiles in 4 genotypes with 3 biological replicates each.

first: Hongwei

last: Guo

first: Xinyan

last: Zhang


title: Drug-based modulation of endogenous stem cells promotes functional remyelination in vivo

city: Clev

first: Paul

middle: J.

last: Tesar

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University School of Medicine

summary: Multiple sclerosis involves an aberrant autoimmune response and progressive failure of remyelination in the central nervous system. Prevention of neural degeneration and subsequent disability requires remyelination through the generation of new oligodendrocytes, but current treatments exclusively target the immune system. Oligodendrocyte progenitor cells are stem cells in the central nervous system and the principal source of myelinating oligodendrocytes. These cells are abundant in demyelinated regions of patients with multiple sclerosis, yet fail to differentiate, thereby representing a cellular target for pharmacological intervention. To discover therapeutic compounds for enhancing myelination from endogenous oligodendrocyte progenitor cells, we screened a library of bioactive small molecules on mouse pluripotent epiblast stem-cell-derived oligodendrocyte progenitor cells. Here we show seven drugs function at nanomolar doses selectively to enhance the generation of mature oligodendrocytes from progenitor cells in vitro. Two drugs, miconazole and clobetasol, are effective in promoting precocious myelination in organotypic cerebellar slice cultures, and in vivo in early postnatal mouse pups. Systemic delivery of each of the two drugs significantly increases the number of new oligodendrocytes and enhances remyelination in a lysolecithin-induced mouse model of focal demyelination. Administering each of the two drugs at the peak of disease in an experimental autoimmune encephalomyelitis mouse model of chronic progressive multiple sclerosis results in striking reversal of disease severity. Immune response assays show that miconazole functions directly as a remyelinating drug with no effect on the immune system, whereas clobetasol is a potent immunosuppressant as well as a remyelinating agent. Mechanistic studies show that miconazole and clobetasol function in oligodendrocyte progenitor cells through mitogen-activated protein kinase and glucocorticoid receptor signalling, respectively. Furthermore, both drugs enhance the generation of human oligodendrocytes from human oligodendrocyte progenitor cells in vitro. Collectively, our results provide a rationale for testing miconazole and clobetasol, or structurally modified derivatives, to enhance remyelination in patients.

overall_design: RNA sequencing of oligodendrocyte progenitor cells treated with vehicle, miconazole or clobetasol for 0, 2, 6, or 12 hours. Cells were plated 1.5 hours prior to addition of drug.

first: Fadi

last: Najm

first: Daniel

last: Factor


title: EZH2 inhibitor efficacy in non-Hodgkin lymphoma does not require suppression of H3K27 mono-methylation [RNA-Seq]

first: Barbara

last: Bryant

overall_design: RNA-seq of KARPAS-422 cell line RNA, in duplicate, treated with DMSO as control, and EZH2 inhibitors CPI360, EPZ-6438 and GSK126. Eight samples in total.


title: Analysis of the RDR6-dependent ein5 ski2 transcriptome profile in Arabidopsis

summary: Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3’-5’ mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5’-3’ exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). Compared with Col-0, 4394 genes exhibited differential expression in ein5-1 ski2-3, much more than those in the ein5-1 (1138 genes) or ski2-3 (1040 genes) single mutant (2-fold cutoff, p < 0.01, FDR < 0.05), suggesting a largely disturbed transcriptome in the absence of both EIN5 and SKI2. While a small overlap was found between the differentially expressed genes in e/C and s/C comparisons, the gene lists from es/C, es/e and es/s comparisons (2-fold cutoff, p < 0.01, FDR < 0.05) largely overlapped with each other, indicating a collaborative function of EIN5 and SKI2 on a transcriptome-wide scale. The 1670 genes overlapped in the es/C, es/e and es/s comparisons included 1306 upregulated genes and 360 downregulated genes with only 4 genes as exception. 994 of the 1306 upregulated genes (76.1%) and 273 of the 360 downregulated genes (75.8%) were differentially expressed in the es/res comparison like that in es/C, es/e and es/s, indicating a substantial supression of the redundant function of EIN5 and SKI2 by RDR6. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5’-3’ and 3’-5’ cytoplasmic mRNA decay pathways.

