title: Deep profiling of the novel intermediate-size noncoding RNAs in intraerythrocytic Plasmodium falciparum

first: Chunyan

last: Wei

address: 5# Dong Dan San Tiao

department: Department of Microbiology and Parasitology

institute: Institute of Basic Medical Sciences, CAMS & School of Basic Medicine, PUMC

summary: Intermediate-size noncoding RNAs (is-ncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. However, they have not been thoroughly explored in Plasmodium falciparum, which is the most virulent malaria parasite infecting human being. By using Illumina/Solexa paired-end sequencing of an is-ncRNA-specific library, we performed a systematic identification of novel is-ncRNAs in intraerythrocytic P. falciparum, strain 3D7. A total of 1,198 novel is-ncRNA candidates, including antisense, intergenic, and intronic is-ncRNAs, were identified. Bioinformatics analyses showed that the intergenic is-ncRNAs were the least conserved among different Plasmodium species, and antisense is-ncRNAs were more conserved than their sense counterparts. Twenty-two novel snoRNAs were identified, and eight potential novel classes of P. falciparum is-ncRNAs were revealed by clustering analysis. The expression of randomly selected novel is-ncRNAs was confirmed by RT-PCR and northern blotting assays. An obvious different expressional profile of the novel is-ncRNA between the early and late intraerythrocytic developmental stages of the parasite was observed. The expression levels of the antisense RNAs correlated with those of their cis-encoded sense RNA counterparts, suggesting that these is-ncRNAs are involved in the regulation of gene expression of the parasite. In conclusion, we accomplished a deep profiling analysis of novel is-ncRNAs in P. falciparum, analysed the conservation and structural features of these novel is-ncRNAs, and revealed their differential expression patterns during the development of the parasite. These findings provide important information.

overall_design: One RNA sample (50-500 nt ) from the mixed intraerythrocytic stage of P. falciparum 3D7, subjected to Illumina/Solexa paired-end sequencing

first: Tengfei

last: Xiao

first: Peng

last: Zhang

first: Zhensheng

last: Wang

first: Xiaowei

first: Lianhui

first: Meixue

last: Yao

first: Runsheng

first: Heng


title: Genome-wide analysis of RXRa binding in mouse liver chromatin with ChIP-SEQ.

status: Public on Apr 01 2014

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

country: USA

institute: Texas A&M University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: For the genome-wide analysis using ChIP-Seq on mouse liver cells, a full accounting of all RXRÎ± binding sites and of RXRa related gene regulations is expected to address the main knowledge gap around RXRÎ±.

overall_design: Liver tissue of wild type and hs-RXRa-del-exon4-/- mice, male and female for each genotype have been ChIP-Seq'ed for RXRa and Pol2.

first: Deqiang

last: Sun


title: Meiotic recombination cold spots in chromosomal cohesion sites

status: Public on Mar 31 2014

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

country: Japan

institute: Osaka University

type: Genome binding/occupancy profiling by genome tiling array

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

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Refer to individual Series


title: Transcriptomics analysis of the Bordetella holmesii response to human serum exposure

status: Public on Mar 28 2014

city: Baltimore

first: Kent

last: Shefchek

state: Maryland

address: 801 West Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

type: Expression profiling by high throughput sequencing

summary: We performed RNA-Seq transcriptomics analyses of the Bordetella holmesii type strain ATCC 51541T under in vitro growth conditions that mimic exposure to the human bloodstream. We sequenced 3 biological replicates of each of the following conditions of exposure to heat-inactivated human serum: 5% serum, 0.5% serum, and a no serum control.

overall_design: RNA-Seq was performed on the Bordetella holmesii type strain ATCC 51541T grown under three conditions: 5% heat-inactivated human serum, 0.5% heat-inactivated human serum, and a no serum control.

first: Hervé

last: Tettelin

first: Thomas

middle: A

last: Hooven

first: Xuechu

last: Zhao

first: Ryan

last: Rampersaud

first: Sean

middle: C

last: Daugherty

first: Naomi

last: Sengamalay

first: Luke

middle: J

last: Tallon

first: Lisa

last: Sadzewicz

first: Claire

middle: M

last: Fraser

first: Adam

last: Ratner


title: Transient expression of Bcl6 is sufficient for oncogenic function and induction of mature B-cell lymphoma

first: Michael

middle: R

last: Green

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

type: Methylation profiling by high throughput sequencing

summary: Reduced representation bisulfite sequencing (RRBS) of hematopoeitic stem/progenitor cells and mature B-cells from wild-type mice and mice transiently expressing Bcl6 under control of the Sca1 promoter.

overall_design: CBAxC57BL/6J mice were engineered to transiently express a Bcl6 cDNA in hematopoeitic stem/progenitor cells under control of the Sca1 promoter and then delete the transgene by cre-mediated recombination upon expression of Cd79a (Sca1-BCL6Δ). Hematopoeitic stem/progentior cells (HSPC, Sca1+Lin-) from the bone marrow and mature B-cells (B220+) from the peripheral blood were isolated from these mice and wild-type CBAxC57BL/6J mice by fluorescence activated cell sorting. Cells from 6-9 mice were pooled, for a total of 4 experimental conditions. DNA was extracted for each condition and analyzed by reduced representation bisulfite sequencing.

first: Ash

last: Alizadeh

first: Isidro

last: Sanchez-Garcia


title: BAF155 methylation at R1064 creates unique chromatin association patterns

city: madison

first: Lu

last: Wang

state: wisconsin

address: 1400 university ave

department: Oncology

institute: UW madison

summary: CARM1, a coactivator for various cancer-relevant transcription factors, is overexpressed in breast cancer. To elucidate the functions of CARM1 in tumorigenesis, we knocked out CARM1 from several breast cancer cell lines using Zinc-Finger Nuclease technology, which resulted in drastic phenotypic and biochemical changes. The CARM1 KO cell lines enabled identification of novel CARM1 substrates, notably the SWI/SNF core subunit BAF155. Methylation of BAF155 at R1064 was found to be an independent prognostic biomarker for cancer recurrence and to regulate breast cancer cell migration and metastasis. Further, CARM1-mediated BAF155 methylation affects gene expression by directing methylated BAF155 to unique chromatin regions (e.g., c-Myc pathway genes). Collectively our studies uncover a mechanism by which BAF155 acquires tumorigenic functions via arginine methylation.

overall_design: Examination of methylation of BAF155 (R1064) in breast cancer cells

first: Mark

last: Meyer

first: J

middle: W

last: Pike

first: Wei

last: Xu


title: Ribosomal footprinting and RNASeq in two strains of yeast and their diploid hybrid

city: Los Angeles

first: Frank

middle: Wolfgang

last: Albert

state: CA

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: UCLA

summary: Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we addressed this question by using ribosomal footprinting to examine how genetic differences between two strains of the yeast S. cerevisiae affect translation. Strain differences in translation were observed for hundreds of genes, more than half as many as showed genetic differences in mRNA levels. Similarly, allele specific measurements in the diploid hybrid between the two strains found roughly half as many cis-acting effects on translation as were observed for mRNA levels. In both the parents and the hybrid, strong effects on translation were rare, such that the direction of an mRNA difference was typically reflected in a concordant footprint difference. The relative importance of cis and trans acting variation on footprint levels was similar to that for mRNA levels. Across all expressed genes, there was a tendency for translation to more often reinforce than buffer mRNA differences, resulting in footprint differences with greater magnitudes than the mRNA differences. Finally, we catalogued instances of premature translation termination in the two yeast strains. Overall, genetic variation clearly influences translation, but primarily does so by subtly modulating differences in mRNA levels. Translation does not appear to create strong discrepancies between genetic influences on mRNA and protein levels.

overall_design: Ribsosomal footprinting and RNASeq in the two yeast strains BY and RM as well as their diploid hybrid. We generated one library each for the BY and RM parents, and two libraries (biological replicates) for the hybrid data.

first: Dale

last: Muzzey

first: Jonathan

last: Weissman

first: Leonid

last: Kruglyak


title: Matrine derivative 1b(MASM) offers radioprotection and modulates acute lethal total-body irradiation-induced alterations of gene expression

city: ShangHai

first: Jian-Zhong

last: Li

address: Guo He Road 325#

country: China

institute: Second Military Medical University

summary:
To further investigate the potential molecular basis of the protective effects of MASM on irradiation (6.5Gy)  damage, gene expression analysis was conducted on rats liver tissues using microarrays. Pre-treatment with MASM prevented differential expression of 53% (766 genes) of 1445 genes differentially expressed in response to radiation.
Pathway enrichment analysis indicated that these genes were mainly involved in a total of 21 pathways, such as metabolic pathways, pathways in cancer, and MAPK signaling pathway.

overall_design: The rats were randomly assigned to one of the three following treatment groups (10-12 animals per group): normal control, radiation and MASM dose (30 mg/kg body weight/day) + radiation. MASM dissolved in double distilled water were administered intragastrically to the male animals for 3 consecutive days before irradiation. Radiation induced gene expression in rat liver was measured at 24 hours after 6.5 Gy exposure.

first: Jian

middle: Z


title: Expression profiling by high throughput sequencing

city: Yokohama

first: Yasutaka

last: Motomura

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: Innate immune cells control acute eosinophilic lung inflammation induced by cystein proteases. Here we characterize the dynamic change of gene expression profile in basophils, natural helper cells and eosinophils during lung inflammation via cystein protease

overall_design: Examination of mRNA levels in individual cell populations, basophils, natural helper cells and eosinophils of the lung from naïve mice and papain treated mice.

first: Masato

last: Kubo


title: The age and genomic integrity of neurons after cortical stroke in humans

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

summary: It has been unclear whether ischemic stroke induces neurogenesis or neuronal DNA-rearrangements in the human neocortex. We show here that neither is the case, using immunohistochemistry, transcriptome-, genome- and ploidy-analyses, and determination of nuclear bomb test-derived 14C-concentration in neuronal DNA. A large proportion of cortical neurons display DNA-fragmentation and DNA-repair short time after stroke, whereas neurons at chronic stages after stroke show DNA-integrity, demonstrating the relevance of an intact genome for survival.

