title: Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing [RNA-seq]

overall_design: 3 replicates from GM12878 and HL-60 cell lines collected for differential gene expression analysis.

first: Riza

last: Daza

first: Andrew

last: Adey

first: Hannah

last: Pliner

first: Lena

last: Christiansen

first: Kevin

last: Gunderson

first: Frank

last: Steemers

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: An alternative pluripotent state confers interspecies chimaeric competency [WGBS]

status: Public on May 06 2015

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

country: USA

institute: University of California, San Diego (UCSD)

type: Methylation profiling by high throughput sequencing

summary: In this study, we show that by simple modulation of extrinsic signaling pathways, a new class of pluripotent stem cells, referred to as region selective epiblast stem cells (rsEpiSCs), could be efficiently derived from different stages of the early embryo. rsEpiSCs share features of primed pluripotency yet are distinct from EpiSCs in their molecular characteristics and ability to colonize post-implantation embryos. We performed whole-genome bisulfite sequencing (WGBS) experiments to compare the DNA methylation landscapes of conventional EpiSCs and rsEpiSCs.

overall_design: Compare the DNA methylation profiles in 2 pluripotent stem cell types (LP-EpiSCs and conventional EpiSCs) in mouse. Two replicates are examined for each cell type.

first: Yupeng

last: He

first: Chongyuan

last: Luo

first: Zhuzhu

last: Zhang


title: Genome wide maps of H3K4me3 and H3ac histone modifications in C6 rat glioma cells [Illumina]

status: Public on May 07 2015

city: Uppsala

first: Marcin

last: Kruczyk

address: Husargatan 3

country: Sweden

institute: Uppsala University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report maps of H3K4me3 and H3ac - activiting expression histone modifications in C6 rat glioma cells.  The data was obtained using whole genome high throughput technology. The sequencing was performed on HiSeq Ilumina platform.

overall_design: Examination of  H3K4me3 histone modification and H3ac histone modification in C6 rat glioma cell line

first: Bozena

last: Kaminska

first: Jan

last: Komorowski


title: Transcriptome analysis of cucumber response to nitrogen deficiency

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

country: China

institute: Nissi Biotech

type: Expression profiling by high throughput sequencing

summary: Nitrogen is the most important mineral nutrient of plant. As a worldwide and economically important vegetable, cucumber (Cucumis sativus L.) has a strong nitrogen-dependence. We took whole transcriptome sequencing approach to compare the gene expression profiles of cucumber leaves and roots grown under sufficient or insufficient nitrate supply. Analysis of the transcriptome data revealed that the root and leaf adapt different response mechanisms to long-term nitrogen deficiency. Photosynthesis and carbohydrate biosynthetic process were pronouncedly and specifically reduced in leaf, while the ion transport function, cell wall and phosphorus-deficiency response function seem systematically down-regulated in root. Genes in nitrogen uptake and assimilation are decreased in root, but some are increased in leaf under nitrogen deficiency. Several lines of evidence suggest that the altered gene expression networks support the basic cucumber growth and development likely through successful nitrogen remobilization involving in the induced expression of genes in ABA and ethylene pathways.

overall_design: cucumber leaf and root mRNA of 28-day after sowing nitrogen deficiency and sufficiency deep sequencing, using Illumina HiSeq 2000

first: Zhiwei

last: Qin


title: Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity for Pluripotency and Reprogramming

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

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

overall_design: Refer to individual Series


title: Small RNA and transcriptome profiling of mice deficient in either germline Dgcr8 or Dicer

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: We used Illumina Small RNA and RNA-Seq kits to prepare both small RNA and RNA-Seq libraries from total RNA isolated from either leptotenze/zygotene or pachytene spermatocytes purified from either Dgcr8 or Dicer germline conditional knockout mice.

overall_design: Conditional knockout mice were generated by using a Ddx4 promoter to drive cre excision of either Dgcr8 or Dicer at embryonic day 18.  Mixed leptotene/zygotene or pachytene spermatocytes were then isolated from the testis of adult conditional knockout mice, along with paired WT littermates as a control.  RNA was isolated from these spermatocytes using Trizol.  Small RNA or RNA-Seq libraries were then prepped using Illumina's sequencing library preparation kits.

first: Stephanie

last: Hilz

last: Modzelewski

first: Elizabeth

last: Fogarty

first: Paula

last: Cohen


title: Comparative anterior pituitary miRNA and mRNA expression profiles of Bama minipigs and Landrace pigs reveal potential molecular network involved in animal postnatal growth

status: Public on May 05 2015

city: Guangzhou

first: Ruisong

last: Ye

state: Guangdong

address: 483 Wushan Tianhe

institute: South China Agricultural University


title: An alternative pluripotent state confers interspecies chimaeric competency [ChIP-seq]

summary: Here we show that by simple modulation of extrinsic signaling pathways, a new class of pluripotent stem cells, referred to as region selective epiblast stem cells (rsEpiSCs), could be efficiently derived from different stages of the early embryo. rsEpiSCs share features of primed pluripotency yet are distinct from EpiSCs in their molecular characteristics and ability to colonize post-implantation embryos. We performed ChIP-seqencing experiments using antibodies against H3K4me3 and H3K27me3, comparing conventional EpiSCs and rsEpiSCs, as well as comparing conventional human H1 ESCs and human H1 ESCs cultured in mouse rsEpiSCs based culture conditions (H1 rsESCs).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of 2 different histone modifications (H3K4me3, H3K27me3) in 2 pluripotent stem cell types in mouse and human.

first: Jun

last: Wu


title: Histone modifications in the marine diatom Phaeodactylum tricornutum

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Genome wide mapping of five histone marks (H3K4me2, H3K9me2, H3K9me3, H3K27me3 and H3AcK9/14) as well as nucleosome occupancy was generated by chromatin immunoprecipitation followed by deep sequencing. To gain insights into the dynamic nature of the P. tricornutum epigenome in response to an environmental cue, we analyzed the impact of nitrate depletion. We specifically examined three histone modifications (H3K4me2, H3K9/14Ac and H3K9me3) using Chip-seq.

overall_design: Examination of 5 different histone modifications.

first: Achal

last: Rastogi

first: Xin

last: Lin

first: Maximo

last: Rivarola

middle: E

last: Allen

first: Chris

last: Bowler

first: Leïla

last: Tirichine


title: Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

type:
Expression profiling by array
Other


title: An alternative pluripotent state confers interspecies chimaeric competency [RNA-Seq]

first: Christopher

last: Benner

summary: Here we show that by simple modulation of extrinsic signaling pathways, a new class of pluripotent stem cells, referred to as region selective epiblast stem cells (rsEpiSCs), could be efficiently derived from different stages of the early embryo. rsEpiSCs share features of primed pluripotency yet are distinct from EpiSCs in their molecular characteristics and ability to colonize post-implantation embryos. We performed RNA-sequencing experiments and examined the global gene expression profiles of EpiSCs, rsEpiSCs, in vivo isolated four regions of E6.5 mouse epiblasts: AP (anterior-proximal), AD (anterior-distal), PP (posterior-proximal) and PD (posterior-distal), human H1 ESCs, H1 rsESCs, H9 ESCs, H9 rsESCs, rhesus monkey ORMES23 rsESCs, and chimpanzee rsiPSCs.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens
Mus musculus

overall_design: Examination of global gene expression profiles in 2 pluripotent stem cell types across multiple species.


title: Comparative anterior pituitary miRNA and mRNA expression profiles of Bama minipigs and Landrace pigs reveal potential molecular network involved in animal postnatal growth [mRNA-Seq]

summary: The anterior pituitary is the most important endocrine organ modulating animal postnatal growth, mainly by controlling growth hormone (GH) gene transcription, synthesis, and secretion. As an ideal model for animal postnatal growth studies, the Bama minipig is characterized as having a lower growth performance and fewer individual differences compared with larger pig breeds. In this study, anterior pituitaries from Bama minipig and Landrace pig were used for miRNA and mRNA expression profile analysis using miRNA microarrays and mRNA-seq. Consequently, a total of 222 miRNAs and 12,909 transcripts were detected, and both miRNAs and mRNAs in the two breeds showed high correlation (r > 0.97). Additionally, 41 differentially expressed miRNAs and 2,254 transcripts were identified. Pathways analysis indicated that 32 pathways significantly differed in the two breeds. Importantly, two GH-regulation-signalling pathways, cAMP and inositol 1, 4, 5-triphosphate (IP3), and multiple GH-secretion-related transcripts were significantly down-regulated in Bama minipigs. Moreover, target prediction by two algorithms (TargetScan and RNAhybrid) indicated that most miRNA–mRNA target pairs (63.68–71.33%) presented a negatively correlated expression pattern. A possible network among miRNAs, mRNAs, and GH-regulation pathways was also proposed. These data will be helpful in understanding the possible molecular mechanisms involved in animal postnatal growth.

overall_design: mRNA profiling in the anterior pituitary from two different pig breeds.2 pooled samples were analyzed. A pool of 3 pig anterior pituitary was used for Bama minpigs(YB) and Landrace pigs(YC),respectively.

first: Yongliang

last: Zhang


title: Composite macroH2A/NRF-1 Nucleosomes Suppress Noise and Generate Robustness in Gene Expression

city: Athens

first: Dimitris

last: Thanos

address: 4 Soranou Ephessiou

department: Basic Research II

country: Greece

institute: BIOMEDICAL RESEARCH FOUNDATION ACADEMY OF ATHENS (BRFAA)

summary: The histone variant macroH2A has been implicated in transcriptional repression, but the molecular mechanisms that contribute to global macroH2A-dependent genome regulation remain elusive. Using ChIP-seq coupled with transcriptional profiling in macroH2A knock-down cells (GSE53103) we demonstrate that singular macroH2A nucleosomes occupy transcription start sites of subsets of both expressed and repressed genes with opposing regulatory consequences. Specifically macroH2A nucleosomes mask repressor binding sites in expressed genes, but activator binding sites in repressed genes thus generating distinct chromatin landscapes limiting genetic or extracellular inductive signals. We show that composite nucleosomes containing macroH2A and NRF-1 are stably positioned on gene regulatory regions and can buffer the transcriptional noise typifying antiviral responses. In contrast, macroH2A nucleosomes without NRF-1 bind promoters weakly and mark genes with noisier gene expression patterns. Thus, the strategic position and stabilization of macroH2A nucleosomes in human promoters defines robust gene expression patterns.

