title: Transcriptional mechanisms controlling direct motor neuron programming

first: Shaun

last: Mahony

summary: Transcriptional programming of cell identity promises to open up new frontiers in regenerative medicine by enabling the efficient production of clinically relevant cell types. We examine if such cellular programming is accomplished by transcription factors that each have an independent and additive effect on cellular identity, or if programming factors synergize to produce an effect that is not independently obtainable. The combinations of Ngn2-Isl1-Lhx3 and Ngn2-Isl1-Phox2a transcription factors program embryonic stem cells to express a spinal or cranial motor neuron identity respectively. The two alternate expression programs are determined by recruitment of Isl1/Lhx3 and Isl1/Phox2a pairs to distinct genomic locations characterized by two alternative dimeric homeobox motifs. These results suggest that the function of programming modules relies on synergistic interactions among transcription factors and thus cannot be extrapolated from the study of individual transcription factors in a different cellular context.

overall_design:
In this study, we functionally characterize induced motor neurons that have been directly generated from ES cells via the forced expression of two different combinations of three transcription factors. Spinal motor neurons are induced via the expression of Ngn2, Isl1, and Lhx3 (iNIL), while cortical motor neurons are induced via the expression of Ngn2, Isl1, and Phox2a (iNIP). Here we profile the gene expression patterns of both types of induced motor neurons, directed differentiation motor neurons, and control cells. In all, 20 microarray experiments are provided in this submission, including 3 replicates of a control condition, 3 replicates of cells that have 24hrs induction of iNIL, 2 replicates of induced spinal motor neurons (induction of iNIL for 48hrs) that have been Hb9-GFP sorted, 3 replicates of induced spinal motor neurons exposed to retinoic acid that have been Hb9-GFP sorted, 3 replicates of motor neurons that have been differentiated in vitro using RA and Hh signalling, 3 replicates of induced cortical motor neurons (induction of iNIP for 48hrs), and 3 replicates of cells in which Isl1 in induced alone (induction of iI for 48hrs).
For ChIP-Seq Samples: In this study, we functionally characterize induced motor neurons that have been directly generated from ES cells via the forced expression of two different combinations of three transcription factors. Spinal motor neurons are induced via the expression of Ngn2, Isl1, and Lhx3 (iNIL), while cortical motor neurons are induced via the expression of Ngn2, Isl1, and Phox2a (iNIP). The genome-wide binding of some of the programming factors is characterized here using ChIP-seq. We characterize the binding of Lhx3 and Isl1/2 in iNIL cells, Phox2a and Isl1/2 in iNIP cells, and Isl1/2 in cells in which Isl1 is induced alone (iI). There are 7 Illumina sequence datasets in this submission; one replicate for each of iLhx3-V5 and Isl1/2 in iNIL cells, two replicates for each of iPhox2a-V5 and Isl1/2 in iNIP cells, and one replicate for Isl1/2 in iI cells. An appropriate pseudo-IP control experiment is included.

first: Esteban

last: Mazzoni

first: Carolyn

last: Morrison

first: Stephane

last: Nedelec

last: Gifford

first: Hynek

last: Wichterle


title: Genome wide RNA-seq analysis of E14.5 Smchd1 wild type and mutant placenta

status: Public on Jul 03 2013

city: Brisbane

first: Graham

last: Kay

address: 300 Herston Rd

country: Australia

institute: Queensland Institute of Medical Research

type: Expression profiling by high throughput sequencing

summary: We report the deregulation of expression in Fi (C57Bl6/J x FVB/n) E14.5 male mouse placenta are that homozygous for a mutant allele of the Smchd1 gene (ie Smchd1MommeD1/MommeD1).

overall_design: RNA-seq analysis of Smchd1+/+ vs Smchd1MommeD1/MommeD1

middle: F

first: Arne

middle: W

last: Mould


title: Genome wide RNA-seq analysis of E9.5 Smchd1 wild type and mutant embryos

summary: We report the deregulation of expression in E9.5 male mouse embryos are that homozygous for a mutant allele of the Smchd1 gene (ie Smchd1MommeD1/MommeD1).


title: Epigenomic alterations in localized and advanced prostate cancer

city: New York

first: Pei-Chun

last: Lin

state: NY

address: 1300 York Ave

department: Pathology and Laboratory Medicine

country: USA

institute: Cornell Weill Medical College

type: Methylation profiling by high throughput sequencing

summary: Here we used Illumina NGS for high-throughput profiling of the DNA methylome in seven human benign prostate tissues, seven human primary prostate cancer and six human castration resistant prostate cancer patient samples. These data were used to profile the CpG cytosine methylation pattern at single base resolution in each sample and to determine differentially methylated cytosines and regions among samples.

overall_design: Enhanced Reduced Representation Bisulfite Sequencing (ERRBS, MspI,150–400 bp size fractions) of 20 human prostate tissues (benign prostate tissues, localized and metastatic prostate cancer)

middle: C

first: Mark

middle: A

last: Rubin

first: Olivier

last: Elemento


title: Genome wide RNA-seq analysis of Smchd1 wild type and mutant

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

overall_design: Refer to individual Series


title: Characterization and Comparison of the Leukocyte Transcriptomes of Three Cattle Breeds

status: Public on Jul 02 2013

city: East Lansing

first: Wen

last: Huang

state: MI

address: 474 S Shaw Ln, Anthony Hall 1205F

department: Animal Science

institute: Michigan State University

summary: In this study, we use mRNA-Seq to characterize and compare the leukocyte transcriptomes of Holstein, Jersey, and Cholistani with respect to variations in sequence, expression, and splicing.

sample_organism:
Bos taurus
Bos indicus

platform_organism:
Bos taurus
Bos indicus

overall_design: Poly A+ RNA are extracted from leukocytes of pools of blood drawn from cows of three different breeds, Holstein, Jersey, and Cholistani. The objective of the study is to compare sequence variation and gene expression of the three cattle breeds.

first: Hasan

last: Khatib


title: Genome-wide maps of histone modifications in male and female mouse liver

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here we map six chromatin modifications -- H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K9me3, and H3K27me3 -- genome-wide in male and female mouse liver in order to identify histone modifications that characterize sex-biased genes and sex-biased DNase hypersensitive sites and their regulation by plasma growth hormone (GH) profiles, which are sexually dimorphic. We find distinct mechanisms of regulation in male liver and female liver: sex-dependent K27me3-mediated repression is an important mechanism of repression of female-biased, but not of male-biased, genes, and a sex-dependent K4me1 distribution, suggesting nucleosome repositioning by pioneer factors, is observed at male-biased, but not female-biased, regulatory sites.  STAT5-mediated activation is most strongly associated with sex-biased chromatin modifications, while BCL6-mediated repression primarily occurs in association with sex-independent chromatin modifications, both at binding sites and at target genes. These samples are part of a study on chromatin states in male and female mouse and their role in sex-biased liver gene expression (A Sugathan and DJ Waxman (2013) Molec Cell Biol).

overall_design: Examination of six different histone modifications in male and female mouse liver.

first: Aarathi

last: Sugathan

first: Ekaterina

middle: V

last: Laz

middle: J


title: Reconstructing de novo silencing of an active plant retrotransposon: dynamics, mechanisms, biological implications

city: Zurich

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

country: Switzerland

institute: ETHZ

type: Non-coding RNA profiling by high throughput sequencing

summary: In plants, maintenance-methylation mediated by METHYLTRANSFERASE-1 (MET1), siRNA-directed de-novo methylation, and chromatin remodeling by DECREASE IN DNA METHYLATION -1 (DDM1) promote transcriptional gene-silencing of transposable elements (TEs). This process is mostly investigated at steady states reflecting how long-established silent conditions are maintained, faithfully re-iterated or temporarily modified during growth, stress and over generations. How invasive TEs are detected and silenced de novo, however, remains largely unknown. Using inbred lineages of hybrid Arabidopsis epigenomes combining wild-type and met1 or ddm1 chromosomes, we have deciphered the timing, spatial distribution and mechanisms underpinning the proliferation and eventual demise of the endogenous retrotransposon évadé (EVD). Both developmental and molecular features of EVD biology, including a remarkable ability to evade RNA interference, ultimately contribute to its silencing over multiple generations. The underlying processes are accompanied by widespread diversification of the Arabidopsis genome and de-novo epiallelism creating an extensive reservoir of selectable and potentially adaptive traits.

overall_design: Differential expression of EVADE small RNAs between three generations of one specific Col0 met1 derived EpiRIL.

first: Arturo

last: Marí-Ordóñez

first: Mathilde

last: Etcheverry

first: Vincent

last: Colot

last: Voinnet


title: High resolution view of bacteriophage lambda gene expression by ribosome profiling

status: Public on Jul 01 2013

city: Tianjin

first: Huifeng

last: Jiang

address: #32XiQiDao Tianjin airport economic park

country: China

institute: Tianjin Institute of Industrial Biotechnology

summary: Bacteriophage lambda is one of the most extensively studied organisms, and has been a primary model for understanding basic modes of genetic regulation.  Here we examine the progress of lambda gene expression during phage development by ribosome profiling, and thereby provide a very high resolution view of lambda gene expression.  The known genes are expressed in a predictable fashion, authenticating the analysis.  But many previously unappreciated potential open reading frames become apparent in the expression analysis, revealing an unexpected complexity in the pattern of lambda gene function.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We chose temperature induction of the classic cI857 repressor mutation in a lysogen of E. coli MG1655 in order to synchronize the lytic process, sampling the lysogen and control non-lysogen both before and 2, 5, 10, and 20 minutes after shifting the temperature from 32° to 42°.  The last sample time was chosen to be before any significant cell lysis, but during the later stages of lytic gene expression. Total protected nucleotides within open reading frames were summed to determine the density of translation of each reading frame.  We take this number to indicate the overall rate of translation, although obviously this assumes that pauses in translation do not excessively affect the overall rate.  Since the expression level is not normalized for the copy number of the replicating phage DNA, it thus encompasses both the effect of DNA template availability on mRNA synthesis and the efficiency of utilization of messengers by ribosomes.

first: Xiaoqiu

last: Liu

first: Zhenglong

last: Gu

first: Jeffrey

last: Roberts


title: The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

city: Philadelphia

first: Justin

last: Cotney

state: PA

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

summary: The evolution of human anatomical features likely involved changes in gene regulation during development. However, the nature and extent of human specific developmental regulatory functions remain unknown. We obtained a genome-wide view of cis regulatory evolution in human embryonic tissues by comparing the histone modification H3K27ac, which provides a quantitative readout of promoter and enhancer activity, during human, rhesus, and mouse limb development. Based on increased H3K27ac, we find that 13% of promoters and 11% of enhancers have gained activity on the human lineage since the human-rhesus divergence. These gains largely arose by modification of ancestral regulatory activities in the limb or potential co-option from other tissues and are likely to have heterogeneous genetic causes. Most enhancers that exhibit gain of activity in humans originated in mammals. Gains at promoters and enhancers in the human limb are associated with increased gene expression, suggesting they include molecular drivers of human morphological evolution.