overall_design: Analyze of potential fusion transcripts in 13 samples, seven cortical ischemic stroke tissue and six control cortex, by deep sequencing using Illumina HiSeq 2000

first: Hagen

middle: B

last: Huttner

first: Olaf

last: Bergmann

first: Mehran

last: Salehpour

first: Attila

last: Rácz

first: Jemal

last: Tatarishvili

first: Emma

last: Lindgren

first: Tamás

last: Csonka

first: László

last: Csiba

first: Tibor

last: Hortobágyi

first: Gábor

last: Méhes

first: Elisabet

last: Englund

first: Beata

last: Solnestam

first: Sofia

last: Zdunek

first: Christian

last: Scharenberg

first: Lena

last: Ström

first: Patrik

last: Ståhl

first: Benjamin

last: Sigurgeirsson

first: Andreas

last: Dahl

first: Stefan

last: Schwab

first: Göran

last: Possnert

first: Samuel

last: Bernard

first: Zaal

last: Kokaia

first: Olle

last: Lindvall

first: Jonas

last: Frisén


title: Genome-wide analysis of liver in male and female mice

first: deqiang

last: sun


title: A role for H3K4 mono-methylation in facultative heterochromatin assembly and partitioning of chromatin readers

status: Public on Mar 29 2014

city: New York

first: Roy

last: Blum

state: NY

address: 552 First Ave

department: Cancer Institute

institute: New York University

summary: Mono-methylation of lysine 4 on histone H3 (H3K4me1) is a well-established feature of enhancers and promoters, although its function is unknown. Remarkably, we find H3K4me1 at the promoter regions of conditionaly-repressed muscle and stimulus-dependent inflammatory response genes in myoblasts. During myogenesis, muscle genes are activated and become H3K4-trimethylated. On the promoters of active genes, we find that H3K4me1 spatially restricts the recruitment of “readers” of H3K4me3, including ING1, which, in turn, recruits Sin3A. Our findings point to a unique role for H3K4 mono-methylation in establishing boundaries that restrict the recruitment of chromatin-modifying enzymes to defined regions within promoters.

overall_design: Mapping of Wdr5, Menin, MLL1, Sin3A, and LSD1 in growing myoblasts (MB) and ING1 in growing myoblasts (MB) and fully differentiated myotubes (MT).

first: Jemmie

last: Cheng

first: Brian

middle: D

last: Dynlacht


title: Transcriptome analysis of mouse embryonic stem cells treated with MS-275

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: This study describes transcriptome profiling of mouse ES cells treated with MS-275. We included RNA-Seq of ds_cDNA synthesized from double poly(A) selected mRNA

overall_design: RNA-Seq profiling on mouse ES cells treated with MS-275

first: Gianluigi

last: Franci

first: Hendrik

middle: G

first: Lucia

last: Altucci

first: Roberta

last: Menafra


title: Hydroxymethylation at gene regulatory regions directs stem cell commitment during erythropoiesis

city: Chicago

first: Jozef

last: Madzo

state: Illinois

address: 900 E 57th Street, KCBD

department: Medicine Hem/Onc.

institute: The University of Chicago

summary: CD34 positive hematopoietic stem cells were differentiated into erythroid lineage. Next generation sequencing (NGS) of 5hmC affinity pulldown and RNAseq were performed in four time point of different stages of erythroid differentiation.

overall_design: 4 RNA-Seq Samples (d0, d3, d7 and d10); 4 affinity-pulldown  (d0, d3, d7 and d10), and 4 input samples  (d0, d3, d7 and d10).

first: Hui

last: Liu

first: Alex

last: Rodriguez

first: Aparna

last: Vasanthakumar

first: Sriram

last: Sundaravel

first: Donne

last: Caces

first: Tim

last: Looney

first: Li

last: Zhang

first: Janet

last: Lepore

first: Alan

middle: H

last: Shih

first: Chun-Xiao

last: Song

first: Yiting

last: Yu

first: Robert

last: Grossman

first: Brigitte

last: Raumann

first: Amit

middle: K

last: Verma

first: Chuan

last: He

first: Ross

middle: L

last: Levine

first: Don

last: Lavelle

first: Bruce

middle: T

last: Lahn

first: Amittha

last: Wickrema

first: Lucy

last: Godley


title: Genome-wide maps of HIF1a binding sites in ccRCC cell line under hypoxia condition

status: Public on Mar 27 2014

city: Beijing

first: Jing

address: 1130 St Nicholas Ave ICRC, room403

institute: Columbia University Medical Center

summary: We report the application of chromatin immunoprecipitation and next generation sequencing technology for  HIF1a binding sites at genome wide level  in a RCC (renal cell carcinoma) cell line under hypoxia conditions. We found HIF1a binding sites in Caki-2 cell line under hypoxia conditions. Especially, we found HIF1a bind to SPOP under hypoxia condition, which was further validated.

overall_design: Examination of HIF1a binding sites in Caki-2 cell line under hypoxia condition

first: Guoqiang

last: Li


title: RNA-seq of Tumor Initiating Cells (TICs) from Lung Squamous Cell Carcinoma (LSCC) lines reveals PRKCI dependent Hedgehog (HH) Signalling

city: Jacksonville

first: Michael

middle: Patrick

last: Walsh

state: Florida

address: 4500 San Pablo Road

department: Cancer Basic Science

institute: Mayo Clinic Jacksonville

summary: RNA-seq analysis was performed on TICs and the parental counterparts of 4 LSCC cell lines. In addition, PRKCI knock down (KD) variants of these cells were sequenced. Subsequent analysis revealed that activation of HH signaling, a known driver of the TIC phenotype, is dependent on PRKCI expression.

overall_design: Examination of TICS, parental cells, parental PRKCI KD cells, and TIC PRKCI KD cells

middle: P

last: Fields

first: Verline

last: Justilein

first: E

last: Thompson


title: High-resolution analysis of gene activity during the Xenopus mid-blastula transition

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

country: United Kingdom

institute: University of Exeter Medical School

summary: The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilization wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the 7th cleavage and extending beyond the MBT at the 12th cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal genes whose mRNAs are deadenylated shortly after fertilization, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organization of gene regulatory networks in the early

overall_design: Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization

first: Clara

last: Collart

first: Leena

last: Bhaw-Rosun

first: Brook

last: Cooper

first: Elena

last: De Domenico

first: Ilya

last: Patrushev

first: Abdul

last: Sesay

first: James

middle: N

last: Smith

last: Gilchrist


title: The Menin–Bach2 axis is critical for regulating CD4 T cell senescence and homeostasis

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

summary: Although CD4 T cell senescence plays an important role in immunosenescence, the mechanisms remain unclear.  We found that T cell-specific Menin deficiency results in the premature senescence of CD4 T cells, accompanied by the senescence-associated secretory phenotype (SASP) after antigenic stimulation.  TH1 and TH2 differentiation was dysregulated in Menin-knockout CD4 T cells.  Bach2, which regulates SASP and TH differentiation, was identified as a Menin target.  Menin binds to the Bach2 locus, and controls its expression through maintenance of histone acetylation.  These findings reveal a critical role of the Menin-Bach2 pathway in regulating CD4 T cell senescence and homeostasis, thus indicating the involvement of this pathway in the inhibition of age-associated development of inflammatory diseases, which are induced by immunosenescence.

overall_design: Examination of transcriptional factor Menin binding and histone modefications in Menin WT and KO CD4 T cells

first: Makoto

last: Kuwahara

first: Masakatsu

last: Yamashita


title: Gene expression analysis of hair cell regeneration in the zebrafish lateral line

status: Public on Mar 26 2014

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However, non-mammalian animals (e.g. birds, amphibian and fish) regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates, we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA-Seq analyses on regenerating support cells purified by fluorescence activated cell sorting (FACS). The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration, because these cells can be acutely killed by exposure to neomycin, after which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. Tg(sqET20) larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 days post fertilization (dpf) Tg(sqET20) larvae at 1, 3 and 5 hours post neomycin treatment, as well as from a non-treated control.

overall_design: Transgenic zebrafish Tg(sqET20) larvae at 5 days post fertilization were exposed to neomycin, dissociated, and FACS sorted into GFP positive and GFP negative populations at 1, 3, and 5 hours following treatment, along with a mock treated 1 hr control. The experiment was performed in triplicate, for a total of 24 samples.

first: Linjia

last: Jiang

first: Andres

last: Romero-Carvajal

first: Jeff

middle: S

last: Haug

first: Christopher

first: Tatjana

last: Piotrowski


title: The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans

first: Huan

last: Yang

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA interference (RNAi) is a potent mechanism for down-regulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary siRNAs. Exogenous double stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition.  The RDE-10/RDE-11 complex and the RNA dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis.  However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear if the sub-cellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved FG domain containing DEAD-box helicase, localizes in P-granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA targeted mRNA in distinct cytoplasmic compartments.

overall_design: Examination of exogenous dsRNA trigger derived siRNA in wildtype and rde-12 mutant animals

first: Jim

last: Vallandingham

first: H

last: Mak


title: Induced Cdx2 binding in embryonic stem cells and endodermal cells

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary:
Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across multiple experiments for binding event discovery.  We demonstrate that our framework enables the simultaneous modeling of sparse condition-specific binding changes, sequence dependence, and replicate-specific noise sources. MultiGPS encourages consistency in reported binding event locations across multiple-condition ChIP-seq datasets and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS’s multi-experiment modeling approach thus provides a reliable platform for detecting differential binding enrichment across experimental conditions.
We demonstrate the advantages of MultiGPS with an analysis of Cdx2 binding in three distinct developmental contexts. By accurately characterizing condition-specific Cdx2 binding, MultiGPS enables novel insight into the mechanistic basis of Cdx2 site selectivity. Specifically, the condition-specific Cdx2 sites characterized by MultiGPS are highly associated with pre-existing genomic context, suggesting that such sites are pre-determined by cell-specific regulatory architecture. However, MultiGPS-defined condition-independent sites are not predicted by pre-existing regulatory signals, suggesting that Cdx2 can bind to a subset of locations regardless of genomic environment.

