title: Maternal hematopoietic TNF, via milk chemokines, programs hippocampal development and memory

first: Shifra

middle: Liba

last: Klein

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell

summary: TNF is a proinflammatory cytokine with established roles in host defense and immune system organogenesis.  Here we report a novel physiological function of TNF that extends its effect beyond the host into the developing offspring.  A partial/complete maternal TNF-deficit, specifically in hematopoietic cells, resulted in reduced milk levels of chemokines IP-10, MCP-1/-3/-5, and MIP-1β, which in turn, augmented offspring postnatal hippocampal proliferation, leading to improved adult spatial memory.  These effects were reproduced by the postpartum administration of a clinically used anti-TNF agent.  Chemokines, fed to suckling pups of TNF-deficient mothers, restored both postnatal proliferation and adult spatial memory to normal levels.  This work identifies a TNF-dependent “lactrocrine” pathway that programs offspring hippocampal development and memory.  The level of ambient TNF is known to be downregulated by physical activity/exercise and adaptive stress; thus, we propose that the maternal TNF-milk chemokine pathway evolved to promote offspring adaptation to post-weaning environmental challenges/competition.

overall_design: Examined transcriptomes of TNF wild type offspring of TNF wild type or heterozygouse mothers

first: Bing

last: Liu

first: Bojana

last: Zupan

first: Emma

last: Laird

first: Georgia

last: Gleason

first: Marjan

last: Bozinoski

first: Judit

last: Gal

first: Miklos

last: Toth


title: Genome wide analysis of transcriptome and microRNAs in early stage of Alzheimer's disease

status: Public on Dec 01 2013

city: Ansan

first: Hyemyung

last: Seo

address: Hanyang University

country: South Korea

institute: Hanyang University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome wide analysis of transcriptome and microRNAs in early stage of Alzheimer’s disease (microRNA)

summary:
We addressed the integrated analysis of mRNA and miRNA expression levels of Tg6799 AD model mice at 4 month and 8 months of age. Total 8 gene cluster modules for co-expression network were predicted from transcriptome data and 6 modules were show relation  with AD or aging. We constructed early stage AD network using data integration between mRNA and miRNA profiles and predicted miRNAs strongly involved in module regulation. We found that ARRDC3 showed AD mutation dependent changes of expression and was related metabolic dysfunction in early stage AD.
These results demonstrate that candidate genes on the simultaneous profiling of mRNA and miRNA expressions in genome wide can be used for the understanding of non-coding RNA related gene expression in early stage AD. We suggested that our results could be future candidate to be developed as early biomarkers in progressive AD pathology.  This result can be used for the further application in neurodegenerative diseases.

overall_design: Tg6799 transgenic mice were purchased from The Jackson Laboratory (USA) and were housed under a 12h light-dark cycle with free access to food and water. Female Tg6799 mice are maintained until 4 months and 8 months of age (for littermate control: LM and mutant subjects: MT). RNA samples were isolated from hippocampus of mice using TRI-Reagent (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions. Gene expression was analyzed with GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix, Santa Clara, CA), which is comprised of over 45,000 probe sets representing approximately 28,700 well-characterized mouse genes. The  Ion Total RNA-Seq Kit v2 (Lifetechnologies, USA) was used for the preparation of micro RNA libraries according to the manufacturer's instructions. Total numbers of subject used are as followed: 1) LM 4 months : MT 4 months : LM 8 months : MT 8 months (2:4:2:4) for screening mRMA and miRNA, 2) LM 4 months : MT 4 months : LM 8 months : MT 8 months (4:4:4:4) for expression verification.

first: S

middle: M


title: Alternative splicing in PTBP2 knockout mouse brain

city: Los Angeles

first: Areum

last: Han

state: CA

address: 6577 MacDonald Research Lab. 675 Charles E. Young Dr. South

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing


title: RNA-seq analysis of recombinant Synechocystis sp. 6803 provides important insights for understanding polyhydroxyalkanoate production in cyanobacteria under photoautotrophic conditions

city: Tsurumi, Yokohama

first: Minami

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho,

department: Biomass Engineering Program

country: Japan

institute: Riken Yokohama Institute

summary: The direct photosynthetic production of polyhydroxyalkanoate in cyanobacteria was improved by increasing carbon flux to biosynthetic pathway and introducing enzyme with higher activity. To understand the global transcriptional changes under photoautotrophic PHA biosynthesis conditions, RNA-seq analysis was performed.

overall_design: Transcriptomes of recombinant Synechocystis sp. with different PHA-producing potential (three strains, two biological replicates for each strain) were analyzed.

first: Nyok-Sean

last: Lau

first: Choon

middle: P

last: Foong

first: Yukio

last: Kurihara

first: Kumar

last: Sudesh


title: Detection of small RNAs generated during early infection of human HEK 293 cells by the alphavirus Sindbis virus

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

summary:
A time course of infection of the alphavirus Sindbis virus (SINV) was used to investigate the presence of viral specific vsRNA and the changes in miRNAs profiles in human embryonic kidney 293 cells (HEK293) by high throughput DNA sequencing.
Deep sequencing of small RNAs early in SINV infection (4 and 6 hpi) showed low abundance (0.8%) of viral specific RNAs (vsRNAs) , with a random uniform distribution not typical of Dicer products, suggesting they arise from non-specific degradation.
Sequencing showed little variation of cellular microRNAs (miRNAs) at 4 and 6 hpi compared to uninfected cells. Twelve miRNAs exhibiting some minor differential expression by sequencing, showed insignificant modulation by Northern blot analysis.

overall_design: RNA was isolated from mock infected and SINV inoculated HEK 293 cells at 4hpi and 6hpi cDNA libraries were generated for the small RNA (sRNA) content of the cells and sequenced using Illumina GA II, which yielded between 29.1M and 30.5M reads per sample

first: Andras

last: Donaszi-Ivanov

first: Tamas

last: Dalmay

first: Penny

last: Powell


title: Compound loss of muscleblind-like function in myotonic dystrophy

city: Gainesville

first: Maurice

last: Swanson

state: Fl

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Myotonic dystrophy (DM) is a multi-systemic disease that severely impacts cardiac and skeletal muscle functions as well as the central nervous system. DM is unusual because it is RNA-mediated disease due to the expression of C(C)UG expansion RNAs that inhibit the activities of the muscleblind-like (MBNL) proteins. In mice, studies using Mbnl1 and Mbnl2 single knockouts have revealed that Mbnl1 plays a predominant role in skeletal and heart muscle alternative splicing regulation while Mbnl2 performs an analogous splicing function in the brain. However, Mbnl single knockout models fail to recapitulate the full-range of adult-onset DM muscle symptoms. Here, we report that Mbnl1; Mbnl2 double knockouts are embryonic lethal while Mbnl1-/-; Mbnl2+/- mice, which express no Mbnl1 and reduced levels of Mbnl2, are viable but develop cardinal features of adult-onset DM cardiac and skeletal muscle disease including reduced lifespan, heart conduction block, severe myotonia and progressive skeletal muscle weakness. Mbnl2 protein levels are elevated in both Mbnl1-/- and Mbnl1-/-; Mbnl2+/- knockouts where Mbnl2 targets Mbnl1-regulated exons. These findings support the MBNL loss-of-function model for DM and provide novel Mbnl compound knockout models to investigate the molecular pathways disrupted by RNA-mediated disease.

overall_design: Mbnl2 protein-RNA interactions were assessed in 4-month-old WT and Mbnl1-/- quadriceps muscles in triplicates by HITS-CLIP.

first: Mini

last: Manchanda


title: Gene Expression and Exon Splicing Change Analysis of Mouse N2A Cell Transcriptome upon Polypyrimidine tract-binding protein depletion.

summary:
Purpose : Splicing factors regulate splice site choices in pre-mRNA and determine final exon set in mRNA. To understand mechanisms of splicing regulation, it is important to identify and characterize exon targets of splicing factors. Recently, development of RNA-seq technology enables researchers to investigate exon splicing profiles as well as gene expression profiles in transcriptome-wide. The goal of this study is to investigate transcriptome changes by splicing factors, Polypyrimidine Tract Binding proteins (PTB). In this study, we analyzed exon and gene expression changes followed by Ptbp1 knock down.
Methods : The knockdown experiment was performed in mouse neuroblastoma (N2A) cells. Total RNA was collected from cells and further treated with DNase I to avoid DNA contamination. RNA-seq libraries were constructed in a strand specific way using dUTP and Uracil-Specific Excision Reagent enzyme. The libraries were subjected to 100bp paired-end sequencing (Illumina HiSeq2000 platform).

overall_design: Poly(A)-mRNA and exon profiles of N2A mouse blastoma cells in two samples: shRNA transfection control, single knock down of ptbp1. RNA-seq libraries were generated in strand specific way using dUTP and USER enzyme and sequenced using Illumina HiSeq2000.


title: Combinatorial role of Jmjd2b and Jmjd2c in mESCs identity

city: Shanghai

first: Zhen

last: Shao

address: 320 Yueyang Road

country: China

institute: Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide occupancy of biotinylated Jmjd2b, Jmjd2c from mESCs, as well as occupancy of selected factors and histone marks from wild-type mESCs, Anti-GFP KD, Jmj2b KD and Jmjd2c KD mESCs genome

overall_design: To identify genome-wide binding target sites of Jmjd2b and Jmjd2c in the mESCs genome, and genome-wide binding sites for selected factors and histone marks from Anti-GFP KD, Jmjd2b KD and Jmjd2c KD mESCs

first: Partha

last: Das

first: Stuart

middle: H

last: Orkin


title: C/EBPa is required for self-renewal, lineage priming and maintenance of epigenetic configurations in hematopoietic stem cells

city: Copenhagen

first: Bo

middle: Torben

last: Porse

address: Ole Maaloes vej 5

department: BRIC/Finsen Laboratory

country: Denmark

institute: University of Copenhagen/Rigshospitalet

summary: Transcription factors are key regulators of hematopoieticstem cells (HSCs) and act through their ability to bind DNA andimpact on gene transcription. Their functions are interpreted inthe complex landscape of chromatin but current knowledge on howthis is achieved is very limited. C/EBPa is an importanttranscriptional regulator of hematopoiesis, but its potentialfunctions in HSCs have remained elusive. Here we report that C/EBPaserves to protect adult HSCs from apoptosis and to maintain theirquiescent state. Consequently, deletion of Cebpa is associatedwith loss of self-renewal and HSC exhaustion. By combining geneexpression analysis with genome-wide assessment of C/EBPa bindingand epigenetic configurations, we show that C/EBPa acts tomodulate the epigenetic states of genes belonging to molecularpathways important for HSC function. Moreover, we demonstrate thatC/EBPa acts as a priming factor at the HSC level to activelypromote myeloid differentiation and counteract lymphoid lineagechoice. Taken together our results show that C/EBPa is a keyregulator of HSC biology, which influences the epigeneticlandscape of HSCs in order to balance different cell fate options.