overall_design:
ChIP-seq experiments were performed in human Namalwa B cells and Hela epithelial cells in order to investigate the function of specialized nucleosomes containing the macroH2A histone variant and the transcription factor NRF-1. Native ChIP, Native RecHIP or crosslink ChIP  were performed in replicates, sequenced and aligned to the reference genome (hg18).
mRNA-seq experiments were performed in human Namalwa B cells using a strand-specific protocol.
Please see manuscript for details.

first: Matthieu

middle: D

last: Lavigne


title: microRNA atlas of dendritic cell (DC) development

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

summary: We determined the microRNA profile of conventional DCs, plasmacytoid DCs, in vitro derived conventional DCs, and DC precursors in the bone marrow. We then compared conventional DCs to plasmacytoid DCs, conventional DCs and in vitro conventional DCs. In addition, we used MDS analysis to compare all the profiles.

overall_design: 14 profiles were produced. Duplicates of LSKs, CMPs, CLPs, CDPs, conventional DCs, plasmacytoid DCs, in vitro cDCs were sequenced.

middle: M


title: Histone H3.3 is required for endogenous retroviral element silencing and genome stability

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center


title: Histone H3.3 is required for endogenous retroviral element silencing and genome stability [RNA-Seq]

summary: Endogenous retroviruses (ERVs) have provided an evolutionary advantage in the diversification of transcript regulation and are thought to be involved in the establishment of extraembryonic tissues during development. However, silencing of these elements remains critical for the maintenance of genome stability. Here, we define a new chromatin state that is uniquely characterized by the combination of the histone variant H3.3 and H3K9me3, two chromatin ‘marks’ that have previously been considered to belong to fundamentally opposing chromatin states. H3.3/H3K9me3 heterochromatin is fundamentally distinct from ‘canonical’ H3K9me3 heterochromatin that has been under study for decades and this unique functional interplay of a histone variant and a repressive histone mark is crucial for silencing ERVs in ESCs. Our study solidifies the emerging notion that H3.3 is not a histone variant associated exclusively with “active” chromatin and further suggests that its incorporation at unique heterochromatic regions may be central to its function during development and the maintenance of genome stability.

overall_design: RNA-seq analysis of three embryonic stem cell lines WT, H3.3 KO1, and H3.3 KO2)

middle: A

first: Simon

last: Elsasser

first: C

last: Allis


title: RNA-seq analysis of epididymal adipose tissue from wild-type and Maf1 knockout mice

status: Public on May 04 2015

city: Bronx

first: Ian

last: Willis

address: 1300 Morris Park Ave

department: Biochemsitry

institute: Albert Einstein College of Medicine

summary: Purpose: To profile the effect of the Maf1 knockout on RNA polymerase II and RNA polymerase III transcriptomes in white adipose tissue

overall_design: Methods: Epididymal adipose tissue was harvested from overnight fasted 22-24 week old male mice that had been fed ad libitum on a chow diet. Total RNA was prepared from three biologically independent samples per genotype and subject to single-end directional RNA sequencing on the Illumina HiSeq platform.  Sequence reads that passed quality filters were aligned against the Mm9 Mouse genome assembly using GSNAP and uniquely mapped reads were counted using HTseq-counts.

first: Nouria

last: Hernandez


title: Histone H3.3 is required for endogenous retroviral element silencing and genome stability [ChIP-Seq]

overall_design: Native ChIP analysis of H3K9me3 in two mouse embryonic stem cell lines (Control and H3.3KD1). Inputs with GSE42155. Crosslinking ChIP analysis of H3.3, and H3.1/2 in two ESC lines (Control and H3.3KD1). Inputs sequenced. Crosslinking ChIP analysis of H3K9me3, DAXX, and KAP1 in three ESC lines (WT, H3.3KO1, H3.3KO2). Native ChIP of H3-HA addback in H3.3KD1 and H3.3KO1 ESC. Native ChIP of H3.3-HA and H3K9me3 in WT and DAXX null ESC. Inputs sequenced. Native H3.3-HA and H3K9me3 ChIP in WT and ATRX null ESC. Inputs sequenced. Crosslinking ChIP of H3.3 in two WT and ATRX null ESC. Inputs sequenced. Crosslinking H3.3 ChIP in KAP1 WT and null ESC. Inputs sequenced. Crosslinking H3.3 and H3.3-H3K9me3 sequential (Re)-ChIP in ESET WT and null ESC. Inputs sequenced.

middle: J


title: Wnt3a-Activin A Synergy Induces eRNAPII Pause-Release and Counteracts a Yap1 Elongation Block during hESC Differentiation

city: La Jolla, San Diego

first: conchi

last: estaras

address: 10010 N Torrey Pines Rd

department: Regulatory Biology

institute: The Salk Institute

summary: The Wnt3a/β-catenin and Activin/Smad2,3 signaling pathways synergize to induce endodermal differentiation of human embryonic stem cells, however the mechanism is not well-understood. Using ChIP-seq and GRO-seq analyses, we report here that hESC enhancers, including Wnt3a/LEF-1 sites, hold enhancer RNAPII complexes (eRNAPII) containing high levels of Ser5P and low Ser7P. In Wnt3a signaling, β-catenin recruits cohesin to the LEF-1:eRNAPII sites to induce enhancer-promoter looping and activate transcription of mesoendodermal (ME) genes. However, paused Ser5P-RNAPII complexes accumulate at these genes, indicating that elongation remains limiting. Subsequent Activin/Smad2,3 signaling increases P-TEFb occupancy, CTD-Ser7P, and productive elongation at ME genes. Additionally, ME genes, including EOMES and MIXL1, are repressed by the Hippo regulator, Yap1, an essential pluripotency factor. GRO-seq experiments indicate that Yap1 blocks nascent transcription and controls NELF occupancy on ME genes. Thus, Wnt3a/β-catenin and Activin/Smad2,3 pathways up-regulate transcription initiation and elongation, respectively, to overcome Yap1 repression during early hESC differentiation

overall_design: ChIP-seq and GROseq experiments in H1 hESCs. Cells were treated with Wnt3a (200ng/ml), Activin A (100ng/ml) or Wnt3a+Activin A (W200ng/ml+A100ng/ml)  for 4h (ChIP-seq) or 6h (GRO-seq). GRO-seq in YAP depleted cells were carried out following  transfection with control or YAP siRNAs . After 48h transfection, cells were left untreated or treated with Wnt3a+Activin (W200ng/ml+A100ng/ml) for additional 6h.

first: Conchi

last: Estaras


title: H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription

status: Public on May 02 2015

city: Göttingen

first: Steven

last: Johnsen

state: Niedersachsen

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

country: Germany

institute: University Medical Center Göttingen

summary: Hormone-dependent gene expression requires dynamic and coordinated epigenetic changes. Estrogen receptor-positive (ER+) breast cancer is particularly dependent upon extensive chromatin remodeling and changes in histone modifications for the induction of hormone-responsive gene expression. Our previous studies established an important role of bromodomain-containing protein-4 (BRD4) in promoting estrogen-regulated transcription and proliferation of ER+ breast cancer cells. Here, we investigated the association between genome-wide occupancy of histone H4 acetylation at lysine 12 (H4K12ac) and BRD4 in the context of estrogen-induced transcription. Similar to BRD4, we observed that H4K12ac occupancy increases near the transcription start sites (TSS) of estrogen-induced genes as well as at distal ERα binding sites in an estrogen-dependent manner. Interestingly, H4K12ac occupancy highly correlates with BRD4 binding and enhancer RNA production on ERα-positive enhancers. Consistent with an importance in estrogen-induced gene transcription, H4K12ac occupancy globally increased in ER-positive cells relative to ER-negative cells and these levels were further increased by estrogen treatment in an ERα-dependent manner. Together, these findings reveal a strong correlation between H4K12ac and BRD4 occupancy with estrogen-dependent gene transcription and further suggest that modulators of H4K12ac and BRD4 may serve as new therapeutic targets for hormone-dependent cancers.

overall_design: ChIP-seq profiles of H4K12ac in MCF7 cells treated with +/- estrogen treatment and MCF10A cells.

first: Sankari

last: Nagarajan


title: A cross-comparison of technologies for the detection of microRNAs from FFPE samples of hepatoblastoma patients

status: Public on May 03 2015

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

platform_organism:
Homo sapiens
synthetic construct


title: Host transcriptional reprogramming across diverse strains of the rice bacterial leaf streak pathogen Xanthomonas oryzae pv.oryzicola

status: Public on May 01 2015

first: Adam

last: Bogdanove

address: 334 Plant Science Building

department: Plant Pathology and Plant-Microbe Biology

summary: We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with 10 geographically diverse strains of Xanthomonas oryzae pv. oryzicola, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease.

overall_design: Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation with 10 strains of Xanthomonas oryzae pv.oryzicola with three biological replicates for each compared to three replicates of mock inoculated O sativa as the control

first: Katherine

last: Wilkins

first: Nicholas

last: Booher

first: Li

last: Wang


title: Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv.oryzae constitutively expressing the X. oryzae pv. oryzicola TAL2a effector from the high copy vector pKEB31

summary: We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with  Xanthomonas oryzae pv. oryzae strain PXO99A heterologously expressing the Tal2a effector, the designer TAL effector dT280 which targets a sequence overlapping the predicted Tal2a binding sequence in UCH, or the Tal11b effector. Results provide insight into the genes differentially regulated in a Tal2a- and dT280-specific manner.

overall_design: Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation. Each leaf was considered a separate biological replicate.

first: Aaron

middle: W

last: Hummel

first: Raúl

last: Cernadas


title: Nucleosome profiling in human embryonic stem cells

city: Irvine

first: Puya

last: Yazdi

state: Ca

address: University of California at Irvine

institute: University of California at Irvine

summary: Paired-end sequencing of MNase digested H1 and H9 hESCs.