overall_design: In this study, we characterize the binding of Cdx2 in embryonic stem cells, endodermal cells, and progenitor motor neurons using V5- or FLAG-tagged doxycycline inducible Cdx2 ESC lines (iCdx2). Endoderm and progenitor motor neurons are generated from the ES cells using directed differentiation approaches. The cells are then exposed to Dox to express the tagged Cdx2 construct. The genome-wide binding of the induced full-length Cdx2 transcription factor is profiled using ChIP-seq with an anti-V5 or anti-FLAG antibody. We also examine the binding behavior of a truncated version of the Cdx2 protein, where a protein interaction domain contained in the first 59 amino acids has been deleted. An appropriate pseudo-IP control experiment for these ChIP-seq experiments has been previously submitted under accession number GSM766062.

first: Esteban

middle: O

last: Mazzoni

first: Richard

middle: I

last: Sherwood

first: Carolyn

middle: A

last: Morrison

first: David

last: Gifford

first: Hynek

last: Wichterle


title: The IclR-family regulator BapR controls biofilms formation in B. cenocepacia H111

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

summary: In Burkholderia cenocepacia H111, the large surface protein BapA plays a crucial role in the formation of highly structured communities, known as biofilms. We have recently demonstrated that Quorum sensing (QS) is necessary for the maximal expression of bapA. In this study we identify a protein from the IclR family of transcriptional regulators that, in conjunction with QS, controls biofilm formation by affecting the expression of bapA. We present evidence that, in addition to BapA,  BapR influences the expression of extracellular protease, swimming motility and has a profound impact in the abundance of persister cells, making this regulator an interesting target for persister and biofilm eradication.

overall_design: Identification of a new regulator BapR controlling biofilm formation

first: Claudio

last: Aguilar

first: Nadine

last: Schmid

first: Martina

last: Lardi

first: Leo

last: Eberl


title: Transcriptomic analysis of WT and larp1 mutant 21 days old seedling at 20°C or following a heat stress (15 min at 38°C)

city: Perpignan

first: Jean-Marc

last: Deragon

address: 58 avenue Paul Alduy

department: Biology

country: France

institute: Université de Perpignan, CNRS

summary: We report the identification of a heat-stress mediated mRNA decay in arabidopsis that is mediated by the XRN4 exonuclease and LARP1 RNA-binding protein.

overall_design: mRNA population in WT and larp1 mutant at 20°C or 15 min at 38°C

first: Cécile

last: Bousquet-Antonelli


title: CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity

status: Public on Mar 25 2014

city: Frederick

first: Scott

last: Durum

state: MD

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

summary: DNA methylation patterns are established in early embryogenesis and are critical for cellular differentiation. To investigate the role of CG methylation in potential enhancer formation, we assessed H3K4me1 modification in murine embryonic fibroblasts (MEFs) derived from the DNA methylation mutant Lsh(-/-) mice. We report here de novo formation of putative enhancer elements at CG hypomethylated sites that can be dynamically altered. We found a subset of differentially enriched H3K4me1 regions clustered at neuronal lineage genes and overlapping with known cis-regulatory elements present in brain tissue. Reprogramming of Lsh(-/-) MEFs into induced pluripotent stem (iPS) cells leads to increased neuronal lineage gene expression of premarked genes and enhanced differentiation potential of Lsh(-/-) iPS cells toward the neuronal lineage pathway compared with WT iPS cells in vitro and in vivo. The state of CG hypomethylation and H3K4me1 enrichment is partially maintained in Lsh(-/-) iPS cells. The acquisition of H3K27ac and activity of subcloned fragments in an enhancer reporter assay indicate functional activity of several of de novo H3K4me1-marked sequences. Our results suggest a functional link of H3K4me1 enrichment at CG hypomethylated sites, enhancer formation, and cellular plasticity.

overall_design:
[ChIP-Seq] Genome-wide maps of H3K4me1 in Lsh WT and KO primary MEFs.
We report here differentiated enrichment of H3K4me1 at Lsh WT and KO mouse embryonic fibroblasts (MEFs). We found a subset of differentially enriched H3K4me1 regions in Lsh KO MEFs, and they clustered at neuronal lineage genes and overlapping with known cis-regulatory elements present in brain tissue. Reprogramming of Lsh-/- MEFs into induced pluripotent stem (iPS) cells leads to increased neuronal lineage gene expression of premarked genes and enhanced differentiation potential of Lsh-/- iPS cells toward the neuronal lineage pathway compared with WT iPS cells in vitro and in vivo. The state of H3K4me1 enrichment is partially maintained in Lsh-/- iPS cells, suggesting the regions are preserved as potential enhancers.

[MethylC-Seq] MethylC-Seq from Mus musculus primary MEFs.
Whole-genome single-base resolution methylcytosine map reveals profound changes that occur after Lsh deletion during embryonic development in primary WT and Lsh-/- MEFs. Lsh deletion leads to widespread decreases of CG methylation level at uniquely mapped genomic regions compared to wild type, including TSSs at protein-coding genes, and non-coding RNA genes.

first: Weishi

last: Yu

first: Carl

last: McIntosh

first: Ryan

last: Lister

first: Iris

last: Zhu

first: Yixing

last: Han

first: Jianke

last: Ren

last: Landsman

first: Eunice

last: Lee

first: Victorino

last: Briones

first: Minoru

last: Terashima

first: Robert

last: Leighty

first: Joseph

middle: R

last: Ecker

first: Kathrin

last: Muegge


title: Distinctive Profile of IsomiR Expression and Novel MicroRNAs in Rat Heart Left Ventricle

city: Belfast

first: Anthony

last: Collins

state: NI

address: Clinical Sciences, Block A, Grosvenor Rd.

department: Centre for Experimental Medicine

institute: Queen's University Belfast

summary: MicroRNAs (miRNAs) are single-stranded non-coding RNAs that negatively regulate target gene expression through mRNA cleavage or translational repression. There is mounting evidence that they play critical roles in heart disease. The expression of known miRNAs in the heart has been studied at length by microarray and quantitative PCR but it is becoming evident that microRNA isoforms (isomiRs) are potentially physiologically important. It is well known that left ventricular (patho)physiology is influenced by transmural heterogeneity of cardiomyocyte phenotype, and this likely reflects underlying heterogeneity of gene expression. Given the significant role of miRNAs in regulating gene expression, knowledge of how the miRNA profile varies across the ventricular wall will be crucial to better understand the mechanisms governing transmural physiological heterogeneity. To determinine miRNA/isomiR expression profiles in the rat heart we investigated tissue from different locations across the left ventricular wall using deep sequencing. We detected significant quantities of 145 known rat miRNAs and 68 potential novel orthologs of known miRNAs, in mature, mature* and isomiR formation. Many isomiRs were detected at a higher frequency than their canonical sequence in miRBase and have different predicted targets. The most common miR-133a isomiR was more effective at targeting a construct containing a sequence from the gelsolin gene than was canonical miR-133a, as determined by dual-fluorescence assay. We identified a novel rat miR-1 homolog from a second miR-1 gene; and a novel rat miRNA similar to miR-676. We also cloned and sequenced the rat miR-486 gene which is not in miRBase (v18). Signalling pathways predicted to be targeted by the most highly detected miRNAs include Ubiquitin-mediated Proteolysis, Mitogen-Activated Protein Kinase, Regulation of Actin Cytoskeleton, Wnt signalling, Calcium Signalling, Gap junctions and Arrhythmogenic Right Ventricular Cardiomyopathy. Most miRNAs are not expressed in a gradient across the ventricular wall, with exceptions including miR-10b, miR-21, miR-99b and miR-486.

overall_design: The hearts of 3 male 8 month old Sprague-Dawley rats were rapidly extracted after euthanasia with sodium pentobarbital. A section of the free wall of the left ventricle was dissected into epicardium, mid-myocardium and endocardium by cutting approximately 1 mm from the epicardial and endocardial surfaces. Small RNA was extracted (miRNeasy Kit; Qiagen, Crawley UK), quantified (Nanodrop; Thermo Scientific) and quality assessed for degradation (RNA Nano Chip, Bioanalyser 2100; Aligent Technologies, Wokingham UK; only samples with a RNA integrity no. (RIN) ≥8 were carried forward) and retention of small RNA (Small RNA Chip, Bioanalyser 2100).  Small RNA was preferentially ligated with adapters, reverse transcribed into cDNA and amplified with 9 individually tagged primer indices (TruSeq Small RNA Sample Preparation Kit; Illumina, Little Chesterford, UK) and a library of small RNA created for each sample. After gel purification the cDNA products were again analysed on the bioanalyser using a High Sensitivity DNA Chip and assessed for the presence and concentration of the peak corresponding to ligated and tagged miRNA (approximately 147nt). Only samples with suitable RIN values exhibiting good retention of small RNA species were used for library preparation. After pooling, the samples were sequenced by TrinSeq (Trinity Genome Sequencing Lab & Neuropsychiatric Genetics Group, Trinity College Dublin, Ireland (http://www.medicine.tcd.ie/sequencing); using TruSeq SR Cluster Kit v5 (Illumina) and the resultant data trimmed and aligned to miRBase v18 (CLC Genomics Workbench v4.0; CLC bio, Swansea UK).

first: Mary

last: McGahon

first: Janet

middle: M

last: Yarham

first: Aideen

last: Daly

first: Jasenka

last: Guduric-Fuchs

first: Lyndsey

middle: J

last: Ferguson

first: David

last: Simpson


title: Gene expression profiling of the ileum following vertical sleeve gastrectomy compared to pair-fed sham surgery controls in mice with high-fat diet-induced obesity.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We report the expression profiles of ileal samples extracted from obese male C57Bl6 mice following vertical sleeve gastrectomy or sham surgery, focusing of gene signatures indicative of altered bile acid metabolism.