overall_design: C/EBPaplha binding was assesed in heamatopoietic stem- and progenitor cells (LSK) and in myeloid progenitor cells (GMP) using ChIP-seq

first: Marie

last: Hasemann

first: Felicia

middle: K

last: Lauridsen

first: Johannes

middle: E

last: Waage

first: Janus

middle: S

last: Jakobsen

first: Anne-Katrine

last: Frank

first: Mikkel

middle: B

last: Schuster

first: Nicolas

last: Rapin

first: Frederik

middle: O

last: Bagger

first: Philipp

last: Hoppe

first: Timm

last: Schroeder

middle: T


title: Transcriptional profile (mRNA and sRNA) of Clostridium acetobutylicum to metabolite stress, butanol and butyrate

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: The transcription profile of C. acetobutylicum to two major metabolite stress, butanol and butyric acid, was comprehensively investigated at three different concentrations of each metabolite and at four different time points (15, 30, 60 and 75 min post stress). All experiments were performed in 3 parallel biological replicates and the RNA extraction was perfomed in a manner to retain the small RNAs and hence, investigate their role and expression under stress.

overall_design:
Genome-wide small RNA and mRNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with Illumina HiSeq 2000 platform.
Please note that all the samples were analyzed for both mRNAs and smallRNAs. We used the miRNeasy Kit from Qiagen to ensure the extraction of the low molecular weight small RNA during the extraction of the total RNA and hence, mRNAs and sRNAs were analyzed together in the total RNA-seq.

first: Eleftherios

last: Papoutsakis

first: BlaKe

middle: C

first: Keerthi

last: Venkataramanan

first: Shawn

middle: W

last: Jones

first: Kevin

last: McCormick

first: Sridhar

middle: G

last: Kunjeti


title: Combinatorial role of Jmjd2b and Jmjd2c in mESC identity

first: Zhen

last: Shao


title: Genome-wide maps of HMGD1 and H1-bound nucleosomes.

city: La Jolla

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute

summary: Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins. Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1, in Drosophila S2 cells. Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks. However, the ratio of HMGD1 to H1 is better correlated with chromatin accessibility, gene expression and nucleosome spacing variation than either protein alone suggesting a competitive mechanism between these proteins. Indeed, we show that HMGD1 and H1 compensate each other’s absence by binding reciprocally to chromatin resulting in changes to nucleosome repeat length and distinct gene expression patterns. Collectively our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. This study thus provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation.

overall_design: ChIP-seq of HMGD1 and Histone H1 bound nucleosomes as well as MNase-seq of total nucleosome in Drosophila S2 cells

first: Narasimharao

last: Nalabothula

first: John

last: Maiorano

first: Rebecca

last: Martin

first: Jonathan

last: Pritchard

first: Yvonne

middle: N

last: Fondufe-Mittendorf


title: RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins

city: Stanford

first: Zhipeng

last: Lu

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

summary:
Background: Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of Sm RNPs is critical for understanding their functions.
Results: We developed a multi-targeting RNA-immunoprecipitation sequencing (RIP-seq) strategy to reliably identify Sm-associated RNAs from Drosophila ovaries and cultured human cells. Using this method, we discovered three major categories of Sm-associated transcripts: small nuclear (sn)RNAs, small Cajal body (sca)RNAs and mRNAs. Additional RIP-PCR analysis showed both ubiquitous and tissue-specific interactions. We provide evidence that the mRNA-Sm interactions are mediated by snRNPs, and that one of the mechanisms of interaction is via base pairing. Moreover, the Sm-associated mRNAs are mature, indicating a splicing-independent function for Sm RNPs.
Conclusions: This study represents the first comprehensive analysis of eukaryotic Sm-containing RNPs, and provides a basis for additional functional analyses of Sm proteins and their associated snRNPs outside of the context of pre-mRNA splicing. Our findings expand the repertoire of eukaryotic Sm-containing RNPs and suggest new functions for snRNPs in mRNA metabolism.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: RNA-Immunoprecipitation sequencing of RNA-Sm protein complexes.

first: Xiaojun

last: Guan

first: Casey

middle: A

last: Schmidt

first: A

last: Matera


title: Genome-wide mapping of histone methylation in human melanocytes and melanoma cell lines

city: Houston

first: HAI

last: LONG

state: TX

address: 1515 Holcombe Blvd., Unit 425

department: Leukemia

institute: University of Texas MD Anderson Cancer Center

type: Methylation profiling by high throughput sequencing

summary: Aberrant DNA methylation and histone modifications both contribute to carcinogenesis, but how these two epigenetic factors interact to impact gene expression remain unclear. To address this issue, we studied gene expression profiles, DNA methylation and two key histone modifications (H3K4me3 and H3K27me3), in two types of normal melanocytes (HEMn and HEMa) and two melanoma cell lines SK-MEL-28 and LOXIMVI. Using these data, we analyzed the relationship between epigenetic factors and gene expression status in both normal and melanoma cells, and the impact of epigenetic switches on gene expression during melanomagenesis.

overall_design: ChIP-seq analysis of H3K4me3 and H3K27me3 in two types of normal melanocytes (HEMn and HEMa) and two melanoma cell lines (SK-MEL-28 and LOXIMVI).

first: Hai

last: Long

first: Yue

first: Jean-Pierre

middle: J

last: Issa


title: Modelling and rescuing neurodevelopmental defect of Down syndrome using induced pluripotent stem cells from monozygotic twins discordant for trisomy 21

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

first: Youssef

last: Hibaoui

first: Iwona

last: Grad

last: Sailani

first: Sophie

last: Dahoun

first: Federico

last: Santoni

first: Stefania

last: Gimelli

first: Michel

last: Guipponi

first: Marie

middle: F

last: Pelte

first: Frédérique

last: Béna

first: Stylianos

last: Antonarakis

first: Anis

last: Feki


title: The THO complex regulates pluripotency gene mRNA export to control embryonic stem cell self-renewal and somatic cell reprogramming

status: Public on Nov 30 2013

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH


title: A functional map of DNA-associated proteolysis

first: Andre

last: Catic

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We established an assay to localize DNA-associated proteins that are slated for degradation by the ubiquitin-proteasome system. The genome-wide map we describe here ties proteolysis to active enhancer elements and to transcription start sites of specific gene families.

overall_design: ChIP-sequencing of ubiquitin and transcription factors was performed in the presence or absence of proteasome inhibition.


title: RNA-Seq characterization of select lincRNA knockout mouse models

city: Baltimore

first: Loyal

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: It has become clear that long intergenic noncoding RNAs (lincRNAs) are an important layer of genome regulation. Thousands have been identified in mammals, yet only a few have been tested through genetic ablation in animal models. Of the few that have, many yields weak to unobservable phenotypes, raising the question of their in vivo relevance. To more broadly investigate the functional relevance of lincRNAs in physiological conditions, we developed a collection of 18 lincRNA knockout strains. We found that two knockout strains, linc-Sox2 and linc-Foxf1a (Fendrr), exhibit perinatal lethal phenotypes in addition to multiple developmental abnormalities. Notably, in depth analysis of a third mutant strain, linc-Brn1b-/-, revealed defects in brain development, with distinct abnormalities in class-specific generation of upper layer II/III-IV neurons in the neocortex. Thus far, we found at least 6 of 18 mutant strains exhibit distinct developmental or lethality phenotypes. Therefore, this study demonstrates that lincRNAs are required for life and play critical roles during mammalian development, highlighting the importance of studying them further to better understand the molecular mechanisms leading to disease.

overall_design: Minimum 2 replicates each of select wild type and lincRNA knockout embryonic and postnatal tissues for three distinct lincRNA knockout mouse strains.

first: Martin

last: Sauvageau

first: Simona

last: Lodato

first: Boyan

last: Bonev

first: Abigail

last: Groff

first: Diana

last: Sanchez

first: Chiara

last: Gerhardinger

first: Ezgi

last: Hacisuleyman

first: Eric

last: Li

first: Matthew

last: Spence

first: Mavis

last: Swerdel

first: Michael

last: D'Ecclessis

first: Jennifer

last: Moore

first: Venus

last: Lai

first: Guochun

last: Gong

first: George

middle: D

last: Yancopoulos

first: David

last: Frendewey

first: Manolis

last: Kellis

first: Ronald

middle: P

last: Hart

middle: M

last: Valenzuela

first: Paola

last: Arlotta

first: John

middle: L

last: Rinn


title: Identification of miR-181a target genes in Epithelial Ovarian Cancer

city: Ann Arbor

first: Analisa

last: DiFeo

state: MI

address: 1600 Huron Parkway

department: Pathology

institute: The University of Michigan

summary: We have identified a single miRNA, miR-181a, that can modulate TGF-β signaling to induce and maintain EMT, and effect further downstream events of tumour cell survival, altered response to chemotherapy, migration, invasion and dissemination in vivo. Our present study provides an understanding of how enhanced expression of miR-181a can confer malignant and invasive traits through the modulation of a canonical signaling pathway and a consequent maintenance of a mesenchymal state. Furthermore, inhibition of miR-181a led to a reversion of EMT and subsequent events through decreased TGF-β signaling. Our data confirmed Smad7 as a functional target through which TGF-β-mediated EMT occurs; re-expression of Smad7 lacking its 3'UTR was able to rescue miR-181a-mediated phenotypes, deeming Smad7 as a critical mediator of miR-181a-induced EMT. Other recent studies support the crucial role(s) that miRNAs play in mediating EMT and consequent aggressive disease traits. For example, the miR-106b-25 cluster has also been shown to target Smad7 and mediate TGF-β-induced EMT downstream to Six1 in breast cancer34. miR-9 directly targets E-cadherin and inhibition of miR-9 had led to an inhibition of metastasis35. Conversely, the miR-200 and -205 family was shown to target transcriptional repressors of E-cadherin, ZEB1 and SIP1, and re-expression of these miRNAs led to a mesenchymal-to-epithelial transition and prevented TGF-β -induced EMT36.