overall_design: Examination of transcriptomes in 6 genotypes.


title: Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of miRNA-mRNA Target Pairs in KSHV-Infected Cells

city: Bethesda

first: Coralie

last: Viollet


title: Regulation of T cell cytokine expression by Tet2-mediated DNA demethylation [MeDIP-Seq]

status: Public on Apr 12 2015

city: Seattle

first: Raymond

last: Doty

state: WA

department: Division of Hematology

institute: University of Washington

summary: T cell function is regulated by epigenetic mechanisms. 5-methylcytosine (5mC) conversion to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation (Tet) proteins was identified to mediate DNA demethylation. Here, we characterize the genome-wide distribution of 5hmC in T cells using DNA immunoprecipitation coupled with high-throughput DNA sequencing. 5hmC marks signature genes associated with effector cell differentiation in the putative regulatory elements. Moreover, Tet2 protein is recruited to 5hmC-containing regions, dependent on lineage-specific transcription factors. Deletion of the Tet2 gene in T cells decreased their cytokine expression, associated with reduced p300 recruitment. In vivo, Tet2 plays a critical role in the expression of cytokine genes. Collectively, our findings for the first time demonstrate a key role of Tet-mediated active DNA demethylation in T cells.

overall_design: Examination of 5mC and 5hmC patterns in helper T cell subsets including naïve, Th1, Th2, Th17, and iTreg cells.

first: Kenji

last: Ichiyama

first: Lai

last: Wei

first: Chen

last: Dong


title: Regulation of T cell cytokine expression by Tet2-mediated DNA demethylation


title: AXL mediates resistance to PI3Kα inhibition by activating the EGFR/PKC/mTOR axis in head and neck and esophageal squamous cell carcinomas.

first: Nicholas

last: Socci

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Phosphoinositide-3-kinase (PI3K)-α inhibitors are clinically active in squamous carcinoma (SCC) of the head and neck (H&N) bearing mutations or amplification of PIK3CA. We aimed to identify potential mechanism of resistance and have observed that SCCs cells overcome the antitumor effects of the PI3Kα inhibitor BYL719 by maintaining PI3K-independent activation of the mammalian target of rapamycin (mTOR).  The persistent mTOR activation is mediated by the tyrosine kinase receptor AXL.  We found that AXL is overexpressed in resistant tumors, dimerizes with the epidermal growth factor receptor (EGFR), phosphorylates EGFR tyrosine 1173, resulting in activation of phospholipase Cγ (PLCγ)- protein kinase C (PKC) that, in turn, activates mTOR. Finally, simultaneous treatment with PI3Kα and either EGFR, AXL or PKC inhibitors reverts this resistance.

overall_design: RNAseq from acquired resistant cells CAL33B, K180B were compared to their parental counterpart CAL33 and K180, respectively. K180 is a shortcut of KYSE180, and B stands for BYL719.  Duplicate of parental sensitive cells and K180B, and triplicate for CAL33B.

first: Moshe

last: Elkabets

first: Evangelos

last: Pazarentzos

first: Qing

last: Sheng

first: Raphael

last: Pelossof

first: Samuel

last: Brook

first: Natasha

last: Morse

first: Jenny

last: Yan

first: Manway

last: Liu

first: Rita

last: Das

first: Yan

last: Chen

first: Angela

first: Huiqin

last: Wang

first: Jinsheng

last: Liang

first: Alan

last: Huang

first: Ronald

last: Ghissein

first: Neal

last: Rosen

first: Trever

last: Bivona

first: Maurizio

last: Scaltriti

first: José

last: Baselga

first: Dejan

last: Juric

first: Ana

middle: O

last: Benzaken

first: Jordi

last: Rodon

first: Joseph

last: Gurski

first: Darcy

last: Kerr

first: Rafael

last: Rosell

first: Cristina

last: Teixidó


title: RNA pol II transcript abundance controls condensin accumulation at mitotically upregulated and heat shock-inducible genes in fission yeast