overall_design: We induced obesity in male C57bl6 mice through a high-fat diet.  At 8 weeks, they were submitted to either a vertical sleeve gastrectomy (VSG) or a sham surgery; following surgery VSG mice were fed ad libitum while sham controls were pair-fed (SPF) to the experimental animals.  During the four perioperative days, mice were fed a liquid Osmolite diet. Approximately 8 weeks after surgery mice were fasted overnight and gavaged with .5mL Osmolite; after one hour mice were sacrificed and the terminal ileum were extracted.   RNA was extracted, quantified, and compared between VSG and SPF experimental groups.

first: Rohit

last: Kohli


title: NELF-dependent transcription activation

city: Cleveland

first: Julian

last: Wong

address: 10900 Euclid Ave

department: Molecular Biology & Microbiology

institute: Case Western Reserve University

summary: Jurkat T-cells were latently infected with a defective HIV provirus carrying a GFP reporer gene.  The cells were superinfected with a lentiviral vector expressing shRNA to NELF-E.  The impact of NELF-depletion on RNAP II distribution on cellular genes and the HIV provirus was measured by ChIP-Seq. Data sets contained between 45 and 56 million mapped reads

overall_design: Four samples were compared: Control shRNA, NELF-E shRNA, Control shRNA plus TNF-a, NELF-E shRNA plus TNF-a.

first: Jonathan

last: Karn


title: A new look at adenovirus splicing

city: Melbourne

first: MAOSHAN

last: CHEN

state: Victoria

address: La Trobe University, Bundoora

department: Department of Biochemistry and Genetics

country: Australia

institute: La Trobe University

summary: Adenovirus type 2 RNA splicing sites were mapped by using deep cDNA sequencing. The majority of the previously identified splice sites were detected. In addition, novel splicing sites were identified

overall_design: Total RNA obtained from four time stages of human primary lung fibroblast cells IMR-90 infected by adenovirus type 2 compared to the control mock-infected by adenovirus type 2.

first: Hongxing

last: Zhao

first: Maoshan

last: Chen

first: Ulf

last: Pettersson


title: Escape from X chromosome inactivation occurs within topologically associated domains

city: Chapel Hill

first: Joshua

middle: W

last: Mugford

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: The University of North Carolina at Chapel Hill

summary: The spatial proximity between regulatory elements and their target genes has a profound affect on gene expression. X Chromosome Inactivation (XCI) is an epigenetic process by which an entire chromosome is rendered, for the most part, transcriptionally silent. A few genes are known to escape XCI and the mechanism for this escape remains unclear. Here, using mouse trophectodermal stem cells, we address whether specific chromosomal interactions facilitate escape from XCI by bringing escape-specific regulatory elements in close proximity to gene promoters. Our results suggest a model where escape from XCI occurs within topologically associated domains. As such, escaping genes and the regulatory sequences required for their escape are likely located within close linear proximity to each other. The datasets provided include those generated from allele-specific 4C-Seq of genes escaping XCI, genes subject to XCI, and non-genic regions of the X chromosome. FASTQ files, text files containing genomic coordiantes, and BED aligmnets are provided. All sequences were mapped relative to mouse genome build mm9.

overall_design: Deep sequencing of circular chromosome conformation capture (4C-Seq) of genes escaping X inactivation in mouse trophoblast stem cells

last: Starmer

first: Rex

last: Williams

first: J

last: Calabrese

first: Piotr

last: Mieczkowski

first: Della

last: Yee

first: Terry

last: Magnuson


title: RNA-seq in Oryzias latipes at stage 24

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

summary: Sequencing of the total RNA of whole embryos of medaka at developmental stage 24.

overall_design: 2 Samples, 60 embryos per sample, were sequenced using Illumina HiSeq 2000.

first: Cristina

last: González-Aguilera

first: Ana

last: Fernández-Miñán

first: Helena

last: Parra-Acero

first: Jaime

last: Carvajal

first: Jochen

last: Wittbrodt

first: José

last: Gómez-Skarmeta

last: Martínez-Morales


title: Diatom transcriptomics under nitrate limitation

city: Seattle

first: E. Virginia

last: Armbrust

state: WA

department: School of Oceanography

institute: University of Washington

summary: Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling.

sample_organism:
Thalassiosira pseudonana
Pseudo-nitzschia multiseries
Fragilariopsis cylindrus

overall_design: Transcriptomes were collected for diatom cultures harvested at the onset of stationary phase in low nitrate media (55 μM NaNO3, 212 μM Na2SiO3, 72.4 μM NaH2PO4), or at the onset of stationary phase in low silicic acid media (1764 μM NaNO3, 53 μM Na2SiO3, 72.4 μM NaH2PO4), or during mid-exponential growth in nutrient-replete media (882 μM NaNO3, 106 μM Na2SiO3, 36.2 μM NaH2PO4) in artificial seawater, maintaining three biological replicates per condition and per diatom (N=27). The SOLiD sequencer (version 4) was used to generate the transcriptomes and the SEAStAR software package was used to process the SOLiD reads and to calculate gene counts. Pooled counts for each nutrient-limited treatment were normalized to pooled counts for the nutrient-replete “control” treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor.

first: Sara

last: Bender

first: Colleen

last: Durkin

first: Chris

last: Berthiaume

first: Rhonda

last: Morales

first: E

middle: V


title: Whole genome methylation profiling in developing and developed Zebrafish

city: Bethesda

first: David

last: McGaughey

address: 10 Center Dr

department: NEI

institute: NIH

summary: DNA methylation is a dynamic process through which specific chromatin modifications can be stably transmitted from parent to daughter cells. A large body of work has suggested that DNA methylation influences gene expression by silencing gene promoters. However, these conclusions were drawn from data focused mostly on promoter regions.  With regards to the entire genome, it is unclear how methylation and gene transcription patterns are related during vertebrate development. To identify the genome-wide distribution of CpG methylation we created series of high-resolution methylome maps of Danio rerio embryos during development and in mature, differentiated tissues. We find that embryonic and terminal tissues have unique methylation signatures in CpG islands and repetitive sequences. Fully differentiated tissues have increased CpG and LTR methylation and decreased SINE methylation relative to embryonic tissues. Unsupervised clustering analyses reveal that the embryonic and terminal tissues can be classified solely by their methylation patterning. Novel analyses also identify a previously undescribed genome-wide exon methylation signature. We also compared whole genome methylation with genome-wide mRNA expression levels using publicly available RNA-seq datasets. These comparisons revealed previously unrecognized relationships between gene-expression, alternative splicing and exon methylation. Surprisingly, we find that exonic methylation is a better predictor of mRNA expression level than promoter methylation. We also found that transcriptionally skipped exons have significantly less methylation than retained exons. Our integrative analyses reveal highly complex interplay between gene expression, alternative splicing, development, and methylation patterning in zebrafish.

overall_design:
MBD-Seq with whole embryos (sperm, 1cell, mbt, 3dpf) and adult tissues (eye, brain, heart, liver)

Please note that the mePoor brain lane4 sample raw data files were used as loading/sequencing controls for the following meRich.lane4 samples;
eye_meRich.lane4
heart_meRich.lane4
liver_meRich.lane4
The mePoor brain lane5 sample raw data files were used as loading/sequencing controls for the following meRich.lane5 samples;
1cell_meRich.lane5
mbt_meRich.lane5
sperm_meRich.lane5

first: Lawrence

middle: C

last: Brody


title: Spontaneous tumor regression is driven by Wnt/Retinoic Acid signaling cross-talk

status: Public on Mar 24 2014

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

summary: We have identified by RNA sequencing the molecular signaling pathways that are involved in skin tumor regression and that fail to happen in malignant not regressing skin tumors .

overall_design: mRNA profile from Keratoacanthoma tumors at 0 and 1 week post DMBA treatment was generated in duplicate for each timepoint analyzed

first: Giovanni

last: Zito

first: Ichinko

last: Saotome

first: Zongzhi

last: Liu

first: Enrico

middle: G

last: Ferro

first: Thomas

middle: Y

last: Sun

first: Don

last: Nguyen

first: Kaya

last: Bilguvar

first: Christine

last: Ko

first: Valentina

last: Greco


title: H3K27ac and H3K4me3 ChIP-seq in Oryzias latipes

first: Juan

last: Tena

summary: Here we analyze key epigenetic marks from medaka (O. latipes) during the vertebrate phylotypic period (stage 24).

overall_design: Chromatin immuno-precipitation with histone 3 lysine 27 acetylation and histone 3 lysine 4 trimethylation antibodies.

first: Cristina

last: González-Aguilera

first: Ana

last: Fernández-Miñán

first: Helena

last: Parra-Acero

first: Jaime

last: Carvajal

first: Jochen

last: Wittbrodt

first: José

middle: L

last: Gómez-Skarmeta

last: Martínez-Morales


title: Transcriptome analysis reveals differential splicing events in IPF lung tissue

city: Stanford

first: Tracy

last: Nance

address: 300 Pasteur Dr

institute: Stanford University

summary:
Objectives: Idiopathic pulmonary fibrosis (IPF) is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of genome-wide transcription through RNA sequencing (RNA-Seq) enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments.
Methods: Messenger RNA extracted from 8 IPF lung samples and 7 healthy controls was sequenced on an Illumina HiSeq. Analysis of differential expression and exon usage was performed using Bioconductor packages. The gene periostin was selected for validation of alternative splicing by quantitative PCR, and pathway analysis was performed to determine enrichment for differentially expressed and spliced genes.
Results: There were 873 genes differentially expressed in IPF (FDR 5%), and 440 unique genes had significant differential splicing events (FDR 5%). In particular, cassette exon 21 of the gene periostin was significantly more likely to be spliced out in IPF samples (adj pval = 2.06e-09), and this result was confirmed by qPCR (Wilcoxon pval = 3.11e-4). We also found that genes close to SNPs in the discovery set of a recent IPF GWAS were enriched for genes differentially expressed in our data, including genes like mucin5B and desmoplakin which have been previously associated with IPF.
Conclusions: There is significant differential splicing and expression in IPF lung samples as compared with healthy controls. We found a strong signal of differential cassette exon usage in periostin, an extracellular matrix protein whose increased gene-level expression has been associated with IPF and its clinical progression, but for which differential splicing has not been studied in the context of IPF. Our results suggest that alternative splicing of periostin and other genes may be involved in the pathogenesis of IPF.