overall_design: A2780 ovarian cancer cell lines stably expressing either pBABE (control vector), p181a#1( clone 1 expressing miR-181a) or p181a#2( clone 2 expressing miR-181a)


title: The THO complex regulates pluripotency gene mRNA export to control embryonic stem cell self-renewal and somatic cell reprogramming (RNA-IP)

first: Li

last: Wang

summary: Embryonic stem cell (ESC) self-renewal and differentiation is governed by a comprehensive regulatory network. Although the transcriptional regulation has been extensively investigated, post-transcriptional mechanisms controlling the ESC state are poorly understood. Here we describe a critical role of the THO complex in ESC self-renewal and differentiation. We show that THO preferentially interacts with pluripotency gene transcripts through Thoc5, and is required for self-renewal by regulating their export and expression. During differentiation, THO loses its interaction with those transcripts due to reduced Thoc5 expression, which leads to decreased expression of pluripotency proteins and facilitates differentiation. Finally, THO is also important for the establishment of pluripotency, as its depletion inhibits somatic cell reprogramming and blastocyst development. Together, our data indicates that THO regulates pluripotency gene mRNA export to control ESC self-renewal and differentiation, and uncovers a novel mechanism of post-transcriptional regulation in stem cell fate specification.

overall_design: RNA IP was conducted by use of antibody against Thoc2, the precipitated RNA was used to generate library using illumina Kit, and subsequently sequenced by miSeq

first: Wang

first: Hu

last: Guang


title: m6A-dependent regulation of messenger RNA stability

status: Public on Nov 29 2013

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNA of all higher eukaryotes. Here we present that m6A is selectively recognized by human YTH domain family (YTHDF2) protein to regulate mRNA degradation. By using crosslinking and immunoprecipitation, we have identified over 4000 substrate RNA of YTHDF2 with conserved core motif of G(m6A)C. We further estabilshed the role of YTHDF2 in RNA metabolism by a combination of ribosome profiling, RNA sequencing, m6A level quantification and cell-based imaging: the C-terminal domain of YTHDF2 selectively binds to m6A of mRNA and the N-terminal domain is responsive for localizing mRNA from translatable pool to processing body where mRNA decay occurs.

overall_design: PAR-CLIP and RIP was used to identify YTHDF2 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF2 siRNA knock-down

first: X

first: Z

last: Lu

first: Y

last: Yue

first: D

last: Han

first: G

last: Hon

first: B

last: Ren

first: T

last: Pan

first: C

last: He


title: Pseudopodoces humilis Transcriptome data used for gene annotation

city: Bei Jing

first: Shilin

last: Tian

address: Xueqing Road

department: genome research

institute: Novogene Bioinformatics Technology CO.ltd

summary:
To optimize the genome annotation, two tissue RNA libraries (i.e. liver and muscle) were constructed using the Illumina mRNA-Seq Prep Kit
This study is a part of the Pseudopodoces humilis WGS project (BioProject ID: PRJNA179234) and was used for gene annotation improvement.

overall_design: We sequenced two tissues using illumina Hiseq 2000 platform.

first: Fumin

last: Lei

first: Ruiqiang

last: Li

first: Yanhua

last: Qu

first: Hongwei

last: Zhao


title: Evolution at two regulatory levels in yeast

first: Carlo

middle: G.

last: Artieri

state: California

address: Herrin Labs Rm. 309

department: Biology

summary: Ribosome profiling performed on interspecific hybrids of Sacharromyces cerevisiae and S. paradoxus in order to identify allele-specific expression indicative of cis-regulatory divergence at the level of mRNA abundance and protein translation.

sample_organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

overall_design: Two biological replicate libraries sequenced from ribosome protected fragments as well as poly-A-selected mRNA of hybrids in addition to one biological replicate library of poly-A selected mRNA from each parental strain.

first: Hunter

last: Fraser


title: Genome-wide DNA methylation mapping in preadipocytes

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

summary: DNA methylation plays a crucial role in the regulation of gene transcription. In this study, using MeDIP-seq experiment, we report the mapping of DNA methylation in undifferentiated 3T3-L1 cells (preadipocytes).

overall_design: Examination of DNA methylation pattern in undifferentiated 3T3-L1 cells (preadipocytes)

first: Frédérik

last: Oger

first: P

last: Lefebvre


title: RNAseq analysis of alternative splicing in PTBP2 knockout mouse brain

city: Los Angeles

first: Areum

address: 6577 MacDonald Research Lab. 675 Charles E. Young Dr. South

institute: UCLA

summary: The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. The splicing regulatory proteins PTBP1 and PTBP2 show distinct temporal expression profiles in the developing brain. Neuronal progenitor cells predominantly express PTBP1, whereas developing neurons express high levels of PTBP2, which are subsequently reduced late in neuronal maturation. We show here that PTBP2 and the program of splicing it controls are essential to proper neuronal maturation and survival. To investigate its in vivo function, we generated conditional PTBP2 null alleles in mice. Loss of PTBP2 in neuronal progenitor cells leads to neonatal death without gross defects in brain architecture. Mice with specific depletion of PTBP2 in the cortex and forebrain are viable. However over the first three postnatal weeks, when the normal cortex expands and develops mature circuits, the PTBP2 null cortices degenerate. We find that PTBP2-/- neurons cultured from embryonic brain show the same initial viability as wild type cells with proper early marker expression and neurite outgrowth. Strikingly, between 10 and 20 days in culture PTBP2 null neurons undergo a catastrophic failure to mature and die. To assess the target transcripts leading to these phenotypes, we examined the genomewide splicing changes in the PTBP2 null brains. This identified a large number of mis-regulated exons that share a temporal pattern of regulation; in the absence of PTBP2 many isoforms normally found in adults are precociously expressed in the developing brain. Transcripts following this pattern encode essential neuronal proteins affecting neurite growth, pre- and post-synaptic assembly, and synaptic transmission. Our results define a new genetic regulatory program essential for neuronal survival and maturation, where PTBP2 acts to temporarily repress expression of protein isoforms until the final maturation of the neuron.

overall_design: Mice carrying a conditional "floxed" PTBP2 allele of PTBP2 were crossed to mice carrying Cre recombinase driven by either the nestin or Emx1 promoters. The resulting knockout mutant mouse brains were analyzed for changes in gene expression and alternative splicing. Knockout mice were compared to wildtype littermates. Whole mouse brain polyA plus RNA was isolated from two Nestin-cre knockout embryos at embryonic day 18 and compared to two wildtype littermates. Total polyA plus RNA was isolated from the cortices of an Emx-cre knockout and its wildtype littermate at postnatal day 1. This RNA was converted to standard Illumina paired end libraries using the Truseq kit. The Emx sample and control libraries were strand specific through elimination of the second strand of cDNA using the USER enzyme. Libaries were sequenced on an Illumina HiSeq using the standard paired end protocol. Data was analyzed using the Cufflinks pipeline. Splicing analysis was carried out using the SpliceTrap program.

first: Qin

first: Sika

last: Zheng


title: Genome-wide Profiling of FOXA2 and POL2 binding in the mouse uterus [ChIP-Seq]

city: Columbia

first: Thomas

last: Spencer

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: Forkhead box A2 (FOXA2) is a critical regulator of endometrial gland development in mice. In the adult mouse uterus, FOXA2 is expressed solely in the GE cells of the endometrium. Conditional deletion of Foxa2 after birth in the uterus, using the progesterone receptor Cre mouse (PgrCre), impeded gland development, thereby rendering the adult mouse infertile due to defects in blastocyst implantation stemming from a lack of endometrial glands and their secretions. As a first step to begin understanding the FOXA2 function in the endometrial glands of the uterus, genome-wide investigation of in vivo FOXA2 and RNA polymerase II (POL2) binding target regions in the neonatal and adult uterus was determined by chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq).

overall_design: In order to determine the transcriptional regulatory networks mediating FOXA2 regulation of endometrial gland development and function, chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) was used to create a genome-wide profile of in vivo FOXA2-binding sites in the developing (PD 12) and adult (DOPP 2.5 and 3.5) mouse uterus.

middle: E

first: Justyna

last: Filant

first: John

last: Lydon


title: Principles of nucleation of H3K27 methylation during embryonic development

status: Public on Nov 28 2013

city: Nijmegen

first: Gert Jan

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

summary: During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 K27 trimethylation (H3K27me3). However, the developmental origins of this regulation are unknown. Here, we report on H3K27me3 deposition dynamics in Xenopus embryos, on sequence elements that initiate deposition during pluripotency, and the sequence characteristics that segregate Polycomb-regulated domains from the rest of the genome. Strikingly, although PRC2 binds widely to active enhancers, H3K27me3 is only deposited at a small subset of these sites. Using a Support Vector Machine algorithm these sequences can be predicted accurately on basis of DNA sequence alone, with a sequence signature conserved between humans, frog and fish. The results suggest a genetic-default model in which genomic sequence constrains Polycomb regulation.

overall_design: ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development

first: Simon

last: van Heeringen

first: Robert

last: Akkers

first: Ila

last: van Kruijsbergen

first: Lars

last: Hanssen

first: Nilofar

last: Sharifi

first: Gert-Jan

first: M. Asif

last: Arif


title: Regulatory Modules Controlling Maize Inflorescence Architecture: ChIP-seq data

status: Public on Nov 27 2013

first: Andrea

last: Eveland

address: 975 N. Warson Road

summary: In this study we investigated the developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, and revealed potential mechanisms for repressing branches in distinct stem cell populations in developing maize inflorescences.  To identify targets of RA1 and to distinguish direct vs. indirect interactions, we performed Chromatin Immunoprecipitation (ChIP)-seq and compared the results to gene expression data (RNA-seq datasets for Eveland et al., 2013, submitted).  We mapped genome-wide occupancy of RA1 and showed that it differently regulates modules of target genes based on spatiotemporal context.