city: Onna-son

first: Norihiko

last: Nakazawa

state: Okinawa

address: 1919-1 Tancha

department: G0 Cell Unit

institute: Okinawa Institute of Science and Technology Graduate University

summary: Condensin plays fundamental roles in chromosome dynamics.  In this study, we determined the binding sites of condensin on fission yeast (Schizosaccharomyces pombe) chromosomes at the level of nucleotide sequences using chromatin immunoprecipitation (ChIP) and ChIP-sequencing (ChIP-seq).  We found that condensin binds to RNA polymerase I-, II- and III-transcribed genes during both mitosis and interphase, and we focused on pol II constitutive and inducible genes.  Accumulation sites for condensin are distinct from those of cohesin and DNA topoisomerase II.  Using cell cycle stage- and heat shock-inducible genes, we demonstrate that pol II-mediated transcripts cause condensin accumulation.  First, condensin’s enrichment on mitotically activated genes was abolished by deleting the sep1+ gene that encodes an M-phase-specific forkhead transcription factor.  Second, by raising the temperature, condensin accumulation was rapidly induced at heat shock protein genes in interphase and even during mid-mitosis.  In interphase, condensin accumulates preferentially during the post-replicative phase.  pol II-mediated transcription was neither repressed nor activated by condensin, as levels of transcripts per se did not change when mutant condensin failed to associate with chromosomal DNA.  However, massive chromosome missegregation occurred, suggesting that abundant pol II transcription may require active condensin prior to proper chromosome segregation.

overall_design: Examination of 3 different chromosome-associated proteins in 3 conditions.


title: Tet2-mediated DNA demethylation controls T cell cytokine expression [seq]

first: Raymond

last: Doty

summary: The conversion of 5-methylcytosine (5mC) into 5-Hydroxymethylcytosine (5hmC) by ten-eleven translocation (Tet) family has recently been identified as a key process for active DNA demethylation, whose effects in the immune response is currently unknown.

overall_design:
Examination of both 5mC and 5hmC modifications in 5 Th cell types.
CD2(Cre)Tet2(f/f) mice (previously described in Moran-Crusio et al.,2011) and wild-type littermates on the mixed background were used in experiments.

first: Kenji

last: Ichiyama

first: Xiaowei

last: Yan

first: Chen

last: Dong


title: The tumor virus landscape of AIDS-related lymphomas

status: Public on Apr 11 2015

first: Aaron

last: Arvey

institute: Memorial Sloan-Kettering Cancer Center

summary: Immunodeficiency dramatically increases susceptibility to cancer as a result of reduced immune surveillance and enhanced opportunities for virus-mediated oncogenesis. While AIDS-related lymphomas (ARLs) are frequently associated with known oncogenic viruses, many cases contain no known transforming virus. To discover novel transforming viruses, we profiled a set of ARL samples using whole transcriptome sequencing. We determined that Epstein-Barr virus (EBV) was the only virus detected in the tumor samples of this cohort, suggesting that if unidentified pathogens exist in this disease, they are present in fewer than 10% of cases or undetectable by our methods.  To evaluate the role of EBV in ARL pathogenesis, we analyzed viral gene expression and found highly heterogeneous patterns of viral transcription across samples. We also found significant heterogeneity of viral antigen expression across a large cohort, with many patient samples presenting with restricted type I viral latency, indicating that EBV latency proteins are under increased immunosurveillance in the post-CART era. Furthermore, EBV infection of lymphoma cells in HIV-positive individuals was associated with a distinct host gene expression program. These findings provide insight into the joint host-virus regulatory network of primary ARL tumor samples and expand our understanding of virus-associated oncogenesis. Our findings may also have therapeutic implications, as treatment may be personalized to target specific viral and virus-associated host processes that are only present in a subset of patients.

overall_design:
AIDS-related lymphoma samples were sequenced and analyzed by presnce/absence of EBV.
-------------------------------------------------
Raw data not provided - IRB decided that consent form was not consistent with any disclosure of genotyping data, including through dbGaP.  This an atypical and highly irregular dataset.