overall_design: mRNA sequencing of 8 IPF and 7 control lung tissue samples.

first: Kevin

last: Smith

first: Vanessa

last: Anaya

first: Rhea

last: Richardson

first: Lawrence

last: Ho

first: Mauro

last: Pala

first: Sara

last: Mostafavi

first: Alexis

last: Battle

first: Carol

last: Feghali-Bostwick

first: Glenn

last: Rosen

first: Stephen

last: Montgomery


title: RNA-seq in whole mouse embryos at stage E10.5

first: Juan

last: Tena

summary: An increasing number of studies, including mutant expression profiling and comparative transcriptomic analyses, require reference RNA-seq data collections in mice. Particularly, to complement previous profiling data sets based on arrays, a full RNA-seq developmental series will be required for whole embryos. E10.5 is a key reference stage as it represents the early organogenesis stage. Here, we have performed high-throughput sequencing of total RNA form whole mice embryos at embryonic stage E10.5.

overall_design: Sequencing of the total RNA of whole embryos of mouse at embryonic stage E10.5.

first: Cristina

last: González-Aguilera

last: Fernández-Miñán

first: Joe

last: Cross


title: Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin

city: Vienna

first: Daria

last: Shlyueva

address: Dr. Bohr-gasse,7

country: Austria

institute: IMP

summary: Steroid hormones act as important developmental switches and their nuclear receptors regulate many genes. However, few hormone-dependent enhancers have been characterized and important aspects of their sequence architecture, cell type-specific activating and repressing functions, or the regulatory roles of their chromatin structure have remained unclear. We used STARR-seq, a recently developed enhancer-screening assay, and ecdysone signaling in two different Drosophila cell types to derive the first genome-wide hormone-dependent enhancer activity maps. We demonstrate that enhancer activation depends on cis-regulatory motif combinations that differ between cell types and can predict cell type-specific ecdysone targeting. Activated enhancers are often not accessible prior to induction. Enhancer repression following hormone treatment is independent of receptor motifs and receptor binding to the enhancer as we show using ChIP-seq, but appears to rely on motifs for other factors, including Eip74. Our strategy is applicable to study signal-dependent enhancers for different pathways and across organisms.

overall_design: STARR-seq was performed in S2 and OSC cells treated with ecdysone in two replicates. DHS-seq before and after treatment was done with single-end sequencing in two replicates. RNA-seq (with and without ecdysone) was performed with a strand-specific protocol using single-end sequencing in two replicates in S2. ChIP-seq (with and without ecdysone) was performed single-end sequencing in two replicates in S2 cells.

first: Christoph

last: Stelzer

first: Daniel

last: Gerlach

first: Jorge

last: Yáñez-Cuna

first: Martina

last: Rath

first: Lukasz

last: Boryń

first: Cosmas

middle: D

last: Arnold

first: Alexander

last: Stark


title: Characterization and comparison of lactating mouse and bovine mammary gland miRNomes

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

institute: INRA

summary:
Background: The mammary gland is a dynamic organ that undergoes important physiological changes during reproductive cycles. Until now, data regarding the characterisation of miRNA in the mammary gland have been scarce and mainly focused on their abnormal expression in breast cancer. Our goal was to characterise the microRNA (miRNA) involved in mechanisms regulating the mammary function, with particular focus on the lactation stage
Methodology/principal findings: Using high-throughput sequencing technology, an exhaustive repertoire of miRNA (miRNome) expressed in mouse and bovine mammary glands during established lactation was identified, characterised and compared. Furthermore, in order to obtain more information on miRNA loading in the RNA-induced silencing complex (RISC), the miRNome was compared with that obtained from RNA associated with the AGO2 protein (AGO2-miRNome) in mouse lactating mammary gland. This study enabled the identification of 164 and 167 miRNA in mouse and bovine, respectively. Among the 30 miRNA most highly expressed in each species, 24 were common to both species and six of them tended to be more highly expressed in lactating than in non-lactating mammary gland. The potential functional roles of these 24 miRNA were deduced using DIANA-miRPath software, based on miRNA/mRNA interactions. Moreover, seven putative novel miRNA were identified. Using DAVID analysis, it was concluded that the predicted targets of two of these putative novel miRNA are involved in mammary gland morphogenesis.
Conclusion/significance: Our study provides an overview of the characteristics of lactating mouse and bovine mammary gland miRNA expression profiles. Moreover, species-conserved miRNA involved in this fundamental biological function were identified. These miRNomes will new be used as references for further studies during which the impact of animal breeding on the miRNA expression will be analysed.

sample_organism:
Bos taurus
Mus musculus

platform_organism:
Bos taurus
Mus musculus

overall_design: microRNA profiles of mammary glands from 2 FVB/N mice at lactation day-12 and mammary biopsies from 4 Holstein dairy cows at mid-lactation, generated by deep sequencing, using Illumina HiSeq 2000.

first: Sandrine

last: Le Guillou

first: Denis

last: Laloë

first: Johann

last: Laubier

first: Lenha

last: Mobuchon

first: Christine

last: Leroux

first: Fabienne

last: Le Provost


title: FIREWACh: High-throughput Functional Detection of Transcriptional Regulatory Modules in Mammalian Cells

status: Public on Mar 22 2014

city: New York

first: Matthew

last: Murtha

address: 550 First Ave

department: Microbiology

institute: NYU School of Medicine

summary: We report a new method called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), a high-throughput functional assay for directly identifying active promoter and enhancer elements. FIREWACh simultaneously assessed over 80,000 DNA fragments derived from “nucleosome-free regions” within embryonic stem cell (ESC) chromatin to identify 6,364 new active regulatory elements.  Many FIREWACh DNAs represent newly discovered ESC-specific enhancers and their analyses identified enriched binding site motifs for ESC transcription factors including SOX2, POU5f1 (OCT4), and KLF4. Thus FIREWACh identifies endogenous regulators of gene expression and can be used for the discovery of key cell-specific transcription factors. The application of FIREWACh to additional cultured cell types will facilitate functional annotation of the genome and expand our view of transcriptional network dynamics.

overall_design: Nucleosome free DNA (i.e. "open chromatin") is isolated enzymatically from cross-linked nuclei of cells (e.g. mouse embryonic stem cells, mESC) and cloned upstream of a minimal promoter driving GFP within a lentivral reporter construct. Virus is made from a pooled library of these plasmids, and used to transfect the target cell (mESC). GFP positive cells contain active NFRs and can be sorted by FACS. The loci of the NFR is determined using high throughput sequencing and mapping.

first: Lisa

last: Dailey


title: Genetic differences underlying chromatin discordance between monozygotic twins [FAIR-seq]

city: Choongchung-Buk-do

first: Hyo-Jeong

last: Ban

address: OHTAC, Yeonje-ree 643, Osong-eup, Chungwon-Koon

department: bioinformatics

country: South Korea

institute: KCDC

summary: Open chromatin is implicated in regulatory processes, and thus variation in chromatin structure may contribute to variation in gene expression and other molecular phenotypes. In this work, we performed a targeted deep sequencing to identify somatic mutations and genetic polymorphisms underlying accessible chromatin in the genomes of 72 monozygotic twins.

overall_design: Open chromatin sequencing based on FAIRE assay for 36 pairs of monozygotic twins

first: Kwoneel

last: Kim


title: H3K27me3 ChIP-seq in DNMT triple knock-out mESCs

city: Basel

first: Philip

middle: Martin

last: Jermann

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

summary: We immunoprecipitated formaldehyde crosslinked chromatin from DNMT triple knockout cells using an antibody against methylated lysine 27 on histone H3. Subsequent high-throughput sequencing allowed us to study the genome-wide distribution of this histone mark in the absence of DNA methylation.

overall_design: Examination of a histone modification in mESCs lacking DNA methylation.

first: Lukas

last: Burger

first: Dirk

last: Schübeler


title: Identification of dysregulated genes after deletion of miR-1-1 and miR-1-2

city: New York City

first: Yong

last: Zhao

address: 1470 Madison Ave

department: Mindich Child Health and Development Institute

institute: Icahn School of Medicine at Mount Sinai

summary: Purpose: The goals of this study are to identify dysregulated mRNAs in the heart after deletion of miR-1-1 and miR-1-2.  Methods: Total RNAs were extracted from hearts at embryonic E15.5 (E15.5) or postnatal 2.5 days (P2.5) of miR-1s dHET and miR-1s dKO mice. mRNAs were purified using a poly-A selection approach and sequenced using Illumina HiSeq 2000. The sequence reads were aligned to the mouse reference genome (NCBI Build 37/mm9) using TopHat program (Bowtie algorithm). Transcript assembles and identification of differentially expressed genes were achieved using Cufflinks package. To account for expression bias due to transcript length, each sample transcript expression was normalized by using cufflinks algorithm with a FDR of 0.05.  Results: Using 1.5-fold change as a cutoff, 997 and 653 transcripts were found to be upregulated and downregulated, respectively, in miR-1s dKO heart at P2.5. 423 transcripts were found to be upregulated and 653 were down-regulated in miR-1s dKO heart at E15.5. Many upregulated genes are directly involved in a fetal gene program.  Conclusions: miR-1 directly represses a fetal gene program.

overall_design: We performed RNA deep-seq using postnatal 2.5 days (P2.5) heart from miR-1-1 and miR-1-2 double knockout mice and compared it to that of littermate control.


