title: A Stable Transcription Factor Complex Nucleated by Dimeric AML1-ETO Controls Leukaemogenesis

first: Yanwen

last: Jiang

institute: Weill Cornell Medical College

summary: AML1-ETO, a fusion protein generated by the t(8;21) translocation in acute myeloid leukemia, is a transcription factor implicated in both gene repression and activation. We now show that, in leukemic cells, AML1-ETO resides in and functions through a stable protein complex (AETFC) that contains several hematopoietic transcription factors and cofactors. In conjunction with biochemical and leukemia pathological studies, the ChIP-seq and RNA-seq analyses of the AETFC components in leukemic cells reveal that these components stabilize the complex through multivalent interactions, provide multiple DNA-binding domains for diverse target genes, colocalize genome-wide, cooperatively regulate gene expression, and contribute to leukemogenesis.

overall_design:
RNA-seq analyses gene expression upon knockdown of each AETFC component, including AML1-ETO, HEB, E2A, LYL1, LDB1 and LMO2, and double-knockdown of HEB and E2A, in Kasumi-1 cells.
ChIP-seq analyses of four AETFC components, namely AML1-ETO, HEB, E2A and LMO2, in Kasumi-1 cells.

first: Xiao-Jian

first: Ari

last: Melnick

first: Robert

middle: G

last: Roeder


title: Sox4 is a master regulator of epithelial-mesenchymal transition (EMT) by controlling Ezh2 expression and epigenetic reprogramming

status: Public on Jun 20 2013

city: Basel

first: Piotr

middle: Jan

last: Balwierz

address: Klingelbergstrasse 50-70

country: Switzerland

institute: University of Basel

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Gene expression profiling has uncovered the transcription factor Sox4 with up-regulated activity during TGFβ-induced EMT in normal and cancerous breast epithelial cells. Sox4 is indispensable for EMT and cell survival in vitro and for primary tumor growth and metastasis in vivo. Among several EMT-relevant genes, Sox4 directly regulates the expression of Ezh2, encoding the Polycomb group histone methyltransferase that trimethylates histone 3 lysine 27 (H3K27me3) for gene repression. Ablation of Ezh2 expression prevents EMT, while forced expression of Ezh2 restores EMT in Sox4-deficient cells. Ezh2-mediated H3K27me3 marks associate with key EMT genes, representing an epigenetic EMT signature that predicts patient survival. Our results identify Sox4 as a master regulator of EMT by governing the expression of the epigenetic modifier Ezh2.

overall_design: Our Dataset comprises of 12 ChIP-seq samples using chromatin from NMuMG cells which was immunoprecipitated using H3K27me3-specific antibody during TGFβ-induced EMT (2ng/ml) at 6 different stages (day 0, 1, 4, 7, 10, 20).

first: Vijay

last: Tiwari

first: Neha

middle: J

first: Phil

last: Arnold


title: Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3’ UTRs

first: Andreas

middle: R

last: Gruber

department: Biozentrum

summary: The RNA helicase UPF1 is best known for its key function in mRNA nonsense-mediated mRNA decay (NMD), but has also been implicated in additional mRNA turnover mechanisms, telomere homeostasis, and DNA replication. In NMD, UPF1 recruitment to target mRNAs is thought to occur through interaction with release factors at terminating ribosomes, but evidence for translation-independent interaction of UPF1 with the 3’ untranslated region (UTR) of mRNAs has also been reported. To map UPF1 binding sites transcriptome-wide, we performed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) in human cells, untreated or after inhibiting translation by puromycin. We found a strong association of UPF1 with 3’ UTRs in undisturbed, translationally active cells and a significant increase in UPF1 binding to coding sequence (CDS) after translation inhibition. These results indicate that UPF1 binds RNA before translation and gets displaced from the CDS by translating ribosomes. This evidence for translation-independent UPF1-RNA interaction, which is corroborated by RNA immunoprecipitations experiments and by our observation that UPF1 also crosslinks to long non-coding RNAs, suggests that the decision to trigger NMD occurs after association of UPF1 with the mRNA, presumably through activation of RNA-bound UPF1 by aberrant translation termination.

overall_design:
Examination of Upf1 binding preferences via iCLIP in untreated HeLa cells and HeLa cells, where translation is blocked by puromycin treatment
in vivo crosslinking and immunoprecipitation strategy (iCLIP)

first: David

last: Zünd

first: Mihaela

last: Zavolan

first: Oliver

last: Mühlemann


title: Cellular source and mechanisms of high transcriptome complexity in the mammalian testis (RNA-Seq cells)

city: Cambridge

first: Magali

last: Soumillon

state: MA

address: Divinity Avenue 7

country: USA

institute: Harvard University, HSCRB

type: Expression profiling by high throughput sequencing

summary:
Understanding  the  extent  of  genomic  transcription  and  its  functional  relevance  is  a  central  goal  in  genomics research. However, detailed genome‐wide investigations of transcriptome complexities in major mammalian organs  and  their  underlying  cellular  sources,  transcriptional  mechanisms,  and  functional  relevance  have been  scarce.  Here  we  first  show,  using  extensive  RNA‐seq  data,  that  transcription  of  both  functional  and nonfunctional  genomic  elements  is  substantially  more  widespread  in  the  testis  than  in  other  organs  across representative mammals. By scrutinizing the transcriptomes of all main testicular cell types in the mouse, we then  reveal  that meiotic  spermatocytes  and  especially  post‐meiotic  round  spermatids  have  remarkably diverse  transcriptomes,  which  explains  the  high  transcriptome  complexity  of  the  testis  as  a  whole.  The widespread  transcriptional  activity  in  spermatocytes  and  spermatids  encompasses  protein‐coding  genes  and long  noncoding  RNA  genes  but  also  poorly  conserved  intergenic  sequences,  suggesting  that  much  of  it  is  not of  immediate  functional  relevance.  Rather,  our  analyses  of  genome‐wide  epigenetic  data  show  that  this prevalent  transcription,  which  apparently  promoted  the  birth  of  new  genes  during  evolution,  results  from  a highly  permissive  chromatin  state  during  and  after  meiosis  that  may  ultimately  facilitate  the  replacement  of histones by protamines during late spermatogenesis.
To study the cellular source and mechanisms of high transcriptome complexity in the mammalian testis, we generated strand-specific deep coverage RNA‐Seq data for purified sertoli cells, spermatogonia, spermatocytes, spermatids and spermatozoa as well as for brain, liver and the whole testis from the mouse. We prepared 8 sequencing libraries for the polyadenylated RNA fraction of each sample and sequenced each library in 3 lanes of the Illumina Genome Analyser IIx platform, yielding a total of >60 millions strand-specific reads of 76 base pairs per sample. In addition, we generated ChIP-Seq data for the H3K4me2 modification as well as RRBS data for brain, liver, testis, spermatocytes and spermatids. RNA-seq, ChIP-seq and RRBS data were generated from the same individual or pool of individuals, in the case of purified cells.

first: Anamaria

last: Necsulea

first: Manuela

last: Weier

last: Brawand

first: Xiaolan

last: Zhang

first: Hongcang

last: Gu

first: Pauline

last: Barthès

first: Maria

last: Kokkinaki

first: Serge

last: Nef

last: Gnirke

first: Martin

last: Dym

first: Bernard

last: de Massy

first: Tarjei

middle: S

last: Mikkelsen

first: Henrik

last: Kaessmann


title: Genome-wide analysis of FNR and σ70 in E. coli under aerobic and anaerobic growth conditions.

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: We found many binding sites for FNR under glucose fermentative anaerobic growth conditions. Also, many binding sites were identified for σ70  under both aerobic and anaerobic growthin conditions. Descirbed in the manuscript "Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure"

sample_organism: Escherichia coli str. K-12 substr. MG1655star

overall_design: Examination of occupancy of FNR adn σ70 under aerobic and anaerobic growth in conditions.

first: Huihuang

last: Yan

first: Irene

last: Ong

first: Dongjun

last: Chung

first: Kun

last: Liang

first: Frances

last: Tran

first: Sunduz

last: Keles

first: Robert

last: Landick

first: Patricia

last: Kiley


title: Cross-presenting CD103+ dendritic cells are protected from influenza virus infection

status: Public on Jun 19 2013

city: New York

first: Brian

last: Brown

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: CD8+ cytotoxic T cells are critical for viral clearance from the lungs upon influenza virus infection. The contribution of cross-presentation to the induction of anti-viral cytotoxic T cells remains debated. Here, we used a recombinant influenza virus expressing a NS1-GFP reporter gene to visualize the route of antigen presentation by lung dendritic cells (DC) upon viral infection in vivo. We found that lung CD103+ DC are the only subset to carry intact GFP protein to the draining lymph nodes. Strikingly, lung migratory CD103+ DC are not productively infected by influenza virus and thus induce virus-specific CD8+ T cells through the cross-presentation of antigens from virally infected cells. We also show that CD103+ DC resistance to infection correlates with an increased antiviral state in these cells that is dependent on the expression of IFN receptor alpha. In conclusion, these results establish that efficient cross-priming by migratory lung DC is coupled to the acquisition of an anti-viral status, which is dependent on type I IFN signaling pathway.

overall_design: mRNA profiles were generated by deep-sequencing in Illumina HiSeq2000 from alveolar macrophages and CD103+ dendritic cells from lungs of untreated and flu-treated mice

first: Miriam

last: Merad

middle: D

first: Adolfo

last: García-Sastre


title: The APSES Transcription factor Efg1 regulates a novel phenotype switch in Candida parapsilosis [ChIP-seq].