overall_design: Plants expressing complementing RA1 transgenes tagged with HA or YFP were used in parallel experiments.  Ear and tassel primordia were collected and tag-specific antibodies were used to pull down RA1 bound to its target loci.  Genome-wide analysis of RA1 occupancy revealed thousands of putative binding sites (i.e. peaks significantly enriched (p < 1e-05) compared to input DNA).

first: David

last: Jackson

first: Doreen

last: Ware

first: Michael

last: Pautler

first: Kengo

last: Morohashi

first: Erich

last: Grotewold

first: Erik

last: Vollbrecht


title: Derivation of novel human ground state naïve pluripotent stem cells [ChIP-seq; RRBS-seq]

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Mouse embryonic stem (ES) cells are isolated from the inner cell mass of blastocysts, and can be preserved in vitro in a naive inner-cell-mass-like configuration by providing exogenous stimulation with leukaemia inhibitory factor (LIF) and small molecule inhibition of ERK1/ERK2 and GSK3b signalling (termed 2i/LIF conditions). Hallmarks of naive pluripotency include driving Oct4 (also known as Pou5f1) transcription by its distal enhancer, retaining a pre-inactivation X chromosome state, global reduction in DNA methylation and in H3K27me3 repressive chromatin mark deposition on developmental regulatory gene promoters.Upon withdrawal of 2i/LIF, naïve mouse ES cells can drift towards a primed pluripotent state resembling that of the post-implantation epiblast. Although human ES cells share several molecular features with naive mouse ES cells, they also share a variety of epigenetic properties with primed murine epiblast stem cells (EpiSCs). These include use of the proximal enhancer element to maintain OCT4 expression, pronounced tendency for X chromosome inactivation in most female human ES cells, increase in DNA methylation and prominent deposition of H3K27me3 and bivalency acquisition on lineage regulatory genes. The feasibility for establishing human ground state naive pluripotency in vitro with equivalent molecular and functional features to those characterized in rodent ES cells remains to be defined. Here we establish defined conditions that facilitate the derivation of genetically unmodified human naive pluripotent stem cells from already established primed human ES cells, from somatic cells through induced pluripotent stem (iPS) cell reprogramming or directly from blastocysts. The novel naive pluripotent cells validated herein retain molecular characteristics and functional properties that are highly similar to mouse naive ES cells, and distinct from conventional primed human pluripotent cells. This includes competence in the generation of cross-species chimaeric embryos that underwent organogenesis following microinjection of human naive iPS cells into mouse morulas. Collectively, our findings establish new avenues for regenerative medicine, patient-specific iPS cell disease modelling and the study of early human development in vitro and in vivo.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Four chromatin marks H3K4me1, H3K4me3, H3K27ac and H3K27me3 were measured in 5 cell lines: C1, WIBR3, LIS2 and WIS2 (naïve and conventional/primed stem cells), and BGO1 (only naïve stem cells). Reduced representation bisulfite sequencing was performed on primed and naïve (expanded in NHSM-WIS medium) human ESCs. For comparison, RRBS was also performed on primed and naïve mouse pluripotent cells.

first: N

first: L

last: Weinberger

first: E

last: Chomsky

first: J

middle: H

last: Hanna


title: Regulatory Modules Controlling Maize Inflorescence Architecture

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

overall_design: Refer to individual Series


title: Derivation of novel human ground state naïve pluripotent stem cells.


title: Regulatory Modules Controlling Maize Inflorescence Architecture: mRNA-seq data

summary: In this study we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth.  We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching.  These are the RNA-seq datasets used in this study.

overall_design: We profiled changes in gene expression during normal maize ear and tassel development and in developing maize ear primordia upon genetic perturbation of the RAMOSA branching pathway.  For the wild-type ear and tassel developmental series, greenhouse-grown B73 inbred plants were used.  10mm ears were collected and sectioned as follows from tip to base along the developmental gradient: tip 1mm sampled (tip; Inflorescence Meristem/Spikelet Pair Meristem), next 1mm discarded, next 1mm sampled (mid; Spikelet Meristem), next 2mm discarded, next 2 mm sampled (base; Floral Meristem), and immediately frozen in liquid nitrogen.  Sections from ~30 sampled ears were pooled for each of 2 biological replicates to represent tip, mid, and base stages.  Tassels were hand-dissected, measured, separated by stage: 1-2mm (stg1), 3-4mm (stg2), and 5-7mm (stg3), and immediately frozen in liquid N.  For each stage, ~20-30 tassels were pooled for each of 2 biological replicates.  For ramosa mutant series, segregating families (1:1) of ra1-R, ra2-R, and ra3-fea1 mutant alleles, all introgressed at least 6 times into the B73 inbred background, were grown at CSHL Uplands Farm.  Field-grown plants were genotyped and collected 6-7 weeks after germination (V7-V8 stage).  First and second ear primordia were immediately hand-dissected, measured, and frozen in liquid nitrogen.  For ra1, ra2 and ra3 mutants and wild-type controls, ears were pooled into two size classes: 1) 1mm class included a range of 0.7-1.5mm sized ears and nine ears were pooled for each of 2 biological replicates; 2) 2mm class included a range of 1.8-2.5mm sized ears and six ears were pooled for each of three biological replicates.  Wild-type samples were proportional mixtures of heterozygote siblings segregating in ra1, ra2, and ra3 populations.  Variability factors (e.g. ear size within class, ear rank on the plant, and time of collection) were distributed evenly across pooled samples.

first: Alexander

last: Goldshmidt

first: Robert

last: Schmidt


title: Dynamic and Parent-of-Origin Expression of Small RNAs in the Developing Maize Endosperm

status: Public on Nov 26 2013

city: Tucson

first: Xiangfeng

last: Wang

address: 1140 E. South Campus Drive, Marley Building 541C

department: School of Plant Sciences

institute: University of Arizona

summary: In angiosperms, endosperm plays a crucial role in coordinating seed development through genetic balance and molecular interaction, and is the primary tissue where genomic imprinting occurs. To identify small interfering RNA (siRNA) “imprintome” and its paternal transcriptome activation in early developing maize endosperms, we performed high-throughput small RNA sequencing of whole kernels at 0, 3 and 5 days after pollination (DAP) and endosperms at 7, 10 and 15 DAP, using B73 by Mo17 reciprocal crosses. We observed gradually increased expression of paternal siRNAs in 3- and 5-DAP kernels and balanced contribution of parental siRNA transcriptome in 7-DAP endosperm, followed by identification 460 imprinted siRNA loci with majority (456/460, 99.1%) being maternally expressed that occurred at 10 DAP. Genome-wide scanning found 13 imprinted genes harboring imprinted siRNA loci within their 2-Kb flanking regions, which was significantly different from random probability based on simulation analysis. Finally, gene ontology categories of “response to auxin stimulus”, “response to brassinosteroid stimulus” and “regulation of gene expression” for genes harboring 10-DAP specific siRNAs and “nutrient reservoir activity”, “protein localization to vacuole” and “secondary metabolite biosynthetic process” for genes harboring 15-DAP specific siRNAs indicated that siRNAs could be involved in influencing specific cellular or biochemical processes that are essential for endosperm development, e.g. nutrient uptake and allocation. Although the mechanism of how these siRNAs regulating endosperm key events remains unclear, this study provided us an alternative perspective of siRNA function in plant.

overall_design: The unpollinated kernels (0 DAP), the kernels of 3, 5 DAP and endosperms of 7 10, 15 DAP from the B73 and Mo17 reciprocal crosses were used to perform high-throughput sequencing using the Illumina HiSeq2000 platform

first: Mingming

last: Xin

first: Ruolin

last: Yang

first: Yingyin

last: Yao

first: Chuang

last: Ma

first: Qixin

last: Sun

first: Zhongfu

last: Ni


title: A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations

city: Berkeley

first: Johan

middle: Philipp

last: Benz

address: 2151 Berkeley Way

department: Energy Biosciences Institute

institute: UC Berkeley

summary: Filamentous fungi are powerful producers of hydrolytic enzymes for the deconstruction of plant cell wall polysaccharides. However, the central question of how these sugars are perceived in the context of the complex cell wall matrix remains largely elusive. To address this question in a systematic fashion we performed an extensive comparative systems analysis of how the model filamentous fungus Neurospora crassa responds to the three main cell wall polysaccharides: pectin, hemicellulose and cellulose. We found the pectic response to be largely independent of the cellulolytic one with some overlap to hemicellulose, and in its extent surprisingly high, suggesting advantages for the fungus beyond being a mere carbon source. Our approach furthermore allowed us to identify carbon source-specific adaptations, such as the induction of the unfolded protein response on cellulose, and a commonly induced set of 29 genes likely involved in carbon scouting. Moreover, by hierarchical clustering we generated a co-expression matrix useful for the discovery of new components involved in polysaccharide utilization. This is exemplified by the identification of lat-1, which we demonstrate to encode for the physiologically relevant arabinose transporter in Neurospora. The analyses presented here are an important step towards understanding fungal degradation processes of complex biomass.

overall_design: Our data are based on carbon source transfer experiments. For this, N. crassa pregrown in sucrose for 16 hrs was washed in media without carbon and then transferred to either pectin, orange peel powder (OPP), xylan, Avicel (cellulose), sucrose, or media without carbon (NoC) for another 4 hrs. Biological triplicates (pectin, Avicel, sucrose, NoC) or duplicates (OPP) were used to identify differentially expressed genes in WT. For xylan only a single library was prepared, which was found to correlate well with previously published microarray data (Sun et al. 2012; doi: 10.1128/EC.05327-11)

first: Chris

middle: R

last: Somerville


title: Genome-wide mapping of SMRT (silencing mediator of retinoid and thyroid hormone receptors) occupancy in mouse liver at different Zeitgeber times (ZTs).

status: Public on Nov 25 2013

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: We mapped SMRT binding on the genome in mouse livers and found no obvious circadian rhythm.

overall_design: 12-weeks old C57BL/6 male mice were fed ad libum. Livers were harvested at 5 pm (ZT 10) and 5 am (ZT 22) with 4 mice in each group. Anti-SMRT ChIP was performed independently in each mouse and pooled together for deep sequencing.

first: Seo-Hee

last: You

first: Zheng

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: Genome-wide acetylated histone 3 lysine 9 (H3K9ac) in HDAC3-depleted liver rescued with deacectylase-dead HDAC3 mutants