first: Akinyemi

last: Ojesina

first: Joonil

last: Jung

first: Matthew

last: Meyerson

first: Ethel

last: Cesarman


title: A Genome-wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence [ChIP-seq]

city: Long Beach

first: Judy

last: Brusslan

address: 1250 Bellflower Blvd

department: Department of Biological Sciences

institute: California State University Long Beach

summary: The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly twice the gene area as H3K9ac marks. Genes with the greatest fold-change in expression displayed the largest positively-correlated percent change in coverage for both marks. Most senescence up-regulated genes were pre-marked by H3K4me3 and H3K9ac, but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes.

overall_design: H3K4me3 and H3K9ac were measured on a genome-wide scale using ChIP-seq at different stages of leaf aging.

first: Giancarl

last: Bonora

last: Rus-Canterbury

first: Fayha

last: Tariq

first: Artur

last: Jaroszewicz

first: Matteo

last: Pellegrini


title: Splicing function of mitotic regulators links R-loop mediated DNA damage to tumor cell killing

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

summary: We discovered that two mitotic regulators, BuGZ and Bub3, involved in splicing regulation during interphase

overall_design: 8 samples from primary Human foreskin fibroblast cells (HFFs) , 12 samples from TOV21G cells. Control siRNA. BuGZ siRNA or Bub3 siRNA were transfected for 48 h before sample collection. Cells treated with pladienolide B served as positive controls.  For each RNAi experiment, we had two biological replicates.

first: Yihan

last: Wan

first: Xiaobin


title: Salivary Transcriptomic Biomarkers for Insulin Resistance

status: Public on Apr 10 2015

city: Los Angeles

first: yong

last: zhang

address: 650 Charles E. Young Drive South

department: school of dentistry

institute: UCLA

summary: We have performed gene expression microarray analysis to profile transcriptomic signatures between insulin resistance high risk subjects and insulin resistance low risk subjects

overall_design: Participants enrolled in this study were recruited in the overnight fasted state, then the collection and processing of glucose (fasting, 30, 60 and 120 minutes) and insulin from blood samples, hemoglobin A1c (HbA1c) , assessment of medical history, socio-demographic characteristics, lifestyle factors, blood pressure and anthropometric and body composition measurements were conducted. During baseline visit, participants were asked to refrain from eating, drinking and oral hygiene procedures for at least 1-hour prior to saliva collection.5 ml of unstimulated whole saliva samples were consistently collected, stabilized and preserved, the sample supernatants were reserved at -80°C prior to assay. Based on the homeostasis model assessment of insulin resistance (HOMA-IR), using the formula [HOMA-IR= (fasting glucose*fasting insulin)/405], participants were divided into 2 groups: IR high risk group (HOMA-IR value ≥2.5) and IR low risk group (HOMA-IR value <2.5). Total RNA was extracted from saliva and subjected to gene expression microarray analysis using Affymetrix human genome 2.0 plus array

first: Yong

last: Zhang

first: Tristan

last: Grogan

first: Kaumudi

last: Joshipura

first: David

last: Elashoff

last: Wong


title: A Genome-wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence


title: ChIP-seq of GATA4 in mouse skeletal muscle myoblasts

city: Minneapolis

first: Genomics

last: Center

state: MN

address: 312 Church Street SE

institute: University of Minnesota

summary: GATA4 occupancy on the mouse genome of satellite cell-derived primary myoblasts. Proliferating myoblasts cultured in growth medium were immunoprecipitated with anti-GATA4 antibody or control IgG. Precipitated genomic DNAs were subjected to next generation sequencing.

overall_design: Paired-end 150 bp sequence reads of GATA4-ChIP and IgG-ChIP using mouse skeletal muscle myoblasts.

first: Tomohide

last: Takaya

first: Atsushi

last: Asakura


title: Transcriptome analysis reveals that sporulation is used as an iron deficiency resistance mechanism in Paenibacillus riograndensis SBR5

city: Porto Alegre

first: Edilena

middle: Reis

last: Sperb

state: RS

address: Bento Gonçalves

department: Genética

country: Brazil

institute: UFRGS

summary: Transcriptome analysis of Paenibacillus riograndensis SBR5.