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus

overall_design:
ChIP-Seq and RNA-Seq of autopod tissue of developing limb buds of Human (E33-E47), rhesus (E31-E36), and mouse (E10.5-E13.5).

No raw data are provided for human samples. Human alignments were anonymized by removing sequence information and converting to bed format.

first: James

middle: P

last: Noonan


title: Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS


title: Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells (ChIP-seq)

summary: The effects of diverse stresses on promoter selectivity and transcription regulation by the tumor suppressor p53 are poorly understood. We have taken a comprehensive approach to characterizing the human p53 network that includes p53 levels, binding, expression and chromatin changes under diverse stresses. Human osteosarcoma U2OS cells treated with anti-cancer drugs Doxorubicin or Nutlin-3 led to strikingly different p53 gene binding patterns based on ChIP-seq experiments. While two contiguous RRRCWWGYYY decamers is the consensus binding motif, p53 can bind a single decamer and function in vivo. Although the number of sites bound by p53 was 6-times greater for Nutlin-3 than Doxorubicin, expression changes induced by Nutlin-3 were much less dramatic compared to Doxorubicin. Unexpectedly, the solvent DMSO alone induced p53 binding to many sites common to Doxorubicin; however, this binding had no effect on target gene expression. Together, these data imply a two-stage mechanism for p53 transactivation where p53 binding only constitutes the first stage. Furthermore, both p53 binding and transactivation were associated with increased active histone modification H3K4me3. We discovered 149 putative new p53 target genes including several that are relevant to tumor suppression, revealing potential new targets for cancer therapy and expanding our understanding of the p53 regulatory network.

overall_design: ChIP-seq profiles of p53 binding in U2OS cells with no treatment or treated with either Doxorubicin, Nutlin-3, or DMSO. Input sequences were used as controls.

first: Daniel

last: Menendez

first: Thuy-Ai

middle: T

last: Nguyen

first: Johannes

middle: M

last: Freudenberg

first: Viju

last: Mathew

first: Carl

last: Anderson

first: Raja

last: Jothi

first: Michael

last: Resnick


title: Late life rapamycin treatment reverses age-related heart dysfunction

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: We report the mRNA profile of aged mice (24 months old) fed either a control diet or a diet containing Rapamycin (14 ppm) for 3 months. After drug treatement, the hearts of the mice were removed and total mRNA was removed from the tissue. Analysis revealed that there were 700 significantly differentially expressed genes between the control fed group and the Rapamycin diet group by our analysis.

overall_design: Heart tissue samples from age-matched control mice (n=10) and rapamycin fed mice (n=10) were extracted for total RNA. The samples were sequenced using Illumina HiSeq 2000 (50 basepair paired-end sequencing). The sequencing yielded quality scores greater than 30 with an average of 10 million reads per sample. 34,293 genes were mapped back to the MGSCv37 C57BL/6J mouse genome (maximum paired distance=300 and minimum=130, minimum number of reads per mapping = 5, maximum number of mismatches= 2, with the reads being mapped to unique sites in the genome).

last: Flynn

first: Monique

middle: N

last: O’Leary

first: Christopher

last: Zambataro

first: Emmeline

last: Academia

last: Presley

first: Brittany

last: Garrett

first: Artem

last: Zykovich

first: Sean

middle: D

last: Mooney

first: Randy

last: Strong

first: Clifford

last: Rosen

last: Nelson

first: Pankaj

last: Kapahi

first: Brian

middle: K

last: Kennedy


title: Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

summary: Most eukaryotic genes express mRNAs with alternative polyadenylation sites at their 3’ ends.  Here we show that polyadenylated 3’ termini in three yeast species (S. cerevisiae, K. lactis, D. hansenii) are remarkably heterogeneous.  Instead of a few discrete 3’ ends, the average yeast gene has an “end zone”, a >200 bp window with >60 distinct poly(A) sites, the most utilized of which represents only 20% of the mRNA molecules. The pattern of polyadenylation within this zone varies across species, with D. hansenii possessing a higher focus on a single dominant point closer to the ORF terminus. Some polyadenylation occurs within mRNA coding regions with a strong bias towards the promoter. The polyadenylation pattern is determined by a highly degenerate sequence over a broad region and by a local sequence that relies on A residues after the cleavage point.  Many dominant poly(A) sites are predicted to adopt a common secondary structure that may be recognized by the cleavage/polyadenylation machinery.  We suggest that the end zone reflects a region permissive for polyadenylation, within which cleavage occurs preferentially at the A-rich sequence.  In S. cerevisiae strains, D. hansenii genes adopt the S. cerevisiae polyadenylation profile, indicating that the polyadenylation pattern is mediated primarily by species-specific factors.

sample_organism:
Saccharomyces cerevisiae
Debaryomyces hansenii
Kluyveromyces lactis

overall_design: Four sequencing lanes containing direct RNA sequence from S. cerevisiae (strains JGY2000 and two replicates of AB1380), K. lactis strain CLIB209, D. hansenii strain NCYC2572, and S. cerevisiae strains JYAC06 and JYAC07, each harboring D. hansenii sequences on a YAC.   AB1380 is the non-YAC-containing S. cerevisiae parental strain for JYAC06 and JYAC07.

first: Joseph

last: Geisberg

first: Yi

last: Jin

first: Xiaochun

last: Fan

first: Kevin

last: Struhl


title: Whole transcriptome RNA-seq of undiseased human prefrontal cortex

first: Paul

last: Ryvkin

address: 423 Guardian Dr, 1404 Blockley Hall

department: Pathology

institute: University of Pennsylvania

summary: We report the application of high-throughput RNA sequencing to the human prefrontal cortex. The brain dataset was obtained by sequencing total RNAs extracted from the dorsolateral prefrontal cortex of five deceased human patients with no apparent pathology, followed by depletion of ribosomal RNA to obtain all non-rRNA coding and non-coding RNAs in the human brain transcriptome.

overall_design: Five samples were sequenced, four coming from frozen brain tissue (frontal cortex) of deceased female human patients with no remarkable pathology, and one from a male patient with no remarkable pathology.

first: Li-San

last: Wang

last: Gregory


title: H3K9ac.L3.Solexa

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_5102
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina  NGS sequencing platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K9ac (target is H3K9ac); Developmental Stage 3rd Instar Larvae

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron


title: Oncogenic Hras-dependent epidermal growth is inhibited following RNAi-mediated depletion of Ctnnb1 and Mllt6

city: Seattle

first: Slobodan

last: Beronja

address: PO Box 19024, Mailstop D4-100

institute: Fred Hutchinson Cancer Research Center

summary: Genome-wide RNAi screens in mice identified Ctnnb1 and Mllt6 as physiological regulators of HrasG12V-dependent epidermal hyperplasia. To probe the consequences of Ctnnb1 and Mllt6 on HrasG12V-dependent oncogenic growth, we examined how their depletion impacts gene expression in the HrasoncoX2 epidermis. We performed RNA-seq analysis of FACS-purified embryonic epidermal cells, followed by network analysis of differentially regulated transcripts. Whether Ctnnb1 or Mllt6, knockdown markedly enhanced activity of genes restricting growth, and decreased expression of genes promoting epidermal proliferation. This contrasted with known transcriptional changes that typically follow epidermal expression of oncogenic Hras. Moreover, there was a significant overlap in genes whose expression was affected by Mllt6 and β-catenin, further implying a level of shared function.

overall_design: Transcriptional profiles of epidermal progenitors of embryonic day 18.5 animals of wild-type, HrasG12V, and HrasG12V depleted of Ctnnb1 or Mllt6 backgrounds.

first: Brice

last: Keyes


title: ER and GR crosstalk at the Genomic Level in mouse mammary cells

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: We report changes in ER and GR binding profiles genome-wide upon co-treatment with Dex and E2 when compared to Dex or E2 treatments alone.

overall_design: We examine ER and GR binding under four different treatments (unt, Dex, E2, and Dex + E2).

first: Tina

middle: B

last: Miranda

first: Gordon

last: Hager

first: Myong-Hee

last: Sung


title: RACK1 function in the miRNA pathway

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

summary:
MicroRNAs (miRNAs) regulate plant development by post-transcriptional regulation of target genes. In Arabidopsis thaliana, DCL1 processes precursors (pri-miRNAs) to miRNA duplexes, which associate with AGO1. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) or AGO1, respectively, to facilitate efficient and precise pri-miRNA processing and miRNA loading. In this study, we show that the
accumulation of plant microRNAs depends on RECEPTOR FOR ACTIVATED C KINASE 1 (RACK1), a scaffold protein found in all higher eukaryotes. miRNA levels are reduced in rack1 mutants and our data suggest that RACK1 affects the microRNA pathway via several distinct mechanisms involving direct interactions with known microRNA factors: RACK1 ensures the accumulation and processing of some pri-miRNAs, directly interacts with SERRATE and is part of an AGO1 complex. As a result, mutations in RACK1 lead to misregulation of miRNA target genes, which is important for ABA responses and phyllotaxy. In conclusion, our study discovered complex functioning of RACK1 proteins in the Arabidopsis miRNA pathway, which are important for miRNA production and therefore plant development.

overall_design: sequencing of small RNAs from WT and rack1abc mutants (two biological replicates each)

first: Corinna

last: Speth

first: Eva-Maria

last: Willing

first: Korbinian

last: Schneeberger


title: Characterization of small RNAs and their targets in Amborella trichopoda

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: The small RNAs and their targets were characterized in Amborella genome by deep sequencing the small RNA populations of leaf tissue and opened-female flower tissue. The small RNA targets were also validated from degradome populations of leaf tissue and opened-female flower tissue.

overall_design: We generated integrative maps of small RNA profiles (sRNA-seq) and degradome (PARE-seq) profiles to characterize the miRNAs and their targets from Amborella.