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

summary: We found that several deacetylase-dead HDAC3 mutants were able to rescue the metabolic phenotype of HDAC3-depleted livers. Here we profile the histone acetylation in the presence of different HDAC3 mutants in mouse liver.

overall_design: Deacetylase-dead HDAC3 mutants, including HAHA, KA, YF and HEBI, were introduced into HDAC3-depleted (Cre) mouse livers by virus along with wild-type (WT) HDAC3 as a control. Livers were harvested at 5 pm (ZT 10) and subjected to ChIP with anti-H3K9ac antibodies followed by deep sequencing.

first: Dan

last: Feng


title: Systematic evaluation of DNase-seq experimental parameters

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

country: Canada

institute: UNIVERSITY HEALTH NETWORK

summary: We systematicaly evaluated two major factors, enzyme digestion level and fragment size, that would affect DNase-seq experiment. We found that while under- or over-digestion sigificantly decreases the DNase-seq signal, there is a broad range of suitable digestion level. In addition, we found fragment smaller than nucleosome size is optimal to identify transcription factor binding events.

overall_design: We tested digestion level of 5U, 25U, 50U, 75U, 100U and fragment size of 50-100bp, 100-200bp, 200-300bp

first: Clifford

last: Meyer

first: Sheng'en

middle: S

last: Hu

first: Henry

last: Long

first: X

last: Liu

first: Myles

last: Brown


title: Transcriptome-wide mapping of human Staufen1 binding sites

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

summary:
Purpose: We performed RNA-Immunoprecipitation in Tandem (RIPiT) experiments against human Staufen1 (Stau1) to identify its precise RNA binding sites in a transcriptome-wide manner. To monitor the consequences of Stau1 binding in terms of target mRNA levels and ribosome occupancy, we modified the levels of endogenous Stau1 in cells by siRNA or overexpression and performed RNA-sequencing and ribosome-footprinting experiments.
Staufen1 (Stau1) is a double-stranded RNA (dsRNA) binding protein implicated in mRNA transport, regulation of translation, mRNA decay and stress granule homeostasis. Here we combined RNA-Immunoprecipitation in Tandem (RIPiT) with RNase footprinting, formaldehyde crosslinking, sonication-mediated RNA fragmentation and deep sequencing to map Staufen1 binding sites transcriptome-wide. We find that Stau1 binds complex secondary structures containing multiple short helices, many of which are formed by inverted Alu elements in annotated 3'UTRs or in "strongly distal" 3'UTRs extending far beyond the canonical polyadenylation signal. Stau1 also interacts with both actively translating ribosomes and with mRNA coding sequences (CDS) and 3'UTRs in proportion to their GC-content and internal secondary structure-forming propensity.  On mRNAs with high CDS GC-content, higher Stau1 levels lead to greater ribosome densities, suggesting a general role for Stau1 in modulating the ability of ribosomes to elongate through secondary structures located in CDS regions.

overall_design: We used HEK293 cells expressing near endogenous levels of wild-type Flag-Stau1 (65KDa isoform with an N-Terminal Flag tag). As a control we used a mutant version of Stau1 that is not functional for dsRNA binding. Formaldehyde crosslinking experiments and RNase footprinting experiments were done in two biological replicates. All RNASeq, Ribosome footprinting and PAS-Seq were done in two biological replicates.

first: Emiliano

last: Ricci

first: Melissa

last: Moore


title: FOXO3 selectively amplifies enhancer activity to establish target gene regulation.

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: Forkhead Box O (FOXO) transcription factors are versatile players in diverse cellular processes, affecting tumorigenesis, metabolism, stem cell maintenance and lifespan. To understand the transcriptional output of FOXO3 activation, we investigate features that define the subset of enhancer binding events that actually contribute to gene regulation. We show FOXO3 transcriptional output is determined by the amount of bound FOXO3, which in turn is determined by motif presence, pre-existing enhancer activity and accessibility. In this manner, FOXO3 amplifies pre-existing levels of activity marks and potentiates enhancer RNA transcription. We conclude that not only enhancer presence and sequence content, but also the pre-existing activity dictates FOXO3 binding and transcriptional output. Considering the flexible and cell type specific nature of regulatory regions and their activity, our observations provide a novel explanation for the diversity in FOXO transcriptional programs and introduce chromatin context as a new player in the regulation of FOXO activity in ageing and disease.

overall_design: Examination of histone modifications and transcriptome changes upon FOXO activation


title: ChIP-seq using a Dp1 antibody in Drosophila S2R+ cells

first: Elizaveta

middle: V

last: Benevolenskaya

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: Here we report the identification of genomic regions of DNA bound by Dp1 in Drosophila S2R+ cells. Dp1 is a dimerization partner of several E2F transcription factors and is needed for E2F target promoter binding. We find that Dp1 binds the promoter regions of genes important for oxidative phosphorylation. This result is important since our data demonstrates that expression of several oxidative phosphorylation genes is down-regulated in dDP mutant Drosophila 3rd instar larval eye imaginal discs. These ChIP-seq results suggest that the mechanism by which dDP regulates expression of these genes is direct. In addition, we have confirmed a number of these Dp1 bound gene promoters by conventional Chromatin Immunoprecipitation.

overall_design: Examination of Dp1 bound regions of genomic DNA in S2R+ cells.

first: Aaron

last: Ambrus

first: Abul

middle: B

last: Islam

first: Maxim

last: Frolov


title: Identification and Characterization of the Mammalian Nuclear RNA N6-Adenosine Methyltransferase Core Complex

first: Dali

last: Han

address: 5801 South Ellis Avenue

department: Department of Chemisty

summary: N6-methyladenosine (m6A) is the most prevalent internal modification found in mammalian messenger and non-coding RNAs. The discoveries of functionally significant demethylases that reverse this methylation as well as the recently revealed m6A distributions in mammalian transcriptomes strongly indicate regulatory functions of this modification. Here we report the identification and characterization of the mammalian nuclear RNA N6-adenosine methyltransferase core (RNMTC) complex. Besides METTL3, a methyltransferase which was the only known component of RNMTC in the past, we discovered that a previously uncharacterized methyltransferase, METTL14, exhibits a N6-adenosine methyltransferase activity higher than METTL3. Together with WTAP, the third component that dramatically affects the cellular m6A level, these three proteins form the core complex that orchestrates m6A deposition on mammalian nuclear RNA. Biochemistry assays, imaging experiments, as well as transcriptome-wide analyses of the binding sites and their effects on m6A methylation support methylation function and reveal new insights of RNMTC.

overall_design: PAR-CLIP and m6A-seq in HeLa cells

first: Yanan

last: Yue

first: Jianzhao

first: Chuan


title: Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe [NGS_Illumina]

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

country: Spain

institute: Instituto de Biología Funcional y Genómica (IBFG)

summary: Sequencing of mononucleosomal DNA during asynchronous mitosis and 0, 3 and 5 hours into meiosis in Schizosaccharomyces pombe.

overall_design: Two samples from mononucleosomal DNA from asynchronous mitosis (haploid 972 h- and diploid pat1.114) and three samples from 0, 3 and 5 hours into meiosis (from diploid pat1.114) were sequenced (Illumina Genome Analyzer IIx) using the single-end read protocol.

first: Ignacio

last: Soriano

first: Francisco

last: Antequera


title: Lympho-myeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

summary: An immune-restricted lymphomyeloid-primed progenitor with the capacity to contribute to both myeloid and lymphoid lineages in the developing embryo emerges prior to definitive HSCs.

overall_design:
Examination of fetal sorted lymphoid primed progentors and adult progenitors

The fastq files are not provided at this time due to further analyses.

first: C

last: Böiers

first: Sten

last: Jacobsen


title: Transcriptional profile in the colon in response to C. rodentium infection.

city: New York

first: Amanda

last: Marchiando

state: NY

address: 545 First Ave

department: Skirball Institute

institute: NYU School of Medicine

summary: The identification of Atg16L1 as a susceptibility gene has implicated antibacterial autophagy in the pathogenesis of Crohn's disease, a major type of inflammatory bowel disease (IBD). However, the role of Atg16L1 during extracellular bacterial infections of the intestine has not been sufficiently examined and compared to the function of other IBD susceptibility genes such as Nod2. We now find that Atg16L1 mutant mice are extraordinarily resistant to intestinal disease induced by the model bacterial pathogen Citrobacter rodentium. We further demonstrate that Atg16L1 deficiency alters the intestinal environment to mediate an enhanced immune response that is dependent on monocytic cells, and that Atg16L1/Nod2 double mutant mice lose this advantage. These results reveal an unappreciated immuno-suppressive function of an IBD gene, and raise the possibility that gene variants that affect the autophagy pathway were evolutionarily maintained to protect against certain life-threatening infections.

overall_design: Twenty samples have been analyzed. All are colonic tissue from mice. Controls are uninfected WT mice, uninfected Atg16L1 mutant mice (Atg16L1HM)  (n=3/genotype). Treatment conditions are tissue from WT and Atg16L1 mutant mice 6 days after C. rodentium infection (n=4/genotype) and 15 days after infection (n=3/genotype).

first: Ken

last: Cadwell


title: Digital gene expression (DGE) of alkali-stressed cucumber leaves

city: Tai'an

first: Zhongxi

last: Gao

address: Daizong street no. 61

institute: Shandong Agricultural University

summary: Here we performed a transcriptomic study on the effect of sodium nitroprusside (SNP) on cucumber leaves under alkali stress using Solexa/Illumina's high-throughput digital gene expression (DGE) system. Two DGE libraries (from one NaHCO3-treated sample and one NaHCO3 + SNP-treated sample) were constructed, and the gene expression variations between the two samples were compared. Hundreds of differentially expressed genes were obtained by the comparison, and GO analysis of these genes suggested that many biological processes, molecular function, cellular components were related to SNP’s mitigated effect on alkaline stress. The authenticity of the DGE data was further confirmed by analyzing real-time RT-PCR using several random-selected genes.

overall_design: The experiment had 2 treatments: 30 mM NaHCO3 (alkali stress treatment, indicated as Na) and 30 mM NaHCO3+100 μM sodium nitroprusside (indicated as SNP). Samples from Na- and SNP-treated leaves, used for RNA isolation, were harvested, and the two corresponding tag libraries of samples were constructed in parallel. Illumina sequencing of transcripts from Na- and SNP-treated samples to get gene information for cucumber leaves in different treatments.