middle: G

first: Brian

last: Pedersen

first: Ping

middle: H


title: An alternative pluripotent state confers interspecies chimaeric competency

first: Christopher

last: Benner

platform_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens
Mus musculus


title: RNA-sequencing of DYRK1A-deficient (CKO) pre-B and pre-T cells

city: Chicago

first: John

last: Crispino

state: IL

institute: The University of Chicago

summary: Pre-B and pre-T lymphocytes must orchestrate a transition from a highly proliferative state to a quiescent one during development. Cyclin D3 is essential for these cells’ proliferation, but little is known about its post-translational regulation at this stage. Here, we show that the dual specificity tyrosine-regulated kinase 1A (DYRK1A) restrains Cyclin D3 protein levels by phosphorylating T283 to induce its degradation. Loss of DYRK1A activity, via genetic inactivation or pharmacologic inhibition, caused accumulation of Cyclin D3 protein, incomplete repression of E2F-mediated gene transcription, and failure to properly couple cell cycle exit with differentiation. Expression of a non-phosphorylatable Cyclin D3 T283A mutant recapitulated these defects, while inhibition of Cyclin D:CDK4/6 mitigated the effects of DYRK1A inhibition. These data uncover a previously unknown role for DYRK1A in lymphopoiesis, and demonstrate how Cyclin D3 protein stability is negatively regulated during exit from the proliferative phases of B and T cell development.

overall_design: 5 cell populations were analyzed (small pre-B cells, large pre-B cells, quiescent CD4+CD8+ thymocytes, cycling CD4+CD+ thymocytes, and mature granulocytes) from 2 Control mice (pooled) and 2 DYRK1A-deficient mice (pooled) for a total of 10 samples.

first: Benjamin

last: Thompson


title: inaseedarray-INASEEDarray

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: au14-04_inaseed - inaseedarray - Analyse a signalling pathway necessary for embryonic cuticle reinforcement during seed development in Arabidopsis - Transcriptome comparison of ale1 and gso1/gso2 mutants compared to Col-0 seeds at two developmental stages (globular and heart)

overall_design: 12 dye-swap - gene knock out

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Gwyneth

last: Ingram

first: Marie-Laure

last: Martin-Magniette


title: Cancer Cells Hijack PRC2 to Modify Multiple Cytokine Pathways

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia [RNA-Seq]

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

summary: The bromodomain and extraterminal (BET) protein Brd4 is a validated drug target in leukemia, yet its regulatory function in this disease is not well understood. Here, we show that Brd4 chromatin occupancy in acute myeloid leukemia closely correlates with the hematopoietic transcription factors (TFs) Pu.1, Fli1, Erg, C/EBPα, C/EBPβ, and Myb at nucleosome-depleted enhancer and promoter regions. We provide evidence that these TFs, in conjunction with the lysine acetyltransferase activity of p300/CBP, facilitate Brd4 recruitment to their occupied sites to promote transcriptional activation. Moreover, chemical inhibition of BET bromodomains is found to suppress the functional output each hematopoietic TF, thereby interfering with essential lineage-specific transcriptional circuits in this disease. These findings reveal a chromatin-based signaling cascade comprised of hematopoietic TFs, p300/CBP, and Brd4, which supports leukemia maintenance and is suppressed by BET bromodomain inhibition.

overall_design: PolyA selected RNA-Seq for drug treated or shRNA-expressing MLL-AF9 transformed acute myeloid leukemia cells (RN2)

first: Jae

middle: S

middle: R

last: Vakoc


title: Targeted bisulfite sequencing to detect TALE-DNMT mediated targeted DNA methylation in human cells

city: Philadelphia

first: Diana

last: Bernstein

address: 3400 Civic Center Blvd Bldg 421

department: Department of Genetics, IDOM

institute: University of Pennsylvania

summary: We use NGS to assess the ability of TALE-guided DNA methyltranferases to make targeted changes to DNA methylation

overall_design: Targeted bisulfite sequencing of cells infected with wild-type or mutant TALE-DNMT constructs directed to the CDKN2A (p16) locus

first: Klaus

last: Kaestner


title: BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia [ChIP-Seq]

overall_design: ChIP-Seq for regulatory factors of Brd4 in MLL-AF9 transformed acute myeloid leukemia cells (RN2)


title: BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia


title: smRNA sequencing analysis to identify p53-dependent non-coding RNA networks in Chronic Lymphocytic Leukemia

city: Heidelberg

first: Thorsten

last: Zenz

address: Im Neuenheimer Feld 460

department: Department of Translational Oncology

institute: German Cancer Research Center (DKFZ)

summary: Mutations of the tumor suppressor p53 lead to chemotherapy resistance and a dismal prognosis in chronic lymphocytic leukemia (CLL). Comparing miRNA/non-coding RNA expression profiles between p53 wild-type and p53 mutant samples in response to DNA damage, we exploit the impaired transcriptional activity of mutant p53 to map out p53 targets in primary CLL by small RNA sequencing. Focusing on miRNAs, we identify a set of p53-dependent miRNAs (miR-182-5p, miR-7-5p, miR-320c/d) in addition to the key p53 target miR-34a. Beyond miRNAs, the long non-coding RNAs (lncRNAs) NEAT1 and lincRNA-p21 are induced in response to DNA damage in the presence of functional p53 but not in CLL with p53 mutation.

overall_design: Quantification of mature miRNA, other ncRNA and mRNA expression profiles in 68 paired CLL primary samples 24h after irradiation or no treatment.

first: Blume

last: Carolin

first: Hotz-Wagenblatt

last: Agnes

first: Hielscher

last: Thomas

first: Jauch

last: Anna

first: Zenz

last: Thorsten


title: Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence

city: West Lafayette

first: Karen

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

institute: USDA-ARS

summary: We use RNA sequencing technology in a time course study to measure transcript abundance from three developmental stages in cotyledons and five stages in the trifoliate leaf of Glycine max to identify genes with distinct temporal patterns of expression during leaf or cotyledon development.  We also examine the diffrences between these two photosynthetic tissues.

overall_design: Timecourse Expression analysis of Cotyledon Development and Leaf Development using RNAseq on distinct timepoints. 3 stages of the cotyledon were sequenced with 3 biological replicates in each stage. Five stages of the leaf were sequenced with 3 biological replicates for each stage.

first: Anne

middle: V

last: Brown


title: A cross-comparison of technologies for the detection of microRNAs from FFPE samples of hepatoblastoma patients [sequencing]

first: Aniruddha

last: Chatterjee

summary: This work highlights similarities and differences between three platforms (next-generation sequencing, microarray and NanoString) for detecting miRNAs and compares their strengths and weaknesses.

overall_design: miRNA expression profiles were determined in 6 Hepatoblastoma FFPE samples using a next-generation sequencing platform.

first: Anna

middle: L

last: Leichter

first: Vicky

last: Fan

first: Peter

last: Tsai

first: Rachel

last: Purcell

first: Michael

last: Sullivan

last: Eccles


title: Toxoplasma proteins GRA17 and GRA23 mediate the movement of small molecules between the host and the parasitophorous vacuole.

city: Cambridge

first: Daniel

last: Gold

state: Massachusetts

address: 77 Massachusetts Ave 68-264d

department: Biology

institute: MIT

summary:
Purpose: Two secreted Toxoplasma proteins (GRA17 and GRA23) mediate the passage of small molecules between the host cytoplasm and the parasite-containing vacuole. This provides the first molecular explanation to how intracellular, vacuole-residing parasites in the phylum Apicomplexa, like Plasmodium, gain access to host nutrients.
Methods: Mouse-derived Bone Marrow Macrophages were infected with Toxoplasma tachyzoites of either WT, dGRA17, dGRA23, or dGRA17rescue genetic background for 4 hours.
Results: GRA23 gene expression levels are elevated in the dGRA17 strain but not vice versa.
Conclusions: GRA17 and GRA23 are synergistically required for permeability of small molecules into the Toxoplasma parasitophorous vacuole.

sample_organism:
Mus musculus
Toxoplasma gondii RH

platform_organism:
Mus musculus
Toxoplasma gondii RH

overall_design: Toxoplasma and Mouse gene expression profiles from BMDMs infected with either WT (control), dGRA17, gGRA23, or dGRA17rescue (control) tachyzoites were obtained by RNA-Seq on an Illumina HiSeq2000 instruments at 4 hours post-infection.

first: Jeroen

middle: P

last: Saeij


title: Physiological and transcriptome responses to elevated CO2 and magnesium in Arabidopsis thaliana

city: Hangzhou

first: Gulei

last: Jin

state: Zhejiang

address: Yuhangtang Road 388#

institute: Zhejiang University

summary:
Background: The unprecedented rise in atmospheric CO2 concentration and injudicious fertilization or heterogeneous distribution of Mg in the soil warrant further research to understand the synergistic and holistic mechanisms involved in the plant growth regulation. The objective of this work is to understand responses in plants along with interactive effect of elevated CO2 and Mg levels by comparing data on single stress with that of combined stresses.
Results: This study investigated the influence of elevated CO2 (800 μL L−1) on physiological and transcriptomic profiles in Arabidopsis cultured in hydroponic media treated with 1 μM (low), 1000 μM (normal) and 10000 μM (high) Mg2+. Following 7-d treatment, elevated CO2 increased the shoot growth and chlorophyll content under both low and normal Mg supply, whereas root growth was improved exclusively under normal Mg nutrition. Notably, the effect of elevated CO2 on mineral homeostasis in both shoots and roots was less than that of Mg supply. Irrespective of CO2 treatment, high Mg increased leaf number but decreased root growth and absorption of P, K, Ca, Fe and Mn whereas low Mg increased the concentration of P, K, Ca and Fe in leaves. Elevated CO2 decreased the expression of genes related to cadmium response, cell redox homeostasis and lipid localization, but enhanced photosynthesis, signal transduction, protein phosphorylation, NBS-LRR disease resistance proteins and subsequently programmed cell death in low-Mg shoots. By comparison, elevated CO2 enhanced the response of lipid localization (mainly LTP transfer protein/protease inhibitor), endomembrane system, heme binding and cell wall modification in high-Mg roots. Some of these transcriptomic results are substantially in accordance with our physiological and/or biochemical analysis.
Conclusions: Contrasting changes were found between roots and shoots with the shoot transcriptome being more severely affected by low Mg while the root transcriptome more affected by high Mg. Elevated CO2 had a greater effect on transcript response in low Mg-fed shoots as well as in high Mg-fed roots. The present findings broaden our current understanding on the interactive effect of elevated CO2 and Mg levels in the Arabidopsis, which may help to design the novel metabolic engineering strategies to cope with Mg deficiency/excess in crops under elevated CO2.