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

summary: We use ChIP-seq to identify the targets of Efg1 in Candida parapsilosis. We show that Efg1 binds to 502 promoter regions, including 70 potential transcription factors or regulatory proteins. Several of the transcription factors belong to networks that regulate biofilm development and white-opaque switching in C. albicans. Efg1 also binds to its own promoter. The binding site for C. parapsilosis Efg1 resembles that of orthologs in other fungi. Many Efg1 targets are probably also regulated by the Ndt80 transcription factor.

overall_design: Efg1 in C. parapsilosis was tagged in situ using a myc epitope. Examination of Efg1-myc DNA binding sites by ChIP-seq. Three immunoprecipitated samples were sequenced and three input samples (pre-immunoprecipitation) were sequenced as controls.

first: Leona

last: Connolly

first: Alessandro

last: Riccombeni

first: Denise

last: Lynch

first: Linda

last: Holland


title: A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure.

city: Davis

first: Weston

last: Powell

state: CA

address: 3426 Tupper Hall

department: MMI

institute: UC Davis

summary: Prader-Willi syndrome (PWS), a genetic cause of childhood obesity, is characterized by intellectual disabilities and sleep abnormalities. PWS-causing deletions include a neuronal long, non-coding RNA (lncRNA) processed into small nucleolar RNAs and a spliced lncRNA,116HG. We show that 116HG forms a subnuclear RNA cloud that co-purifies with the transcriptional activator RBBP5 and active metabolic genes, remains tethered to the site of its transcription and increases in size in postnatal neurons. Snord116del mice lacking 116HG exhibited increased energy expenditure corresponding to dysregulation of diurnally expressed Mtor and circadian genes Clock, Cry1, and Per2. Genomic and metabolic analyses demonstrate altered diurnal energy regulation in the Snord116del mouse cortex and link the loss of 116HG to the energy imbalance observed in PWS.

overall_design: Examination of lncRNA binding sites by ChIRP-seq using an oligo-based purification method from WT and Snord116del (+/-) mouse brain with specific and nonspecific control oligos.  Transcript abundance levels by RNA-seq analysis of 3 adult WT and 2 adult Snord116del (+/-) mouse brain cortices at Zt+6 and 2 adult WT and 2 adult Snord116del (+/-) mouse brain cortices at Zt+16.

middle: T


title: RNA-seq of RNase R treated poly(A)-/ribo- RNAs from H9 cells

status: Public on Jun 18 2013

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

summary: We have used RNA-seq to examine circular RNAs from RNase R treated poly(A)-/ribo- RNAs in human embryonic stem cells

overall_design: Examine circular RNAs in human embryonic stem cells

first: Yang

last: Zhang

first: Xiao-Ou

first: Tian

last: Chen

first: Jian-Feng

last: Xiang

first: Qing-Fei

last: Yin

first: Yu-Hang

last: Xing

first: Shanshan

last: Zhu

first: Ling-Ling


title: Genome-wide identification of CTCF and Cohesin binding sites in neonatal mouse brain

city: London

first: Rebecca

last: Oakey

address: Great Maze Pond

department: Medical and Molecular Genetics

country: United Kingdom

institute: King's College London

summary: ChIP-seq for CTCF and  Rad21 in 3 week old mouse brain from reciprocal BxC and  CxB crosses. One biological replicate of each.

overall_design: Examination of CTCF and Cohesin binding sites in neonetal mouse brain

first: Adam

last: Prickett

first: Nikolaos

last: Barkas

first: Ruth

middle: B

last: McCole

first: Siobhan

last: Hughes

first: Samuele

middle: M

last: Amante

first: Reiner

last: Schulz


title: Genome-scale Analysis of E. coli FNR Reveals Complex Features of Transcription Factor Binding

first: Kevin

last: Myers

type: Genome binding/occupancy profiling by genome tiling array

type: Expression profiling by genome tiling array

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

platform_organism: Escherichia coli str. K-12 substr. MG1655star

overall_design: Refer to individual Series


title: Development of GRO-cap (GRO-seq followed by 5'-cap enrichment) to map transcription start sites in C. elegans

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

summary: Dosage Compensation is required to correct for uneven gene dose between the sexes. We utilized global run-on sequencing (GRO-seq) to examine how Caenorhabditis elegans dosage compensation reduces transcription of X-linked genes. To facilitate these experiments, we required accurate 5’-ends of genes that have been missing due to a co-transcriptional trans-splicing event common in nematodes. We developed a modified GRO-seq protocol to identify TSSs that are supported by transcription, and determined that TSSs lie more than 1 kb upstream of the previously annotated TSS for nearly one-quarter of all genes. We then investigated the changes that occur in transcriptionally engaged RNA Polymerase when dosage compensation is disrupted, and find that dosage compensation controls recruitment of RNA Polymerase to X-linked genes.

overall_design: GRO-cap reactions were performed with TAP, and without TAP as a control.

first: William

last: Kruesi

first: Leighton

last: Core

first: Colin

last: Waters

first: John

last: Lis


title: Cellular source and mechanisms of high transcriptome complexity in the mammalian testis (RRBS and ChIP-Seq)

first: Magali

last: Soumillon

type: Methylation profiling by high throughput sequencing

overall_design: ChIP-Seq data for the H3K4me2 modification as well as RRBS data for brain, liver, testis, spermatocytes and spermatids

first: Anamaria

last: Necsulea

first: Manuela

last: Weier

first: David

last: Brawand

first: Xiaolan

last: Zhang

first: Hongcang

last: Gu

first: Pauline

last: Barthès

first: Maria

last: Kokkinaki

first: Serge

last: Nef

first: Andreas

last: Gnirke

first: Martin

last: Dym

first: Bernard

last: de Massy

first: Tarjei

last: Mikkelsen

first: Henrik

last: Kaessmann


title: Using GRO-seq experiments to determine the mechanism of C. elegans dosage compensation's control of transcription

first: Barbara

last: Meyer

overall_design: GRO-seq experiments (two biological replicates) were performed in nuclei from many wild-type states and a dosage compensation mutant

first: William

last: Kruesi

first: Leighton

last: Core


title: Binding of the C. elegans dosage compensation complex protein DPY-27

overall_design: Two biological replicates of ChIP with DPY-27 and a random rabbit IgG

first: Colin

last: Waters

first: John

last: Lis


title: Next-generation sequencing of Okazaki fragments extracted from Saccharomyces cerevisiae

first: Wenchao

last: Yang

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: We investigated the genome-wide distribution of Okazaki fragments in the commonly used laboratory Saccharomyces cerevisiae strain S288C to study the DNA replication model adopted by the budding yeast. The method based upon lambda exonuclease digestion for purification of RNA-primed replication intermediates was first improved to be suitable for the purification of Okazaki fragments. Then, we used this improved method to purify Okazaki fragments from S288C yeast cells, followed by Illumina sequencing. We found that the expected asymmetric distribution of Okazaki fragments around confirmed replication origins, which was derived from the semi-discontinuous DNA replication model, was not observed on S. cerevisiae chromosomes. Even around two highly efficient replication origins, ARS522 and ARS416, the ratios of Okazaki fragments on both strands were inconsistent with the semi-discontinuous DNA replication model. Our study supported the discontinuous DNA replication model. Besides, we also observed that Okazaki fragments were overpresented in the transcribed regions in S. cerevisiae mitochondrial genome, which indicated the interplay between transcription and DNA replication.

overall_design: Examination of the distribution of Okazaki fragments in Saccharomyces cerevisiae strain S288C.

first: Xinhui

last: Li


title: Global gene expression analysis of the zoonotic parasite Trichinella spiralis revealed novel genes in host parasite interaction

city: Changchun

first: Xiaolei

last: Liu

address: 5333 Xian Road

institute: Key Laboratory of Zoonosis, Jilin University

summary: Trichinellosis of human and other mammals was caused through the ingestion of the parasite，Trichinella spiralis，contaminated meat. It is a typical zoonotic disease that affects more than 10 million people world-wide. Parasites of Trichinella genus are unique intracellular pathogens. Adult Trichinella parasites directly release newborn larvae which invade striated muscle cells and causes diseases. In this study, we profiled the global transcriptome in the three developmental stages of T. spiralis. The transcriptomic analysis revealed the global gene expression patterns from newborn larval stage through muscle larval stage to adults. Thousands of genes with stage-specific transcriptional patterns were described and novel genes involving host-parasite interaction were identified. More than 45% of the protein-coding genes showed evidence of transcription from both sense and antisense strands which suggests the importance of RNA-mediated gene regulation in the parasite. This study presents a first deep analysis of the transcriptome of T. spiralis, providing insight information of the parasite biology.

overall_design: Messenger RNA from three developmental stages of T. spiralis was selectively purified from total RNA using oligo-(dT) conjugated magnetic beads. Complementary DNA (cDNA) was synthesized guided by oligo-(dT) as a primer.

first: Yanxia

last: Song

first: Qijun

last: Chen


title: High-throughput Solexa sequencing of total RNA from Escherichia coli wild type and ∆fnr strain (PK4854)

first: Kevin

last: Myers

summary: Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆fnr mutant, compared to the wild-type strain.  The mutations engineered into this strain produce a strain lacking the FNR protein.

overall_design: A RNA-seq study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 WT and two separate cultures of the ∆fnr mutant strain.The results are further described in the article "Genome-scale Analysis of E.coli FNR Revealse the Complexity of Bacterial Regulon Structure".

first: Huihuang

last: Yan

first: Irene

last: Ong

first: Dongjun

last: Chung

first: Kun

last: Liang

first: Frances

last: Tran

first: Sunduz

last: Keles

first: Robert

last: Landick

first: Patricia

last: Kiley


title: A blood based 12-miRNA signature of Alzheimer patients

status: Public on Jun 17 2013

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

type: Non-coding RNA profiling by high throughput sequencing

summary: We applied Next-Generation Sequencing (NGS) to miRNAs from blood samples of 48  AD (Alzheimer's Disease) patients and 22 unaffected controls, yielding a total of 140 unique mature miRNAs with significantly changed expression level. Of these, 82 were higher and 58 lower abundant in samples from AD patients. We selected a panel of 12 miRNAs for a qRT-PCR analysis on a larger cohort of 202 samples including not only AD patients and healthy controls but also patients with other CNS illnesses: Multiple Sclerosis, Parkinson's Disease, Major Depression, Bipolar Disorder, Schizophrenia, and Mild Cognitive Impairment, which is assumed to represent a transitional period before the development of AD. MiRNA target enrichment analysis of the selected 12 miRNAs indicated an involvement of miRNAs in nervous system development, neuron projection, neuron projection development, and neuron projection morphogenesis, respectively. Using this 12-miRNA signature we were able to differentiate between AD and controls with an accuracy of 93.3%, a specificity of 95.1%, and a sensitivity of 91.5%. The differentiation of AD from other neurological diseases was possible with accuracies between 73.8% and 77.8%. The differentiation of the other CNS disorders from controls yielded even higher accuracies.

overall_design: Examination of the miRNA profile in blood samples of 48 AD patients and 22 controls

first: Keller

last: Andreas


title: Condensin Controls Recruitment of RNA Polymerase II to Achieve X-Chromosome Dosage Compensation

first: Barbara

last: Meyer

first: William

last: Kruesi

first: Leighton

last: Core

first: Colin

last: Waters

first: John

last: Lis


title: High throughput sequencing enables detailed analysis of S. cerevisiae DNA replication