first: Todd

last: Wehner

first: Hao

last: Chen

first: Yan

last: Lin

first: Qinghua

last: Shi


title: Global analysis of the transcriptional difference between indigenous and invasive whiteflies reveals the possible mechanism of whitefly invasion

status: Public on Nov 24 2013

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

institute: Zhejiang University

summary: The whitefly Bemisa tabaci is a species complex of more than 31 cryptic species which include some of the most destructive invasive pests of many ornamental and glasshouse crops worldwide. Among them, Middle East-Asia Minor 1 (herein MEAM1) and Mediterranean (herein MED) have invaded many countries around the world and displaced the native whitefly species. However, the molecular differences between invasive and indigenous whiteflies remain largely unknown.

overall_design: The global transcriptional difference between the two invasive whitefly Bemisia tabaci species (MEAM1, MED) and one indigenous whitefly species (Asia II 3) were analyzed using the Illumina sequencing technology.

first: Yong-Liang

first: Yu-Jun

first: Jun-Bo

last: Luan

first: Shu-Sheng

last: Liu

first: Xiao-Wei


title: Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

first: Luis

type: Genome binding/occupancy profiling by genome tiling array

type: Expression profiling by genome tiling array


title: RNA-seq analysis generated a comprehensive landscape of transcriptomes and revealed complex patterns of transcripts in Chinese HBV-related hepatocellular carcinoma

city: HangZhou

first: Biaoyang

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

institute: ZheJiang University

summary: RNA-seq is a powerful tool for comprehensive characterization of whole transcriptome at both gene and exon levels and with a unique ability of identifying novel splicing variants. To date, RNA-seq analysis of HBV-related HCC has not been reported. In this study, we performed transcriptome analyses for 10 matched pairs of cancer and non-cancerous tissues from Chinese HBV-related hepatocelluar carcinoma patients using 36bp single-end sequencing approach on Solexa/Illumina GAII platform. On average, about 21.6 million sequencing reads and 10.6 million aligned reads were obtained for samples sequenced on each lane, which was able to identify > 50% of all the annotated genes for each sample. Furthermore, from by far the largest database of transcripts expressed in HCC tissues, we identified 1,378 significantly differently expressed genes (DEGs) and 24, 338 differentially expressed exons (DEEs). Comprehensive function analyses indicated that cell growth-related, metabolism-related and immune-related pathways were most significantly enriched by DEGs, pointing to a complex mechanism for HCC carcinogenesis. Positional gene enrichment analysis showed that DEGs were most significantly enriched at chromosome 8q21.3-24.3. The most interesting findings were from the analysis at exon levels where we characterized three major patterns of expression changes between gene levels and exon levels, implying a much complex landscape of transcript-specific differential expressions in HCC. Finally, we identified a novel highly up-regulated exon-exon junction in ATAD2 (ATPase family, AAA domain containing 2) gene in HCC tissues. Overall, to our best knowledge, our study represents the most comprehensive characterization of the HBV-related HCC transcriptome including exon level expression changes and novel splicing variants, which illustrated the power of RNA-seq and provided important clues for understanding the molecular mechanisms of HCC pathogenesis at system-wide levels.

overall_design:
A comprehensive analysis of transcriptome for 10 match-paired HBV-related Chinese HCC and non-cancerous adjacent tissues.

Processed data files:
Exon-level results, gene-level results, differentially expressed exons, and differently expressed genes (DEGs).

first: Jinliang

last: Xing

first: Hanqiang

first: Qichao

last: Huang

first: Xi

last: Ma

first: Fan

last: Mo

first: Wei

last: Yu

first: Lisha

last: Li

first: Hongwei

first: Tian

last: Tian

first: Dong

last: Wu

first: Feng

last: Shen

first: Zhinan


title: Fusion discovery in breast cancer cell line

status: Public on Nov 22 2013

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: SnowShoes-FTD, a fusion transcript discovery tool, was used to identify fusions in breast cancer cell lines using the RNA-Seq data

overall_design: Total RNA extracted from cell lines. The total RNA was used for construction of RNA-Seq library for RNA-Sequencing.

first: E

last: Thompson

first: Brian

last: Necela

middle: W

first: Gary

last: Schroth

first: Edith

last: Perez


title: Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma

city: Oakland

first: Ravi

last: Sachidanandam

address: 2945 Webster St

institute: Girihlet Inc.

summary: UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish, cultured cells and human tumors, we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples.

overall_design: Total small RNA from 2 batches of Tg(fabp10:has.UHRF1-GFP)High and age matched Tg(fabp10:nls-mCherry) control 5 dpf zebrafish livers was purified for preparation of high-throughput sequencing libraries.

first: Raksha

last: Mudbhary

first: Yujin

last: Hoshida

first: Yelena

last: Chernyavskaya

first: Vinitha

last: Jacob

first: Augusto

last: Villanueva

first: M

middle: I

last: Fiel

first: Xintong

last: Chen

first: Kensuke

last: Kojima

first: Swan

last: Thung

first: Roderick

middle: T

last: Bronson

first: Anja

last: Lachenmayer

first: Kate

last: Revill

first: Clara

last: Alsinet

first: Anal

last: Desai

first: Chinweike

last: Ukomadu

first: Josep

last: Llovet

first: Kirsten

middle: C

last: Sadler


title: Epigenetic regulation of the MEG3-DLK1 microRNA cluster in human Type 2 diabetic islets

first: Ying

state: PA

address: 423 Guardian Drive

summary: Type 2 diabetes mellitus (T2DM) is a complex disease characterized by the inability of the insulin-producing β-cells in the endocrine pancreas to overcome insulin resistance in peripheral tissues. To determine if microRNAs are involved in the pathogenesis of human T2DM, we sequenced the small RNAs of human islets from diabetic and non-diabetic organ donors. We identified a cluster of miRNAs in an imprinted locus on human chromosome 14q32 that is highly and specifically expressed in human β-cells and dramatically down-regulated in islets from T2DM organ donors. The down-regulation of this locus strongly correlates with hyper-methylation of its promoter. Using HITS-CLIP for the essential RISC-component Argonaute, we identified disease-relevant targets of the chromosome 14q32 microRNAs, such as IAPP and TP53INP1 that cause increased β-cell apoptosis upon over-expression in human islets. Our results support a role for microRNAs and their epigenetic control by DNA methylation in the pathogenesis of T2DM.

overall_design: Identification of miRNA-target interaction in human islets using HITS-CLIP, one mRNA library and one miRNA library

first: Vasumathi

last: Kameswaran

first: Nuria

last: Bramswig

first: Lindsay

last: McKenna

first: Melinda

last: Penn

first: Jonathan

last: Schug

first: Nicholas

middle: J

last: Hand

first: Kyoung-Jae

last: Won

first: Anastassios

last: Vourekas

first: Inchan

last: Choi

first: Chengyang

last: Liu

first: Kumar

last: Vivek

first: Ali

last: Naji

first: Joshua

last: Friedman

first: Klaus

last: Kaestner


title: High-resolution mapping of ribosome footprints from Arabidopsis thaliana

status: Public on Nov 23 2013

city: Chatujak

first: Piyada

last: Juntawong

state: Bangkok

address: 50 Ngamwongwan rd.

department: Genetics

country: Thailand

institute: Kasetsart University

summary: Post-transcriptional gene regulation plays a significant role in the response to oxygen deprivation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, mRNA loading on to polysome, and regulation of ribosome activity during mRNA translation in 7-day-old Arabidopsis seedlings subjected to 2 hour hypoxia treatment.

overall_design: 14 samples, 2 conditions (2 hr hypoxia and 2 hr normoxia), 2 bioreplicates of 3 RNA pools (total mRNA, immunopurified (TRAP) polysomal mRNA, ribosome footprints), 1 bioreplicate of 1 RNA pool (immunopurified (TRAP)-ribosome footprints).

first: Thomas

last: Girke

first: Julia

last: Bailey-Serres


title: Variation of gene expression associated with colonisation of an anthropized environment: comparison between African and European populations of Drosophila simulans

city: Gif-sur-Yvette

first: François

last: Wurmser

address: Bât 13, avenue de la Terrasse

department: INEE

institute: CNRS UPR9034

summary: The comparison of transcriptome profiles among populations is a powerful tool for investigating the role of gene expression change in adaptation to new environments. In this study, we use massively parallel sequencing of 39 cDNAs obtained from large samples of adult males, to compare a population of Drosophila simulans from a natural reserve within its ancestral range (eastern Africa) with a derived population collected in the strongly anthropized Rhone valley (France). The goal was to scan for adaptation linked to the invasion of new environments by the species. Among 15,090 genes retained for the analysis, 794 were found to be differentially expressed between the two populations. We observed an increase in expression of reproduction-related genes in eastern Africa, and an even stronger increase in expression of Cytochrome P450, Glutathione transferase and Glucuronosyl transferase genes in the derived population. These three gene families are involved in detoxification processes, which suggests that pesticides are a major environmental pressure for the species in this area. The survey of the Cyp6g1 upstream region revealed the insertion of a transposable element, Juan, in the regulatory sequence that is almost fixed in the Rhoˆne Valley, but barely present in Mayotte. This shows that Cyp6g1 has undergone parallel evolution in derived populations of D. simulans as previously shown for D. melanogaster. The increasing amount of data produced by comparative population genomics and transcriptomics should permit the identification of additional genes associated with functional divergence among those differentially expressed.

overall_design: Two samples for two populations, with diverse medium. Each sample composed of 100 males from a 100 different wild-caught females

first: Tristan

last: Mary-Huard

first: Jean-Jacques

last: Daudin

first: Dominique

last: Joly

first: Catherine

last: Montchamp-Moreau


title: High-throughput sequencing of small RNAs from adult Taenia multiceps

city: Ya'an

first: Guangyou

last: Yang

address: Xinkang Road 46*

department: Department of Parasitology

institute: Sichuan Agricultural University

summary: sRNA profiling from adult Taenia multiceps by Illumina high-throughput sequencing was used to increase our understanding of the molecular regulation mechanisms of the cestode,find novel biomarkers for the parasitic disease and search new strategies to control these parasites.