first: Siwaret

last: Arikit

first: Jixian

last: Zhai


title: The metabolic niche of a prominent sulfate-reducing human gut bacterium [1]

status: Public on Jun 29 2013

city: St Louis

first: Federico

middle: E

last: Rey

address: 4444 Forest Park Blvd

institute: Washington University

summary: Sulfate-reducing bacteria (SRB) colonize the guts of ~50% of humans and produce H2S, a signaling molecule with numerous host effects. We used genome-wide transposon mutagenesis and insertion-site sequencing (INSeq), RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy USA adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of carbohydrates and sulfur sources. Diet was a major determinant of functions expressed by this artificial 9-member community and of the genes that impact D. piger fitness; the latter includes high- and low-affinity systems for utilizing ammonia, a limiting resource for D. piger in mice consuming a polysaccharide-rich diet. While genes involved in hydrogen consumption and sulfate reduction are necessary for its colonization, varying dietary free sulfate levels did not significantly alter levels of D. piger, which can obtain sulfate from the host in part via cross-feeding mediated by Bacteroides-encoded sulfatases. Chondroitin sulfate, a common dietary supplement, increased D. piger and H2S levels without compromising gut barrier integrity. A chondroitin sulfate-supplemented diet together with D. piger impacted the assemblage’s substrate utilization preferences, allowing consumption of more reduced carbon sources, and increasing the abundance of the H2-producing Actinobacterium, Collinsella aerofaciens. Our findings provide genetic and metabolic details of how this H2-consuming SRB shapes the responses of a microbiota to diet ingredients, and a framework for examining how individuals lacking D. piger differ from those that harbor it.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: mRNA profiles of fecal contents from gnotobiotic mice colonized with defined consortia of human gut associated microbes

first: Jeffrey

middle: I

last: Gordon


title: Vitamin C induces Tet-dependent DNA demethylation in ES cells to promote a blastocyst-like methylome [MeDIP-Seq]

status: Public on Jun 30 2013

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 675 West 10th Avenue

department: Epigenomics

institute: BCCA Genome Sciences Centre

summary: DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germline and may be mediated by Tet (ten-eleven-translocation) enzymes, which convert 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC). Tet enzymes have been extensively studied in mouse embryonic stem (ES) cells, which are generally cultured in the absence of Vitamin C, a potential co-factor for Fe(II) 2-oxoglutarate dioxygenase enzymes like Tets. Here we report that addition of Vitamin C to ES cells promotes Tet activity leading to a rapid and global increase in hmC. This is followed by DNA demethylation of numerous gene promoters and up-regulation of demethylated germline genes. Tet1 binding is enriched near the transcription start site (TSS) of genes affected by Vitamin C treatment. Importantly, Vitamin C, but not other antioxidants, enhances the activity of recombinant human Tet1 in a biochemical assay and the Vitamin C-induced changes in hmC and mC are entirely suppressed in Tet1/2 double knockout (Tet DKO) ES cells. Vitamin C has the strongest effects on regions that gain methylation in cultured ES cells compared to blastocysts and in vivo are methylated only after implantation. In contrast, imprinted regions and intracisternal A-particle (IAP) elements, which are resistant to demethylation in the early embryo, are resistant to Vitamin C-induced DNA demethylation. Collectively, this study establishes that Vitamin C is a direct regulator of Tet activity and DNA methylation fidelity in ES cells.

overall_design: Oct4-GiP mouse embryonic stem (ES) cells were cultured in the presence or absence of Vitamin C (L-ascorbic acid 2-phosphate, 100 μg/ml) for 12 or 72 hours. Cells were maintained in N2B27 medium supplemented with LIF (1000 U/ml), MEK inhibitor PD0325901 (1 μM), and GSK3β inhibitor CHIR99021 (3 μM). Genomic DNA was used for DNA immunoprecipitation with antibodies against 5-hydroxymethylcytosine (hmC) or 5-methylcytosine (mC).  Immunoprecipitated DNA was adaptor-ligated for paired-end sequencing on an Illumina HiSeq and sequence reads were aligned to the mm9 mouse reference genome for analysis.

first: Kathryn

last: Blaschke

first: Kevin

last: Ebata

first: Mohammed

last: Karimi

first: Matthew

last: Lorincz

first: Miguel

last: Ramalho-Santos


title: ER, GR, and E2

first: Songjoon

last: Baek

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

overall_design: Refer to individual Series


title: Control of Reproductive Floral Organ Identity Specification in Arabidopsis by the C Function Regulator AGAMOUS

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD


title: Changes in DNaseI hypersensitivity upon co-treatment of cells with Dex and E2

summary: We report changes in DNaseI accessibility genome-wide upon co-treatment with Dex and E2 when compared to Dex or E2 treatments alone.

first: Tina

last: Miranda

first: Gordon

last: Hager

first: Myong-Hee

last: Sung


title: Analysis of the nitrate-responsive transcriptome of the Arabidopsis root

city: Santiago

first: Elena

last: Vidal

address: Avenida Libertador Bernardo O'Higgins 340

department: Genetica Molecular y Microbiologia

country: Chile

institute: Pontificia Universidad Catolica de Chile

summary: Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out. In this work, we employed the Illumina high throughput sequencing technology to perform an integrated analysis of the poly-A+ enriched and the small RNA fractions of the Arabidopsis thaliana root transcriptome in response to nitrate treatments. Our sequencing strategy identified new nitrate-regulated genes including 40 genes not represented in the ATH1 Affymetrix GeneChip, a novel nitrate-responsive antisense transcript and a new nitrate responsive miRNA/TARGET module consisting of a novel microRNA, miR5640 and its target, AtPPC3. This nitrate-responsive miRNA/target module might be involved in controlling carbon flux to assimilate nitrate into amino acids, suggesting that microRNAs can have both developmental and metabolic functions in the nitrate response of Arabidopsis roots.

overall_design: Arabidopsis thaliana wild-type Col-0 plants were grown in hydroponic nitrate-free medium with 0.5 mM ammonium succinate as the only N-source for two weeks and were treated with 5 mM KNO3, or 5 mM KCl as control, for 2 hours. Total RNA from two independent sets of plants (biological replicates) was extracted from roots, and poly-A+ enriched and sRNA fractions were used to construct libraries for Illumina sequencing.

first: Tomás

last: Moyano

first: Gabriel

last: Krouk

first: Manpreet

middle: S

last: Katari

first: Milos

last: Tanurdzic

first: W

middle: R

last: Mc Combie

first: Gloria

last: Coruzzi

first: Rodrigo

last: Gutiérrez


title: Promoter directionality is controlled by U1 snRNP and polyadenylation signals

status: Public on Jun 28 2013

city: New York

first: Xuebing

last: Wu

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

summary: Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-coding genes is limited by unknown mechanisms. In particular, although RNA polymerase II (RNAPII) initiates divergently from most active gene promoters, productive elongation occurs primarily in the sense-coding direction. Here we show in mouse embryonic stem cells that asymmetric sequence determinants flanking gene transcription start sites control promoter directionality by regulating promoter-proximal cleavage and polyadenylation. We find that upstream antisense RNAs are cleaved and polyadenylated at poly(A) sites (PASs) shortly after initiation. De novo motif analysis shows PAS signals and U1 small nuclear ribonucleoprotein (snRNP) recognition sites to be the most depleted and enriched sequences, respectively, in the sense direction relative to the upstream antisense direction. These U1 snRNP sites and PAS sites are progressively gained and lost, respectively, at the 5' end of coding genes during vertebrate evolution. Functional disruption of U1 snRNP activity results in a dramatic increase in promoter-proximal cleavage events in the sense direction with slight increases in the antisense direction. These data suggest that a U1-PAS axis characterized by low U1 snRNP recognition and a high density of PASs in the upstream antisense region reinforces promoter directionality by promoting early termination in upstream antisense regions, whereas proximal sense PAS signals are suppressed by U1 snRNP. We propose that the U1-PAS axis limits pervasive transcription throughout the genome.

overall_design: 3' end sequencing of poly (A) + RNAs in mouse ES cells with and without U1 snRNP inhibition using antisense morpholino oligonucleotides (AMO). Each with two biological replicates.

first: Albert

last: Almada

first: Andrea

last: Kriz

first: Christopher

last: Burge

first: Phillip

last: Sharp


title: Vitamin C induces Tet-dependent DNA demethylation in ES cells to promote a blastocyst-like methylome

first: Martin

last: Hirst


title: Control of Reproductive Floral Organ Identity Specification in Arabidopsis by the C Function Regulator AGAMOUS (ChIP)

first: Pat

last: Ryan

summary: Characterization of the activities of the transcription factor that AG encodes throughout flower development using perturbation assays and ChIP-Seq in combination with a floral induction system (FIS) that allows a stage-specific analysis of flower development.

overall_design: Examination of genomic regions bound by fully functional AG-GFP protein at approx floral stage 4-5 as compared to a negative control sample.

first: Diarmuid

last: Ó’Maoiléidigh

first: Samuel

last: Wuest

first: Patrick

last: Raganelli

first: Frank

last: Wellmer


title: Chromatin maps of the Drosophila melanogaster TrxG protein Ash1 and FSH

city: Basel

first: Christian

last: Beisel

address: Mattenstrasse 26

department: Biosystems Science and Engineering

institute: ETH Zurich

summary: Trithorax group (TrxG) proteins counteract Polycomb silencing by an as yet uncharacterized mechanism. A well-known member of the TrxG is the histone methyltransferase Absent, Small, or Homeotic discs 1 (ASH1). In Drosophila ASH1 is needed for the maintenance of Hox gene expression throughout development, which is tightly coupled to preservation of cell identity. In order to understand the molecular function of ASH1 in this process, we performed affinity purification of tandem-tagged ASH1 followed by mass spectrometry (AP-MS) and identified FSH, another member of the TrxG as interaction partner. Here we provide genome-wide chromatin maps of both proteins based on ChIP-seq.

overall_design: Our Dataset comprises of 4 ChIP-seq samples using chromatin from S2 cells which was immunoprecipitated, using antibodies against Ash1, FSH-L and FSH-SL.