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary: For rapid characterisation of replication dynamics in wild-type cells from an unperturbed cell cycle we have obtained replicating (S phase) and non-replicating (G2 phase) cells by fluorescence activated cell sorting (FACS) and subjected the DNA to copy number analysis.

overall_design: Measurement of genome replication time for various S. cerevisiae strains. For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase).

first: Carolin

last: Müller

first: Michelle

last: Hawkins

first: Renata

last: Retkute

first: Martin

last: Blythe

first: Sunir

last: Malla

first: Raymond

last: Wilson


title: Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Erythropoiesis is dependent on the activity of transcription factors, including the erythroid-specific erythroid Kruppel-like factor (EKLF). ChIP followed by massively parallel sequencing (ChIP-Seq) is a powerful, unbiased method to map transfactor occupancy. We used ChIP-Seq to study the interactome of EKLF in mouse erythroid progenitor cells and more differentiated erythroblasts. We correlated these results with the nuclear distribution of EKLF, RNA-Seq analysis of the transcriptome, and the occupancy of other erythroid transcription factors. In progenitor cells, EKLF is found predominantly at the periphery of the nucleus, where EKLF primarily occupies the promoter regions of genes and acts as a transcriptional activator. In erythroblasts, EKLF is distributed throughout the nucleus, and erythroblast-specific EKLF occupancy is predominantly in intragenic regions. In progenitor cells, EKLF modulates general cell growth and cell cycle regulatory pathways, whereas in erythroblasts EKLF is associated with repression of these pathways. The EKLF interactome shows very little overlap with the interactomes of GATA1, GATA2, or TAL1, leading to a model in which EKLF directs programs that are independent of those regulated by the GATA factors or TAL1. (Blood.2011;118(17):e139-e148)

overall_design: We used ChIP-Seq to study the interactome of EKLF in mouse erythroid progenitor cells and more differentiated erythroblasts and RNA-Seq analysis of the transcriptome.

first: Andre

last: Pilon

first: Subramanian

last: Ajay

first: Swathi

last: Kumar

first: Laurie

last: Steiner

first: Praveen

middle: F

last: Cherukuri

first: Stephen

last: Wincovitch

first: Stacie

last: Anderson

first: James

middle: C

last: Mullikin

first: Patrick

last: Gallagher

first: Elliott

middle: H

last: Margulies

first: David

last: Bodine


title: The APSES Transcription factor Efg1 regulates a novel phenotype switch in Candida parapsilosis [RNA-seq].

first: Geraldine

last: Butler

summary: In Candida albicans the Efg1 transcription factor (a member of the APSES family) is an important regulator of hyphal growth, and of the white-to-opaque transition. In contrast, we show that the Efg1 ortholog in Candida parapsilosis is a major regulator of a different morphological switch at the colony level, from a concentric to smooth morphology. The rate of switching is at least 100-fold increased in an efg1 knockout relative to wild type. Deleting efg1 also reduces biofilm formation, and results in increased sensitivity to SDS, Congo red, caspofungin and calcofluor white in cells of both morphologies. Biofilm reduction is more dramatic in in vitro than in in vivo models. We use ChIP-seq to show that Efg1 binds to 502 promoter regions, including 70 potential transcription factors or regulatory proteins. Several of the transcription factors belong to networks that regulate biofilm development and white-opaque switching in C. albicans. Efg1 also binds to its own promoter. The binding site for C. parapsilosis Efg1 resembles that of orthologs in other fungi. Many Efg1 targets are probably also regulated by the Ndt80 transcription factor. We show that a paralog of Efg1 (Efh1) is restricted to Candida species. Efh1 does not regulate concentric-smooth phenotype switching, biofilm formation or stress response in C. parapsilosis. Our analysis supports the hypothesis that Efg1 has an ancient role as regulator of development in fungi, but we have identified a new role in C. parapsilosis as a regulator of colony switching that is distinct from the white-opaque switch in C. albicans.

overall_design: RNA was isolated from  C. parapsilosis wild type (three biological replicates, concentric phenotype), and from efg1 deletion strains (three biological replicates from both concentric and smooth phenotype). Gene expression was determined using strand-specific RNA-seq.

first: Leona

last: Connolly

first: Alessandro

last: Riccombeni

first: Denise

last: Lynch

first: Linda

last: Holland


title: The APSES Transcription factor Efg1 regulates a novel phenotype switch in Candida parapsilosis.


title: Transcriptomic profiles of zebrafish embryos exposed to silver (nanoparticles, bulk and ions) using HT-SuperSAGE in a Illumina GA2 platform

city: Exeter

first: Ronny

last: van Aerle

state: Devon

address: Stocker Road

department: Biosciences, College of Life and Environmental Sciences

institute: University of Exeter

summary: Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk- and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24h of exposure, but with a recovery at 48h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24h, but not at 48h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms.

overall_design: mRNA profiles of whole zebrafish embryos at 24 and 48 hours post-fertilisation (hpf) exposed to silver in nano, bulk and ionic forms were generated by deep sequencing using HT-SuperSAGE (Illumina GA2).

first: Anke

last: Lange

first: Alex

last: Moorhouse

first: Konrad

last: Paszkiewicz

first: Katie

last: Ball

first: Blair

last: Johnston

first: Eliane

last: de-Bastos

first: Timothy

last: Booth

first: Charles

last: Tyler

first: Eduarda

last: Santos


title: Cellular source and mechanisms of high transcriptome complexity in the mammalian testis (RNA-Seq organs)

first: Magali

last: Soumillon

summary:
Understanding  the  extent  of  genomic  transcription  and  its  functional  relevance  is  a  central  goal  in  genomics research. However, detailed genome‐wide investigations of transcriptome complexities in major mammalian organs  and  their  underlying  cellular  sources,  transcriptional  mechanisms,  and  functional  relevance  have been  scarce.  Here  we  first  show,  using  extensive  RNA‐seq  data,  that  transcription  of  both  functional  and nonfunctional  genomic  elements  is  substantially  more  widespread  in  the  testis  than  in  other  organs  across representative mammals. By scrutinizing the transcriptomes of all main testicular cell types in the mouse, we then  reveal  that meiotic  spermatocytes  and  especially  post‐meiotic  round  spermatids  have  remarkably diverse  transcriptomes,  which  explains  the  high  transcriptome  complexity  of  the  testis  as  a  whole.  The widespread  transcriptional  activity  in  spermatocytes  and  spermatids  encompasses  protein‐coding  genes  and long  noncoding  RNA  genes  but  also  poorly  conserved  intergenic  sequences,  suggesting  that  much  of  it  is  not of  immediate  functional  relevance.  Rather,  our  analyses  of  genome‐wide  epigenetic  data  show  that  this prevalent  transcription,  which  apparently  promoted  the  birth  of  new  genes  during  evolution,  results  from  a highly  permissive  chromatin  state  during  and  after  meiosis  that  may  ultimately  facilitate  the  replacement  of histones by protamines during late spermatogenesis.
To study the cellular source and mechanisms of high transcriptome complexity in the mammalian testis, we generated strand-specific deep coverage RNA‐Seq data for purified sertoli cells, spermatogonia, spermatocytes, spermatids and spermatozoa as well as for brain, liver and the whole testis from the mouse. We prepared 8 sequencing libraries for the polyadenylated RNA fraction of each sample and sequenced each library in 3 lanes of the Illumina Genome Analyser IIx platform, yielding a total of >60 millions strand-specific reads of 76 base pairs per sample. In addition, we generated ChIP-Seq data for the H3K4me2 modification as well as RRBS data for brain, liver, testis, spermatocytes and spermatids. RNA-seq, ChIP-seq and RRBS data were generated from the same individual or pool of individuals, in the case of purified cells.

overall_design: RNA-Seq of brain, liver and the whole testis

first: Anamaria

last: Necsulea

first: Manuela

last: Weier

last: Brawand

first: Xiaolan

last: Zhang

first: Hongcang

last: Gu

first: Pauline

last: Barthès

first: Maria

last: Kokkinaki

first: Serge

last: Nef

first: Andreas

last: Gnirke

first: Martin

last: Dym

first: Bernard

last: de Massy

first: Tarjei

last: Mikkelsen

first: Henrik

last: Kaessmann


title: Transcriptome sequencing of Myotis brandtii

city: shenzhen

first: zhiyong

last: huang

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

institute: BGI-Shenzhen, Shenzhen 518083, China

summary: Deep sequencing of mRNA from Myotis brandtii.  Analysis of poly(A)+ RNA of livers, kidneys and brains from M. brandtii hibernated for 2 months, hibernated for 6 months and summer active animals.

overall_design: Livers, kidneys and brains from M. brandtii hibernated for 2 and 6 months, and summer active animals.

first: Vadim

middle: N

last: Gladyshev

first: Xiaodong

last: Fang


title: Activation of the aryl hydrocarbon receptor by dioxin during embryonic stem cell differentiation disrupts the expression of homeobox transcription factors that control cardiomyogenesis

status: Public on Jun 15 2013

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that regulates the expression of xenobiotic detoxification genes and is a critical mediator of gene-environment interactions.  In addition, many AHR target genes that have been identified by genome-wide profiling have morphogenetic functions, suggesting that AHR activation may play a role in embryonic development.  To address this hypothesis, we studied the consequences of AHR activation by TCDD, its prototypical ligand, during spontaneous mouse ES cell differentiation into contractile cardiomyocytes.  Treatment with TCDD or shRNA-mediated AHR knockdown significantly decreased the ability of cardiomyocytes to contract and the expression of cardiac markers in these cells.  An AHR-positive embryonic stem cell lineage was generated that expressed puromycin resistance and eGFP under the control of the AHR-responsive Cyp1a1 promoter.  Cells of this lineage were over 90% pure and expressed AHR as well as cardiomyocyte markers. Analysis of temporal trajectories of global gene expression in these cells shows that activation of the AHR/TCDD axis disrupts the concerted expression of genes that regulate multiple signaling pathways involved in cardiac and neural morphogenesis and differentiation, including dozens of genes encoding homeobox transcription factors and Polycomb and Trithorax Group genes.  More than 50% of the homeobox factors so regulated do not have AhRE sites in their promoters, indicating that AHR activation may establish a complex regulatory network that reaches beyond direct AHR signaling and is capable of disrupting various aspects of embryonic development, including cardiomyocyte differentiation.