title: Systematic identification of regulatory elements in conserved 3’-untranslated regions of human transcripts

status: Public on Mar 21 2014

first: Panos

last: Oikonomou

state: New York

address: 1150 St. Nicholas Ave

department: Biological Sciences

institute: Columbia University

summary: We present a combined experimental/computational technology to reveal a catalogue of functional regulatory elements embedded in 3’UTRs of human transcripts. We used a bidirectional reporter system coupled with flow cytometry and high-throughput sequencing to measure the effect of short, non-coding vertebrate-conserved RNA sequences on transcript stability and translation. Information-theoretic motif analysis of the resulting sequence-to-gene-expression mapping revealed linear and structural RNA cis-regulatory elements that positively and negatively modulate the post-transcriptional fates of human transcripts.

overall_design:
We explored the functional role of 16332 short human 3'UTR sequences (C3U Library) evolutionarily conserved with P. troglodytes, M. musculus and G. gallus. For sorting the C3U library into subpopulations, we gated the population using FACS into bins each containing 10% of the total number of cells. We collected cells for the top four high expression bins (H10, H20, H30, H40) and the bottom four low expression bins (L10, L20, L30, L40)
Multiple samples (C3U library subpopulations) were pooled for each illumina index (decribed n the 'library construction protocol' field). For example, six samples (A-L10 I & II, B-L10 I & II, A-L20 I & II) were all pooled in illumina index CGATGTAT. Therefore, each individual fastq file corresponds to multiple samples. The individual samples were sorted in the processing step using identifiers inside the sequence reads. One single pooled sample was run on both lanes (the extra lane was run for additional reads).
The expression level (H: high, L:low or background) and library replicates (A or B) of the pooled library subpopulations are indicated in the sample title.

first: Hani

last: Goodarzi

first: Saeed

last: Tavazoie


title: Genetic differences underlying chromatin discordance between monozygotic twins

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

overall_design: Refer to individual Series


title: Deep sequencing shows multiple oligouridylations are required for 3' to 5' degradation of histone mRNAs on polyribosomes

status: Public on Mar 20 2014

first: William

middle: F

last: Marzluff

address: 207 Fordham Hall

summary:
We developed a customized RNA-Seq strategy to identify the 3' termini of degradation intermediates of histone mRNAs. Using this strategy, we identified two types of oligouridylated degradation intermediates: RNAs ending at different sites of the 3' side of the stemloop that resulted from initial degradation by 3'hExo and intermediates near the stop codon and within the coding region.
We established a method for identifying degradation intermediates for replication-depdendent histone mRNAs.  Histone mRNAs are present in large amounts in S-phase cells.  Inhibition of DNA replication results in a rapid degradation of histone mRNA.  We developed an approach to selectively amplify the 3' ends of histone mRNA molecules, including degradation intermediates, which we then sequenced.  Using a novel bioinformatics platform we identified degradation intermediates including many that had untemplated nts added to the 3' end.  We identified a large variety of degradation intermediates that contained oligo(U) tails.  We were able to deduce the 3' to 5' pathway of histone mRNA degradation.

overall_design:
RNA-seq with a custom 3' linker:
The samples analyzed included two biological replicates of RNAs before and 20 min after HU treatment (samples 1, 26, 27) capped RNAs from cells treated with HU for 20 min (samples 2,3,16,17) RNA isolated from polyribosomes 20 min after HU treatment, from untreated cells (samples 4-9) and cells treated with pactamycin for 5 min (samples 10-15); from cells in which the exosome subunit Pml/SC100 had been knocked down (samples 22-23) and cells treated with the control siRNA (samples 20-21).

Please note that, for Sample 2 and Sample 3, the sequencer was unable to recover both ends in the mate pairs for these two sequencing runs, but we chose to use these data anyway since the reads that were recovered included the 3' linker that we used to determine the presence of untemplated additions.

first: Joshua

last: Welch


title: Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

city: Ithaca

first: Iris

middle: Helene

last: Jonkers

address: Biotechnology Building 417

department: Molecular Biology & Genetics

institute: Cornell University

summary: Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ~3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1,000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes.

overall_design: We isolated replicates of nuclei of untreated mESCs and cells treated for 2, 5, 12.5, 25 and 50 min with 300nM flavopiridol, as well as nuclei treated for 12.5, 25, and 50 min with 500nM triptolide and performed GRO-seq with these.

first: Hojoong

last: Kwak

first: John

middle: T

last: Lis


title: A bioinformatics approach reveals novel mechanisms of the OVOL transcription factors in the regulation of epithelial-mesenchymal cell programming and cancer progression.

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: We find significant evidence of the OVOL, AP1, STAT1, STAT3, and NFKB1 TFs having important roles in MET. We prioritize known gene/drug targets for follow-up in the clinic, and show that the AP1/MYC TF pair is a strong candidate for intervention.

overall_design: Examination of the effects of OVOL1 and OVOL2 overexpression common to prostate cancer and breast cancer models.

first: Ken

last: Pienta


title: The 3′-tag digital gene expression library construction and Illumina sequencing analysis of Wild Type and SPL-/- ovules with placenta Transcriptomes

city: shang hai

first: lihua

last: zhao

state: shang hai

address: FengLin road 300#

institute: Shanghai Institutes for Biological Sciences, CAS

summary: To elucidate the molecular basis underlying early female reproductive development, Here, we used high-throughput tag-sequencing analysis to identify genes preferentially expressed in female meiocytes (FMs) by comparing gene expression profiles from wild type ovules undergoing megasporogenesis with those from the lacking megasporogenesis spl mutant ovules. A total of 862 genes were identified as FMs with levels that are consistently reduced in spl ovules in two biological replicates. Genes involved in biogenesis, metabolism, transporter activity and DNA binding were over-represented in female meiocytes, suggesting that female meiocytes are synthetically and metabolically more active.

overall_design: Total mRNA profiles of stage 10-11 old ﬂoral buds wild type (WT) and SPL-/- ovules with placenta were generated by deep sequencing, Repeat twice, using Illumina adaptor 2 (GEX adapter 2).

first: Lihua

first: Yuan

last: Qin


title: Genomic and Transcriptomic Analyses of the Facultative Methanotroph, Methylocystis Strain SB2

first: Alexey

last: Vorobev

address: 2350 Hayward Street

summary: Here we present the assembled genome of the facultative methanotroph, Methylocystis strain SB2, along with assessment of its transcriptome when grown on methane vs. ethanol.  As expected, transcriptomic analyses indicate methane is converted to carbon dioxide via the canonical methane oxidation pathway for energy generation, and that carbon is assimilated at the level of formaldehyde via the serine cycle.  When grown on ethanol, it appears this strain converts ethanol to acetyl-CoA and then utilizes the TCA cycle for energy generation and the ethylmalonyl CoA pathway for the production of biomass.

overall_design:
All cultures were grown in triplicates for subsequent DNA and RNA extraction as well as for subsequent sequencing using Illumina.
Transcriptomic analysis results presented in this Series.

first: Jeremy

last: Semrau


title: SRF is required for neutrophil migration in response to inflammation

first: Stephanie

last: Halene

address: 300 George St. 786E

department: Hematology/YCCC

institute: Yale University School of Medicine

summary: RNA expression in Srf wildtype and knockout primary bone marrow derived mature neutrophils was determined via RNA sequencing

overall_design: Mature Gr1 high, 7/4 high, SSC high neutrophils were sorted from Srf WT and KO mouse bone marrow and submitted for RNA sequencing


title: Fate changes leading to multipotency of isolated mesenchymal cells

city: La Jolla

first: Ofer

last: Shoshani

state: California

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research


title: Fate changes leading to multipotency of isolated mesenchymal cells [ChIP-Seq]

summary: Mesenchymal populations include a fraction of cells exhibiting multipotency as well as others with limited differentiation range. It has been assumed that the mesenchymal cellular cascade is topped by a multipotent cell, which gives rise to progeny with diminishing differentiation potentials.  Here we show that cultured mesenchymal cells, a priori exhibiting a limited differentiation potential, may gain new capacities and become multipotent following single cell isolation. These fate changes were accompanied by up-regulation of differentiation promoting genes, many of which also became H4K20me1 methylated. Early events in the process included TGFβ and Wnt modulation, and down-regulation of hypoxia signaling. Indeed, hypoxic conditions inhibited the observed cell changes. Overall, cell isolation from neighboring partners caused major molecular changes and particularly, a newly established epigenetic state. It is suggested that MSCs behave non-deterministically and non-hierarchically and should therefore be defined primarily by their capacity to undergo fate changes triggered by environmental cues.

overall_design: MSC 21 population and one of its derived clones (4L.1.4) were grown to confuence, and IP of fragmented DNA using an antibody directed against H4K20ME1, or non-immune serum (control) was done. Pulled DNA was then sequenced.

first: Dena

last: Leshkowitz

first: Hassan

last: Massalha

first: Orly

last: Ravid

first: Dov

last: Zipori


title: Characterization of the Merkel cell carcinoma miRNome

city: Nashville

first: Thomas

last: Andl

state: Tennessee

address: A2310 Medical Center North

department: Department of Medicine

institute: Vanderbilt University Medical Center

summary: MicroRNAs have been implicated in various skin cancers, including melanoma, squamous cell carcinoma, and basal cell carcinoma; however, the expression of microRNAs and their role in Merkel cell carcinoma (MCC) have yet to be explored in depth. To identify microRNAs specific to MCC (MCC-miRs), next-generation sequencing (NGS) of small RNA libraries was performed on different tissue samples including MCCs, other cutaneous tumors, and normal skin. Comparison of the profiles identified several microRNAs upregulated and downregulated in MCC. For validation, their expression was measured via qRT-PCR in a larger group of MCC and in a comparison group of non-MCC cutaneous tumors and normal skin. Eight microRNAs were upregulated in MCC: miR-502-3p, miR-9, miR-7, miR-340, miR-182, miR-190b, miR-873, and miR-183. Three microRNAs were downregulated: miR-3170, miR-125b, and miR-374c. Many of these MCC-miRs, with the miR-183/182/96a cistron in particular, have connections to tumorigenic pathways implicated in MCC pathogenesis. In situ hybridization confirmed that the highly expressed MCC-miR, miR-182, is localized within tumor cells. Furthermore, NGS and qRT-PCR reveals that several of these MCC-miRs are highly expressed in the patient-derived MCC cell line, MS-1.  These data indicate that we have identified a set of MCC-miRs with high implications for MCC research.