overall_design: SBR5 strain was grown in sufficient iron media and limited iron media.

first: Michelle

middle: T

last: Sfeir

first: Raul

last: Sperotto

first: Gabriela

last: Fernandes

first: Fábio

last: Pedroza

first: Emanuel

last: Souza

first: Luciane

last: Passaglia


title: Transcriptomic analysis of vulvovaginal candidiasis identifies a role for the NLRP3 inflammasome

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: RNA-seq analysis of an in vivo murine model of vulvovaginal candidiasis

overall_design: Murine vaginas were infected with Candida albicans and harvested for RNA-seq analysis 3 days post-infection

first: Vincent

last: Bruno

first: Brian

last: Peters


title: Transcriptional reprogramming of engineered cellobiose-utilizing Saccharomyces cerevisiae in response to cellobiose revealed by RNA-Seq

city: Tianjin

first: Yuping

last: Lin

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Saccharomyces cerevisiae cannot metabolize cellobiose in nature. Here, S. cerevisiae was engineered to achieve cellobiose utilization by introducing both a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (gh1-1) from Neurospora crassa. We sequenced mRNA from anaerobic exponential cultures of engineered S. cerevisiae grown on cellobiose or glucose as a single carbon source in biological triplicate. Differences in gene expression between cellobiose and glucose metabolism revealed by RNA deep sequencing indicated that cellobiose metabolism induced mitochondrial activation and reduced amino acid biosynthesis under fermentation conditions.

overall_design: mRNA levels in cellobiose-grown and glucose-grown cells of engineered cellobiose-utilizing Saccharomyces cerevisiae were examined by deep sequencing, in triplicate, using Illumina Genome Analyzer-II. We sequenced 3 samples from cellobiose-grown cells and 3 samples from glucose-grown cells and identified differential expressions in the cellobiose versus glucose fermentations by using mRNA levels of glucose-grown cells as a reference.

first: Jamie

last: Cate


title: Modeling Familial Cancer with iPSC Approaches

first: Betty

last: Chang

address: 1425 Madison Ave

institute: Mount Sinai School of Medicine

summary: In vitro modeling of human disease has recently become feasible with the adoption of induced pluripotent stem cell (iPSC) technology. Here, we established patient-derived iPSCs from an Li-Fraumeni Syndrome (LFS) family and investigated the role of mutant p53 in the development of osteosarcoma (OS). Several members of this family carried a heterozygous p53(G245D) mutation and presented with a broad spectrum of tumors including OS. Osteoblasts (OBs) differentiated from iPSC-derived mesenchymal stem cells (MSCs) recapitulated OS features including defective osteoblastic differentiation (OB differentiation) as well as tumorigenic ability. Systematic analyses revealed that the expression of genes enriched in LFS-derived OBs strongly correlated with decreased time to tumor recurrence and poor patient survival. In silico cytogenetic region enrichment analysis (CREA) demonstrated that LFS-derived OBs do not have genomic rearrangements and hence are a particularly valuable tool for elucidating early oncogenic events prior to the accumulation of secondary alterations. LFS OBs exhibited impaired upregulation of the imprinted gene H19 during osteogenesis. Restoration of H19 expression in LFS OBs facilitated osteogenic differentiation and repressed tumorigenic potential. By integrating human imprinted gene network (IGN) and functional genomic analyses, we found that H19-mediates suppression of LFS-associated OS through the IGN component DECORIN (DCN). Downregulation of DCN impairs H19-mediated osteogenic differentiation and tumor suppression. In summary, these findings demonstrate the feasibility of studying inherited human cancer syndromes with iPSCs and also provide molecular insights into the role of the IGN in p53 mutation-mediated tumorigenesis.

overall_design: mRNAseq profiling during mesenchymal stem cell differentiation to osteoblasts.