overall_design: mRNA profiles of WT and selected AHR positive cells at different differentiation days treated with and without TCDD in duplicates

first: Qin

last: Wang

first: Jing

last: Chen

first: Chia-I

last: Ko

first: Yunxia

last: Fan

first: Vinicius

last: Carreira

first: Yinglei

first: Alvaro

last: Puga


title: The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter proximal nucleosomes

status: Public on Jul 08 2013

city: Augusta

first: Wei-Hua

last: Wu

state: GA

address: 1462 Laney Walker Blvd

department: Neurology

institute: IMMAG/MCG/GRU


title: Next Generation Sequencing  Analysis of Saccharopolyspora erytharea transcriptomes

city: St Lucia

first: Esteban

last: Marcellin

state: QLD

address: Corner college and Coopers Rd

department: AIBN

country: Australia

institute: The University of Queensland

summary: We report the high-throughput profiling of saccharopolyspora erythraea life cycle in bioreactors. RNA was harvested at seven time-points from bioreactors, three points immediately before, one during and three following the metabolic switch (as evidenced by biomass cell dry weight). We prepared unstranded RNA libraries and sequenced 363 million reads for a total of 32.7Gb and a mean ~4,000 fold coverage of the genome. Our comprehensive sequencing showed the S.erythraea genome to be prevalently transcribed, with at least 85.8% of genome sequence from either strand being transcribed.

overall_design: We sequenced a  bioreactor fermentation at seven time points.

first: Tim

last: Mercer

first: Cuauhtemoc

last: Licona-Cassani

first: Robin

middle: W

last: Palfreyman

first: Marcel

middle: E

last: Dinger

first: Jenifer

last: Steen

first: Dennis

middle: K

last: Gascoigne

first: John

last: Mattick

first: Lars

last: Nielsen


title: Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

city: Cambridge

first: Laurie

last: Boyer

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

overall_design: Refer to individual Series

first: Jeffrey

last: Alexander

first: Joseph

last: Wamstad


title: The Obesity-associated Fto gene regulates activity of the dopaminergic midbrain circuitry [WT]

first: Christopher

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Here we use MeRIP-Seq to analyze global adenosine methylation (m6A) in mRNAs in the midbrain and striatum of Fto-deficient mice.  We find that Fto deficiency leads to increased methylation within a subset of mRNAs important for neuronal signaling, including many within the dopaminergic signaling pathway. Collectively, our results show that Fto regulates demethylation of specific mRNAs in vivo, and this activity relates to control of dopaminergic transmission.

overall_design: Profiling of m6A in midbrain and striatum from wild type mice

first: Martin

last: Hess

first: Simon

first: Kate

last: Meyer

first: Linda

last: Verhagen

last: Koch

first: Hella

last: Brönneke

first: Marcelo

middle: O

last: Dietrich

first: Sabine

last: Jordan

first: Olivier

last: Elemento

first: Bengt

last: Belgardt

first: Thomas

last: Franz

first: Tamas

middle: L

last: Horvath

first: Ulrich

last: Rüther

first: Samie

last: Jaffrey

first: Peter

last: Kloppenburg

first: Jens

last: Brüning


title: The Obesity-associated Fto gene regulates activity of the dopaminergic midbrain circuitry [FTO KO]

overall_design: Profiling of m6A in midbrain and striatum from FTO knockout mice

middle: R


first: Laurie

last: Boyer

summary: We interrogated the transcriptome using RNA-seq at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol.  These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively.  This study revealed many dynamic patterns of mRNAs and long non-coding RNAs (lncRNAs) and identified groups of genes with similar expression patterns during differentiation.

overall_design: RNA-seq analysis of global RNA levels at 4 stages of directed cardiac differentiation of mouse embryonic stem cells.  Each stage in biological duplicates

first: Jeffrey

last: Alexander

first: Joseph

last: Wamstad


title: mRNA sequencing identifies differential gene expresssion profiles between ASCC3 knock-down cells and control cells

city: Saint Louis

first: Jianqing

last: Li

state: MO

address: 660 S Euclid Ave.

department: Molecular Microbiology

institute: Washington University in St. Louis, School of Medicine

summary: We sequenced mRNAs from HeLa cells transduced with either scrambled shRNA or shRNA targeting ASCC3. The results have shown differential gene expression in ASCC3 knockdown cells, suggesting a regulatory role for ASCC3 in certain cellular pathway.

overall_design: mRNA from HeLa cells transduced with either scrambled shRNA (ni) or shRNA targeting ASCC3 (ai) were harvested and used for deep sequencing by Illumina HiSeq 2000 sequencing instruments.

first: Kevin

last: Chen


title: The Obesity-associated Fto gene regulates activity of the dopaminergic midbrain circuitry

city: New York

first: Christopher

last: Mason

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

first: Martin

last: Hess

first: Simon

first: Kate

last: Meyer

first: Linda

last: Verhagen

last: Koch

middle: S


title: Genome-wide methylation and expression analysis of two breast cancer cell lines [RNA-Seq]

city: St. Louis

first: Nathan

last: VanderKraats

address: 660 S. Euclid Ave

department: Center for Pharmacogenomics

summary: To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq.  Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. 2010, Genome Research).

overall_design: RNA-Seq was used to generate mRNA expression profiles of MCF7 and T47D cells under standard growth conditions.

middle: D

first: John

last: Edwards

last: Hiken

first: Keith

last: Decker


title: Transcriptomic profiling of Aspergillus flavus in response to 5-azacytidine & gallic acid

city: Guangzhou

first: Zhumei

last: He

address: 135 Xingangxi Street

department: School of Life Sciences

institute: Sun Yat-sen University

summary: Aspergillus flavus is a common saprophyte and opportunistic pathogen producing aflatoxin (AF) and many other secondary metabolites. 5-Azacytidine (5-AC), a derivative of nucleoside cytidine, is widely used for studies in epigenetics and cancer biology as an inactivator of DNA methyltransferase and is also used for studying secondary metabolism in fungi. Our previous studies showed that 5-AC affects development and inhibits AF production in A. flavus, and that A. flavus lacks DNA methylation. How this common DNA methyltransferase inhibitor affects development and AF production is not clear. In this study, we applied an RNA-Seq approach to elucidate the mechanism of 5-AC’s effect on A. flavus. In our current study, we identified 240 significantly differently expressed (Q-value<0.05) genes after 5-AC treatment, including two backbone genes in secondary metabolite clusters #27 and #35, which are involved in development or survival of sclerotia. With 5-AC treatment, about three quarters of the genes in the AF biosynthetic gene cluster in A. flavus were down-regulated to a certain degree. Strikingly, at least two genes aflI and aflLa, were completely inhibited. Interestingly, several genes involved in fungal development were down-regulated, especially veA, which is a gene that encodes protein bridges VelB and LaeA. This result supports the hypothesis that 5-AC affects development and AF production through weakening or even interrupting the connection between VelB and LaeA and then causing dysregulation of the expression pattern of genes involved in development and secondary metabolism. Our results improved the A. flavus genome annotation, provided a comprehensive view of the transcriptome of A. flavus responding to 5-AC and confirmed that fungal development and secondary metabolism are co-regulated. In  additon, the RNA-Seq data of another sample treated with gallic acid was used to improve A. flavus genome annotation.

overall_design: mRNA of Aspergillus flavus cultured in three different culture media PDB, PDB+5-AC(5-Azacytidine),and PDB+GA(gallic acid) was subjected to sequence independently.


title: Genome-wide methylation and expression analysis of two breast cancer cell lines [Methyl-MAPS]

overall_design: DNA Methylation was assayed for two breast cancer cell lines using Methyl-MAPS.


summary: We interrogated the genome-wide occupancy of histone modifications and RNA polymerase II at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol.  These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively.  This study revealed many dynamic patterns of histone modifications during differentiation that are coordinated with stage-specific gene expression including a novel preactivation chromatin pattern found at genes associated with cardiac function.  In addition, this study identified distal enhancer elements and enriched transcription factor motifs within enhancer regions for each stage of differentiation, which were used to predict novel transcription regulatory networks.

overall_design: ChIP-seq analysis of histone modifications and RNA polymerase II at 4 stages of directed cardiac differentiation of mouse embryonic stem cells.  Each stage in biological duplicate or triplicate


title: Density and methylation state of CpG dinucleotides define histone variant specific retention of nucleosomes in mouse spermatozoa

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: Nucleosomes are the principal packaging units of chromatin and critical for gene regulation and genome stability. In mammals, a subset of nucleosomes fail to be replaced by protamines during spermatogenesis and are retained in mature spermatozoa providing opportunities for paternal epigenetic transmission. In humans, the remaining 10% localize at regulatory elements of genes. To assess evolutionary conservation and to dissect the molecular logic underlying nucleosome retention, we determined the genome wide nucleosome occupancy in mouse spermatozoa that only contain 1% residual histones. In striking contrast to mammalian somatic cells and haploid round spermatids, we observe high enrichment of nucleosomes at CpG-rich sequences throughout the genome, at conserved regulatory sequences as well as at intra- and intergenic regions and repetitive DNA. This preferred occupancy occurs mutually exclusive with DNA methylation both in mouse and human sperm. At unmethylated CpG-rich sequences, residing nucleosomes are largely composed of the H3.3 histone variant, and trimethylated at lysine 4 (H3K4me3). Both canonical H3.1/H3.2 and H3.3 variant histones are present at promoters marked by Polycomb-mediated H3K27me3, which is strongly predictive for gene repression in pre-implantation embryos. Our data indicate important roles of DNA sequence composition, DNA methylation, variant H3.3 and canonical H3.1/H3.2 histones and associated modifications in nucleosome retention versus eviction during the histone-to-protamine remodeling process in elongating spermatids and potentially in epigenetic inheritance by nucleosomes between generations.

overall_design: Identification of histone, histone variant and histone modification states in round spermatids and sperm

first: Serap

last: Erkek

first: Mizue

last: Hisano

first: Rabih

last: Murr

first: Dirk

last: Schuebeler

first: Michael

last: Stadler


title: In vivo development, differentiation and function of brown fat proceeds in the absence of miRNAs 193b and 365-1

status: Public on Jun 14 2013

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

summary: Brown adipose (BAT) development and function are unaffected by the absence of miR-193b/365-1

overall_design: We refer to wild-type mice (+/+) as WT and to mice lacking the mir-193b (-/-) as Null mice.