overall_design: To identify microRNAs specific to Merkel cell carcinoma (MCC) next-generation sequencing (NGS) of small RNA libraries was performed on different tissue samples including MCCs, other cutaneous tumors, and normal skin

first: Matthew

middle: S

last: Ning


title: Mammary morphogenesis and regeneration require the inhibition of EMT at terminal end buds by Ovol2 transcriptional repressor

status: Public on Mar 19 2014

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: Riken

summary: Epithelial cells possess remarkable plasticity, having the ability to become mesenchymal cells through alterations in adhesion and motility (epithelial-to-mesenchymal transition or EMT). However, it is still unknown whether and how epithelial plasticity is kept in check in epithelial cells during development. Here we show that restricting the EMT of mammary epithelial cells by transcription factor Ovol2 is required for proper morphogenesis and regeneration. Deletion of Ovol2 blocks mammary ductal morphogenesis, depletes stem/progenitor cell reservoirs, and leads epithelial cells to undergo EMT in vivo to become non-epithelial cell types. Ovol2 directly represses myriad EMT inducers and its absence switches response to TGF-beta from growth arrest to EMT. Furthermore, forced expression of the repressor isoform of Ovol2 is able to reprogram metastatic breast cancer cells from a mesenchymal to an epithelial state. Our findings underscore the critical importance of exquisitely regulating epithelial plasticity in development and cancer.


title: A Model System for Studying the Transcriptomic and Physiological Changes Associated with Mammalian Host-Adaptation by Leptospira interrogans Serovar Copenhageni

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: Leptospirosis, an emerging zoonotic disease with worldwide distribution, is caused by spirochetes belonging to the genus Leptospira. More than 500,000 cases of severe leptospirosis are reported annually, with .10% of these being fatal. Leptospires can survive for weeks in suitably moist conditions before encountering a new host. Reservoir hosts, typically rodents, exhibit little to no signs of disease but shed large numbers of organisms in their urine. Transmission occurs when mucosal surfaces or abraded skin come into contact with infected urine or urine-contaminated water or soil. In humans, leptospires can cause a variety of clinical manifestations, ranging from asymptomatic or mild fever to severe icteric (Weil’s) disease and pulmonary haemorrhage. Currently, little is known about how Leptospira persist within a reservoir host. Prior in vitro studies have suggested that leptospires alter their transcriptomic and proteomic profiles in response to environmental signals encountered during mammalian infection. However, no study has examined gene expression by leptospires within a mammalian host-adapted state. To obtain a more faithful representation of how leptospires respond to host-derived signals, we used RNA-Seq to compare the transcriptome of L. interrogans cultivated within dialysis membrane chambers (DMCs) implanted into the peritoneal cavities of rats with that of organisms grown in vitro. In addition to determining the relative expression levels of ‘‘core’’ housekeeping genes under both growth conditions, we identified 166 genes that are differentially-expressed by L. interrogans in vivo. Our analyses highlight physiological aspects of host adaptation by leptospires relating to heme uptake and utilization. We also identified 11 novel non-coding transcripts that are candidate small regulatory RNAs. The DMC model provides a facile system for studying the transcriptional and antigenic changes associated with mammalian host-adaption, selection of targets for mutagenesis, and the identification of previously unrecognized virulence determinants.

sample_organism: Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130

overall_design: Transcriptome analysis of L. interrogans Copenhageni FIOCRUZ L1-130 using RNA from 2 different conditions using RNA-seq. Also, the reproducibility and robustness of data is ensured by three biological replicates from each condition.

first: Melissa

last: Caimano

first: Anna

last: Allard

first: Daniel

last: Hurley

first: Karsten

last: Hokamp

first: André

middle: A

last: Grassmann

first: Jay

last: Hinton

first: Jarlath

middle: E

last: Nally


title: Gene expression of early craniofacial development through RNA-seq

status: Public on Mar 18 2014

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We report gene expression patterns in embryonic mice (E8.5, E9.5, E10.5) through RNA-seq of 13 tissue/stage combinations in order to generage an atlas of early mouse craniofacial gene expression.

overall_design: Embryos  at E8.5, E9.5, and E10.5 CD1 were collected from CD1 mice, fom multiple micro-regions whose development, differentiation and signaling are responsible for the construction of the mammalian face.

first: Steve

last: Potter

first: Bruce

last: Aronow


city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

summary:
The human genome harbors a large number of sequences encoding for RNAs that are not translated but control cellular functions by distinct mechanisms. The expression and function of the longer transcripts namely the long non-coding RNAs (lncRNAs) in the vasculature is largely unknown.
Here, we characterized the expression of lncRNAs in human endothelial cells and elucidated the function of the highly expressed metastasis-associated lung adenocarcinoma transcript 1 (MALAT1; also known as MALAT-1 or NEAT2).
Endothelial cells of different origin express high levels of the conserved lncRNAs MALAT1, TUG1, MEG, linc00657 and linc00493. MALAT1 was significantly increased by hypoxia and controls a phenotypic switch in endothelial cells. Silencing of MALAT1 by siRNAs or GapmeRs induced a pro-migratory response and increased basal sprouting and migration, whereas proliferation of endothelial cells was inhibited. If angiogenesis was further stimulated by VEGF, MALAT1 siRNAs induced discontinuous sprouts indicative of defective proliferation of stalk cells. In vivo studies confirmed that genetic ablation of MALAT1 inhibited proliferation of endothelial cells and reduced neonatal retina vascularization. Gene expression profiling followed by confirmatory qRT-PCR demonstrated that silencing of MALAT1 impaired the expression of various cell cycle regulators.
Silencing of MALAT1 tips the balance from a proliferative to a migratory endothelial cell phenotype in vitro and its genetic deletion reduces neonatal vascular growth in vivo.

overall_design: Human endothelial polyA+ RNA expression analysis. We used two replicate samples of human umbilical vein endothelial cells.

first: Stefanie

last: Dimmeler


title: DGE analysis of transcriptome change during photoperiodic regulation of potato tuber formation

city: Wuhan

first: Jianwei

last: Shan

state: Hubei province

address: shizishan street

department: college of life of science

institute: huazhong agricultural university

summary: We analyzed the transcriptome change during photoperiodic regulation of potato tuber formation

overall_design: 3 samples from longday condition and 2 samples from shortday condition were sequenced

first: Jun

last: Liu

last: Zhou

first: Wei

last: Song

first: Xiaohuan

last: Wang

first: Xiaoxi

last: Go

first: Tingting

last: Xie

first: Conghua


title: Global Transcriptome Analyses of Mammalian Terminal Erythroid Differentiation

city: New Haven

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary:
Purpose:The purpose of this study is to create unbiased, stage-specific transcriptomes by RNA-seq analyses of pure populations of both murine and human erythroblasts at distinct developmental stages.
Methods: Recently developed FACS-based methods (Chen et al, PNAS, Liu et al, Blood, Hu et al Blood) were employed to purify morphologically and functionally discrete populations of cells, each representing specific stages of terminal erythroid differentiation. RNA was prepared from these cells and subjected to RNA-seq analyses.
Results: There were vast temporal changes in gene expression across the differentiation stages, with each stage exhibiting unique transcriptomes.Clustering and network analyses revealed that differing stage-specific patterns of expression across differentiation were transcriptionally enriched for genes of differing function. Numerous differences were present between human and murine transcriptomes, with significant variation in the global patterns of gene expression.
Conclusions: These data provide a significant resource for studies of normal and perturbed erythropoiesis, allowing a deeper understanding of mechanisms of erythroid development, differentiation, and inherited and acquired disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Both murine and human erythroblasts at distinct developmental stage mRNA profiles were generated by deep sequencing, in triplicate, using IlluminaHiSeq 2000.

first: Xiuli

last: An

first: Vincent

middle: P

first: Jing

first: Fumin

last: Xue

first: Jingping

last: Hu

first: Narla

last: Mohandas

first: Patrick

last: Gallagher

first: Jie

last: Li

first: Kunlu

last: Wu


title: PAR-CLIP-seq reveals RNAs directly interacting with CTCF in human transformed cell line U2OS

first: Danny

last: Reinberg

address: 522 First Avenue, 2nd floor Rm 211

institute: NYU School of Medicine / HHMI

summary: This experiment sought to determine the genome-wide interactome of CTCF in human cells.

overall_design: PAR-CLIP seq for CTCF was performed in U2OS cells in 2 biological replicates

first: Ricardo

last: Saldaña-Meyer


title: RNA-seq analysis of transcriptome and glucosinolate metabolism in seeds and sprouts of broccoli (Brassica oleracea var. italica)

city: Harbin

first: Jinjun

last: Gao

state: Heilongjiang

address: Mucai Street

department: Life Sciences

institute: Northeast Agricultural University

summary:
Purpose: The goals of this study are to analyze the transcriptome of five time point in broccoli seed germination and sprout development and to find the putative glucosinolate metabolism genes in the stage.
Methods: Total mRNA of germinated seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas of wild-type broccoli were harvested. Each sample was harvested in three independent biological replicates with equal weight and subsequently pooled together for sequencing. The sequence reads that passed quality filters were de novo assembled using VELVET followed by OASES. Then the assembled unigenes were used for the abundance and functional analysis.
Results: A total of ~85million 251bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and Nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues,as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolismgenes sharing 62.04-89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinaseTGG2 was 20-130 times higher.These results along with the previous reports that glucosinolate concentration decreased exponentially once after germination indicate the breakdown products of glucosinolates may play important roles in broccoli seed germination and sprout development.
Conclusion: Our study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts to develop functional vegetables containing high levels of the anticarcinogenic glucosinolates. They will also provide new insight into the genomic research of this species and its relatives.