first: Tobias

last: Kockmann

first: Renato

last: Paro


title: Bach2 represses effector programmes to stabilize Treg-mediated immune homeostasis

status: Public on Jun 27 2013

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

summary: Through their functional diversification, CD4+ T cells play key roles in both driving and constraining immune-mediated pathology. Transcription factors are critical in the generation and maintenance of cellular diversity and negative regulators antagonistic to alternate fates often act in conjunction with positive regulators to stabilize lineage specification1. Polymorphisms within the locus encoding a transcription factor BACH2 are associated with diverse immune-mediated diseases including asthma2, multiple sclerosis3, Crohn¹s disease4-5, coeliac disease6, vitiligo7 and type 1 diabetes8. A role for Bach2 in maintaining immune homeostasis, however, has not been established. Here, we define Bach2 as a broad regulator of immune activation that stabilizes immunoregulatory capacity while repressing the differentiation programmes of multiple effector lineages in CD4+ T cells. Bach2 was required for efficient formation of regulatory (Treg) cells and consequently for suppression of lethal inflammation in a manner that was Treg cell dependent. Assessment of the genome-wide function of Bach2, however, revealed that it represses genes associated with effector cell differentiation. Consequently, its absence during Treg polarization resulted in inappropriate diversion to effector lineages. In addition, Bach2 constrained full effector differentiation within Th1, Th2 and Th17 cell lineages. These findings identify Bach2 as a key regulator of CD4+ T-cell differentiation that prevents inflammatory disease by controlling the balance between tolerance and immunity.

overall_design:
The role of Bach2t to regulate immune homeostasis was investigated by mapping DNA binding profiles of Bach2 in iTreg condition.
The function of Bach2 was also evaluated by comparing transcriptome in WT and Bach2-deficient iTreg cells and further comparison was done with transcriptome in naive, Th1, Th2, and Th17 conditions.

first: Rahul

last: Roychoudhuri

first: Kiyoshi

last: Hirahara

first: Kambiz

last: Mousavi

first: Hossein

last: Zare

first: Hongwei

last: Sun

first: Hayato

last: Takahashi

first: Vittorio

last: Sartorelli

first: Yuka

last: Kanno

first: John

last: O'Shea

first: Nicholas

last: Restifo


title: FANCD2 Activates Transcription of TAp63 and Suppresses Tumorigenesis

city: BOSTON

first: eunmi

last: Park

address: 44 Binney street

institute: Dana-Farber Cancer Institute

summary: Fanconi Anemia (FA) is a rare genetic disorder characterized by an increased susceptibility to squamous cell cancers.   Fifteen FA genes are known, and the encoded proteins cooperate in a common DNA repair pathway.  A critical step is the monoubiquitination of the FANCD2 protein, and cells from most FA patients are deficient in this step.  How monoubiquitinated FANCD2 suppresses squamous cell cancers is unknown.  Here we show that Fancd2-deficient mice are prone to Ras oncogene-driven skin carcinogenesis, while Usp1-deficient mice, expressing elevated cellular levels of Fancd2-Ub, are resistant to skin tumors.  Moreover, Fancd2-Ub activates the transcription of the tumor suppressor TAp63, thereby promoting cellular senescence and blocking skin tumorigenesis.  For FA patients, the reduction of FANCD2-Ub and TAp63 protein levels may account for their susceptibility to squamous cell neoplasia. Taken together, Usp1 inhibition may be a useful strategy for upregulating TAp63 and preventing or treating squamous cell cancers in the general non-FA population.

overall_design: Examination of FANCD2 binding after UV treatment in 293T cells

first: Eunmi

first: Alan

last: D'Andrea


title: Pruning of the adipocyte cistrome by hematopoietic master regulator PU.1

first: Joanna

last: DiSpirito

address: Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: IDOM


title: Enhanced upregulation of CRH mRNA expression in the rat nucleus accumbens after a delayed second injection of methamphetamine

city: Baltimore

first: Jean Lud

last: Cadet

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

summary: Methamphetamine (METH) is a widely abused illicit amphetamine that causes acute biochemical and molecular changes in the brain.  However, there are very few studies that have investigated the long-term effects of a single METH exposure in adult animals. The purpose of this study was thus to determine the consequences of a single injection of METH (10) mg/kg) on the biochemical and transcriptional effects of a second challenge injection of the drug (2.5 mg/kg) given one month later. Towards that end, we measured monoamine levels and gene expression by microarray and quantitative PCR analyses in the nucleus accumbens (NAc) of 4 groups of rats: saline-pretreated and saline-challenged (SS); saline-pretreated and METH-challenged (SM); METH-pretreated and saline-challenged (MS); and METH-pretreated and METH-challenged (MM). The rats were euthanized 2 hours after the acute challenge injection and NAc samples were harvested. The acute METH challenge caused increases in NAc DA and HVA levels in both the SM and MM groups. Microarray analyses revealed that an injection of METH (2.5 mg/kg) produced acute changes (1.8-fold; p < 0.01) in the expression of 418 (358 up-, 60 downregulated) genes including several immediate early genes (IEGs) such as Arc, c-fos, and fosB in the SM group. Several neuropeptides including Cart, Crf (Crh), and vasopressin were upregulated in that group.  Injection of the higher dose of METH (10 mg/kg) did not influence monoamine levels but caused changes in 510 (345 up-, 165 downregulated) transcripts measured one month later (MS group). This list included Cart and Crf but not any IEGs. The MM group showed changes in 774 (572 up-, 202 downregulated) genes that also included vasopressin, Cart, and Crf whose expression was enhanced by the second METH injection.  Quantitative PCR confirmed the METH-induced changes in the expression of the neuropeptides. We also confirmed the METH-induced potentiation of Crf expression in the METH-pretreated group.  These observations suggest that a single injection of a moderate dose of METH can produce long-lasting changes in gene expression in the rodent NAc. The long-term increases in Crf expression also suggest that a single injection of a moderate METH dose can cause prolonged dysregulation in the endogenous stress system in the rat brain.

first: Jean

middle: L

first: Christie

last: Brannock

first: Jonathan

last: Katz

first: Munanchu

last: Poudel

first: Joshua

last: Newman

first: Bruce

last: Ladenheim

first: Michael

last: McCoy

first: Irina

last: Krasnova

first: Elin

last: Lehrmann

first: Kevin

last: Becker

first: Subramaniam

last: Jayanthi


title: CLIP-seq of S. cerevisiae Drn1-TAP and Dbr1-TAP

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: Data for replicate Drn1-TAP and Dbr1-TAP CLIP-seq experiments to identify RNA-protein interactions

overall_design: Drn1-TAP and Dbr1-TAP CLIP-seq


title: Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing

city: Gießen

first: Andreas

last: Gogol-Döring

address: Wiesenstraße 14

department: MNI

institute: Technische Hochschule MIttelhessen

summary: The Drosophila melanogaster gene Dscam can generate thousands of different ectodomains via mutual exclusive splicing of three large exon clusters. The isoform diversity plays a profound role in both neuronal wiring and pathogen recognition. However, it remained unexplored how many isoforms are indeed expressed, whether the splicing choice between the clusters is independent and why the diversity encoded in the gene locus seems to be beyond necessity. To address these questions, we developed IsomSeq, a novel multiple segment sequencing method that allows to directly quantify the alternatively spliced exon combination of Dscam isoforms within an entire cellular and organismal transcriptome.

overall_design: We sequenced the dscam repertoire of adult brain, S2 cell line, and 5 different developmental stages (embryo, L1, L2, L3, pupa)

first: Wei

last: Sun

first: Xintian

last: You

first: Haihuai

last: He

first: Yoshiaki

last: Kise

first: Ansgar

last: Klebes

first: Dietmar

last: Schmucker

last: Chen


title: Multiplexed Illumina sequencing libraries from picogram quantities of DNA

city: Boston

first: Sarah

middle: Keating

last: Bowman

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

summary: High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Application of this method allows whole genome studies from samples where material or yields are limiting.

overall_design: Comparison of ChIP-seq libraries constructed from 100 pg DNA (this study) and nanograms of DNA (modENCODE). ChIP antibody: H3K27me3, Active Motif 31955.

first: S

first: R

last: Kingston


title: Gene expression analysis of murine peritoneal macrophages deficient for SAMHD1 and IFNAR

city: Dresden

first: Tina

last: Schumann

address: Fetscherstraße 74

department: Medical Faculty "Carl Gustav Carus"

institute: Institute of Immunology

summary: To investigate the contribution of type-1 IFN signalling to the upregulation of IFN- stimulated genes in SAMHD1-deficient cells, we performed global gene expression analysis of SAMHD1-deficient IFNAR-/- macrophages.

overall_design: Peritoneal macrophages from ten SAMHD1-deficient IFNAR-/-  and six SAMHD1-deficient controls were FACS sorted. RNA was subjected to next generation mRNA sequencing.

first: Rayk

last: Behrendt

last: Dahl

first: Dimitra

last: Alexopoulou


title: Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer

city: Tampere

first: Janne

last: Seppälä

address: Biokatu 8

country: Finland

institute: Institute of Biomedical Technology

summary: Androgen receptor (AR) is overexpressed in the majority of castration-resistant prostate cancers (CRPCs). Our goal was to study the effect of AR overexpression on the chromatin binding of the receptor and to identify AR target genes that may be important in the emergence of CRPC. We have established two sublines of LNCaP prostate cancer (PC) cell line, one overexpressing AR 2–3-fold and the other 4–5-fold compared with the control cells. We used chromatin immunoprecipitation (ChIP) and deep-sequencing (seq) to identify AR-binding sites (ARBSs). We found that the number of ARBSs and the AR-binding strength were positively associated with the level of AR when cells were stimulated with low concentrations of androgens. In cells overexpressing AR, the chromatin binding of the receptor took place in 100-fold lower concentration of the ligand than in control cells. We conﬁrmed the association of AR level and chromatin binding in two PC xenografts, one containing AR gene ampliﬁcation with high AR expression, and the other with low expression. By combining the ChIP-seq and expression proﬁling, we identiﬁed AR target genes that are upregulated in PC. Of them, the expression of ZWINT, SKP2 (S-phase kinase-associated protein 2 (p45)) and FEN1 (ﬂap structure-speciﬁc endonuclease 1) was demonstrated to be increased in CRPC, while the expression of SNAI2 was decreased in both PC and CRPC. FEN1 protein expression was also associated with poor prognosis in prostatectomy-treated patients. Finally, the knock-down of FEN1 with small interfering RNA inhibited the growth of LNCaP cells. Our data demonstrate that the overexpression of AR sensitizes the receptor binding to chromatin, thus, explaining how AR signaling pathway is reactivated in CRPC cells.

overall_design: Examination of AR binding with 9 cell line samples + control and 2 xenograft samples + control. ChIPseq with AR antibody in 3 different LNCaP derivative cell lines overexpressing AR upon treatment with different androgen concentrations and 2 different tumor xenografts expressing different AR levels.