first: Yonatan

last: Feuermann


title: RNAseq Mycobacterium Tuberculosis

status: Public on Jun 13 2013

city: Bogota

first: Patricia

last: Del Portillo

address: Carrera 5 No. 66A-34

country: Colombia

institute: corpogen

summary: We analyzed the genes expressed, or the transcriptome, of bacilli (Mycobacterium tuberculosis) growing in fatty acids as sole carbon source. Using new technologies to massively sequence of RNA molecules we identified a group of genes that provides novel insight regarding the metabolic pathways and transcriptional regulation of latent M. Tuberculosis.

overall_design: Comparative Transcriptomics between two carbon source (Dextrose, Long Fatty Acids), at two states of growth (Exponential and Stationary Phase)

first: Juan

middle: G

last: Rodriguez

first: Adriana

last: Hernandez

first: Cecilia

last: Helguera-Repetto

first: Diana

last: Aguilar Ayala

last: Anzóla

first: Jose

last: Bustos

first: María

last: Zambrano

first: Jorge

last: González-y-Merchand

middle: J

last: García


title: Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus infected mice

city: Philadelphia

first: Megan

middle: Ruth

last: Elliott

address: 3610 Hamilton Walk

institute: University of Pennsylvania

summary: We use transcriptome analysis to study the spinal cord transcriptome during MHV-induced demyelinating disease and find important biological pathways for demyelinating pathology.  We find evidence of a Th1 cytokine response, ongoing antigen presentation and lymphocyte proliferation, lipid metabolism changes, and eicosanoid inflammation.  In addition, we report several genes important for osteoclast function have augmented expression in the CNS during demyelination, suggesting a parallel between the osteoclast and microglial functions in maintaining homeostasis and the fidelity of specialized extracellular matrices in their respective compartments.

overall_design: RNA-seq of mock-infected and MHV-infected spinal cord tissue at 33 days post-infection, the peak of demyelination.

first: Ruth

first: Susan

last: Weiss


title: Induction of a hemogenic program in mouse fibroblasts

first: Betty

last: Chang

address: 1425 Madison Ave

institute: Mount Sinai School of Medicine

summary: Definitive hematopoiesis emerges during embryogenesis via an endothelial-to-hematopoietic transition. We attempted to induce this process in mouse fibroblasts by screening a panel of factors for hemogenic activity. We identified a combination of four transcription factors, Gata2, Gfi1b, cFos, and Etv6 that efficiently induces endothelial-like precursor cells with the subsequent appearance of hematopoietic cells. The precursor cells express a human CD34 reporter, Sca1 and Prominin1 within a global endothelial transcription program. Emergent hematopoietic cells possess nascent/specifying hematopoietic stem cell gene expression profiles and cell surface phenotypes. After transgene silencing and reaggregation culture, the specified cells generate hematopoietic colonies in vitro. Thus, we have shown that a simple combination of transcription factors is sufficient to induce a complex, dynamic and multi-step developmental program in vitro. These findings provide insights into the specification of definitive hemogenesis and a platform for future development of patient-specific stem/progenitor cells as well as more differentiated blood products.

overall_design: mRNA-seq profiling on populations generated after transduction with Gata2, Gfi1b, cFos and Etv6 at day 20 and day 35.

first: Carlos

last: Pereira

first: Kateri

last: Moore

first: Ihor

last: Lemischka


title: Predicting and manipulating drug inactivation by the human gut microbiome

city: San Francisco

first: Peter

middle: James

last: Turnbaugh

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

summary: The trillions of microorganisms in the human gastrointestinal tract are an underexplored aspect of pharmacology. Despite numerous examples of microbial effects on drug efficacy and toxicity, there is often an incomplete understanding of the underlying mechanisms. Here, we dissect the inactivation of the commonly prescribed cardiac glycoside, digoxin, by Eggerthella lenta. Whole genome transcriptional profiling, comparative genomics, and culture-based assays revealed a cytochrome-encoding operon up-regulated by digoxin, absent in non-metabolizing E. lenta strains, and predictive of the efficiency of digoxin inactivation by the human gut microbiome. Digoxin inactivation was further enhanced by microbial interactions and inhibited by arginine. Pharmacokinetic studies using gnotobiotic mice revealed that increasing dietary protein reduces the in vivo metabolism of digoxin by E. lenta, with significant changes to drug concentration in the urine and serum. These results emphasize the importance of viewing pharmacology from the perspective of both our human and microbial genomes.

overall_design: RNA-Seq analysis of Eggerthella lenta cultured with or without digoxin.

first: Henry

last: Haiser


title: Genome-wide methylation and expression analysis of two breast cancer cell lines

first: Nathan

last: VanderKraats


title: Molecular profiling of human mammary gland links breast cancer risk to a p27+ cell population with progenitor characteristics

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Gene expression, DNA and histone methylation profiles were performed on multiple cell types purified from normal human nulliparous and parous breast tissue using SAGE-seq, MSDK-seq and ChIP-seq [GSE26141].

overall_design: SAGE-seq, MSDK-seq and ChIP-seq libraries were made from individual cell types and integrated to find a comprehensive view of parity associated changes.

first: Sibgat

middle: A

last: Choudhury

first: Reo

last: Maruyama


title: Effect of ETV1 knockdown on genome wide AR binding in LNCaP Cells

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Translocation of ETS transcription factors including ERG and ETV1 occur in half of all prostate cancers. LNCaP cells harbor an ETV1 translocation. We performed ChIP-Seq analysis to determine the role of ETV1 on AR binding. The localization of enhancers were determined by H3K4me1 ChIP-Seq.

overall_design: To determine ETV1 and H3K4me1 localization, logarithmically growing cells

first: Charles

last: Sawyers


title: Frac-seq reveals preferential polyribosome association of minor mRNA isoforms

city: Santa Cruz

first: Jeremy

last: Sanford

address: 1156 High Street

department: MCD Biology

institute: UC Santa Cruz

summary: The goal of this study was to test the hypothesis that minor alternative mRNA isoforms can be preferentially translated.

overall_design: Included are Cytoplasm and Polyribosome samples in duplicate from both Control and Rapamycin treated cells.

first: Timothy

last: Sterne-Weiler


title: ChIP-Seq analysis of Candida albicans Sfl1p and Sfl2p

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

summary: Sfl1p and Sfl2p are two homologous heat shock factor-type transcriptional regulators that antagonistically control morphogenesis in Candida albicans, while being required for full pathogenesis and virulence. To understand how Sfl1p and Sfl2p exert their function, we combined genome-wide location and expression analyses to reveal their transcriptional targets in vivo together with the associated changes of the C. albicans transcriptome. We show that Sfl1p and Sfl2p bind to the promoter of at least 113 common targets through divergent binding motifs and modulate directly the expression of key transcriptional regulators of C. albicans morphogenesis and/or virulence. Surprisingly, we found that Sfl2p additionally binds to the promoter of 75 specific targets, including a high proportion of hyphal-specific genes (HSGs; HWP1, HYR1, ECE1, others), revealing a direct link between Sfl2p and hyphal development. Data mining pointed to a regulatory network in which Sfl1p and Sfl2p act as both transcriptional activators and repressors. Sfl1p directly represses the expression of positive regulators of hyphal growth (BRG1, UME6, TEC1, SFL2), while upregulating both yeast form-associated genes (RME1, RHD1,YWP1) and repressors of morphogenesis (SSN6, NRG1). On the other hand, Sfl2p directly upregulates HSGs and activators of hyphal growth (UME6, TEC1), while downregulating yeast form-associated genes and repressors of morphogenesis (NRG1, RFG1, SFL1). Using genetic interaction analyses, we provide further evidences that Sfl1p and Sfl2p antagonistically control C. albicans morphogenesis through direct modulation of the expression of important regulators of hyphal growth. Bioinformatic analyses suggest that binding of Sfl1p and Sfl2p to their targets occurs with the co-binding of Efg1p and/or Ndt80p. Indeed, we show that Sfl1p and Sfl2p targets are bound by Efg1p and that both Sfl1p and Sfl2p associate in vivo with Efg1p. Taken together, our data suggest that Sfl1p and Sfl2p act as central “switch on/off” proteins to coordinate the regulation of C. albicans morphogenesis.

overall_design: ChIP was performed in 2 independently grown C. albicans sfl1 or sfl2 homozygous mutant strains expressing (sfl1-CaEXP-SFL1-HA or sfl2-CaEXP-SFL2-HA, respectively) or not (sfl1-CaEXP or sfl2-CaEXP, respectively) SFL1-HA or SFL2-HA (-HA, 3'-triple-HA-tagged alleles of SFL1 or SFL2) under the control of a methionine-repressible promoter (Total samples = 8; 2xCaEXP-SFL1-HA, 2xCaEXP-SFL2-HA, 2xCaEXP control for SFL1-HA ChIP and 2xCaEXP control for SFL2-HA ChIP).


title: Multiple RNA recognition patterns during microRNA biogenesis in plants

status: Public on Jun 12 2013

city: Rosario

first: Uciel

middle: Pablo

last: Chorostecki

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

summary: MicroRNAs (miRNAs) are processed from longer precursors with fold-back structures. While animal MIRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach (SPARE) to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the evolutionary conserved miRNAs present in Arabidopsis thaliana. We found that plant MIRNAs are processed by four mechanisms, depending on the sequential direction of the processing machinery and the number of cuts required to release the miRNA. Classification of the precursors according to their processing mechanism revealed specific structural determinants for each group. We found that the complexity of the miRNA processing pathways occurs in both ancient and evolutionary young sequences, and that members of the same family can be processed in different ways. We observed that different structural determinants compete for the processing machinery and that alternative miRNAs can be generated from a single precursor. The results provide a mechanistic explanation for the structural diversity of MIRNA precursors in plants and new insights towards the understanding of the biogenesis of small RNAs.

overall_design: Approach to systematically analyze miRNA processing intermediates and characterize the biogenesis of conserved and young miRNAs present in Arabidopsis thaliana. MiRNA processing intermediates profiles of Wild type and Fiery mutants Arabidopsis plants were analyzed, using Illumina GAIIx.