overall_design: examination of 6 individuals of adult stage of Taenia multiceps (pooled)

first: Xuhang

last: Wu


title: The long non-coding RNA Paupar regulates the expression of both local and distal genes

status: Public on Nov 21 2013

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series

first: Keith

last: Vance

middle: N

first: Sheena

last: Lee

first: Vladislava

last: Chalei

first: Lesheng

last: Kong

first: Sarah

last: Cooper

first: Peter

last: Oliver

first: Chris

middle: P

last: Ponting


title: Single Cell RNA-Seq

city: Pasadena

first: Diane

last: Trout

state: CA

address: 1200 E California Blvd M/C 156-29

department: Biology

institute: California Institute of Technology

summary: RNA-seq transcriptome measurements are typically performed by isolating RNA from large numbers of cells in culture or tissues. While highly informative, such experiments mask the variability in gene expression patterns that exists between individual cells. To gain insight into the dynamics of gene expression on the level of single-cells, we have carried out the transcriptomes of single-cells from the GM12878 cell line using RNA-seq.

overall_design: Single GM12878 cells were picked and RNA-seq libraries were generated using the SMART-seq protocol. We also carried out RNA-seq experiments on pools of 10, 30 and 100 cells, on 100pg and 10ng of total RNA, and on pools of 10 cells that were subsequently split into 10 separate sample and processed as if they were single cells in order to assess technical variation in our experiments.

first: Barbara

last: Wold

first: Georgi

last: Marinov

first: Brian

last: Williams


title: Two New Stromal Signatures Stratify Breast Cancers with Different Prognosis

city: Stanford

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

summary:
Purpose:  Multiple studies from last decades have shown that the microenvironment of carcinomas plays an important role in the initiation, progression and metastasis of cancer.  Our group has previously identified novel cancer stroma gene expression signatures associated with outcome differences in breast cancer by gene expression profiling of two tumors of fibroblasts as surrogates for physiologic stromal expression patterns.  The aim of this study is to find additional new types of tumor stroma gene expression patterns.
Results:  53 tumors were sequenced by 3SEQ with an average of 29 million reads per sample.  Both the elastofibroma (EF) and fibroma of tendon sheath (FOTS) gene signatures demonstrated robust outcome results for survival in the four breast cancer datasets.  The EF signature positive breast cancers (20-33% of the cohort) demonstrated significantly better outcome for survival.  In contrast, the FOTS signature positive breast cancers (11-35% of the cohort) had a worse outcome.  The combined stromal signatures of EF, FOTS, and our previously identified DTF, and CSF1 signatures characterize, in part, the stromal expression profile for the tumor microenvironment for between 74%-90% of all breast cancers.
Conclusions:  We defined and validated two new stromal signatures in breast cancer (EF and FOTS), which are significantly associated with prognosis.

overall_design: Gene expression profiling by 3SEQ was performed on 8 additional types of fibrous tumors, to identify different fibrous tumor specific gene expression signatures.  We then determined the significance of the fibrous tumor gene signatures in four publically available breast cancer datasets (GSE1456, GSE4922, GSE3494, NKI Dataset).

first: Shirley

middle: X

last: Zhu

first: Alayne

middle: L

last: Brunner

first: Matt

last: van de Rijn

first: Robert

last: West


title: Global transcriptome analysis of the pH regulator pacC in Colletotrichum gloeosporioides

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

institute: Weizmann Institute of Science

summary: Colletotrichum gloeosporioides, a widely distributed economically important agent in postharvest fruit disease thrives by massive secretion of ammonia to alkalize its environment and activate its pathogenicity genes. We sequenced the C. gloeosporioides transcriptomes of WT and a ∆pacC mutant, a major gene regulator under changing pH, under pH 7.0 in order to examine pacC regulation. Transcriptome analysis of the ∆pacC strain showed that 468 and 458 genes were up or down regulated, respectively. Both the up and down regulated genes were clustered into similar functions including: transporters to maintain cellular homeostasis, cell wall degrading enzymes to optimize pathogenicity and GATA-like transcription factors. Suggesting that activation of pacC under alkaline condition regulates genes expression to fit their optimal PKa. The transcript level predictions were verified by growth in different pH and fruit infection. Further analyses showed pacC binding sites were over-represented in the promoters of the pacC up-regulated genes but not in the promoters of the down-regulated genes, where instead, GATA-like binding sites were prominent. Evolutionary conservation of pacC control was sought by examining the gene orthologs in 5 fungal genomes whose members display contrasting alkaline or acidifying pathogenicity strategies. The results showed that irrespective of pathogen colonization strategy, only orthologs of up-regulated genes showed over-representation of pacC binding sites. Significantly, the down regulated orthologs revealed cross-genome over-representation of GATA transcription factor binding sites. Thus, pacC is a phylogenetically conserved fungal mechanism exerting dual pH control for maintaining homeostasis and pathogenicity in changing environments.

overall_design: Examination of C. gloeosporioides WT and a ∆pacC mutant grown under pH 7.0

first: Noam

last: Alkan

first: Eli

last: Reuveni

first: Dov

last: Prusky

last: Fluhr


title: Genome-wide identification of KANADI1 target genes

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

country: Germany

institute: Max Planck Institute for Developmental Biology

summary: A combination of ChIP-Seq and genome-wide mRNA expression profiling using tilling arrays was used to identify genes bound and regulated by the KANADI1 transcription factor.

overall_design:
A. thaliana KAN1 ChIP-seq w. control, 2 replicates

This submission represents ChIP-Seq component of study.

first: Stephan

last: Wenkel

first: Marcus

last: Heisler

first: Yakun

last: Xie

first: Paz

last: Merelo


title: M. tuberculosis Rv3263 Knockout

city: College Station

first: Thomas

last: Ioerger

address: Interdisciplinary Life Sciences Building

department: Computer Science

institute: Texas A&M University

summary: We determine gene expression profile for the knockout of Rv3263 (DNA Methyltransferase) and compared to wildtype M. tuberculosis.

overall_design: Two RNA-Seq datasets are included: wildtype (H37Rv_SS1) and knockout  (delta_Rv3263)

first: Scarlet

last: Shell

first: Sarah

last: Fortune


title: High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: N6-methyladenosine (m6A) is the most ubiquitous mRNA base modification, but little is known about its precise location, temporal dynamics, and regulation. Here, we generated genomic maps of m6A sites in meiotic yeast transcripts at nearly single-nucleotide resolution, identifying 1,308 putatively methylated sites within 1,183 transcripts. We validated 8/8 methylation sites in different genes with direct genetic analysis, demonstrated that methylated sites are significantly conserved in a related species, and built a model that predicts methylated sites directly from sequence. Sites vary in their methylation profiles along a dense meiotic time-course, and are regulated both locally, via predictable methylatability of each site, and globally, through the core meiotic circuitry. The methyltransferase complex components localize to the yeast nucleolus, and this localization is essential for mRNA methylation. Our data illuminates a conserved, dynamically regulated methylation program in yeast meiosis, and provides an important resource for studying the function of this epitranscriptomic modification.

overall_design: Examination of m6A methylation under various conditions

first: Agarwala

last: Sudeep

first: Eric

last: Lander

first: Gerald

last: Fink

first: Aviv

last: Regev


title: Commensal microbe-derived butyrate epigenetically induces colonic regulatory T cells

status: Public on Nov 20 2013

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN


title: Genome-wide analyses of the DRB response of the histone H3 Lys36 methylation state, as well as Ash1l occupancy in mouse embryonic stem cells.

summary: Using wild type and Ash1l ∆SET mutant embryonic stem cells, against a prevalent notion, here we report di-,tri-methylation of histone H3 Lys36 occur independently of ongoing transcription. Ash1l ∆SET mutant shows the impaired methylation levels in broad range of genome. Intriguingly, data implicate that a binding of retinoic acid receptor to a certain genomic region promotes installation of the tri-methylation in the retinoic acid receptor-associated gene independent of its ongoing transcription.

overall_design: Examination of 2 different histone modifications in 2 cell types in 2 different conditions. Examination of Ash1l occupancy in 2 different conditions.

first: Kenichi

last: Nishioka

first: Ken

last: Higashimoto

first: Jafar

last: Sharif

middle: A


title: Deep sequencing of the small RNA transcriptome of blood leukocytes from Parkinson's disease patients prior to and following deep brain stimulation (DBS) and as compared with healthy control volunteers

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

institute: UCL

summary: We report the application of small RNA sequencing technology for high-throughput profiling of microRNA molecules (miRNAs) in blood leukocytes of Parkinson's Disease (PD) patients. Expression changes which may contribute to PD pathogenesis and reaction to treatment were identified in RNA preparations from blood leukocyte samples collected from PD patients prior to and following DBS neurosurgery on stimulation and following a short one hour cessation of the electrical stimulation (which enabled dissociation of the surgery effects from the electrical stimulation alone) and from matched healthy control volunteers, all under signed informed consents.

overall_design: Examination of four states: Parkinson's Disease (PD) patients 1 day prior to DBS, PD patients a few weeks after DBS neurosurgery (upon symptoms stabilization) both on and following one hour electrical stimulation cessation, and age-matched healthy control volunteers.

first: Hagai

last: Bergman

first: Michal

last: Bronstein

first: Zvi

last: Israel

first: Hermona


title: Global Analysis of the Transcriptional Response of Whitefly to Entomopathogenic Fungi Beauveria bassiana Reveals New Insights on Host-Pathogen Interactions

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

summary: We investigated the transcriptional response of invasive Mediterranean (MED) species of the whitefly B. tabaci complex (commonly referred to as Q biotype) to entomopathogenic fungi Beauveria bassiana using Illumina sequencing technology.

overall_design: Nearly 1,000 of control whiteflies, 48h fungal-induced whiteflies and 72h fungal-induced whiteflies were collected, respectively.

first: Jun

last: Xia

first: Chang

middle: R

last: Zhang

first: Xiao

first: Shu

last: Liu


title: Identification of differentially expressed small RNAs of colon cancer stem cells.