overall_design: Examination of two CO2 concentration and three Mg levels of shoot and root Arabidopsis

first: Yaofang

last: Niu

first: Caixian

last: Tang

first: Golam

last: Ahammed

first: Longbiao

last: Guo

first: Jingquan

last: Yu


title: RNA-Sequencing of human papillary thyroid carcinomas

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

country: Italy

institute: National Research Council

summary: RNA-Sequencing analysis of 18 papillary thyroid carcinoma biopsies and of 4 healthy donors' thyroids. In this analysis we assessed differential gene expression and investigated the mutational landscape in this tumor type. Analysis of gene fusion was also performed, leading to the identification of a novel chimeric transcript, potential driver in tumor initiation.

overall_design: Total RNA isolated from 18 papillary thyroid carcinoma biopsies and 4 healthy donors' thyroids.

first: Roberta

last: Esposito

first: Pierlorenzo

last: Pallante

first: Alfredo

last: Fusco

last: Ciccodicola


title: Dual regulation of Fbw7 function and oncogenic transformation by Usp28

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: Fbw7, the substrate recognition subunit of SCF(Fbw7) ubiquitin ligase, mediates turnover of multiple proto-oncoproteins and promotes its own degradation. Fbw7-mediated substrate degradation is antagonized by the Usp28 deubiquitinase. We now show, using knockout mice, that Usp28 preferentially deubiquitinates and stabilizes Fbw7. Monoallelic deletion of Usp28 maintains stable Fbw7 but destabilizes Fbw7 substrates. In contrast, complete knockout of Usp28 promotes Pin1-dependent autocatalytic turnover of Fbw7, accumulation of Fbw7 substrates and oncogenic transformation. Overexpression of Usp28 stabilizes both Fbw7 and its substrates and similarly enhances transformation. We propose that dual regulation of Fbw7 activity by Usp28 maintains physiological levels of Fbw7 substrates, and that both loss and overexpression of Usp28 in human cancer promote Fbw7 substrate accumulation.

overall_design: RNAseq experiments of E13.5 murine embryonic fibroblasts (MEFs) derived from animals in which Usp28 was either deleted (-/-), wildtype (+/+) or heterozygous (+/-). In a first set of experiments immortalized MEFs of all three genotypes were analysed in biological triplicates. In a second set of experiments immortalized and Ras transformed MEFs of all three genotypes and MEFs which overexpress USP28 (+/+/+) where sequenced in duplicates.

first: Christina

last: Schülein-Völk

first: Jing

last: Zhu

first: Wenshan

last: Xu

first: Lyudmyla

last: Taranets

first: Andreas

last: Hellmann

first: Elmar

last: Wolf

first: Nikita

last: Popov


title: A microRNA expression atlas of grapevine based on small RNA library sequencing

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Genetic and epigenetic regulations, mostly driven by small non-coding RNAs, play a crucial role to define genetic programming in plant biology and development. In this work, we focus on miRNAs, the most representative class of small RNAs, to present the first comprehensive miRNA expression atlas in Vitis vinifera L. Our atlas gives a clear picture of miRNA regulation and homeostasis in the whole plant during its lifecycle.  We analyzed 68 small RNA libraries, which were prepared from a rich and diverse number of tissues (13)  harvested on different developmental stages. We identified 110 known miRNAs and annotated 176 novel, some of which belonging to known families and others completely new.   We found that very few miRNAs may be defined as tissue specific. However, interestingly, in the stamen 22 miRNAs were found highly specific. Most of the identified miRNAs show low expression levels, whereas, 32 miRNAs are present in all tissues and mainly highly expressed. Additionally, in each organ, the different developmental stages share 30—70% of miRNAs and their modulation leads the regulation of plant development. We also present a target prediction analysis and suggest a first functional description of hundreds of miRNAs. Our findings represent the most complete expression atlas for grapevine and any other woody species, paving the ground for future functional studies.

overall_design: Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation and Illumina Small RNA Sample Prep kit  followed by high-throughput sequencing with Illumina HiSeq 2000 and GA IIx Illumina Sequencer  platforms for 13 different organs/tissues of grapevine in different developmental stages, with two replicates each, comprising a total of 70 samples

first: Daniela

last: Pinto

first: Jayakumar

middle: B

last: Kullan

first: Edoardo

last: Bertolini

first: Marianna

last: Fasoli

first: Sara

last: Zenoni

first: Mario

last: Pezzotti

middle: C

first: Lorenzo

last: Farina

last: Pè

first: Erica

last: Mica


title: Insights into the proliferation and invasiveness of breast cancer from genome-wide profiling of estrogen receptor beta 2

city: Stockholm

first: Li

address: Hälsovägen 7-9

department: Biosciences and Nutrition

institute: Karolinska Institute

summary: The human ERβ variant, ERβ2, is expressed at higher levels than ERβ1 in many breast cancer cell lines and breast tumours and increasing evidence supports the hypothesis that ERβ2, in contrast to ERβ1, is associated with aggressive phenotypes of various cancers. We identified a breast cancer cell line that expresses endogenous ERβ2, but not ERα or ERβ1, allowing studies of ERβ2 in the absence of other ER isoforms. Importantly, we show that knockdown of endogenous ERβ2 inhibited cell proliferation and cell invasion. To  gain insights into the molecular mechanism responsible for these cellular phenotypes, we assayed ERβ2 dependent global gene expression profiles. A total of 263 genes were identified as potentially ERβ2-upregulated genes and 662 as ERβ2-downregulated genes. ERβ2-regulated genes were involved in cell morphology, DNA replication and repair, cell death and survival. Our findings demonstrate that ERβ2 alone has a key role in enhancing cell proliferation and invasion, beyond modulation of ERα and ERβ1 signalling.

overall_design: BT549 cells grown in antibiotic free medium were transfected with a control siRNA, siRNA targeting ERβ2, ERβ2 cDNA, empty vector control, and then global gene expression profiles were assessed. Three biological replicates were used for each group.

first: Chunyan

last: Zhao

first: Jan-Åke

last: Gustafsson

first: Karin

last: Dahlman-Wright


title: Gene Expression Signature in Adipose Tissue of Acromegaly Patients

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

institute: St. Jude Children's Research Hospital

summary:
OBJECTIVE: Acromegaly is a rare endocrine disorder with excess growth hormone (GH) production. This disorder has important metabolic effects in insulin resistance and lipolysis. The objective of this study was to explore transcriptional changes induced by GH in adipose tissue.
METHODS: The patients underwent clinical and metabolic profiling including assessment of HOMA-IR. Explants of adipose tissue were assayed ex-vivo for lipolysis and ceramide levels. Adipose tissue was analyzed by RNA sequencing (RNA-seq).
RESULTS: There was evidence of reduced insulin sensitivity based on the increase in fasting glucose, insulin and HOMA-IR score. We observed several previously reported transcriptional changes (IGF1, IGFBP3) as well as several novel transcriptional changes, some of which may be important for GH signal regulation (PTPN3 and PTPN4) and the effect of GH on growth and proliferation. Several transcripts could potentially be important in GH-induced metabolic changes. Specifically, induction of LPL, ABHD5, and ACVR1C could contribute to enhanced lipolysis and may explain the suggestive enhancement of adipose tissue lipolysis in acromegaly patients as reflected by glycerol release from the explants of the two groups of patients (p=0.09). Higher expression of SCD and TCF7L2 could contribute to insulin resistance. Expression of HSD11B1 was reduced and GR was increased, predicting modified glucocorticoid activity in acromegaly.
CONCLUSIONS: We identified the acromegaly gene expression signature in human adipose tissue. The significance of altered expression of specific transcripts will enhance our understanding of the metabolic and proliferative changes associated with acromegaly.

overall_design: DESIGN: Patients with acromegaly (n=9) or non-functioning pituitary adenoma (n=11) were prospectively observed from March 2011 to June 2012. Sequencing was performed on RNA from 7 acromegaly patients and 11 controls.

middle: T

first: Dave

last: Bridges


title: The role of SMCHD1 in the formation of constitutive heterochromatin

city: MONTPELLIER CEDEX 5

first: Jérôme

last: Déjardin

address: 141, rue de la Cardonille

institute: Institute of Human Genetics

summary: A large portion of the mammalian genome is assembled into constitutive heterochromatin which is highly compact and transcriptionally silent throughout the cell cycle. On the molecular level it is characterized by DNA methylation, “repressive” histone marks (hypoacethylation, H3K9 trimethylation, H4K20 trimethylation) and the presence of heterochromatin protein 1 (HP1). Regions of constitutive heterochromatin such as telomeres, pericentromeres and centromeres play a critical role in the maintenance of the genome integrity. Using a technique called Proteomics of Isolated Chromatin Segments (PICh) we have identified SMCHD1 as a novel component of telomeres and pericentomeres. SMCHD1 was previously shown to be involved in the inactivaction of the X chromosome and imprinting, but the its exact role in these processes is not understood. Our study aims to unravel the role of SMCHD1 in the formation and/or maintenance of constitutive chromatin. Using human cancer cells as research model we are trying to discover its mechanism of action by identifying its interacting partners, characterizing its genome wide binding sites and characterizing the effect of SMCHD1 knockout on the heterochromatin function.

overall_design: Characterization of SMCHD1 binding sites in HCT-116 cells.

first: Agnieszka

last: Nowak

first: Claudia

last: Armenise

first: Elodie

last: Rey


title: Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis [ChIP-seq]

status: Public on Apr 30 2015

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

country: United Kingdom

institute: School of Life Sciences, University of Dundee

summary: DNA methylation is tightly regulated throughout mammalian development and altered DNA methylation patterns are a general hallmark of cancer. The methylcytosine dioxygenase TET2 is frequently mutated in hematological disorders, including acute myeloid leukemia (AML), and has been suggested to protect CpG islands and promoters from aberrant DNA methylation. In this study, we present a novel Tet2-dependent leukemia mouse model that closely recapitulates gene expression profiles and hallmarks of human AML1-ETO induced AML. Using this model, we show that the primary effect of Tet2 loss in pre-leukemic hematopoietic cells is progressive and widespread DNA hypermethylation affecting up to 25% of active enhancer elements. In contrast, CpG island and promoter methylation does not change in a Tet2-dependent manner, but increase relative to population doublings. We confirm this specific enhancer hypermethylation phenotype in human AML patients with TET2 mutations. Analysis of immediate gene expression changes reveals rapid deregulation of a large number of genes implicated in tumorigenesis, including many downregulated tumor suppressor genes. Hence, we propose that TET2 prevents leukemic transformation by protecting enhancers from aberrant DNA methylation, and that it is the combined silencing of several tumor suppressor genes in TET2-mutated hematopoietic cells that contribute to increased stem cell proliferation and leukemogenesis.