first: Nicolas

last: Bologna

first: Arnaldo

last: Schapire

first: Jixian

last: Zhai

first: Jerome

last: Boisbouvier

first: Blake

last: Meyers

first: Javier

middle: F

last: Palatnik


title: Tcf-1 expression in murine thymus

city: Bethesda

first: Marei

last: Dose

state: MD

address: 9000 Rockville Pk

institute: National Institutes of Health

summary: The DNA binding factor Tcf-1 is one of the most prominently expressed genes in thymocytes yet its global DNA binding pattern remained unknown. Here we have assessed by ChIP-seq the Tcf-1 binding pattern in murine thymocytes in WT B6 mice and in mice expressing a stabilized form of the Tcf-1 binding partner beta-Catenin (CAT mice).

overall_design: Tcf-1 ChIP-seq of 2 samples and 2 input controls and H3K4mel3 ChIP-seq of 1 sample and 1 input control.

first: Fotini

last: Gounari


title: Experimental characterization of the human non-sequence-specific nucleic acid interactome

city: Vienna

first: Gerhard

last: Duernberger

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM

summary: The interactions between proteins and nucleic acids have a fundamental function in many biological processes well beyond nuclear gene transcription and include RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins binding individual mRNAs in mammalian cells has greatly been augmented by recent surveys, no systematic study on the native proteins of human cells differentially engaging various types of nucleic acids in a non sequence-specific manner has been reported. We designed an experimental approach to cover the non sequence-specific RNA and DNA binding space broadly, including methylation, and test for its ability to interact with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high confidence direct binders, 249 of which were devoid of previous experimental evidence for binding nucleic acids. We could assign 513 specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and to individual domains. The evolutionary conserved protein YB-1, previously associated with cancer and gene regulation, is shown to bind methylated cytosine preferentially conferring YB-1 a potential epigenetic function. Collectively, the dataset represents a rich resource of experimentally determined nucleic acid-specific binding proteins in humans and, indirectly, for other species.

overall_design: Identification of genomic YB-1 binding sites in HEK293 cells

first: Jacques

last: Colinge


title: Identification of novel imprinted differentially methylated regions by global analysis of human parthenogenetic induced pluripotent stem cells

first: Rahul

last: Karnik

address: 419 Broadway

summary: Parental imprinting is an epigenetic phenomenon by which genes are expressed in a monoallelic fashion, according to their parent-of-origin. DNA methylation is considered the hallmark mechanism regulating parental imprinting. To identify imprinted differentially methylated regions (DMRs), we compared the DNA methylation status between multiple normal and parthenogenetic human pluripotent stem cells (PSCs) by performing reduced representation bisulfite sequencing. Our analysis identified over twenty previously unknown imprinted DMRs in addition to the known DMRs. These include DMRs in loci associated with human disorders, and a class of intergenic DMRs that do not seem to be related to gene expression. Furthermore, the study showed some DMRs to be unstable, liable to differentiation or reprogramming. A comprehensive comparison between mouse and human DMRs identified almost half of the imprinted DMRs to be species-specific. Taken together our data map novel DMRs in the human genome, their evolutionary conservation, and relation to gene expression.

overall_design: RRBS profiles were generated from 6 parthenogenetic iPSC lines (hiPS A11, hiPS A20, hIPS A26, hiPS B34, hiPS B36, hiPS B41)  and fibroblasts from the 2 parents whose ovarian teratomas were used to derive the iPSC lines, for a total of 8 samples.

first: Alex

last: Meissner


title: Multiple platform assessment and isomir analysis of the EGF dependent microRNA-ome by microarray and deep sequencing analysis

status: Public on Jun 11 2013

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

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

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Refer to individual Series


title: abc transporters in Dictyostelium discoideum development

city: Ljubljana

first: Marko

last: Toplak

address: Trzaska cesta 25

country: Slovenia

institute: University of Ljubljana

summary: ATP-binding cassette (ABC) transporters can translocate a broad spectrum of molecules across the cell membrane including physiological cargo and toxins. ABC transporters are known for the role they play in resistance towards anticancer agents in chemotherapy of cancer patients. There are 68 ABC transporters annotated in the genome of the social amoeba Dictyostelium discoideum. We have characterized more than half of these ABC transporters through a systematic study of mutations in their genes. We have analyzed morphological and transcriptional phenotypes for these mutants during growth and development and found that most of the mutants exhibited rather subtle phenotypes. A few of the genes may share physiological functions, as reflected in their transcriptional phenotypes. Since most of the abc-transporter mutants showed subtle morphological phenotypes, we utilized these transcriptional phenotypes to identify genes that are important for development by looking for transcripts whose abundance was unperturbed in most of the mutants. We found a set of 668 genes that includes many validated D. discoideum developmental genes. We have also found that abcG6 and abcG18 may have potential roles in intercellular signaling during terminal differentiation of spores and stalks.

overall_design: Transcriptional phenotyping during development of abc transporter mutants in Dictyostelium discoideum

first: Edward

last: Miranda

first: Olga

last: Zhuchenko

first: Balaji

last: Santhanam

first: Blaz

last: Zupan

first: Adam

last: Kuspa

first: Gad

last: Shaulsky


title: Genomic mapping of ERG, AR, histone H3 monomethyl-K4, histone H3 trimethyl-K4 binding sites in mouse prostates in WT, ERG overexpression, Pten loss mouse prostates

first: Yu

last: Chen

summary: Translocation of ETS transcription factors including ERG and ETV1 occur in half of all prostate cancers. We generated a mouse model of ERG ovexpression (Rosa26-ERG) which when crossed into prostate specific probasin-Cre, expressed ERG specifically in the prostate. We crossed Rosa26-ERG into Pten flox/flox allele to generate compound GEMM mouse. Here, we determined the genomic binding sites of ERG, AR, and the histone marks H3K4me1 and H3K4me3 that maps enhancers and promoters respectively in the prostates of these mice.

overall_design: The prostate of four six month old mice of each genotype were pooled. The chromatin was isolated and ChIP-Seq performed.

first: Charles

last: Sawyers


title: Identification of microarray probe signals constantly present in multiple sample types

status: Public on Jun 10 2013

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine


title: Multiple platform assessment and isomir analysis of the EGF dependent microRNA-ome by microarray and deep sequencing analysis [small RNA-seq]

summary: We have used an integrative high content analysis approach to identify the specific miRNAs implicated in EGF signaling in HeLa cells as potential mediators of cancer mediated functions. We have used microarray and deep-sequencing technologies in order to obtain a global view of the EGF miRNA transcriptome with a robust experimental cross-validation. By applying a procedure based on Rankprod tests, we have delimited a solid set of EGF-regulated miRNAs. After validating regulated miRNAs by RT-qPCR, we have derived protein networks and biological functions from the predicted targets of the regulated miRNAs to gain insight into the potential role of miRNAs in EGF-treated cells. In addition, we have analyzed sequence heterogeneity due to editing relative to the reference sequence (isomirs) among regulated miRNAs.

overall_design: Time course experiment comparing HeLa gene expression in response to EGF analyzed by small RNA-seq using Illumina 36-bp read massively parallel sequencing. Three independent experiments were performed where HeLa cells were serum deprived for 24 hours and were either left untreated or treated with EGF for 6h and harvested for RNA extraction.  Thus, a total of 6 samples were analyzed, 3 controls and the 3 respective treated counterparts. These same samples were also analyzed in parallel on two different microarray platforms.

first: Franc

last: Llorens

first: Manuela

last: Hummel

first: Lorena

last: Pantano

first: Xavier

last: Pastor

first: Ana

last: Vivancos

first: Ester

last: Castillo

first: Heidi

last: Mattlin

first: Anna

last: Ferrer

first: Matthew

last: Ingham

first: Marc

last: Noguera

first: Robert

last: Kofler

first: Juliane

middle: C

last: Dohm

first: Raquel

last: Pluvinet

first: Mònica

last: Bayés

first: Heinz

last: Himmelbauer

first: Jose

last: del Rio

first: Eulàlia

last: Martí


title: Lung adenocarcinoma metastasis is suppressed by the alveolar lineage transcription factors GATA6 and HOPX.

city: New Haven

first: Don

last: Nguyen

state: CT

address: 310 Cedar St

institute: Yale Shcool of Medicine

summary: Molecular programs that mediate normal cell differentiation are required for oncogenesis and tumor cell survival in certain cancers. How cell-lineage-restricted genes specifically influence metastasis is poorly defined. In lung cancers, we uncovered a transcriptional program that is preferentially associated with distal airway epithelial differentiation and lung adenocarcinoma (ADC) progression. This program is regulated in part by the lineage transcription factors GATA6 and HOPX. These factors can cooperatively limit the metastatic competence of ADC cells, by modulating overlapping alveolar differentiation and invasogenic target genes. Thus, GATA6 and HOPX are critical nodes in a lineage-selective pathway that directly links effectors of airway epithelial specification to the inhibition of metastasis in the lung ADC subtype.

overall_design: mRNA profiles of human lung Adenocarcinoma PC9 cell lines infected with lentivirus harboring shRNA of control and shRNA of both GATA6 and HOPX were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: William

last: Cheung

first: Minghui

last: Zhao

first: Zongzhi

last: Liu

first: Laura

last: Stevens

first: Paul

last: Cao

first: Justin

last: Fang

first: Tomas

last: Westbrook

middle: X


title: Identification of microarray probe signals constantly present in multiple sample types (part 2)

first: Stephen

last: Krawetz

summary: The correlation of the RNA profiles obtained by microarray analysis was compared with that obtained from RNA-Seq by using reduced complexity sperm datasets. This resolved as a series of discordant probes. The extent of discordancy among other datasets was then determined.

overall_design: A correlative study between probe’s signal intensity from Illumina bead arrays with its transcript level detected by next generation sequencing technique was performed. RNAs from sperm and testis samples were applied

first: Shihong

last: Mao

first: Aletheia

last: Lima-Souza

last: Goodrich


title: A user-friendly chromatographic method to purify small regulatory RNAs

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

institute: CNRS

summary: The discovery of the small regulatory RNA populations has changed our vision of cellular regulations. Indeed, loaded on Argonaute proteins they formed ribonucleoprotein complexes that target complementary sequences and achieved widespread silencing mechanisms conserved in most eukaryotes. The recent development of deep sequencing approaches highly contributed to their detection. Small RNA isolation form cells and/or tissues remains a crucial stage to generate robust and relevant sequencing data. In 2006, a novel strategy based on anion-exchange chromatography has been purposed as an alternative to the standard size-isolation purification procedure. However, the eventual biases of such a method have been poorly investigated. Moreover, this strategy not only relies on advanced technical skills and expensive material but is time consuming and requires an elevated starting biological material amount. Using bioinformatic comparative analysis of six independent small RNA-sequencing libraries of Drosophila ovaries, we here demonstrate that anion-exchange chromatography purification prior to small RNA extraction unbiasedly enriches datasets in bona fide reads (small regulatory RNA reads) and depletes endogenous contaminants (ribosomal RNAs and degradation products). The resulting increase of sequencing depth provides a major benefit to study rare populations. We then developed a fast and basic manual procedure to purify loaded small non coding RNAs using anion-exchange chromatography at the bench. We validated the efficiency of this new method and used this strategy to purify small RNAs from various tissues and organisms. We moreover determined that our manual purification increases the output of the previously described anion-exchange chromatography procedure.