first: Alfonso

last: Urbanucci

first: Biswajyoti

last: Sahu

first: Antti

last: Larjo

first: Kati

last: Waltering

first: Robert

last: Vessella

first: Teuvo

last: Tammela

first: Harri

last: Lähdesmäki

first: Olli

middle: A

last: Jänne

first: Tapio

last: Visakorpi


title: Pruning of the adipocyte cistrome by hematopoietic master regulator PU.1 (ChIP-seq)

city: Philadelphia

first: Joanna

last: DiSpirito

institute: University of Pennsylvania

summary: "Master" transcription factors are the gatekeepers of lineage identity. As such, they have been a major focus of efforts to manipulate cell fate for therapeutic purposes. The ETS transcription factor PU.1 has a potent ability to confer macrophage phenotypes on cells already committed to a different lineage, but how it overcomes the presence of other master regulators is not known. The nuclear receptor PPARγ is the master regulator of the adipose lineage, and its genomic binding pattern is well characterized in adipocytes. Here, we show that when expressed at macrophage levels in mature adipocytes, PU.1 bound a large fraction of its macrophage sites, where it induced chromatin opening and the expression of macrophage target genes. Strikingly, PU.1 markedly reduced the genomic binding of PPARγ without changing its abundance. PU.1 expression repressed genes with nearby adipocyte-specific PPARγ binding sites, while a common macrophage-adipocyte gene expression program was retained. Together, these data reveal unexpected lability within the adipocyte PPARγ cistrome and show that even in terminally differentiated cells, PU.1 can remodel the cistrome of another master regulator.

overall_design: ChIP-seq was performed on 3T3-L1 adipocytes from two treatment groups: (1) adipocytes transduced with a control adenovirus expressing beta-galactosidase (LACZ-Ads) and (2) adipocytes transduced with an adenovirus expressing full-length murine PU.1 cDNA (PU.1-Ads). Nuclear lysates from each group were used for PPARg ChIP. For PU.1-Ads, PU.1 ChIP was also performed. To generate chromatin for ChIP-seq, DNA from three immunoprecipitations per condition was pooled. This process was repreated from a second set of L1 adipocytes to generate two biological replicates for sequencing. Genomic input DNA was sequenced from the first biological replicate only.

first: J

first: B

last: Fang

first: F

last: Wang

first: M

last: Lazar


title: Orchestrated intron retention regulates normal granulocyte differentiation [RNA-Seq]

city: Camperdown

first: william

last: ritchie

state: NSW

address: Building 93

institute: centenary institute

summary: Using mRNA-seq, we determined intron retaining genes that were differentially regulated in FACS purified cells at three progressive stages of mouse granulopoiesis; CD34+Kit+Gr-1low promyelocytes, CD34-Kit-Gr-1mid myelocytes and CD34-Kit-Gr-1high granulocytes. We found that IR affects 86 genes, including those specific to granulocyte (Lyz2 and MMP8) and nuclear architecture (Lmnb1 and Lbr). IR was associated with the decrease in protein levels measured by mass spectrometry (P=0.0015, binomial test). There was a significant overlap of IR between human and mouse (P=2.85E-22, hypergeometric test), showing that IR is conserved.Inhibition of NMD in granulocytes resulted in marked accumulation of 39/86 intron retaining mRNAs (P<0.05, RUV procedure with Holm-Bonferroni correction), indicating that IR triggers NMD to downregulate mRNA and protein expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Sequencing of polyadenylated RNA from three types of myeloid cells (promyelocytes, myelocytes and granulocytes) using Illumina GAIIx

first: William

last: Ritchie

first: Justin

last: Wong


title: Dynamic Expression of Imprinted Genes Associates with Maternally Controlled Nutrient Allocation during Maize Endosperm Development

city: Tucson

first: Xiangfeng

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

department: School of Plant Sciences

institute: University of Arizona

summary: In angiosperms, the endosperm provides nutrients for embryogenesis or seed germination and is the primary tissue where gene imprinting occurs. To map the imprintome of the early developing endosperm in maize, we performed high-throughput transcriptome sequencing of the kernels at 0, 3, 5 days after pollination (DAP) and the endosperms at 7, 10, and 15 DAP produced from the B73 and Mo17 reciprocal crosses. We observed a gradual increase of paternal gene mRNAs in the 3- and 5-DAP kernels. In the 7-DAP endosperm, the majority of the tested genes reached a ratio of 2m:1p suggesting that paternal genes were nearly fully activated by 7 DAP. A total of 116, 234 and 63 imprinted genes exhibiting parent-specific expression were identified in the 7-, 10-, and 15-DAP endosperms, respectively. The highest amount of paternally expressed genes (PEGs) was found at 7 DAP mainly due to the significantly deviated parental allele expression ratio of these genes at this stage, while nearly 80% of the maternally expressed genes (MEGs) were specific to 10 DAP which were primarily attributed to the sharply increased expression levels compared to the other stages. GO enrichment analysis of the imprinted genes indicated the 10-DAP-specific MEGs were involved in the nutrient uptake and allocation through auxin signaling pathway in the maize endosperm coincident with the endosperm developmental stage associated with the beginning of starch and storage protein accumulation

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: Guosheng

last: Li

first: Hao

last: Chen

first: John

last: Laurie

first: Chuang

last: Ma

first: Dongfang

first: Yingyin

last: Yao

first: Brian

last: Larkins

first: Qixin

last: Sun

first: Ramin

last: Yadegari

first: Zhongfu

last: Ni


title: BACH2 mediates negative selection and p53-dependent tumor suppression at the pre-B cell receptor checkpoint.

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: The B cell-specific BACH2 transcription factor is required for affinity maturation of mature B cells. Here, we show that Bach2 mediates negative selection at the pre-B cell receptor checkpoint and functions as a critical safeguard against leukemogenesis. Bach2-mediated activation of p53 is required for stringent elimination of pre-B cells that failed to productively rearrange immunoglobulin VH-DJH gene segments, and thus lack pre-B cell receptor expression. Upon productive VH-DJH gene rearrangement, pre-B cell receptor signaling ends negative selection through BCL6-mediated repression of p53. In patients with pre-B acute lymphoblastic leukemia, Bach2-mediated checkpoint control is frequently compromised and low levels of Bach2 expression represent a strong independent predictor of poor clinical outcome. Bach2+/+ pre-B cells resist leukemic transformation by Myc through Bach2-dependent upregulation of p53. Upon transformation with Myc, Bach2-/- pre-B cells fail to upregulate p53, form large colonies and initiate fatal leukemia in transplant recipient mice. ChIP-seq and gene expression analyses revealed that BACH2 competes with BCL6 for promoter binding and reverses BCL6-mediated repression of p53 and multiple other checkpoint control genes. These findings identify Bach2 as a key activator of p53 in pre-B cells, which is critical to maintain stringency of the pre-B cell receptor checkpoint and an important barrier against leukemic transformation.

overall_design: ChIP-seq using BACH2 and BCL6 antibodies in OCI-Ly7 cells

first: Chuanxin

last: Huang

first: Ari

last: Melnick


title: The developmental life cycle of the enteric parasite Entamoeba invadens: transcriptome analysis reveals a crucial role for phospholipase D in stage conversion

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

summary: RNA-seq was performed on encysting and excysting E. invadens, a parasite of reptiles that is used as a model system to study stage conversion in Entamoeba species, including the human pathogen E. histolytica. The goal of the project was to identify changes to the transcriptome during development, in order to better understand the mechanisms of development.

overall_design: RNA was isolated from trophozoites, from encysting parasites (at 8, 24, 48 and 72 hours after transfer to encystation media) and from excysting parasites (2 and 8 hours after induction of excystation), converted to cDNA, and sequenced on a SOLiD platform. RNA-seq data was used to refine gene models, find potential unannotated genes, and identify genes that are developmentally regulated.

first: Gareth

last: Weedall

first: Neil

last: Hall

first: Upinder

last: Singh


title: Muscleblind-like proteins regulate embryonic stem cell-specific alternative splicing and reprogramming

status: Public on Jun 26 2013

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

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

overall_design: Refer to individual Series


title: Multicolor miRNA fluorescence in situ hybridization for tumor differential diagnosis

last: Renwick

address: 1230 York Ave

institute: Rockefeller University

summary: We profiled and quantitated miRNAs in two skin tumors (Basal cell carcinoma and Merkel cell carcinoma) and identified tumor-specific miRNAs. We used these tumor-specific miRNAs to guide development of miRNA fluorescence in situ hybridization.

overall_design: 2 barcoded sequencing runs, including 40 unique samples (36 used in manuscript). The details of each sample can be found in Supplementary Tables S1 and S2.

first: Pavol

last: Cekan

first: Paul

last: Masry

first: Sean

last: McGeary

first: Jason

last: Miller

first: Markus

last: Hafner

first: Aleksandra

last: Mihailovic

first: Pavel

last: Morozov

first: Miguel

last: Brown

first: Tasos

last: Gogakos

first: Mehrpoya

last: Mobin

first: Einar

last: Snorrason

first: Harriet

last: Feilotter

first: Xiao

last: Zhang

first: Clifford

last: Perlis

first: Hong

last: Wu

first: Mayte

last: Suarez-Farinas

first: Huichen

last: Feng

first: Masahiro

last: Shuda

first: Patrick

last: Moore

first: Victor

last: Tron

first: Yuan

last: Chang

first: Thomas

last: Tuschl


title: Muscleblind-like proteins regulate embryonic stem cell-specific alternative splicing and reprogramming I

first: Manuel

last: Irimia

summary: Previous investigations of the core gene regulatory circuitry that controls embryonic stem cell (ESC) pluripotency have largely focused on the roles of transcription, chromatin and non- coding RNA regulators. Alternative splicing (AS) represents a widely acting mode of gene regulation, yet its role in the regulation of ESC pluripotency and differentiation is poorly understood. Here, we identify the Muscleblind-like RNA binding proteins, MBNL1 and MBNL2, as conserved and direct negative regulators of a large program of AS events that are differentially regulated between ESCs and other cell types. Knockdown of MBNL proteins in differentiated cells causes switching to an ESC-like AS pattern for at least half of these AS events. Among the events is an ESC-specific AS switch in the forkhead family transcription factor FOXP1 that controls pluripotency. Consistent with a central and negative regulatory role for MBNL proteins in pluripotency, their knockdown significantly enhances the expression of key pluripotency genes and the formation of induced pluripotent stem cells (iPSCs) during somatic cell reprogramming.