first: Dung-Fang

last: Lee

first: Ihor

last: Lemischka


title: Time resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells

city: Cork

first: Pavel

middle: V

last: Baranov

state: Co. Cork

address: Western Gateway Building, UCC

department: Biochemistry and Cell Biology

country: Ireland

institute: University College Cork

summary: Oxygen and glucose metabolism plays a pivotal role in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) occurs during ischemia and stroke, resulting in extensive tissue injury and cell death. We applied time-resolved ribosome profiling technique to assess early events at the level of gene expression in rat pheochromocytoma PC12 cells during short-term OGD. Most substantial alterations in transcripts levels and their translation were seen to occur in the first 20 minutes of OGD. The rapid adaptation of translation apparatus to OGD is global and involves altered elongation and initiation rates. We also observed salient and reproducible alterations in ribosome densities of individual mRNAs such as increased translation of particular upstream Open Reading Frames (uORFs); induced site-specific arrests of the ribosomes and synthesis of extended protein isoforms.

overall_design: Ribosome profiling (with mRNA-seq sequencing) was carried out at 0,20,40 and 60 minutes of OGD. Two biological replicates were used.

first: Dmitry

middle: E

last: Andreev

first: Patrick

middle: B

last: O’Connor

first: Alexander

last: Zhdanov

first: Ruslan

middle: I

last: Dmitriev

first: Ivan

middle: N

last: Shatsky

last: Papkovsky


title: Tet2-mediated DNA demethylation controls T cell cytokine expression

first: Raymond

last: Doty

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

overall_design: Refer to individual Series


title: Transcriptome-wide analysis of the genome regulation and pathogenicity mechanisms of a fungal pathogen

city: Wuhan

first: Qi-Jia

last: Wu

address: Nanhu Avenue

institute: ABlife. inc

summary: Transcriptome sequencing is a powerful approach to globally delineate both the transcriptional and post-transcriptional genome regulation in human and other higher eukaryotes. This study sequenced the transcriptomes of two pathogenicity-differential strains of the plant wilt pathogen Verticillium dahliae. Although they showed no growth difference in vitro, hundreds of V. dahliae genes including those synthesizing aflatoxin were preferentially expressed at in the high-virulence strain. Using both the Pfam and GO annotation strategies, some of these putative virulence genes were ambiguously clustered into several known pathogenic mechanisms including hydrophobins secreted from fungal cells and acting as phytotoxin, biosynthesis of melanin protecting the fungal pathogen against host immune responses, membrane proteins of CFEM and major facilitator superfamily MFS1 with known functions in pathogenesis and multi-drug resistance, respectively. These results suggest that some pathogenicity pathways are pre-activated at the transcriptional level prior to the fungal infection of host plants. We developed two algorithms to confidently identify 1518 alternative splicing events in 1,259 Verticillium genes, representing 15.1% of multi-exonic genes. Among the events, 43.5% involving in novel splice sites were classified into nine AS types, the others belong to intron retention. Verticillium AS genes were exclusively enriched in the regulatory biological processes such as mycelium development, reproduction, morphogenesis, cell communication and signal transduction, predicting a primary function of AS regulation when the pathogen infecting its host. This work presents a transcriptome-wide approach for identifying the fungal virulence genes and pathogenicity mechanisms; both the methodology and mechanisms could be generally applicable to other fungal pathogens.

overall_design: Transcriptome analysis of two Verticillium dahliae strains

first: Yi

last: Zhang

first: Dazhao

last: Yu


title: Spatially resolved, highly multiplexed RNA profiling in single cells

status: Public on Apr 09 2015

first: Xiaowei

last: Zhuang

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

summary: Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 – 1000 unique RNA species in hundreds of individual cells. Correlation analysis of the ~10^4 – 10^6 pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins.

overall_design: A single sample is analyzed

first: Kok

middle: H

last: Chen

first: Alistair

last: Boettiger

first: Jeffrey

middle: R

last: Moffitt

first: Siyuan

last: Wang


title: The cytosolic iron-sulfur cluster assembly protein MMS19 regulates transcriptional gene silencing, DNA repair, and flowering time in Arabidopsis