overall_design: Chromatin immunoprecipitation and sequencing (ChIP-seq) of histone marks (H3K4me1, H3K4me3 and H3K27ac) in Tet2-WT and Tet2-KO in-vitro grown hematopoietic cells transduced with AML1-ETO.

first: Guangshuai

last: Jia

first: Jens

last: Johansen

first: Marianne

last: Pedersen

first: Nicolas

last: Rapin

first: Frederik

middle: O

last: Bagger

first: Bo

last: Porse

first: Olivier

last: Bernard

first: Jesper

last: Christensen

first: Kristian

last: Helin


title: Tet2-/-Flt3ITD and WT stem and progenitor cells

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: The study was a comparison of gene expression using RNA-seq. We analyzed the stem and progenitor cells from WT and Vav-cre+ Tet2fl/fl Flt3-ITD (T2F3) mice. We isolated stem cells LSK (lin- sca+ kit+) and granulocyte-macrophage progenitors GMP (lin- sca- kit+ fcgr+ cd34+) cells from bone marrow. Comparisons were made across genotypes WT vs. T2F3 and cell types LSK vs. GMP.

overall_design: Comparison of WT and Tet2-/-Flt3ITD bone marrow stem and progenitor cells.

first: Ross

last: Levine

first: Alan

last: Shin


title: Frequent and Transient Acquisition of Pluripotency During Somatic Cell Trans-Differentiation with iPSCs Reprogramming Factors (ATAC-Seq)

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Recent reports have proposed a new paradigm for obtaining mature somatic cell types from fibroblasts without going through a pluripotent state, by briefly expressing canonical iPSC reprogramming factors Oct4, Sox2, Klf4 and c-Myc (abbreviated as OSKM), in cells expanded in lineage differentiation promoting conditions. Here we apply genetic lineage tracing for endogenous Nanog, Oct4 and X chromosome reactivation during OSKM induced trans-differentiation, as these molecular events mark final stages for acquisition of induced pluripotency. Remarkably, the vast majority of reprogrammed cardiomyocytes or neural stem cells derived from mouse fibroblasts via OSKM mediated trans-differentiation were attained after transient acquisition of pluripotency, and followed by rapid differentiation. Our findings underscore a molecular and functional coupling between inducing pluripotency and obtaining “trans-differentiated” somatic cells via OSKM induction, and have implications on defining molecular trajectories assumed during different cell reprogramming methods.

overall_design: poly RNA-Seq and Chromatin accesibility (ATAC-seq) were measured during conversion of mouse embryonic fibroblasts to neural stem cells using OSKM trans-differentiation method, as well as in mouse emrbyonic fibroblasts, iPSCs and mouse ESCs.

first: Itay

last: Maza

first: Asaf

last: Zviran

first: Jacob

last: Hanna


title: Frequent and Transient Acquisition of Pluripotency During Somatic Cell Trans-Differentiation with iPSCs Reprogramming Factors (RNA-Seq)

overall_design: poly RNA-Seq was measured before, during and after conversion of mouse embryonic fibroblasts to neural stem cells using OSKM trans-differentiation method.


title: Sensing the end: how TUT7 controls the fate of precursor microRNAs by uridylation

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

summary: Terminal uridylyl transferases (TUTs) function as integral regulators of microRNA (miRNA) biogenesis by modifying the end structure of precursor miRNA (pre-miRNA). Using biochemistry and deep sequencing techniques, we here investigate the mechanism how human TUT7 recognizes and uridylates pre-miRNAs. We show that the overhang of a pre-miRNA is the key structural element that TUT7 and its paralogues, TUT4 and TUT2, recognize. For group II pre-miRNAs which have a 1 nt 3’ overhang, TUT7 restores the canonical end structure (2 nt 3’ overhang) by mono-uridylation, and thereby promotes miRNA biogenesis. Interestingly, once the 3’ end is receded into the stem (3’ trimmed pre-miRNAs such as Ago-cleaved-pre-miRNA), TUT7 effectively generates an oligo-U tail that consequently leads to degradation. Our single-molecule study further suggests that a distributive mode is employed for both pathways, but the overhang length determines the frequency of TUT7-RNA interaction. Our results explain how TUT7 and TUT4 differentiate pre-miRNA species and reveal a role for TUT7 and TUT4 in the oligo-uridylation and removal of defective pre-miRNAs.

overall_design: HeLa cells were knocked down of control or TUT2/4/7, then total RNAs were prepared for RNA-seq

first: Boseon

last: Kim

first: V

middle: N


title: Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

summary: The prostate gland mainly contains basal and luminal cells constructed as a pseudostratified epithelium. Annotation of prostate epithelial transcriptomes provides a foundation for discoveries that can impact disease understanding and treatment. Here, we describe a whole-genome transcriptome analysis of human benign prostatic basal and luminal populations by using deep RNA sequencing. Combined with comprehensive molecular and biological characterizations, we show that the differential gene expression profiles account for their distinct functional phenotypes. Strikingly, in contrast to luminal cells, basal cells preferentially express gene categories associated with stem cells, neural and neuronal development and RNA processing. Consistent with their expression profiles, basal cells functionally exhibit intrinsic stem-like and proneural properties with enhanced ribosome RNA (rRNA) transcription activity. Of clinical relevance, the treatment failed castration-resistant and anaplastic prostate cancers molecularly resemble a basal-like phenotype. Therefore, we link the cell-type specific gene signatures to subtypes of prostate cancer development, and identify genes associated with patient clinical outcome.

overall_design: Human total RNA profiles of 3 pairs of benign prostatic basal and luminal populations freshly purified from prostate tissues of three prostate cancer patients by deep RNA-seq.

first: Daechan

last: Park

first: Yue

last: Lu

first: Dean

last: Tang


title: Study the effect of SUZ12 on the responsiveness of IFNg target genes in multiple cancer and non cancer cell lines

city: Toronto

first: Rod

last: Bremner

address: 600 University Ave

institute: Mount Sinai Hospital

summary: We studied the effect of knocking down SUZ12 on the responsiveness of IFNg target genes

overall_design: 12 cell lines were transfected with siRNA against SUZ12 (siSUZ12) or siCtrl and left untreated or treated with IFNg for 6 hours

first: Mohamed

last: Abou El Hassan

first: Katherine

last: Huang

first: Yu

last: Liu


title: Degree of Recruitment of DOT1L to MLL-AF9 Defines Level of H3K79 Di- and Tri-methylation on Target Genes and Transformation Potential

city: Charlottesville

first: John

last: Bushweller

state: VA

address: 1340 Jefferson Park Avenue

department: Molecular Physiology and Biological Physics

institute: University of Virginia

summary: The MLL gene is a common target of chromosomal translocations found in human leukemia. MLL-fusion leukemias are consistently poor prognosis. One of the most common translocation partners is AF9 (a.k.a. MLLT3). MLL-AF9 recruits DOT1L, a histone 3 lysine 79 methyltransferase (H3K79me1/me2/me3), leading to aberrant gene transcription. We show that DOT1L has three AF9 binding sites, and present the NMR solution structure of a DOT1L-AF9 complex. We generated structure-guided point mutations with graded effects on recruitment of DOT1L to MLL-AF9. ChIP-Seq analyses of H3K79me2 and H3K79me3 show that graded reduction of the DOT1L interaction with MLL-AF9 results in selective losses in H3K79me2 and me3 marks at MLL-AF9 target genes. Furthermore, the degree of DOT1L recruitment defines the level of MLL-AF9 hematopoietic transformation.

overall_design: Hematopoietic progenitor cells isolated from mouse bone marrow were transduced with retrovirus expressing either wildtype MLL-AF9 (WT), mutants, MLL-AF9 (D544R) and MLL-AF9 (D546R). ChIP-Seq analyses were performed on these wildtype and mutant cells using H3K79me2 and H3K79me3 antibodies. 3 samples corresponding to ChIP-Seq with H3K79me2 antibody: 1) MLL-AF9 (WT) 2) MLL-AF9 (D544R) 3) MLL-AF9 (D546R)  3 Samples Corresponding to ChIP-Seq with H3K79me3 antibody: 4) MLL-AF9 (WT) 5) MLL-AF9 (D544R) 6) MLL-AF9 (D546R)

first: Aravinda

last: Kuntimaddi

first: Jeremy

last: Thorpe

first: Ritambhara

last: Singh

first: Mazhar

last: Adli


title: N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

city: Chicago

first: Guan-Zheng

last: Luo

address: 929 E 57th St

department: Chemistry

institute: UChicago

summary: N6-methyldeoxyadenosine (6mA or m6A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria, and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution, and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms.

overall_design: Multiple sequencing methods are developed to profile the distribution of 6mA in Chlamydomonas including MeDIP-Seq, enzyme-treated DNA-Seq, MNase-Seq and RNA-Seq.

first: Ye

last: Fu

first: Chuan

last: He


title: SaeRS-dependent inhibition of biofilm formation in Staphylococcus aureus Newman

city: Little Rock

first: Chia

middle: Y

last: Lee

state: AR

address: 4301 W. Markham St.

department: Microbiology and Immunology

institute: University of Arkansas for Medical Sciences

summary: The SaeRS two-component regulatory system of Staphylococcus aureus is known to affect the expression of many genes. The SaeS protein is the histidine kinase responsible for phosphorylation of the response regulator SaeR. In S. aureus Newman, the sae system is constitutively expressed due to a point mutation in saeS, relative to other S. aureus strains, which results in substitution of proline for leucine at amino acid 18. Strain Newman is unable to form a robust biofilm and we report here that the biofilm-deficient phenotype is due to the saeSP allele. Replacement of the Newman saeSP with saeSL, or deletion of saeRS, resulted in a biofilm-proficient phenotype. Newman culture supernatants were observed to inhibit biofilm formation by other S. aureus strains, but did not affect biofilm formation by S. epidermidis. Culture supernatants of Newman saeSL or Newman ΔsaeRS had no significant effect on biofilm formation. The inhibitory factor was inactivated by incubation with proteinase K, but survived heating, indicating that the inhibitory protein is heat-stable. The inhibitory protein was found to affect the attachment step in biofilm formation, but had no effect on preformed biofilms. Replacement of saeSL with saeSP in the biofilm-proficient S. aureus USA300 FPR3757 resulted in the loss of biofilm formation. Culture supernatants of USA300 FPR3757 saeSP, did not inhibit biofilm formation by other staphylococci, suggesting that the inhibitory factor is produced but not secreted in the mutant strain. A number of biochemical methods were utilized to isolate the inhibitory protein. Although a number of candidate proteins were identified, none were found to be the actual inhibitor. In an effort to reduce the number of potential inhibitory genes, RNA-Seq analyses were done with wild-type strain Newman and the saeSL and ΔsaeRS mutants. RNA-Seq results indicated that sae regulates many genes that may affect biofilm formation by Newman.