overall_design: mRNA profiles of various embryonic stem cells, tissues and cell lines from human and mouse using high-throughput sequencing data and the role of MBNL proteins in regulation of ESC-differential alternative splicing

first: Yu

last: Liu

last: Han

first: Benjamin

middle: J

last: Blencowe

first: Jeffrey

last: Wrana


title: Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency

status: Public on Jun 25 2013

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

summary: The presence of acetylated histone H3K56 in human embryonic stem cells (ESCs) correlates positively with the binding of Nanog, Sox2 and Oct4 (NSO) transcription factors at their target gene promoters. However, the function of H3K56ac there has been unclear. We now report that Oct4 interacts with K56ac and it is functionally important since K56ac combines with NSO factors in ChIP-Seq to mark the regions associated with pluripotency better than NSO alone. Therefore, our data suggest that K56ac plays a critical role in binding to Oct4 to promote the pluripotency of ESCs.

overall_design: Genome wide location analysis ChIP-Seq was performed in mouse embryonic stem cell lines (E14Tg2a) for histone H3K56ac.

first: Y

last: Xue

first: C

last: Song

first: M

last: Grunstein


title: Identification of LIN28-bound mRNAs reveals features of target recognition and regulation

city: Berlin

first: Robin

last: Graf

address: Robert Rössle Str. 10

department: Immune Regulation and Cancer

institute: Max Delbrueck Center for Molecular Medicine

summary: The conserved human LIN28 RNA-binding proteins function in development, maintenance of pluripotency and oncogenesis. We used PAR-CLIP and a newly developed variant of this method, iDo-PAR-CLIP, to identify LIN28B targets as well as sites bound by the individual RNA binding domains of LIN28B in the human transcriptome at nucleotide resolution. The position of target binding sites reflected the known structural relative orientation of individual LIN28B binding domains, validating iDo-PAR-CLIP. Our data suggest that LIN28B directly interacts with most expressed mRNAs and members of the let-7 microRNA family. The Lin28 binding motif detected in pre-let-7 was enriched in mRNA sequences bound by LIN28B. Upon LIN28B knock down, cell proliferation and the cell cycle were strongly impaired. Quantitative shotgun proteomics of LIN28B depleted cells revealed significant reduction of protein synthesis from its RNA targets that function in translation, mRNA splicing and cell cycle control. Computational analyses provided evidence that the strength of protein synthesis reduction correlated with the location of LIN28B binding sites within target transcripts.


title: Differential expression in Wn5a and vector transduced 4T1 cells.

city: Birmingham

first: Rosa

last: Serra

state: AL

address: 1918 University Blvd. 660 MCLM

department: Cell Biology

institute: University of Alabama at Birmingham


title: Differential expression in Wn5a and vector transduced 4T1 cells. [RNA-Seq]

summary: A highly metastatic breast cancer cell line, 4T1, was used to generate stable Wnt5a expressing and vector only control cells.  Cells were generated using lentivirus infection and selection with blasticidin. Expression of Wnt5a was confirmed using western blot.  Cell behaviour was characterized. Wnt5a expressing cells exhibited reduced migration in a transwell assay and reduced metastasis in a tail vein injection assay. Growth was not significantly affected.

overall_design: One sample of each condition.

first: David

last: Crossman


title: Fine structure analysis and epigenetic properties of a de novo centromere on a chromosome fragment in maize

city: Beijing

first: Junling

last: Pang

address: No.12 Zhongguancun South St.,Haidian District

institute: Chinese Academy of Agricultural Sciences

summary: A small fragment from maize chromosome 3 was created by irradiation by Stadler and Roman and named Duplication 3a (or Dp3a). This small chromosome does not contain any detectable CentC and CRM sequences, but when molecular features of functional centromeres such as CENH3 and CENP-C were examined, they were present. Immunolocalization analysis of phosphorylation of Ser-10 of histone H3 levels on Dp3a shows a pattern typical of a functional centromere. Meiotic analysis revealed that sister chromatids divided equationally at meiosis I as do all small chromosomes examined to date in maize. To examine the sequences associated with CENH3, chromatin immunoprecipitation (ChIP) was carried out with anti-CENH3 antibodies using material from young seedlings with and without Dp3 chromosome as the tissue source. The ChIPed DNA sample was then labeled for FISH detection and prepared for Illumina sequencing.The ChIP-Seq reads were mapped to the B73 reference genome and a significant peak was detected in the Dp3a sample that span 350 kb of the long arm of chromosome 3, which is the candidate region for association with CENH3. ChIP-bisulfite-seq results indicated that there is a slightly increased DNA methylation level after the centromere formation, approaching the level similar to normal centromere regions. Collectively, the results suggest the formation of a de novo centromere on this fragment that initially must have started at the time of X-irradiation release from the progenitor chromosome. These observations add further evidence for the epigenetic nature of centromere function in maize.

overall_design: ChIP-seq was carried out with anti-CENH3 antibodies using material from young seedlings with and without Dp3a chromosome.  For Dp3a, some ChIPed DNA was treated with sodium bisulfite and prepared for Illumina sequencing to test its methylation level.

first: James

last: Birchler

first: Fangpu


title: FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Genome-wide erasure of DNA methylation takes place in primordial germ cells (PGCs) and early embryos but the signalling mechanisms that induce reprogramming are unknown. Here we show that inhibition of Erk1/2 and Gsk3b signalling in mouse embryonic stem cells (ESCs) by small molecule inhibitors (PD0325901 and CHIR99021, hereafter called 2i) induces genome-wide demethylation on a scale similar to that in PGCs and early embryos, with only major satellites, intracisternal A particles (IAPs) and imprinted genes relatively resistant to erasure. Demethylation involves oxidation of 5-methylcytosine (5mC) in part by Tet1 together with repression of the de novo methyltransferases (Dnmt3a, Dnmt3b) and their regulator Dnmt3L and we identify a cis-acting regulatory region in Dnmt3b that is highly responsive to signalling. Notably, this epigenetic and transcriptional ground state of pluripotency resembles closely that of inner cell mass (ICM) cells of the blastocyst. These insights provide a novel framework for understanding how signalling pathways regulate epigenetic reprogramming.

overall_design: mRNA and methylation profiles of ES cells passaged with or without 2i inhibitors were generated by deep sequencing, using Illumina GAIIx and HiSeq.

first: Gabriella

last: Ficz

first: Timothy

last: Hore

first: Fatima

last: Santos

first: Wendy

last: Dean

last: Oxley

first: Simon

last: Cook

last: Andrews

first: Miguel

last: Branco

first: Wolf

last: Reik


title: KSRP-mediated Transcriptome reshaping

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

country: Italy

institute: Università vita e Salute Ospedale San Raffaele

summary: KSRP knock-down and BMP2 treatment produce a largely overlapping reshape of the transcriptome in C2C12 cells. microRNAs (miRNAs) are essential regulators of development, physiology, and evolution with miRNA biogenesis being strictly controlled at multiple levels. Regulatory proteins, such as KH-type splicing regulatory protein (KSRP), modulate rates and timing of the enzymatic reactions responsible for maturation of select miRNAs from their primary transcripts in response to specific stimuli. Induction of myogenic miRNAs (myomiRs) is essential for muscle differentiation with KSRP phosphorylation being required to convey myogenic signals to enhanced myomiR maturation. Here we show that either KSRP silencing or Bone Morphogenetic Protein (BMP)2-signaling activation in mesenchimal C2C12 cells prevented myogenic differentiation while induced osteoblastic differentiation as revealed by the reshaping of the whole transcriptome analyzed by RNA deep-sequencing. The most striking feature common to both BMP2 signaling activation and KSRP silencing was a blockade of myomiR maturation. Our results demonstrate that phosphorylated SMAD proteins, the transducers of BMP signaling, associate with KSRP and block its interaction with primary-myomiRs. This, in turn, abrogates KSRP-dependent myomiR maturation with the knock-down of SMAD4, 5, and 9 being able to rescue KSRP function. SMAD-induced blockade of KSRP-dependent myomiR maturation, in parallel to the well known SMAD function on gene transcription, inhibits C2C12 cell differentiation into myofibers and contributes to orient cells towards osteoblast lineage. We propose that remodeling of co-regulatory complexes affecting primary-miRNA processing is a mechanism well suited to guide cell fate determination in eukaryotes.

overall_design: Total RNA was prepared from 1. untreated mock-transfected C2C12 cells; 2. BMP2-treated mock-transfected C2C12 cells; 3. untreated shKSRP-transfected C2C12 cells and analyzed by RNA-seq

last: Pasero

last: Giovarelli

first: G

first: R

last: Gherzi

first: P

last: Briata


title: Genome-wide transcriptome analysis of maize (Zea mays c.v. Nathan) plants infected by Colletotrichum graminicola strains.

city: Halle (Saale)

first: Ely

middle: Oliveira

last: -Garcia

state: Sachen-Anhalt

address: Betty Heimann Straße 3

department: Institut für Agrar- und Ernährungswissenschaften (IAEW)

summary:
In order to characterize defense responses not only cytologically, but also on the transcript level, genome-wide sequencing of mRNA isolated from non-infected control leaves and from leaves inoculated either with the WT or with GLS1 overexpressing strains was performed, using Illumina Next Generation Sequencing Technology. In order to identify transcripts specifically induced in leaves infected by β-1,3-glucan-exposing strains, transcript patterns of leaves inoculated with GLS1 overexpressing PtrpC:GLS1 strains were compared with those of the WT.

In PtrpC:GLS1-inoculated leaves, a total of 2179 genes were more than 2.5-fold increased, with many genes known as genes typically up-regulated in PAMP-triggered defense responses. These genes include genes encoding PR proteins enzymes involved in cell wall re-inforcemen, and terpene synthases possibly involved in phytoalexin synthesis. Furthermore, increased transcript abundance of genes encoding serine-threonine receptor-like kinases calmodulin, as well as zinc-finger and WRKY transcription factors have been identified. Other up-regulated genes encode proteins involved in protein degradation, i.e. proteases, ubiquitin ligases, as well as enzymes involved in synthesis of auxin or cytokinin phytohormones.