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Colorectal carcinoma (CRC) is one of the most common cancers worldwide. Re-evaluating our current knowledge on CRC and developing novel therapeutic strategies is still crucial. Accumulating evidence suggests that cancer cells possess characters reminiscent of those of normal stem cells. Unveiling small RNAs responsible for cell stemness and chemoradioresistance should eventually lead to the development of novel therapeutic approaches.

overall_design: Expression profiles of parental CRC cells and cancer spheres expanded under stem cell medium cultivation were generated for identifying key regulators.

first: Hsei-Wei


title: Hdac6 regulates Tip60-p400 function in stem cells

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR


title: Viral small RNAs in Sindbis virus-infected mammalian cells

status: Public on Nov 19 2013

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: Small RNAs play a critical role in host-pathogen interaction. In insects, for instance, small RNA-mediated silencing or RNA interference (RNAi) represents the main antiviral defense system. However, the antiviral role of RNAi has not been clearly proven in higher vertebrates. On the contrary, it is well established that the cell response relies on the recognition of viral RNAs by host pattern recognition receptors (PRR) to trigger the activation of the interferon pathway. Based on this evidence, we wished to contribute to this research field by identifying and characterizing small non-coding RNAs produced in mammalian cells upon RNA virus infection. We focused on Sindbis virus (SINV), the prototypical arbovirus, which by definition, is able to infect both vertebrate hosts and invertebrate vectors and triggers the interferon pathway or RNAi, respectively.

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design: Taking advantage of large scale sequencing, we cloned and sequenced small RNAs from both mock and SINV-infected mammalian cells (HEK 293 and VERO). We identified a novel population of viral small RNAs (vsRNAs) that accumulate as 20 to 30 nt species during infection. We assessed that this viral small RNA population is modified in 3'end and derived from the activation of the cellular antiviral endoribonuclease RNaseL. Altogether our results indicate a potential role for the SINV-derived small RNAs in the host defense mechanism.

first: Erika

last: Girardi

first: Béatrice

last: Chane-Woon-Ming

first: Mélanie

last: Messmer

first: Pasi

last: Kaukinen


title: Characterization of Snail-associated small RNAs in colon cancer cells

platform_organism:
Primates
Homo sapiens


title: Hdac6 regulates Tip60-p400 function in stem cells (sequencing)

summary: The Tip60 (also known as Kat5) lysine acetyltransferase functions broadly as a transcriptional co-activator that acetylates histones. In contrast, Tip60 functions in embryonic stem cells (ESCs) both to silence genes that promote differentiation and to activate genes required for proliferation. The mechanism by which Tip60 functions as a repressor is unknown. Here we show that the class II histone deacetylase Hdac6 co-purifies with Tip60-p400 complex from ESCs and is necessary for complete silencing of most differentiation genes targeted by Tip60. In contrast to differentiated cells, where Hdac6 is mainly cytoplasmic and does not interact with Tip60, Hdac6 is largely nuclear in ESCs and neural stem cells (NSCs) and interacts with Tip60-p400 in both cell types. Hdac6 is enriched at promoters bound by Tip60-p400 in ESCs, but while Tip60 binds on both sides of transcription start sites (TSSs), Hdac6 binding overlaps with only the downstream Tip60 peak. Surprisingly, Hdac6 does not deacetylate histones at these sites, but rather is required for Tip60 binding. These data suggest that nuclear exclusion of Hdac6 during differentiation plays a major role in modulation of Tip60-p400 function.

overall_design:
We determined the genome-wide localization of Tip60 and Hdac6 in mouse ES cells, and examined genomic binding profiles of Tip60 and Hdac6 upon indicated knockdown by ChIP-seq.
We examined genomic binding profiles of p400 upon indicated knockdown by ChIP-seq.

first: Poshen

first: Jui-Hung

last: Hung

first: Taylor

last: Hickman

first: Andrew

middle: H

last: Coles

first: James

middle: F

last: Carey

first: Zhiping

last: Weng

first: Feixia

last: Chu

first: Thomas

middle: G

last: Fazzio


title: Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation [ChIP-Seq]

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

summary:
Here, we have focused on studying the link between metabolic changes driven by the differentiation into mature adipocytes of a human preadipocyte cell line (SGBS) and their regulation, through a combined experimental and computational approach.
By collecting data on gene expression, PPARg, CEBPa, LXR and H3K4me3 genome-wide ChIP-seq profles and transcriptome-wide microRNA target identification for miR-27a, miR29a and miR-222, and using constraint-based modeling to estimate metabolic reaction activity, we obtained a comprehensive set of information highlighting how epigenetic, transcriptional and post-transcriptional regulation impacts the metabolic network.

overall_design: Illumina Solexa sequencing: Six samples in total. Two ChIP-seq samples were prepared using an antibody against H3K4me3 active TSS chromatin marker from human SGBS preadipocyte and day 10 differentiated SGBS adipocyte cells. From day 10 differentiated SGBS cells additional three samples were prepared using an antibody against PPARg, CEBPa and LXRa to determine their genome-wide binding. One input control sample is included.

first: Mafalda

last: Galhardo

first: Lasse

last: Sinkkonen

last: Sauter


title: The long non-coding RNA Paupar regulates the expression of both local and distal genes [CHART-seq]

city: Oxford

first: Stephen

last: Sansom

summary: Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis. Here, we describe the genomically local and more distal functions of Paupar, a vertebrate-conserved and central nervous system-expressed lncRNA transcribed from a locus upstream of the gene encoding the Pax6 transcription factor. Knockdown of Paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neuronal differentiation. Paupar acts in a transcript-dependent manner both locally, to regulate Pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with Pax6 protein. Paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is modulated by Paupar transcript levels. Our findings demonstrate that a lncRNA can function in trans at transcriptional regulatory elements distinct from its site of synthesis to control large-scale transcriptional programmes.

overall_design: The genome-wide binding profile of Paupar was determined using Capture Hybridisation Analysis of RNA Targets (CHART)-Seq technique (Simon et al, Proc Natl Acad Sci U S A 108: 20497-20502, 2011) in N2A cells. Following the CHART-seq protocol, we used RNase H elution to recover genomic DNA associated with endogenous Paupar transcripts and genomic DNA associated with a control oligonucleotide (corresponding to the E.coli LacZ sequence). We identified Paupar binding sites in comparison both to DNA recovered using the control LacZ oligonucleotide and to an input DNA sample from N2A cells.

first: Keith

last: Vance

first: Sheena

last: Lee

first: Vladislava

last: Chalei

first: Lesheng

last: Kong

first: Sarah

middle: E

last: Cooper

first: Peter

last: Oliver

first: Chris

last: Ponting


title: Gene expression analysis of Ash1l mutant mouse embryonic stem cells.

first: Takaho

last: Endo

summary: Using wild type and Ash1l deltaSET mutant embryonic stem cells, here we report differences of gene expression pattern under undifferentiated state and differentiated state. Interestingly, gene expression changes are frequently observed in a subset of gene group that is regulated by Polycomb group proteins.

overall_design: Examination of 2 cell types in 2 different conditions.

first: Kenichi

last: Nishioka

first: Ken

last: Higashimoto

first: Jafar

last: Sharif


title: Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs

city: Montreal

first: Soizik

last: Berlivet

state: Quebec

address: 110, avenue des Pins Ouest

institute: Institut de Recherches Cliniques de Montreal

summary: HoxA genes exhibit central roles during development and causal mutations have been found in several human syndromes including limb malformation.  Despite their importance, information on how these genes are regulated is lacking.  Here, we report on the first identification of bona fide transcriptional enhancers controlling HoxA genes in developing limbs and show that these enhancers are grouped into distinct topological domains at the sub-megabase scale (sub-TADs). We provide evidence that target genes and regulatory elements physically interact with each other through contacts between sub-TADs rather than by the formation of discreet "DNA loops".  Interestingly, there is no obvious relationship between the functional domains of the enhancers within the limb and how they are partitioned among the topological domains, suggesting that sub-TAD formation does not rely on enhancer activity.  Moreover, we show that suppressing the transcriptional activity of enhancers does not abrogate their contacts with HoxA genes.  Based on these data, we propose a model whereby chromatin architecture defines the functional landscapes of enhancers.  From an evolutionary standpoint, our data points to the convergent evolution of HoxA and HoxD regulation in the fin-to-limb transition, one of the major morphological innovations in Vertebrates.

overall_design: The chromatin binding of the RNA polymerase II and the sub-unit Med12 of the Mediator complexe were analysed by ChIP-sequencing mouse distal E11.5 forelimb. This approach allowed us to identify the position of limb-specific enhancers.

first: David

last: Langlais

first: Josée

last: Dostie

first: Marie

last: Kmita


title: Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation

first: Merja

last: Heinäniemi

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

overall_design: Refer to individual Series


title: Prediction of gene activity based on an integrated multi-omics approach.

city: Baltimore

first: Karen

last: Reddy

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

institute: Johns Hopkins University

summary: An increasingly common method for predicting gene activity is genome-wide chromatin immunoprecipitation of ‘active’ chromatin modifications followed by massively parallel sequencing (ChIP-seq). Using a novel ChIP-seq quantification method (cRPKM), we tested the power of such ChIP-seq strategies to predict relative protein and RNA levels at the pre-pro-B and pro-B differentiation stages in early B cell lymphopoiesis. Using a multi-omics approach that compares promoter chromatin status (ChIP-seq; published in GSE:21978) with ongoing active transcription (GRO-seq; published in GSE:40173), steady state mRNA (RNA-seq), inferred mRNA stability, and relative proteome abundance measurements (iTRAQ), we demonstrate that active chromatin modifications at promoters are a good indicator of transcription and steady state mRNA levels. Moreover, we found that promoters with active chromatin modifications exclusively in one of these cell states frequently predicted differentially expressed proteins. However, we found that many genes whose promoters have non-differential but active chromatin modifications also displayed changes in expression of their cognate proteins. This large class of developmentally and differentially regulated proteins that was uncoupled from chromatin status used mostly post-transcriptional mechanisms. Interestingly, the most differentially expressed protein in our B-cell development system, 2410004B18Rik, was regulated by a post-transcriptional mechanism, which further analyses indicated was mediated by an identified miRNA. These data provide a striking example of how our integrated multi-omics data set can be useful in uncovering regulatory mechanisms.

overall_design: Total RNA from mouse pre-pro-B and pro-B cells, depleted of rRNA and small RNAs, was sequenced using a strand specific, single end sequencing strategy.

first: Mohammad

last: Heydarian

first: Jevon

last: Cutler

first: Teresa

last: Romeo-Luperchio

last: Mitchell

first: Min-Sik

last: Kim

first: Akhilesh

last: Pandey

first: Barbara

last: Sollner-Webb