overall_design: use RNA seq to compare mRNAs in three Staphylococcus aureus strains with different saeS alleles

first: David

last: Cue


title: Transcriptional Landscape of B cell Early Activation

city: Boston

first: Trent

last: Fowler

state: MA

address: 150 Harrison Ave

department: Dept. of Devleopmental, Chemical, and Molecular Biology

institute: Tufts University

summary: The physiological responses to B cell receptors (BCR) and Toll-like receptors (TLRs) so vital to immunity are well known but the transcriptional signatures and regulatory mechanisms that initiate activation and release cells from quiescence remain unclear.  Here, we show that BCR- or TLR-mediated activation of B cells involves a large shared transcriptional signature and a smaller subset of distinct signal-specific transcriptional responses.  Signal-specific transcription is observable within 2 hours of ligand exposure; suggesting different modes of activation begin soon after ligand binding and long before the well-documented BCR and TLR-dependent physiological responses occur. Ligand-specific differences in regulatory mechanisms including RNA Pol II recruitment, activating (H3K4me3) and repressing (H3K27me3) histone marks, transcription factor binding sites in responsive gene promoters, and miRNA expression were observed. These results begin to define the transcriptional landscape of early B cell activation revealing more ligand-specific regulation and character than occurs much earlier than previously expected.

overall_design: CD43- mouse resting B cells were stimulated with ligands against the B cell receptor and TLR4 (LPS). RNA-sequencing was performed to describe differential transcription and ChIP-sequencing was performed to describe regulatory mechanism responses.

first: Ananda

last: Roy


title: Transcriptional response to aminoglycoside antibiotics in cochlear hair cells at 3 hour

city: Los Angeles

first: Litao

last: Tao

state: California

address: 1425 San Pablo St.

department: Stem Cell and Regenerative Medicine

institute: University of Southern California

summary: We purified Atoh1-GFP positive hair cells from organotypic cultures of P1 cochlea 3 hours after 0.5mM gentamicin treatment and performed RNA sequencing to profile the early transcriptional response of hair cells to aminoglycoside antibiotics.

overall_design: Levels of mRNA in gentamicin-treated hair cells (three replicates) were compared to untreated hair cells (three replicates). GFP negative, non-hair cells populations from treated organs were compared to those from untreated organs (three replicates for each condition).

first: Neil

last: Segil


title: Rapid acclimation of juvenile corals to CO2-mediated acidification by up-regulation of HSP and Bcl-2 genes

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

institute: The Australian National University

summary: We compared the effect of acute (Moya et al 2012)  and chronic exposure to elevated pCO2 on gene expression in primary polyps of Acropora millepora

overall_design: Examination of transcriptome in Acropora millepora primary polyps at 380 and 750 ppm CO2 (air) after 9 days exposure

first: Aurelie

last: Moya

first: Lotte

last: Huisman

first: Jean-Pierre

last: Gattuso

last: Hayward

first: Eldon

middle: E

last: Ball

middle: J

last: Miller


title: Spatiotemporal brassinosteroid signaling and antagonism with auxin control Arabidopsis root growth.

city: Stanford

first: Juthamas

last: Chaiwanon

state: CA

address: 260 Panama St.

department: Plant Biology

institute: Carnegie Institution

summary: Analysis of brassinosteroid (BR) and auxin effects on gene expression in Arabidopsis roots. Our genomic results indicate that BR and auxin induce largely opposite gene expression responses in primary roots.

overall_design: RNA-Seq for 7-day-old Arabidopsis Col-0, dwf4, bri1-116, and bri1-116;bzr1-1D roots grown on regular medium and treated with brassinolide, auxin or mock solution for 4 hr.

first: Zhiyong

last: Wang


title: The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells

status: Public on Apr 29 2015

first: Bernard

last: Khor

address: 185 Cambridge St MCPZN 7106

department: Pathology

institute: Massachusetts General Hospital

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

overall_design: Refer to individual Series


title: Frequent and Transient Acquisition of Pluripotency During Somatic Cell Trans-Differentiation with iPSCs Reprogramming Factors

first: Noa

last: Novershtern


title: Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development

city: Wenjiang,Chengdu

first: hongjun

last: liu

state: Sichuan

address: 211 Huimin Road

institute: Sichuan Agricultural University

summary: The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutants analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development.

overall_design: Seeds of the maize inbred line 18-599 (Maize Research Institute, Sichuan Agricultural University, Chengdu, China) were grown in a growth chamber at 24°C/18°C (day/night) with 12 h illumination per day. Ears were collected as described previously [10] at four developmental stages: the growth point elongation, spikelet differentiation, floret primordium differentiation, and the floret organ differentiation phases. In brief, ears were manually collected at the four developmental stages. All the samples were harvested and immediately frozen in liquid nitrogen, and stored at -80°C until used for RNA isolation.

first: Hongjun

last: Liu*

first: Xuerong

last: Yang*

first: Xinhui

last: liao*

first: Tao

last: Zuo

first: Cheng

last: Qin

first: Shiliang

last: Cao

first: Ling

last: Dong

first: Huangkai

last: Zhou

first: Yongzhong

last: Zhang

first: Sisi

last: Liu

first: Yaou

last: Shen

first: Haijian

last: Lin

first: Thomas

last: Lübberstedt

first: Zhiming

last: Zhang#

first: Guangtang

last: Pan#


title: LRP8-Reelin-regulated Neuronal (LRN) Enhancer signature underlying learning and memory formation (GRO-seq)

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

summary: A comprehensive landscape of epigenomic events regulated by the Reelin signaling through activation of specific cohort of cis-regulatory enhancer elements (LRN-enhancers), which involves the proteolytical processing of the LRP8 receptor by the gamma-secretase activity and is required for learning and memory behavior

overall_design: All GRO-Seq experiments were designed to understand the unique signature of LRN-enhancers and  to evaluate the transcriptional response to Reelin treatment in neuronal cells.

first: Francesca

last: Telese


title: The PRC2-associated factor C17orf96 is a novel CpG island regulator in mouse ES cells

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

summary:
CpG islands (CGIs) are key DNA regulatory elements in the vertebrate genome and are often found at gene promoters. In
mammalian embryonic stem (ES) cells, CGIs are decorated by either the active or repressive histone marks, H3K4me3 and
H3K27me3, respectively, or by both modifications (‘bivalent domains’), but their precise regulation is incompletely understood.
Remarkably, we find that the polycomb repressive complex 2 (PRC2)-associated protein C17orf96 (a.k.a. esPRC2p48 and
E130012A19Rik) is present at most CGIs in mouse ES cells. At PRC2-rich CGIs, loss of C17orf96 results in an increased
chromatin binding of Suz12 and elevated H3K27me3 levels concomitant with gene repression. In contrast, at PRC2-poor CGIs,
located at actively transcribed genes, C17orf96 colocalizes with RNA polymerase II and its depletion leads to a focusing of
H3K4me3 in the core of CGIs. Our findings thus identify C17orf96 as a novel context-dependent CGI regulator.

overall_design: ChIP-seq of C17orf96, H3K4me3 and H3K27me3 in mouse ES cells (E14).

first: Yang

last: Shi


title: LRP8-Reelin-regulated Neuronal (LRN) Enhancer signature underlying learning and memory formation (RNA-Seq 1)

overall_design: All RNA-Seq experiments were designed to evaluate the transcriptional program regulated by the Reelin-LRP8 signaling pathway in neuronal cells


title: LRP8-Reelin-regulated Neuronal (LRN) Enhancer signature underlying learning and memory formation (ChIP-Seq)

overall_design: All ChIP-Seq experiments were designed to understand the unique signature and function of LRN-enhancers in signaling pathways of learning and memory.


title: LRP8-Reelin-regulated Neuronal (LRN) Enhancer signature underlying learning and memory formation (4C-Seq)

overall_design: All 4C-Seq experiments were designed to evaluate the physycal interaction between selected Fos promoter and putative regulatory enhancers regions


title: LRP8-Reelin-regulated Neuronal (LRN) Enhancer signature underlying learning and memory formation


title: The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells [seq]

first: Bernard

last: Khor

summary: Using an unbiased chemical biology approach, we discover harmine as a novel regulator of Treg/Th17 differentiation. Harmine enhances Treg differentiation (working in conjunction with low levels of exogenous TGFb) and inhibits Th17 differentiation. Analysis of global gene expression of Tregs generated using low TGFb + harmine reveals significant similarity to Tregs generated using high TGFb only and suggests relevance of harmine-engaged mechanisms to IBD.

overall_design: Naïve murine CD4+CD62L+ T cells were stimulated with anti-CD3/28, transduced with control or Dyrk1a shRNA, and treated with harmine or control.

first: B

first: G

last: Goel

first: M

last: Schirmer

first: R

last: Xavier


title: Epigenetic regulation of Atrophin1 by lysine-specific demethylase 1 is required for cortical progenitor maintenance

city: Philadelphia

first: Feng

state: PA

address: 415 Curie Boulevard

department: Department of Neuroscience and Mahoney Institute for Neurosciences

institute: Perelman School for Medicine, University of Pennsylvania

summary: Lysine-specific demethylase 1 (LSD1) is involved in gene regulation and development; however, its precise function, molecular targets and underlying mechanisms during development are poorly understood. Here, we show that LSD1 is required for neuronal progenitor cell (NPC) maintenance during cortical development. A ChIP-seq analysis identified a LSD1 binding site (LBAL) downstream of Atrophin1 (ATN1). Surprisingly, tranylcypromine (LSD1 inhibitor) treatment increased H3K4 methylation at LBAL, leading to ATN1 repression and NPC differentiation. Knockdown of LSD1 and ATN1 phenocopied each other in inducing NPC premature differentiation and depletion which could be rescued by ATN1 overexpression, suggesting that LSD1 controls NPC differentiation via regulation of ATN1 methylation status and expression. The involvement of LSD1 in ATN1 expression and NPC maintenance were confirmed in knockout mice. These findings hint at the potential application for the clinical drug, tranylcypromine, in the prevention and/or treatment of ATN1-associated degenerative disease, dentatorubral-pallidoluysian atrophy.