overall_design: Comparison of small  regulatory RNA populations obtained after three different small RNA purification procedures

first: Thomas

last: Grentzinger

first: Claudia

last: Armenise

first: Alain

last: Pelisson

first: Christine

last: Brun

first: Bruno

last: Mugat

first: Séverine

last: Chambeyron


title: RNA-seq analysis of ES cell populations with different functional potentials in serum/LIF and 2i/LIF, as well as analysis of the transcriptional effect of LIF in ground state (2i) culture conditions.

city: Copenhagen

first: Joshua

last: Brickman

address: Blegdamsvej 3B

department: The Danish Stem Cell Centre (DanStem)

country: Denmark

institute: University of Copenhagen

summary: We report that ES cells cultured in ground state (2i and 2i/LIF) culture conditions are heterogeneous and show heterogeneus expression of extraembryonic markers. Using a highly sensitive reporter for the endoderm marker Hex we can sort Hex high and low populations from either serum/LIF or 2i/LIF and demonstrate that they have different functional properties. Here we explored the transcriptional basis of these functional differences and noted that Hex low (HV-) and Hex high (HV+) populations showed  more distinct expression profiles in 2i/LIF than in serum/LIF. Additionally in 2i/LIF the HV+ population showed an upregulation of extraembryonic markers (such as trophoblast stem cell specific genes) and also imprinted genes compared to the HV- population, which is not observed when these populations are sorted from serum/LIF. We also analysed the transcriptional effect of LIF in 2i by analysing unsorted ES cells cultured in either 2i alone or 2i with LIF. We observed that the addition of LIF led to an upregulation of extraembryonic markers but did not effect the expression of pluripotency genes, other than Klf4. Additionally, the most significantly upregulated genes from 2i/LIF cultured ES cells compared to 2i cultured ES cells showed the greatest correlation to placental tissue when compared to the GNF tissue specific expression database. This analysis, alongside functional experiments, suggested that HV+ ES cells in 2i/LIF corresponded to an extraembryonically primed population of cells and that the addition of LIF supported this population.

overall_design: RNA-seq of sorted Hex low and high expressing ES cell populations cultured in serum/LIF or 2i/LIF as well as unsorted ES cells from 2i or 2i/LIF.

first: Sophie

last: Morgani


title: Investigating the sRNA and mRNA transcriptional response to antibiotics in methicillin-resistant Staphylococcus aureus using Illumina RNAseq

city: Heidelberg

first: Ben

last: Howden

state: VIC

address: Austin Health

department: Infectious Diseases Department

institute: Austin Health

summary: Coordinated protein-coding sequence transcriptional responses of Staphylococcus aureus to antimicrobial exposure are well described but little is known of the role of bacterial non-coding, small RNAs (sRNAs) in these responses. Here we used RNAseq to investigate the sRNA response of the epidemic multiresistant hospital ST239 S. Aureus strain JKD6009 and its vancomycin-intermediate clinical derivative, JKD6008, after exposure to four antibiotics representing the major classes of antimicrobials used to treat methicillin-resistant S. Aureus infections. These agents included vancomycin, linezolid, ceftobiprole, and tigecycline. We identified 410 potential sRNAs (sRNAs) and then compared global sRNA and mRNA expression profiles at 2 and 6 hours, without antibiotic exposure, and after exposure to 0.5 x MIC for each antibiotic, for both JKD6009 (VSSA), and JKD6008 (VISA).

overall_design: Two strains were used (JKD6009, vancomycin-susceptible S. Aureus; JKD6008, in vivo derived vancomycin-intermediate S. Aureus). The complete JKD6008 genome seqeuce was used as the reference. Two time points, 2 hours and 6 hours after culture in Mueller Hinton broth. Strains were exposed to no antibiotic, or 0.5 x MIC for 10 mins for the following antibiotics; vancomycin, linezolid, ceftobiprole, tigecycline. RNA isolation procedures enriched for mRNA or sRNA. The 40 cDNA libraries were sequenced using a whole flowcell (8 lanes) in an Illumina genome analyzer GAII for 36 cycles. Data was analyzed using the BioConductor package limma, and by applying non-negative matrix factorization to determine the impact of antibiotic exposure on the sRNA and mRNA transcriptional profiles.

first: Benjamin

middle: P


title: An epigenetic signature of developmental potential in neural stem cells and early neurons [ChIP-seq]

status: Public on Jun 09 2013

city: London

first: Matt

last: Burney

address: 125 Coldharbour Lane

institute: King's College London

summary: A cardinal property of neural stem cells (NSCs) is their ability to adopt multiple fates upon differentiation. The epigenome is widely seen as a read-out of cellular potential and a manifestation of this can be seen in embryonic stem cells (ESCs), where promoters of many lineage-specific regulators are marked by a bivalent epigenetic signature comprising trimethylation of both lysine 4 and lysine 27 of histone H3 (H3K4me3 and H3K27me3, respectively). Bivalency has subsequently emerged as a powerful epigenetic indicator of stem cell potential. Here, we have interrogated the epigenome during differentiation of ESC-derived NSCs to immature GABAergic interneurons. We show that developmental transitions are accompanied by loss of bivalency at many promoters in line with their increasing developmental restriction from pluripotent ESC through multipotent NSC to committed GABAergic interneuron. At the NSC stage, the promoters of genes encoding many transcriptional regulators required for differentiation of multiple neuronal subtypes and neural crest appear to be bivalent, consistent with the broad developmental potential of NSCs. Upon differentiation to GABAergic neurons, all non-GABAergic promoters resolve to H3K27me3 monovalency, whereas GABAergic promoters resolve to H3K4me3 monovalency or retain bivalency. Importantly, many of these epigenetic changes occur prior to any corresponding changes in gene expression. Intriguingly, another group of gene promoters gain bivalency as NSCs differentiate toward neurons, the majority of which are associated with functions connected with maturation and establishment and maintenance of connectivity. These data show that bivalency provides a dynamic epigenetic signature of developmental potential in both NSCs and in early neurons.

overall_design: Neural stem cells derived from mouse embryonic stem cells were differentiated into neurons and FACS purified based on RedStar fluorescence driven by the Tau promoter. Chromatin was prepared from NSCs and neurons (n=1), sonicated to roughly 300bp and immunoprecipitated with antibodies against H3K4me3, H3K27me3, total Histone H3 and total IgG, alongside a 5% input sample. K4/K27 and corresponding input samples were analysed by ChIPSeq

first: Matthew

first: Caroline

last: Johnson

first: Kee-Yew

last: Wong

first: Siaw-Wei

last: Teng

first: Vassilios

last: Beglopoulos

first: Lawrence

middle: W

last: Stanton

first: Brenda

last: Williams

first: Angela

last: Bithell

first: Noel

last: Buckley


title: An epigenetic signature of developmental potential in neural stem cells and early neurons


title: Uniform optimal framework for integrative next-gen sequence analysis

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Here, we have collapsed multiple analysis problems into two coherent categories, signal detection and signal estimation and adapted linear-optimal solutions from signal processing theory. Our algorithms for detection (DFilter) and estimation (EFilter) extend naturally to integration of multiple datasets. In benchmarking tests, DFilter outperformed assay-specific algorithms at identifying promoters from histone ChIP-seq, binding sites from transcription factor (TF) ChIP-seq and open chromatin regions from DNase- and FAIRE-seq data. EFilter similarly outperformed an existing method for predicting mRNA levels from histone ChIP-seq data (Spearman correlation: 0.81 - 0.89). We performed H3K4me3 and H3K36me3 ChIP-seq on e11.5 mouse forebrain and used DFilter and EFilter to predict promoters and developmental gene expression, uncovering plausible gene targets for SNPs associated with neurodevelopmental disorders.

overall_design: Generated two histone modifiction ChiP-seq in developing embryo mouse forebrain and using them for making bioligical inferences

first: Shyam

last: Prabhaker

first: MURATANI

last: Masafumi


title: Differential programming of B cells in Aicda-/- mice

status: Public on Jun 07 2013

city: Amsterdam

first: Marc

middle: Arnaud

last: Hogenbirk

address: Plesmanlaan 121

department: biological stress response

country: Netherlands

institute: the Netherlands Cancer Institute


title: The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline

city: Princeton

first: Trudi

last: Schupbach

state: NJ

address: Washington Rd

department: Molecular Biology

institute: HHMI/Princeton University

summary: In a broad range of organisms, Piwi-interacting RNAs (piRNAs) have emerged as core components of a surveillance system that protects the genome by silencing transposable and repetitive elements. A vast proportion of piRNAs is produced from discrete genomic loci, termed piRNA clusters. The molecular mechanisms and the factors that govern the expression of these loci are largely unknown. We have preciously shown the Cutoff (Cuff), a protein with similarity to yeast Rai1, is a component of the piRNA pathway. In order to understand the function of the Cuff protein in piRNA production, we produced small RNA libraries from cn, bw (wt) and cuffwm25 mutant ovaties. The analysis of these libraries revealed that approximately 80% of the total piRNA population is depleted in the absence of a functional Cuff protein. We also determined that Cuff is mostly a nuclear protein and is enriched at the level of certain piRNA clusters. Our results point to a role for Cuff in the transcriptional regulation of piRNA generating loci and in the production of the proper piRNA complement during Drosophila oogenesis.

overall_design: piRNA profiling in ovaries from cn, bw and cuffwm25 mutant ovaries

first: Attilio

last: Pane

first: Peng

last: Jiang

first: Dorothy

middle: Y

last: Zhao

first: Mona

last: Singh


title: TGF-b Signaling Is Associated with Endocytosis  at the Pocket Region of the Primary Cilium

status: Public on Jun 06 2013

first: Mads

last: Bak

address: Blegdamsvej 3

summary: Digital gene expression tag profiling of P19CL6 cell model during differentiation to cardiomyocytes

overall_design:
Four replicates were anlyzed at five time-points during differentiation; day 1, day 4, day 7, day 10 and day 14. Spontanously beating cardiomyocytes was observed at day 14
Spreadsheet with Log2 difference expression values is filtered by FDR and thus incomplete.