overall_design: Wild-type broccoli mRNA profiles of seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas were generated by deep sequencing, three biological replicates pooling together for each tissue, using Illumina Myseq platform.

first: Xinxin

last: Yu

first: Fengming

last: Ma


title: mRNA profile in DR-related mutants

city: Köln

first: Corinna

last: Klein

address: Joseph-Stelzmann-Straße 9b

country: Germany

institute: Max Planck Institute for Biology of Ageing

summary: Dietary restriction (DR) extends lifespan in a wide variety of species, yet the underlying mechanisms are not well understood. Here we show that the Caenorhabditis elegans HNF4α-related nuclear hormone receptor NHR-62 is required for metabolic and physiologic responses associated with DR-induced longevity. nhr-62 mediates the longevity of eat-2 mutants, a genetic mimetic of dietary restriction, and blunts the longevity response of DR induced by bacterial food dilution at low nutrient levels. Metabolic changes associated with DR, including decreased Oil Red O staining, decreased triglyceride levels, and increased autophagy are partly reversed by mutation of nhr-62. Additionally, the DR fatty acid profile is altered in nhr-62mutants. Expression profiles reveal that several hundred genes induced by DR depend on the activity of NHR-62, including a putative lipase required for the DR response. This study provides critical evidence of nuclear hormone receptor regulation of the DR longevity response, suggesting hormonal and metabolic control of life span.

overall_design: Young adult worms before bearing eggs inside were collected. N2 serves as the control of wild type. 3 biological replicates included in this experiment.

first: Yidong

last: Shen

first: Adam

last: Antebi


title: miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis (small RNA-seq)

city: Cold Spring Harbor

first: Kate

middle: M

last: Creasey

state: NY

address: 1 Bungtown Road

department: Plant Sciences

institute: Cold Spring Harbor Laboratory

summary: Utilizing whole-genome sRNA-seq to analyze transposon derived siRNAs in DNA methylation mutants, and RNAi mutants, compared to wildtype.

overall_design: Total RNA extracted from plant inflorescence tissue, small RNA sequenced Illumina HiSeq, read size 18-nt to 26-nt, mapping with Bowtie (Tuxedo)

first: K

first: R

last: Martienssen


title: miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis (bisulfite-seq)

summary: Utilizing whole-genome BIS-seq to analyze transposon methylation in DNA methylation mutants, and RNAi mutants, compared to wildtype.

overall_design: DNA extracted from plant inflorescence tissue, bisulphite-treated and libraries sequenced Illumina HiSEq, mapped by BiSMark.


title: Identification of Ovol2 binding regions in HC11 cells

first: Kazuhide

last: Watanabe

summary: Epithelial cells possess remarkable plasticity, having the ability to become mesenchymal cells through alterations in adhesion and motility (epithelial-to-mesenchymal transition or EMT). Recent studies suggest that EMT endows differentiated epithelial cells with stem cell traits, posing the interesting question of how epithelial plasticity is properly restricted to ensure epithelial differentiation during tissue morphogenesis. Here we identify zinc-finger transcription factor Ovol2 as a key suppressor of EMT of mammary epithelial cells. Epithelia-specific deletion of Ovol2 completely arrests mammary ductal morphogenesis, and depletes epithelial stem/progenitor cell reservoirs. Further, Ovol2-deficient epithelial cells undergo EMT in vivo to become non-epithelial cell types, and that Ovol2 directly represses key EMT inducers such as Zeb1 and regulates stem/progenitor cell responsiveness to TGF-beta. We also provide evidence for a suppressive role of Ovol2 in breast cancer progression. Our findings underscore the critical importance of exquisitely regulating epithelial plasticity to balance stemness with epithelial differentiation in development and cancer. We report ChIPseq data illustrating Ovol2 genome-wide targets in mouse mammary epithelial cells, suggesting that Ovol2 regulates a plethora of genes associated with the EMT process.

overall_design: Immunoprecipitated samples from HC11 mouse mammary epithelial cells with antibodies against Ovol2 and control IgG respectively were used for ChIP-seq experiments.

first: Alvaro

last: Villarreal-Ponce

first: Xing

last: Dai


title: The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of  transposon-specific piRNAs

city: Pomona

first: Peter

last: Arensburger

state: CA

address: 3801 Watkins Avenue

department: Dept. of Biology

institute: California State Polytechnic University Pomona

summary: Background: The piRNA pathway has been shown in model organisms to be involved in silencing of transposons thereby providing genome stability. In D. melanogaster the majority of piRNAs map to these sequences. The medically important mosquito species Aedes aegypti has a large genome size, a high transposon load which includes Miniature Inverted repeat Transposable Elements (MITES) and an expansion of the piRNA biogenesis genes. Studies of transgenic lines of Ae. aegypti have indicated that introduced transposons are poorly remobilized and we sought to explore the basis of this. We wished to analyze the piRNA profile of Ae. aegypti and thereby determine if it be responsible for transposon silencing in this mosquito. Results: Estimated piRNA sequence diversity was comparable between Ae. aegypti and D. melanogaster, but surprisingly only 19% of mosquito piRNAs mapped to transposons compared to 51% for D. melanogaster. Ae. aegypti piRNA clusters made up a larger percentage of the total genome than those of D. melanogaster but did not contain significantly higher percentages of transposon derived sequences than other regions of the genome. Ae. aegypti contains a number of protein coding genes that may be sources of piRNA biogenesis with two, traffic jam and maelstrom, implicated in this process in model organisms. Several genes of viral origin were also targeted by piRNAs. Examination of six mosquito libraries that had previously been transformed with transposon derived sequence revealed that new piRNA sequences had been generated to the transformed sequences, suggesting that they may have stimulated a transposon inactivation mechanism. Conclusions: Ae. aegypti has a large piRNA complement that maps to transposons but primarily gene sequences, including many viral-derived sequences. This, together the more uniform distribution of piRNA clusters throughout its genome suggest that some aspects of the piRNA system differ between Ae. aegypti and D. melanogaster.

sample_organism:
Aedes aegypti
Drosophila melanogaster

platform_organism:
Aedes aegypti
Drosophila melanogaster

overall_design: 5 small RNA libraries were generated from total RNA of whole adult Aedes aegypti tissues, two of these libraries were sequenced twice (technical replicates).  1 small RNA library was generated from total RNA of a whole adult Drosophila melanogaster tissue.

first: P

middle: H

last: Hice

first: J

last: Wright

first: N

last: Craig

middle: W

last: Atkinson


title: PID-1 is a novel factor that operates during 21U RNA biogenesis in Caenorhabditis elegans

status: Public on Mar 17 2014

city: Biberach an der Riß

first: Holger

state: Rhineland Palatinate

address: Birkendorfer Str. 65

department: global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim Pharma GmbH & Co KG

summary: Animal germ cells employ small RNA-based mechanisms to recognize and silence DNA that invades their genome. One of these pathways is named the Piwi:piRNA pathway. Biogenesis of piRNAs is poorly understood. In C. elegans, the piRNA (21U-RNA)-binding Argonaute protein PRG-1 is the only known player acting downstream of pre-cursor transcription. From a screen aimed at the isolation of ‘piRNA-induced silencing defective’ mutations we identified, amongst known Piwi-pathway components like MUT-7, RDE-3 and HRDE-1, PID-1 as a novel player. PID-1 is essential for 21U RNA biogenesis and affects an early step in the processing or transport of 21U precursor transcripts.

overall_design: 12 small RNA samples were analyzed as singletons.

first: Bruno

last: de Albuquerque

first: Maartje

middle: J

last: Luteijn

first: Ricardo

last: Rodrigues

first: Petra

last: van Bergeijk

first: Selma

last: Waaijers

first: Lucas

last: Kaaij

first: Mike

last: Boxem

first: René

last: Ketting


title: Allele-specific expression of multiple tissues

city: Stanford

first: Stephen

last: Montgomery

address: 300 Pasteur Lane

institute: Stanford University

summary: We report patterns of allele-specific expression across multiple tissues of a single individual using RNA-Seq and mmPCR-Seq data

overall_design: Examination of ten different tissues

middle: B

first: Jin

last: Li


title: Transcriptional profiling of Drosophila melanogaster heads from experimentally-evolved populations

first: Brian

last: Hollis

state: SC

address: 715 Sumter Street

department: Department of Biological Sciences

institute: University of South Carolina

summary: We used RNA sequencing to examine the transcriptomes of male and female heads from experimentally-evolved D. melanogaster populations after 117 generations of mating system manipulation in order to examine the pattern of evolution in sex-biased genes.

overall_design: Examined head transcriptomes of 3 monogamous populations and 3 polygamous populations, both males and females, for 12 total samples.


title: Rbfox2 controls autoregulation in RNA binding protein networks

city: Cambridge

first: Mohini

last: Jangi

state: MA

address: 500 Main Street

department: Biology

institute: MIT

summary: We generated a global analysis of Rbfox2 splicing regulation combined with a highly specific, single nucleotide-resolution Rbfox2 RNA binding map.  We found that Rbfox2 regulates the splicing and expression of many previously unknown targets, and particularly a number of RNA binding proteins (RBPs), by modulating alternative splicing coupled-NMD. Based on our observations of RBP-Rbfox2 co-regulation with a polarity predicted by Rbfox2 binding, we propose a model whereby Rbfox2 tunes autoregulatory splicing events to control RBP expression levels and in turn alter their respective splicing networks.

overall_design: iCLIP for epitope-tagged Rbfox2 and control untagged Rbfox2; RNAseq of control and Rbfox2 knockdown in mouse embryonic stem cells

first: Phillip

last: Sharp