In comparison, 2164 genes were more than 2.5-fold down-regulated in maize leaves infected by PtrpC:GLS1 strains, as compared to WT-infected leaves. Several of the encoded proteins are known susceptibility factors. Forty-six down-regulated genes code for proteins containing iron or manganese, or are involved in uptake of these ions, suggesting major re-arrangement of the redox-status in maize leaves after β-glucan perception.

overall_design: Examination of plant defense responses in maize plants inoculated with 2 different Colletotrichum graminicola strains.

middle: O

last: Garcia

first: Holger

last: Deising


title: Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity; implications for possible immune adjuvant therapy

status: Public on Jun 23 2013

city: New Orleans

first: Erik

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: Our goal of this study was to perform quantitative and global assessment of EBV gene expression in gastric carcinomas and assess EBV associated cellular pathway alterations.

overall_design: Examination of a gastric carcinoma cell line naturally infected with EBV, SNU-719 using poly-A and ribodepletion RNA-seq data sets

first: Michael

last: Strong

first: Guorong

last: Xu

first: Joseph

last: Coco

first: Carl

last: Baribault

first: Dass

last: Vinay

first: Michelle

last: Lacey

first: Amy

first: Teresa

last: Lehman

last: Seddon

first: Zhen

last: Lin

first: Monica

last: Concha

first: Melody

last: Baddoo

first: MaryBeth

last: Ferris

first: Kenneth

middle: F

last: Swan

first: Deborah

last: Sullivan

first: Matthew

last: Burow

first: Christopher

middle: M

last: Taylor


title: Functional centromere lost centromeric specific sequences but gain new sequences from nearby chromosomal arm.

first: Junling

last: Pang

summary: We identified a newly formed dicentric chromosome (sDic-15) in maize from intrachromosomal recombination and BFB cycles, in which only one centromere is active. The centromeres lost CentC sequences and dramatic reduced the CRM sequences, but when the molecular features of functional centromeres such as CENH3 was examined, they were present. Immunolocalization analysis of phosphorylation of H3T3, H3ser-10 and H2A levels on this new centromere shows a pattern typical of a functional centromere. Meiotic analysis revealed that this dicentric chromosome is table and transmit very well. To examine the new sequences associated with CENH3 in this centromere, chromatin immunoprecipitation (ChIP) was carried out with anti-CENH3 antibodies and material from young seedlings with or without dicentric chromosome. We mapped the ChIP-Seq reads to the reference genome and found a 723kb region from the short arm of maize chromosome 9 involve the new centromere formation. This region is gene-poor and full of TEs, but genes in this region are transcribed. The original 723kb region shows a high DNA methylation level as native centromeres but had no significant change when it involved into new centromere formation. The reactivation of this newly formed centromere indicated that centromere reactivation may not dependent on the relatively intact DNA sequences or topology of original inactive centromere.

overall_design: ChIP-seq was carried out with anti-CENH3 antibodies using material from young seedlings with and without sDic-15 chromosome. For sDic-15, some ChIPed DNA was treated with sodium bisulfite and prepared for Illumina sequencing to test its methylation level.

first: Xiu-Jie

last: Wang

first: Fangpu

last: Han


title: Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor

status: Public on Jun 21 2013

city: Chicago

first: Thien

last: Le

state: IL

institute: University of Chicago


title: Genome wide expression analysis of Ctbp2 knock down mouse F9 cells

city: Amsterdam

first: Prashanth Kumar

last: Bajpe

address: Plesmanlaan 121

department: Molecular Carcinogenesis

country: Netherlands

institute: Netherlands Cancer Institute

summary: Using an RNA interference-based genetic screen in mouse F9 cells we identify the transcriptional corepressor CTBP2 as a coactivator critically required for retinoic acid (RA)-induced transcription. Here we perfom a whole genome transcriptome analysis in F9 cells expressing shRNA for Ctbp2 and Rxr in the absence or presence of retinoic acid (RA). A total of 2,754 genes were found to be upregulated (>2 fold) and 1518 genes were downregulated (>2 fold) in response to RA treatment in the control cells. We find that around 52% and 55% of upregulated genes are dependent on Ctbp2 and Rxr for activation respectively suggesting that Ctbp2 is a coactivator of RA signaling.

overall_design: Whole genome RNA-sequencing in F9 cells expressing shGFP or shCtbp2 or shRxr

first: Prashanth

last: Kumar

first: Sidong

last: Huang


title: Global transcriptome analysis of orange wheat blossom midge, Sitodiplosis mosellana (Gehin) (Diptera: Cecidomyiidae) to identify candidate transcripts regulating diapause

status: Public on Jun 20 2013

city: Zhengzhou

first: ZhongJun

last: Gong

state: Henan

address: HuaYuan Road 116

department: Institute of plant protection

institute: Henan academy of agricultural sciences

summary: Many insects enter a developmental arrest (diapause) that allows them to survive harsh seasonal conditions. Despite the well-established ecological significance of diapause, the molecular basis of this crucial adaptation remains largely unresolved. Sitodiplosis mosellana (Gehin), the orange wheat blossom midge (OWBM), causes serious damage to wheat throughout the northern hemisphere, and sporadic outbreaks occur in the world. Traits related to diapause appear to be important factors contributing to their rapid spread and outbreak. To better understand the diapause mechanisms of OWBM, we sequenced the transcriptome and determined the gene expression profile of this species.

overall_design:
Examination of  different gene expression in DOL and NDOL
Total RNA was extracted separately from DOL and NDOL using Trizol Reagent following manufacturer’s instructions. Approximately 10μg RNA from each sample was used to construct individual DGE libraries. mRNA was isolated as described under cDNA library construction. The cDNA fragments were purified by agarose gel electrophoresis and enriched by PCR amplification. Each library had an insert size of 200 bp, and 42 - 50 bp sequences were generated by Illumina HiSeq 2000 in a single run using paired-end technology.
SRA Study SRP019201.

first: Zhong

first: Yu

middle: Q

last: Wu


title: REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary:
Genome-wide analysis of REST and Polycomb binding in Rest-/- and Eed-/- mouse embryonic stem (mES) cells showed that Rest was required for PRC1 recruitment to a subset of Polycomb regulated neuronal genes. Furthermore, we found that PRC1 can be recruited to Rest binding sites independently of CpG islands and the H3K27Me3 mark., and that PRC2 was frequently increased around Rest binding sites located in CpG-rich regions in the Rest2/2 mES cells.
Published here: PLoS Genet 8(3): e1002494. doi:10.1371/journal.pgen.1002494

overall_design: Examination of REST and Polycomb binding in Rest-/-, Eed-/-, and wt mES cells using ChIP-sequencing. Submitter cannot locate the raw data for GSM1169003, GSM1169004, GSM1169011, GSM1169012, GSM1169015, and GSM1169016.

first: Nikolaj

last: Dietrich

first: Eskild

last: Landt

first: Shuchi

last: Agrawal-Singh

last: Bak

first: Niels

last: Tommerup

first: Juri

last: Rappsilber

first: Erik

last: Södersten

first: Klaus

last: Hansen


title: mRNA and Ribosome Profiling in Four Nematode Species Traversing a Shared Developmental Transition

first: Michael

last: Stadler

address: 300 Pasteur Dr.

institute: Stanford University

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans
Caenorhabditis remanei
Caenorhabditis brenneri

overall_design: mRNA-seq and Ribo-seq

first: Andrew

last: Fire


title: Role for DNA methylation in Gata4-binding in embryonic stem cells-derived mesoderm

status: Public on Jun 24 2013

city: Kyoto

first: Masaki

last: Shigeta

state: Kyoto

address: 465 Kajii-cho, Kawaramachi-street, Hitokojiagaru, Kamigyo-ku

department: Department of Anatomy and Developmental Biology

country: Japan

institute: Kyoto prefectural university of medicine

summary: During embryogenesis, many key transcription factors are used repeatedly, achieving different outcomes depending on cell type and developmental stage. The epigenetic modification of the genome functions as a memory of a cell’s developmental history, and it has been proposed that such modification shapes the cellular response to transcription factors. To investigate the role of DNA methylation in the response to transcription factor Gata4, we have tried to identify GATA4-binding associated genes of WT-type and Dnmt3a-/-Dnmt3b-/-(DKO) in Flk1-based mesoderm progenitor by Gata4 ChIP-analysis.

overall_design: Wild-type and DKO ES cell clones stably expressing dexamethasone (Dex)-inducible Gata4 were generated by introducing an expression plasmid for Gata4 fused with the ligand-binding domain of the human glucocorticoid receptor (Gata4GR) driven by the CAG promoter, by electroporation. For mesoderm differentiation, 5.4 x 10^5 ES for WT, 6.5 x 10^5 ES cells for DKO, were plated onto OP9 stroma-culture in 15-cm dish. Day. 4.5-differentiated cells were treated with 100 nM Dex for 3 hours and then collected as single-cell suspensions using 0.25% trypsin-EDTA, followed by incubation in differentiation medium at 37˚C to allow cell-surface markers to recover. Flk1(+) cells were sorted by AutoMACS (Miltenyi Biotec) and crosslinked with 1% formaldehyde for Gata4 ChIP-seq analysis.

first: Hitoshi

last: Niwa


title: Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling

city: Charlotte

first: Zhengchang

last: Su

address: 9201 University City Blvd

department: Bioinformatics and Genomics

institute: UNC Charlotte

summary: Using a highly efficient and strand-specific RNA-seq method combined with a highly accurate and robust algorithm and tool we developed, TruHMM for assembling full-length transcriptomes,  to profile the transcriptome of E.coli K12 under different culture conditions and growth phases, we showed that the dynamic transcriptome structures appears to be culture condition and growth phases dependent.

overall_design: mRNA profiles of E.coli K12 cultured under different treaments including LB (OD=0.87), Heatshock (15min, 30min, 60min), and MOPS-P(0h,2h,4h).

first: Shan

last: Li

first: Xia

last: Dong


title: Targeting the treponemal microbiome of digital dermatitis infections by deep coverage pyrosequencing

city: Frederiksberg

first: Kirstine

last: Klitgaard

address: Bulowsvej 27

institute: National Veterinary Laboratory

type: Genome variation profiling by high throughput sequencing

summary: We examined 36 biopsies taken from digital dermatitis lesions of  Holstein cows. The target was the V3 -V4 variable region of 16S rRNA using Treponema specific primers. We identified 20 different taxa of Treponema using this approach.

overall_design: Phylogenetic study of the Treponema taxa found in digital dermatitis lesions of Holstein cows.

first: Antoni

last: Bretó

first: Mette

last: Boye

first: Tim

middle: K

last: Jensen


title: Histone Demethylase Lsd1 is Required to Repress Hematopoietic Stem and Progenitor Cell Signatures During Blood Cell Maturation

city: Boston

first: Marc

middle: A.