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: To study how MMS19 and ABO4 affect gene expression, we performed RNA deep sequencing for the seedlings materials Col, mms19-1,and abo4 mutants.

overall_design: Compare the mRNA profiles of 14-day old seedlings materials of mutants (mms19-1 and abo4) to wild type Col by Illumina suquencing.

first: Xinjian

last: He

first: Yongfeng

last: Han

first: Huanwei

last: Huang


title: A Genome-wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence [RNA-seq]

first: Judy

last: Brusslan

overall_design: RNA-seq data at different stages of leaf aging.

first: Giancarl

last: Bonora

first: Ana

last: Rus-Canterbury

first: Fayha

last: Tariq

first: Artur

last: Jaroszewicz

first: Matteo

last: Pellegrini


title: Small RNA profiling of human cumulus cells and oocytes

city: Montpellier

first: Said

last: Assou

address: 80, Av. Augustin Flich

institute: INSERM

summary: Cumulus cells are biologically distinct from other follicular cells and perform specialized roles, transmitting signals within the ovary and supporting oocyte maturation during follicular development. The bi-directional communication between the oocyte and the surrounding cumulus cells is crucial for the acquisition of oocyte competence. Using Illumina/deep-sequencing technology, we dissected the small RNAome of pooled human mature MII oocytes and cumulus cells.

overall_design: Cumulus cells and MII mature oocytes small RNA profiles were generated by deep-sequencing, using Illumina 1G sequencer

first: Samir

last: Hamamah


title: CapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals (ChIP-Seq)

city: Marseille - cedex 09

first: Aurélien

last: Griffon

address: 163, Avenue de Luminy - case 928

institute: TAGC - Inserm U1090

summary: Here we developed CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrated accurate quantification of enhancer activity. Furthermore, we found that enhancer strength correlates with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function.

overall_design: ChIP-seq for the transcription factors HEB and TCF1, the DNaseI and the epigenetic modification H3K9me3 in DP thymocytes.

first: Laurent

last: Vanhille

first: Ahmad

last: Maqbool

first: Joaquin

last: Zacarias

first: Thi

last: Dao

first: Nicolas

last: Fernandez

first: Benoit

last: Ballester

first: Jean-Christophe

last: Andrau

first: Salvatore

last: Spicuglia


title: Dissection of the style’s response to pollination using transcriptome profiling in self-compatible (Solanum pimpinellifolium) and self-incompatible (Solanum chilense) tomato species

city: Shanghai

first: Panfeng

last: Zhao

address: 800 Dongchuan RD. Minhang District

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

summary:
Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data.
Results: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which “Cysteine and methionine metabolism pathway” and “Plant hormone signal transduction pathway” were significantly enriched in SI.
Conclusions: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of “Cysteine and methionine metabolism” and “Plant hormone signal transduction”, which are likely to play important roles in the control of pollen tubes growth in SI species.

sample_organism:
Solanum chilense
Solanum pimpinellifolium

overall_design: 24-h unpollination (UP) and self-pollination (P) styles mRNA profiles from SC and SI tomato species were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform.

first: Lida

last: Zhang

first: Lingxia


title: AKT phosphorylates H3-threonine 45 to facilitate termination of gene transcription in response to DNA damage.

city: Seoul

first: Hong-Duk

last: Youn

address: Daehak-ro Jonno-gu

department: Biomedical Sciences

institute: Seoul National University College of Medicine

summary:
Purpose: In this study, we show that DNA damage-activated AKT phosphorylates threonine 45 of core histone H3 (H3-T45)
Result: By genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) analysis, H3-T45 phosphorylation was distributed throughout DNA damage-responsive gene loci, particularly immediately after the transcription termination site
Conclusion: AKT-mediated phosphorylation of H3-T45 regulates the processing of the 3′ end of DNA damage-activated genes to facilitate transcriptional termination

overall_design: MCF10A cells were ChIPed with anti-phosphorylated H3-T45, anti-phosphorylated RNA Pol II-S2 and S5, and anti-H3-K36me3.

first: Jong-Hyuk

last: Lee