overall_design: Examination of LSD1 binding sites in neuronal progenitor cells.

first: Zhiheng

last: Xu


title: RNA-seq profiling of transcriptomes of control and Hif1a mutant E12.5 hearts

city: Claremont

first: Alexander

last: Zambon

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

summary:
Purpose: to identify genes aberrantly expressed upon myocardial ablation of Hif1a
Methods: a floxed Hif1a allele was deleted in mouse embryonic hearts using a NXK2.5Cre line. Total RNA was extracted from E12.5 hearts (n=3 for controls and mutants) usinz Trizol and processed for RNA-seq. Reads were mapped to Mm10 reference genome using TopHat2 and Bowtie2. Transcript expression values were determined after transcript normalization with AltAnalyze
Results: this analysis revealed a total of 1451 genes significantely (|Fold| > 20% and P<0.05) modulated in Hif1a cKO hearts

overall_design: 6 total RNAseq runs with 3 experimental samples and 3 controls samples

first: Nuno

last: Guimarães-Camboa

last: Carlos Zambon


title: Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

city: La Jolla

first: Ferhat

last: Ay

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Background: DNA in the nucleus of a living cell carries out its functions in the context  of a complex, three-dimensional chromatin architecture. Several recently  developed methods, each an extension of the chromatin conformation capture (3C)  assay, have enabled the genome-wide profiling of chromatin contacts between  pairs of loci in yeast, fruit fly, human and mouse. Especially in complex  eukaryotes, data generated by these methods, coupled with other genome-wide  datasets, demonstrated that non-random chromatin folding correlates  strongly with cellular processes such as gene expression and DNA replication.  Here we describe a novel assay to map genome-wide chromatin contacts, tethered  multiple 3C (TM3C), that involves a simple protocol of restriction enzyme  digestion and religation of fragments upon agarose gel beads followed by deep  DNA paired-end sequencing. In addition to identifying contacts between pairs  of loci, TM3C enables identification of contacts among more than two loci  simultaneously.  Results: We use TM3C to assay the genome architectures of two human cell lines: KBM7,  a near-haploid chronic leukemia cell line, and NHEK, a normal diploid human  epidermal keratinocyte cell line. We confirm that the contact frequency maps  produced by TM3C exhibit features characteristic of existing genome architecture  datasets, including the expected scaling of contact probabilities with genomic  distance, as well as a low noise-to-signal ratio between inter- and  intrachromosomal contacts. We also confirm that TM3C captures several known  cell type-specific contacts, ploidy shifts and translocations, such as Ph+  formation in KBM7. Furthermore, we develop a two-phase mapping strategy that  separately maps chimeric subsequences within a single read, allowing us to  identify contacts involving three or four loci simultaneously, potentially  corresponding to combinatorial regulation events.  This mapping strategy also  greatly increases the number of distinct binary contacts identified and,  therefore, the coverage obtained for a fixed number of mapped reads. We  confirm a subset of the triplet contacts involving the IGF2-H19  imprinting control region (ICR) using PCR analysis for KBM7 cells.  Assaying the genome architecture of a near-haploid cell line allows us  to create 3D models of a human cell line without averaging  signal from two homologous copies of a chromosome.  Our 3D models of KBM7 show clustering of small  chromosomes with each other and large chromosomes with each other,  consistent with previous studies of the genome architectures of other  human cell lines.  Conclusion: TM3C is a simple protocol for ascertaining genome  architecture and can be used to identify simultaneous contacts among three  or four loci. Application of TM3C to a near-haploid human cell line  revealed large-scale features of chromosomal organization and  complex chromatin loops that may play a role in regulating reciprocal  expression of the IGF2 and H19 genes.

overall_design: Analysis of the spatial organization of two human cell lines (KBM7, a near-haploid chronic leukemia cell line, and NHEK, a normal diploid human epidermal keratinocyte cell line) using tethered multiple 3C (TM3C), a novel and simple protocol for ascertaining genome architecture which can be used to identify simultaneous contacts among three or four loci in addition to binary contacts that can be identified using traditional chromosome conformation capture coupled with next generation sequencing (Hi-C).

first: Thanh

last: Vu


title: ChIP-seq profiling of loci bound by HIF1a in wild-type E12.5 hearts

summary:
Purpose: to identify genes directly bound by HIF1a in cardiomycoytes
Methods: crosslinked chromatin isolated from E12.5 mouse hearts was precipitated using an anti-HIF1a antibody and processed for sequencing. A list of genes containing a HIF1a peak (Minimum score 3.5) was compared with RNA-seq results to identify genes that are bound by HIF1a and expressed in E12.5 hearts
Results: this analysis identified 1016 genes expressed and bound by HIF1a in embryonic hearts

overall_design: Two experimental replicates and one input


title: Growth signals employ CGGBP1 to suppress transcription of Alu-SINEs

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar


title: IL-33 activates tumor stroma to promote intestinal polyposis

city: Houston

first: Jason

last: Heaney

state: Texas

address: One Baylor Plaza, R810

department: Molecular & Human Genetics

institute: Baylor College of Medicine

summary: Tumor epithelial cells develop within a microenvironment consisting of extracellular matrix, growth factors, and cytokines produced by non-epithelial stromal cells. In response to paracrine signals from tumor epithelia, stromal cells modify the microenvironment to promote tumor growth and metastasis. Here, we identify interleukin (IL)-33 as an epithelial cell-derived regulator of stromal cell activation and mediator of intestinal polyposis. IL-33 expression was elevated in the tumors and serum of colorectal cancer patients and induced in the adenomatous polyps of ApcMin/+ mutant mice. Genetic and antibody suppression of IL-33 signaling in ApcMin/+ mice inhibited proliferation, induced apoptosis, and suppressed angiogenesis in polyps, which reduced both tumor number and size. In ApcMin/+ polyps, IL-33 expression localized to tumor epithelial cells and expression of the IL-33 receptor, IL1RL1, associated with two stromal cell types, namely subepithelial myofibroblasts (SEMFs) and mast cells, whose activation was previously associated with polyposis. In vitro IL-33 stimulation of human SEMFs induced the expression of extracellular matrix components and growth factors associated with intestinal tumor progression. IL-33 deficiency reduced mast cell accumulation in ApcMin/+ polyps and expression of mast cell-derived proteases and cytokines known to promote polyposis. Together, our results suggest that IL-33 is a tumor epithelial cell-derived paracrine signal that promotes polyposis through the coordinated activation of stromal cells and the formation of a reactive stroma microenvironment.

overall_design: Six T-75 flasks of CCD-18Co cells were grown to 80% confluency; three were treated with rhIL-33, three were given vehicle control; cells were trypsinized and split in two--half of each flask used for sequencing and half for qPCR validation post-sequencing

first: Rebecca

last: Maywald

first: Stephanie

middle: K

last: Doerner

first: Luca

last: Pastorelli

first: Carlo

last: de Salvo

first: Susan

middle: M

last: Benton

first: Emily

last: Dawson

first: Denise

middle: G

last: Lanza

first: Nathan

middle: A

last: Berger

first: Sanford

middle: D

last: Markowitz

first: Heinz

last: Lenz

first: Joseph

last: Nadeau

first: Theresa

last: Pizzaro


title: Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures

status: Public on Apr 28 2015

city: Bolpur

first: Jolly

last: Basak

state: West Bengal

address: Santiniketan

department: Biotechnology

institute: Visva-Bharati, Siksha Bhavana

summary: MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99% probability range derived from the available data. We have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80% sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20. There is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets.

overall_design: Small RNA sequencing was done for 10 days old seedlings of Phaseolus vulgaris  Cv. Anupam

first: Chandran

last: Nithin

first: Nisha

last: Patwa

first: Amal

last: Thomas

first: Ranjit

last: Bahdur


title: Transcriptomic analysis of the mouse mammary gland reveals new insights for the role of serotonin in lactation

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Serotonin in the mammary gland is known to regulate processes such as calcium homeostasis, tight junction permeability, and milk protein gene expression. The objective of this study was to discover novel genes, pathways and functions which serotonin modulates during lactation. The rate-limiting enzyme in the synthesis of non-neuronal serotonin is tryptophan-hydroxylase (TPH1). Therefore, we used TPH1 knock-out mice dams (serotonin deficient) and compared them to wild-type dams and also Tph1 deficient dams injected daily with 5-HTP. Mammary gland tissues were collected on day 10 of lactation and then analyzed by RNA sequencing.

overall_design: Genome-wide gene expression profiles of 12 mouse mammary gland samples were evaluated using RNA sequencing; these 12 samples belong to wild-type dams (WT; n = 4), Tryptophan hydroxylase (Tph1) knock-out dams (KO; Tph1 deficient; n = 4), and Tph1 deficient dams injected daily with 5-HTP (RC; n = 4). Mammary tissues were collected on day 10 of lactation and then underwent RNA extraction, library generation, and subsequent sequencing.