last: Kerenyi

state: Massachusetts

address: 1 Blackfan Street - Karp Research Building

department: Hematology / Oncology

institute: Boston Children's Hospital and Dana Farber Cancer Institute

summary: Here we describe that lysine-specific demethylase 1 (Lsd1/KDM1a), which demethylates histone H3 on Lys 4 or Lys 9 (H3K4/K9), is an indispensible epigenetic governor of hematopoietic differentiation. Integrative genomic analysis in primary hematopoietic cells, combining global occupancy of Lsd1, genome-wide analysis of its histone substrates H3K4 mono- and di-methylation and gene expression profiling, reveals that Lsd1 represses hematopoietic stem and progenitor cell (HSPC) gene expression programs during hematopoietic differentiation. We found that Lsd1 function was not restricted to transcription start sites, but is also critical at enhancers. Loss of Lsd1 at these sites was associated with increased H3K4me1 and H3K4me2 methylation levels on HSPC genes and their derepression. Failure to fully silence HSPC genes compromised differentiation of hematopoietic stem cells and mature blood cell lineages.  Our data indicate that Lsd1-mediated concurrent repression of enhancer and promoter activity of stem and progenitor cell genes is a pivotal epigenetic mechanism required for proper hematopoietic maturation.

overall_design: To identify direct target genes of Lsd1 in myeloid cells we mapped global occupancy of Lsd1 in 32D granuolocytic progenitor cells and compared H3K4me1/me2/me3 and H3K27ac histone modifications in Lsd1fl/fl (wild type) vs. Lsd1fl/f Mx1Cre (knockout) Gr1dim Mac1 granuolocytic progenitor cells.

first: Stuart

middle: H

last: Orkin


title: Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor [Gro-Seq]

first: Thien

last: Le

summary: The C4-12/Flag.ERβ cell line which stably expressed Flag.ERβ is used to study ERβ genomic functions without ERα interference. Mapping ERβ binding sites in these cells reveals ERβ unique distribution and motif enrichment patterns. Accompanying our mapping results, nascent RNA profiling is performed on cells at the same treatment time. The combined results allow the identification of ERβ target genes. Gene ontology analysis reveals that ERβ targets are enriched in differentiation, development and apoptosis. Concurrently, E2 treatment suppresses proliferation in these cells. Within ERβ binding sites, while the most prevalent binding motif is the canonical ERE, motifs of known ER interactors are also enriched in ERβ binding sites. Moreover, among enriched binding motifs are those of GFI, REST and EBF1, which are unique to ERβ binding sites in these cells. Further characterization confirms the association between EBF1 and the estrogen receptors, which favors the N-terminal region of the receptor. Furthermore, EBF1 negatively regulates ERs at the protein level. In summary, by studying ERβ genomic functions in our cell model, we confirm the anti-proliferative role of ERβ and discover the novel cross talk of ERβ with EBF1 which has various implications in normal physiology.

overall_design: C4-12/Flag.ERβ cells were treated with 10nM E2 (or ethanol as vehicle control) for 1 hour. Nuclei were extracted and processed with run-on assay. The resultant run-on RNA was reverse-transcribed to generate cDNA library which was subsequently sequenced by Illumina Genome Analyzer II or HiSeq2000. Two samples for each treatment were included in this experiment.

middle: P

first: Miao

last: Sun

first: Xin

last: Luo

first: W

last: Kraus

first: Geoffrey

last: Greene


title: Muscleblind-like proteins regulate embryonic stem cell-specific alternative splicing and reprogramming II

city: Barcelona

first: Manuel

last: Irimia

address: 88 Dr. Aiguader

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

summary: Previous investigations of the core gene regulatory circuitry that controls embryonic stem cell (ESC) pluripotency have largely focused on the roles of transcription, chromatin and non- coding RNA regulators. Alternative splicing (AS) represents a widely acting mode of gene regulation, yet its role in the regulation of ESC pluripotency and differentiation is poorly understood. Here, we identify the Muscleblind-like RNA binding proteins, MBNL1 and MBNL2, as conserved and direct negative regulators of a large program of AS events that are differentially regulated between ESCs and other cell types. Knockdown of MBNL proteins in differentiated cells causes switching to an ESC-like AS pattern for at least half of these AS events. Among the events is an ESC-specific AS switch in the forkhead family transcription factor FOXP1 that controls pluripotency. Consistent with a central and negative regulatory role for MBNL proteins in pluripotency, their knockdown significantly enhances the expression of key pluripotency genes and the formation of induced pluripotent stem cells (iPSCs) during somatic cell reprogramming.

overall_design: mRNA profiles of various embryonic stem cells, tissues and cell lines from human and mouse using high-throughput sequencing data and the role of MBNL proteins in regulation of ESC-differential alternative splicing

first: Hong

last: Han

first: Benjamin

last: Blencowe


title: Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor [ChIP-Seq]

overall_design: C4-12/Flag.ERβ cells were treated with 10nM E2 for 1 hour then crosslinked with 1% formaldehyde; EtOH treatment was used as control. Crosslinked samples were processed for ChIP-seq and sequenced with Illumina Genome Analyzer II and aligned to hg18. QuEST was used as the peak-calling software, using default parameters recommended to analyze transcription factor ChIP-seq data. The entire ChIP-seq process was performed once on each sample (Vehicle or E2-treated).


title: Orchestrated intron retention regulates normal granulocyte differentiation

city: Camperdown

first: william

last: ritchie

address: Building 93

institute: centenary institute

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

overall_design: Refer to individual Series


title: Eukaryote-Specific Insertion Elements Control Human ARGONAUTE Slicer Activity

city: New York

first: Pavel

last: Morozov

state: NY

department: Tuschl Lab

institute: Rockefeller University

summary: We solved the crystal structure of human ARGONAUTE1 (hAGO1) bound to endogenous 5'-phosphorylated guide RNAs. To identify structural changes that evolutionarily rendered hAGO1 inactive, we compared our structure with published structures of guide-RNA-containing and cleavage-active hAGO2. Aside from mutation of a catalytic tetrad residue, proline residues at positions 670 and 675 in hAGO1 introduce a kink in the cS7 loop and thereby forming a convex surface within the hAGO1 nucleic-acid-binding channel near the inactive catalytic site. We predicted that even upon restoration of the catalytic tetrad, hAGO1-cS7 sterically hinders the placement of a fully-paired guide-target RNA duplex into the endonuclease active site. Consistent with this hypothesis, reconstitution of the catalytic tetrad (R805H) led to low level hAGO1 cleavage activity, whereas combining R805H with cS7 substitutions (P670S and P675Q) substantially augmented hAGO1 activity. Evolutionary changes to hAGO1 were subtle and readily reversible, suggesting that loading of guide RNA and seed-based miRNA-target RNA pairing constrain its sequence drift.

overall_design: Structure-guided design of mutations that confer slicer activity to hAGO1. RNAs were isolated from recombinant purified hAGO1 and hAGO2, processed from baculovirus-infected Trichoplusia ni insect cells, and then processed for Illumina HiSeq. In addition, total RNA samples from AGO1 baculouvirus infected vs. non-infected Trichoplusia ni cells were isolated and also processed for Illumina HiSeq.

last: Ascano


title: Gene expression profiling normal murine myeloid cells and myeloid leukemia cells induced by CNTRL-FGFR1

city: Augusta

first: Mingqiang

last: Ren

state: GA

address: 1120 15th Street

department: Cancer Center

institute: Georgia Regents University

summary:
To characterize gene expression changes in AML induced by CNTRL-FGFR1, we used RNA-seq analysis of sorted Mac+Gr1+B220+ AML cells (n = 2) from the SP and BM of leukemic mice, as well as sorted Mac+Gr1+ myeloid cells (n=3) from normal mice.
Methods: cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit following the manufacturer’s instructions. The quality of the resulting cDNA libraries were assessed using a Bioanalyzer DNA 1000 chip (Agilent) and quantified by quantitative PCR (Bio-Rad). The cDNA libraries were sequenced using paired end Illumina Hiseq2000 protocols (50 cycles). The Illumina sequencing pipeline version 1.8 was employed for transferring raw images to base calls, generating sequence reads, and de-multiplexing the reads.  The generated FASTQ files were imported to CLC Genomics Workbench and aligned to the mouse genome, NCBI37/mm9. The transcript expression levels were determined in terms of number of reads per kilobase per million (RPKM) and compared between sorted normal myeloid (Gr1+Mac1+) cells and sorted leukemic myeloid cells.
Results: The result showed a remarkable difference between normal (Gr1+Mac1+) and leukemic (Mac+Gr1+B220+) myeloid cells. Gene Set Enrichment Analysis  and leading-edge analysis suggested that Mac+Gr1+B220+ cells have the potential to differentiate into either myeloid or T-cell, but not a B-cell, lineages. Quantitative RT-PCR analysis of lineage-specific genes showed increased expression of Flt3, Gfi1, and Kit related to early myeloid-lineage commitment, while genes related to myeloid differentiation, Irf8, Klf4, Csf1r, Myc, and Spi1 were decreased compared with normal myeloid cells. Quantitative RT-PCR also confirmed that the Cd3e and Lmo2 T-cell specific genes were markedly increased in AML cells.
Conclusions: We demonstrate that the CNTRL-FGFR1 fusion kinase induces bi-lineage myeloid and T-lymphoid disease in model mice. Genetic and molecular analyses in these models demonstrated that multiple signaling pathways, specifically related to myeloid and T-lymphoid lineages, were altered in neoplasms, which underscores the importance of developing therapies that target all of these signaling pathways to eradicate the leukemia-initiating-cells

first: Ming-Qiang

first: John

last: Cowell


title: Genome wide profiling of RNA polymerase III in Saccharomyces cerevisiae

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

institute: MRC Human Genetics Unit, The University Of Edinburgh

summary: Genome wide mapping of RNA polymearase III binding sites in Saccharomyces cerevisiae under normal growth and nutrient starved condition using ChIP-seq. Chromatin Immuno-precipitation (ChIP) was performed for FLAG tagged version of pol III subunit RPC128 after crosslinking the log-phase cells with formaldehyde. MOCK and IP DNA was sequenced and coverage of pol III was calculated at each base of the genome.

overall_design: RPC128-FLAG ChIP-seq single end seqquencing on Illumina GAII. 2 replicates of IP samples and 1 MOCK sample. Done in under normal growth and nutrient deprivation (4 hours).

first: Purnima

last: Bhargava