first: Søren

middle: T

last: Christensen

first: Lars

last: Larsen


title: A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

country: Switzerland

institute: EPFL


title: Differential programming of B cells in Aicda-/- mice [RNA-Seq]

summary: We sequenced mRNA from naive, in vitro activated, and GC B cells obtained from both Aicda-/- and Aicda+/+ mice.

overall_design: Examination of mRNA levels in naive, in vitro activated, and GC B cells.

first: Heinz

last: Jacobs


title: miRNA-sequencing of human pancreatic islets and enriched beta-cells

city: Oxford

first: Martijn

last: van de Bunt

address: OCDEM, Churchill Hospital, Headington

institute: Oxford Centre for Diabetes, Metabolism & Endocrinology

summary: Recent advances in the understanding of the genetics of type 2 diabetes (T2D) susceptibility have focused attention on the regulation of transcriptional activity within the pancreatic beta-cell. MicroRNAs (miRNAs) represent an important component of regulatory control, and have proven roles in the development of human disease and control of glucose homeostasis. We set out to establish the miRNA profile of human pancreatic islets and of enriched beta-cell populations, and to explore their potential involvement in T2D susceptibility. We used Illumina small RNA sequencing to profile the miRNA fraction in three preparations each of primary human islets and of enriched beta-cells generated by fluorescence-activated cell sorting. In total, 366 miRNAs were found to be expressed (i.e. >100 cumulative reads) in islets and 346 in beta-cells; of the total of 384 unique miRNAs, 328 were shared. A comparison of the islet-cell miRNA profile with those of 15 other human tissues identified 40 miRNAs predominantly expressed (i.e. >50% of all reads seen across the tissues) in islets. Several highly-expressed islet miRNAs, such as miR-375, have established roles in the regulation of islet function, but others (e.g. miR-27b-3p, miR-192-5p) have not previously been described in the context of islet biology. As a first step towards exploring the role of islet-expressed miRNAs and their predicted mRNA targets in T2D pathogenesis, we looked at published T2D association signals across these sites. We found evidence that predicted mRNA targets of islet-expressed miRNAs were globally enriched for signals of T2D association (p-values <0.01, q-values <0.1). At six loci with genome-wide evidence for T2D association (AP3S2, KCNK16, NOTCH2, SCL30A8, VPS26A, and WFS1) predicted mRNA target sites for islet-expressed miRNAs overlapped potentially causal variants. In conclusion, we have described the miRNA profile of human islets and beta-cells and provide evidence linking islet miRNAs to T2D pathogenesis.

overall_design: Examination of the miRNA profiles in 3 preparations of isolated pancreatic islets and 3 preparations of FACS-enriched pancreatic beta-cells

first: Kyle

last: Gaulton

first: Leopold

last: Parts

first: Ignasi

last: Morán

first: Paul

middle: R

last: Johnson

first: Cecilia

middle: M

last: Lindgren

first: Jorge

last: Ferrer

first: Anna

middle: L

last: Gloyn

first: Mark

middle: I

last: McCarthy


title: Global analysis of Upf1 in mESCs reveals expanded scope of nonsense-mediated mRNA decay

city: Cambridge

first: Jessica

last: Hurt

state: MA

address: 77 Massachusetts Avenue

department: Biology

country: USA

institute: Massachusetts Institute of Technology

summary: Nonsense-mediated mRNA decay (NMD) is a conserved RNA surveillance pathway that is an important modulator of disease pathology and is required for embryonic development.  Despite significant research effort, the rules that govern NMD remain incompletely understood. Here we used a combined¬ approach, integrating RNA-Seq, ribosome footprinting, and CLIP-Seq analysis of the essential NMD factor Upf1, to provide a more complete picture of the role of NMD in modulating gene expression in murine embryonic stem cells (mESCs).  We show that presence of an exon-exon junction ≥50 nucleotides (nt) downstream of a termination codon (dEJ) contributes to NMD independently of 3' UTR length, but has stronger effects in genes with shorter 3' UTRs.  We also map translated upstream open reading frames (uORFs) in mESCs and show that they are associated with NMD regulation, especially of genes encoding transcription factors, and we find that lowly translated mRNAs can escape NMD.  Finally, we identify over 200 direct binding targets of Upf1 and describe a pathway of Upf1-dependent gene regulation reliant on Upf1 binding to the 3' UTR and independent of presence of a dEJ.   Together, these analyses characterize known and discover novel determinants of NMD and establish a broader role in mESC gene regulation for Upf1.

overall_design: mRNA-Seq analysis of wildtype (2 samples), translationally inhibited (by cycloheximide treatment, 2 samples),  control-depleted (2 samples),  and Upf1-depleted (4 samples) mouse embryonic stem cells (mESCs); CLIP-Seq analysis of Upf1 (5 samples, and 5 samples of IgG control CLIP-Seq); Ribosome footprint profiling of wildtype (1 sample), control-depleted (1 sample), and Upf1-depleted (1 sample) mESCs

first: Alex

middle: D

last: Robertson

first: Christopher

middle: B

last: Burge


title: Differential programming of B cells in Aicda-/- mice [MethylCap-Seq]

first: Marc

last: Hogenbirk

summary: We determined CpG methylation load from GC B cells obtained from both Aicda-/- and Aicda+/+ mice.

overall_design: Examination of methylation load of Aicda-/- and Acida+/+ GC B cells.


title: Atrial Identity Is Determined by A COUP-TFII Regulatory Network

city: Houston

first: San-pin

last: Wu

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: Contribution of histone methylation to the plasticity of human FOXP3+ Treg cells

status: Public on Jun 08 2013

city: Xi'an

first: Haiqi

last: He

state: Shaanxi

address: West Yanta Road

institute: Xi'an Jiaotong University


title: Atrial Identity Is Determined by A COUP-TFII Regulatory Network (ChIP-Seq)

summary: Embryonic cardiomyocytes possess the plasticity to choose between atrial and ventricular fates. For a limited window of time, the transcription factor COUP-TFII (Nr2f2) sufficiently and essentially confers the atrial identity through direct and indirect regulation of nearly half of chamber specific genes.

overall_design: Examination of COUP-TFII binding sites in embryonic artia

first: Ming-Jer

last: Tsai

first: Sophia


title: Comprehensive, high resolution analysis of cis-acting regulatory networks at the alpha globin locus

first: Richard

middle: J

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine


title: A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs (ChIP-Seq)

first: Marion

last: LELEU

summary: During limb development, Hoxd genes are transcribed in two waves: Early on, when the arm and forearm are specified and subsequently, when digits form. While the latter phase is controlled by enhancers centromeric to the HoxD cluster, we show here that the early phase requires enhancers located in the opposite telomeric gene desert. The transition between the two types of regulations involves a functional switch between two distinct topological domains, as reflected by a subset of genes mapping centrally into the cluster, which initially interact with the telomeric domain and subsequently shift to establish new contacts on the opposite side. This transition between two regulatory landscapes generates an intermediate area of low Hox dose developing into the wrist, the transition between our arms and our hands. This intriguing correspondence between genomic and morphological boundaries illustrates the mechanism underlying collinear Hox gene regulation in our developing appendages.

overall_design: Chromatin ImmunoPrecipitation and Sequencing (ChIP-seq) of H3K27A in developing proximal and distal limbs at E9.5, E10.5 and E12.5

first: G

last: Andrey

first: D

last: Duboule


title: A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs (4C-Seq)

overall_design: Circular Chromosome Conformation Capture (4C seq) at the HoxD locus in developing proximal and distal limbs at E9.5 and E12.5


title: Identification of Oct4-dependent genes in vivo

city: Farmington

first: Paul

last: Robson

address: 10 Discovery Way

institute: The Jackson Laboratory for Genomic Medicine

summary: Transcriptome analysis of Oct4 null and wild type preimplantation mouse embryos by RNA-sequencing

overall_design: N=3 embryos of two genotypes (+/+ or -/-) at each of three time points (E2.5, E3.75, E4.5) were sequenced.

first: Amy

last: Ralston


title: A TAF4 coactivator function for E proteins that involves enhanced TFIID binding

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: The multisubunit TFIID plays a direct role in transcription initiation by binding to core promoter elements and directing preinitiation complex assembly. Although TFIID may also function as a coactivator through direct interactions with promoter-bound activators, mechanistic aspects of this poorly defined function remain unclear. Here biochemical studies show a direct TFIID-E protein interaction that (i) is mediated through interaction of a novel E protein activation domain (AD3) with the TAF homology (TAFH) domain of TAF4, (ii) is critical for activation of a natural target gene by an E protein and (iii) mechanistically, acts by enhancing TFIID binding to the core promoter. Complementary assays establish a gene-specific role for the TAFH domain in TFIID recruitment and gene activation in vivo. These results firmly establish TAF4 as a bona fide E protein coactivator, as well as a mechanism involving facilitated TFIID binding through direct interaction with an E protein activation domain.

overall_design: Genome-wide profiling of mRNA levels in MEF lines with Taf4 loxp/- (ctrl), Taf4 -/- (ko), Taf4 -/- Tg:hTAF4 wt, and Taf4 -/- Tg: hTAF4 Δ (TAFH-deleted).

first: Wei-Yi

last: Chen

first: Jinsong

last: Zhang

first: Zhimei

last: Du

first: Tomoyoshi

last: Nakadai

first: Robert

middle: G

last: Roeder


title: Comprehensive, high resolution analysis of cis-acting regulatory networks at the alpha globin locus (HTS)

summary: We have combined the 4C chromosome conformation capture protocol with high throughput, genome-wide sequence analysis to characterise in full a cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000kb), the 4C approach provides a comprehensive, high resolution analysis of a specific locus with the aim of defining, in detail, all cis- regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model we detected all known local and long-range interactions with this gene cluster. In addition we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the α-globin cluster. Using paired-end sequencing it was possible for the first time to identify interactions between specific subsets of cis-regulatory elements in populations of cells and within individual cells.

overall_design: Two biological replicates of 4C amplification from the promoters of the human HBA gene promoters.  Sequenced as paired end fragments usinig Illumina GAII

first: Jim

last: Hughes