first: Jimena

last: Laporta

first: Laura

middle: L

last: Hernandez


title: RNAi of TbNMD3 in procyclic form Trypanosoma brucei lines

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary: A procyclic form Trypansome brucei RNAi line (PTT parental line, transfected with pALC14 incorporating a TbNMD3 gene fragment) capable of inducing depletion of TbNMD3 was analysed for mRNA expression by RNAseq

overall_design: Cells were grown for 72 hours in culture; RNAi was induced in cells by the addition of 1 microgram/ml of tetracycline

first: Keith

last: Matthews

first: Melanie

last: Buhlmann


title: Screening of a novel strong promoter by RNA sequencing and its application to H2 production in a hyperthermophilic archaeon

city: Ansan-si

first: Min-Sik

last: Kim

state: Gyeonggi-do

address: Haean-ro

department: Department of Marine Biotechnology

institute: Korea Institute of Ocean Science and Technology

summary: A strong promoter increases transcription of the genes of interest and enhances the production of various valuable substances. For a hyperthermophilic archaeon Thermococcus onnurineus NA1, which can produce H2 by carbon monoxide oxidation, we searched for a novel endogenous strong promoter by transcriptome analysis using high-throughput RNA sequencing. Based on the relative transcript abundance, we selected one promoter to encode a hypothetical gene, of which homologs were found only in several Thermococcales strains. This promoter, PTN0510, was introduced into the front of CO-responsible hydrogenase gene cluster encoding a carbon monoxide dehydrogenase (CODH), a hydrogenase and a Na+/H+ antiporter. In the resulting mutant strain, KS0510, transcription and translation level of the gene cluster increased by 4- to 14-folds and 1.5- to 1.9-folds, respectively, in comparison with those of wild-type strain. Additionally, H2 production rate of KS0510 mutant was 4.8-fold higher than that of wild-type strain. The PTN0510 was identified to be much stronger than the well-known two strong promoters, gdh and slp promoters from Thermococcus strains, through RT-qPCR and western blotting analyses and kinetics of H2 production. In this study, we demonstrated that the RNA-seq approach is a good strategy to mine a novel strong promoter of use to a Thermococcus strain when developed as a biotechnologically promising strain to produce valuable metabolites through a metabolic engineering.

overall_design: RNA expreesion profile of T. onnurineus NA1 genes in CO-containing media, in duplicate, using Illumina HiSeq 2500

first: Seong

middle: H

last: Lee

first: Hae

last: Jung

first: Jinwon

first: Jung-Hyun

first: Hyun

middle: S

first: Sung

last: Kang


title: Analysis of genome wide H3K9me3 levels in control and ORCA knockdown cells

city: Urbana

first: Supriya

last: Prasanth

state: IL

address: 601 S. Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois, Urbana-Champaign

summary: Origin Recognition Complex Associated (ORCA) associates with repressive chromatin environments. We carried out H3K9me3 ChIP-seq to determine the affect of ORCA's loss on this repressive mark. Towards this end, we cultured U2OS osteosarcoma cells, performed control and ORCA knockdowns using siRNAs and then carried out H3K9me3 ChIP-seq to determine the regions in the genome which get affected upon ORCA knockdown.

overall_design: Examination of the levels of H3K9me3 in control and ORCA knockdown cells

first: Sumanprava

last: Giri

first: S

first: Julien

last: Pontis

first: Slimane

last: Ait-Si-Ali


title: Effects of Trbp deletion on gene expession in mice hearts

status: Public on Apr 27 2015

city: Boston

first: Da-Zhi

last: Wang

address: 300 Longwood Ave.

department: Cardiology

institute: Boston Children's Hospital

summary: We generated the cardiac-specific knockout of Trbp (Trbp-cKO) in mice. We profiled the transcriptome in both wild-type and Trbp-cKO hearts, and found numerous genes were deregulated by deletion of Trbp. We also profiled miRNA expression both wild-type and Trbp-cKO hearts, and found expression of a subset of miRNA species was altered in Trbp-cKO hearts.

overall_design: Examine expression of mRNAs and miRNAs in wild-type and Trbp-cKO hearts

first: Jian

last: Ding

first: Yanqun


title: s54 -dependent response to nitrogen limitation and virulence in Burkholderia cenocepacia H111

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

summary: Members of the genus Burkholderia are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen Burkholderia cenocepacia H111 to nitrogen limitation at the transcript and protein expression level. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins and the two component regulatory system ntrBC, B. cenocepacia H111 also up-regulated polyhydroxybutyrate (PHB) accumulation and exopolysaccharide (EPS) production in response to nitrogen shortage. A search for consensus sequences in promoter regions of nitrogen responsive genes identified a s54 consensus sequence. The mapping of the s54 regulon as well as the characterization of a s54 mutant suggests an important role of s54 not only in control of nitrogen metabolism, but also in virulence of this organism.

overall_design: Nitrogen limitation and s54 regulon in B. cenocepacia

first: Martina

last: Lardi

first: Claudio

last: Aguilar

first: Alessandro

last: Pedrioli

first: Angela

last: Suppiger

first: Gerardo

last: Cárcamo-Oyarce

first: Nadine

last: Schmid

first: Ulrich

last: Omasits

first: Christian

last: Ahrens

first: Leo

last: Eberl


title: Effects of SO2 on yeast metabolism and changes in the transcriptional profiles

city: Legnaro (PD)

first: Chiara

last: Nadai

address: Viale dell'Università, 16

department: DAFNAE

institute: University of Padova

summary: Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of a vineyard yeast strain collected from the vineyards of the Piave AO (Appellation of origin) (R008 strains) region in North East of Italy and 3 commercial yeast strains (EC1118, VL3 and AWRI796). Yeast cells were collected at the same step of the fermentation curve: at the beginning of the process, when the CO2 produced by the cells was 6 g/l (middle exponential growth phase). The fermentations have been performed for each strain with no SO2 added and with SO2 added at a final concentration of 25 mg/l. Three biological replicates of the fermentations were performed for each strain and samples for RNA-seq were gathered at the beginning of the process. The aim of this experiment was the comparison of the transcriptomes of the four yeast strains to identify the genes characterizing sulphites response.

overall_design: Eight samples were analyzed: R008 strain at middle exponential growth phase (6 g/l CO2 produced) with no SO2 added (previously submitted with ID GSM1092510, experiment GSE44845),  R008 strain at middle exponential growth phase (6 g/l CO2 produced) with 25mg/l of SO2 added, EC1118 strain at middle exponential growth phase (6 g/l CO2 produced) with no SO2 added (previously submitted with ID GSM1092506, experiment GSE44845), EC1118 strain at middle exponential growth phase (6 g/l CO2 produced) with 25mg/l of SO2 added, VL3 strain at middle exponential growth phase (6 g/l CO2 produced) with no SO2 added, VL3 strain at middle exponential growth phase (6 g/l CO2 produced) with 25mg/l of SO2 added, AWRI796 strain at middle exponential growth phase (6 g/l CO2 produced) with no SO2 added, AWRI796 strain at middle exponential growth phase (6 g/l CO2 produced) with 25mg/l of SO2 added.

first: Stefano

last: Campanaro

first: Viviana

last: Corich

first: Alessio

last: Giacomini

first: Laura

last: Treu

first: Michela

last: D'Angelo


title: Innate lymphoid cell development requires TOX-dependent generation of a common ILC  progenitor

city: Los Angeles

first: Wolf

last: Wiedemeyer

address: 8700 Beverly Blvd.

department: BMS

institute: Cedars-Sinai

summary: Subtypes of innate lymphoid cells (ILC), defined by effector function and transcription factor  expression, have recently been identified. In the adult, ILC derive from common lymphoid  progenitors in bone marrow, although transcriptional regulation of the developmental  pathways involved remains poorly defined. TOX is required for development of lymphoid  tissue inducer cells, a type of ILC3 required for lymph node organogenesis, and NK cells, a  type of ILC1. We show here that production of multiple ILC lineages requires TOX, as a result  of TOX-dependent development of common ILC progenitors. Comparative transcriptome  analysis demonstrated failure to induce various aspects of the ILC gene program in the  absence of TOX, implicating this nuclear factor as a key early determinant of ILC lineage  specification.

overall_design: TOX KO vs. wild tyype

first: Corey

last: Seehus

first: Parinaz

last: Aliahmad

first: Brian

last: de la Torre

first: Iliyan

last: Iliev

first: Lindsay

last: Spurka

first: Vincent

last: Funari

first: Jonathan

last: Kaye


title: Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

summary:
Background: Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). These ncRNAs are functionally important in the genome, however, the identification and annotation of ncRNAs in a genome is challenging. The aim of this study was to identify different types of small ncRNAs particularly piRNAs, and the role of piRNA pathway genes in the protection of chicken primordial germ cells (PGCs).
Results: At first, we performed next-generation sequencing to identify ncRNAs in chicken PGCs, and we performed ab initio predictive analysis to identify putative piRNAs in PGCs. Then, we examined the expression of three repetitive sequence-linked piRNAs and 14 genic-transcript-linked piRNAs along with their linked genes using real-time PCR. All piRNAs and their linked genes were highly expressed in PGCs. Subsequently, we knocked down two known piRNA pathway genes of chicken, PIWI-like protein 1 (CIWI) and 2 (CILI), in PGCs using siRNAs. After knockdown of CIWI and CILI, we examined their effects on the expression of six putative piRNA-linked genes and DNA double-strand breakage in PGCs. The knockdown of CIWI and CILI upregulated chicken repetitive 1 (CR1) element and RAP2B, a member of RAS oncogene family, and increased DNA double-strand breakage in PGCs.
Conclusions: Our results increase the understanding of PGC-expressed ncRNAs and the role of piRNA pathway genes in the protection of germ cells.

overall_design: Small ncRNA expression profiling in SSEA-1 positive PGCs, SSEA-1 negative gonadal stromal cells (GSCs), Stage X blastoderms, and chicken embryonic fibroblast (CEFs)

first: Deivendran

last: Rengaraj

first: Sang

middle: I

last: Lee

first: Jae

last: Han


title: Genome-wide binding sites of Progesterone receptor (PGR) isoforms PGR-A and PGR-B during differentiation of human endometrial stromal cells

first: Milan

last: Bagchi

address: 407 S. Goodwin Ave

department: MIP

institute: UIUC

summary: We report the genome-wide binding sites of PGR-A and PGR-B at 2h of in vitro differentiation of human endometrial stromal cells that express either PGR-A or PGR-B. Progesterone, acting through the progesterone receptors (PGRs), is one of the most critical regulators of endometrial differentiation, known as decidualization, which is a key step toward the establishment of pregnancy. Yet a long-standing unresolved issue in uterine biology is the precise roles played by the major PGR isoforms, PGR-A and PGR-B, during decidualization in the human. Our approach, expressing PGR-A and PGR-B individually after silencing endogenous PGRs in human endometrial stromal cells (HESC), enabled the analysis of the roles of these isoforms separately as well as jointly by ChIP-seq and gene-expression analysis.

overall_design: In order to study the cistromes of PGR-A and PGR-B at 2h of in vitro differentiation of human endometrial stromal cells, we generated primary cultures of human endometrial stromal cells expressing flag tagged PGR-A and PGR-B individually after silencing endogenous PGRs. Input DNA was used as the reference sample.

first: Hatice

last: Kaya

first: Indrani