title: Spo11-oligo mapping in zip3 mutants

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Meiotic recombination promotes genetic diversification as well as pairing and segregation of homologous chromosomes, but the double-strand breaks (DSBs) that initiate recombination are dangerous lesions that can cause mutation or meiotic failure. How cells control DSBs to balance between beneficial and deleterious outcomes is not well understood. This study tests the hypothesis that DSB control involves a network of intersecting regulatory circuits. We show that DSBs form in greater numbers in Saccharomyces cerevisiae cells lacking ZMM proteins, a suite of recombination-promoting factors traditionally regarded as acting strictly downstream of DSB formation. This counterintuitive result suggests that homologous chromosomes that have successfully engaged one another stop making DSBs, and provides new insight into phenotypes of zmm and other recombination-defective mutants. A genetically distinct pathway ties DSB formation to meiotic progression through the Ndt80 transcription factor. High-resolution genome-wide DSB maps generated by sequencing short oligonucleotides covalently bound to Spo11 (Spo11 oligos) demonstrate that feedback tied to ZMM function contributes in unexpected ways to spatial patterning of the recombination landscape.

overall_design: Four samples total: two wild type and two zip3 mutant (each an independent culture)

first: Neeman

last: Mohibullah

first: Xuan

last: Zhu

first: Drew

last: Thacker

first: Scott

last: Keeney


title: Small RNA-sequencing of Fibro-Adipogenic Progenitors (FAPs) upon Histone Deacetylase inhibition in young mdx mice

status: Public on Apr 23 2014

city: Roma

first: Pier Lorenzo

last: Puri

address: Via del Fosso di Fiorano, 64

country: Italy

institute: IRCCS Fondazione Santa Lucia

type: Non-coding RNA profiling by high throughput sequencing

summary: Fibro-adipogenic progenitors (FAPs) are emerging cellular components of the skeletal muscle regenerative environment. The alternative functional phenotype of FAPs - either supportive of muscle regeneration or promoting fibro-adipogenic degeneration - is a key determinant in the pathogenesis of muscular diseases, including Duchenne Muscular Dystrophy (DMD). However, the molecular regulation of FAPs is still unknown. We show here that an "HDAC-myomiR-BAF60 variant network" regulates the functional phenotype of FAPs in dystrophic muscles of mdx mice. Combinatorial analysis of gene expression microarray and genome-wide chromatin remodeling by Nuclease accessibility (NA)-seq revealed that HDAC inhibitors de-repress a "latent" myogenic program in FAPs from dystrophic muscles at early stages of disease progression. In these cells HDAC inhibition promoted the expression of two core components of the myogenic transcriptional machinery, MyoD and BAF60C, and upregulated the myomiRs (miRs) miR-1.2, miR-133 and miR-206, which target two alternative BAF60 variants (BAF60A and B) ultimately leading to the activation of a pro-myogenic program at the expense of the fibro-adipogenic phenotype. By contrast, FAPs from dystrophic muscles at late stages of disease progression displayed resistance to HDACi-induced chromatin remodeling at myogenic loci and fail to activate the pro-myogenic phenotype. These results reveal a previously unappreciated disease stage-specific bipotency of mesenchimal cells within the regenerative environment of dystrophic muscles. Resolution of such bi-potency by epigenetic interventions, such as HDACi, provides the molecular rationale for the in situ reprogramming of target cells to promote therapeutic regeneration of dystrophic muscles.

overall_design: miRNA modulation upon Histone Deacetylase inhibition in Fibro-Adipogenic Progenitors (FAPs) derived from young mdx mice was evaluated by small RNA-sequencing in 2 controls and 2 treated samples

first: Valentina

last: Saccone

first: Silvia

last: Consalvi

first: Luca

last: Madaro

first: Pasquale

last: Fasanaro

first: Pier

middle: L


title: Gene expression profiles of antigen-specific CD4+ T cells from mice carrying T cell-specific deletions of MyD88 or IL6Ra

status: Public on Apr 22 2014

city: New Haven

first: Dominik

last: Schenten

state: CT

address: 300 Cedar Street

department: Immunobiology

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: 2W:I-A(b) specific CD4+ T cells were isolated from immunized knock-out mice and wild-type controls on day 7 post immunization and the gene expression profiles of the cells were compared

overall_design: Antigen-specifc CD4+ T cells were isolated and pooled from 4 independent experiments. The samples represent antigen-specific T cells from 15-30 mice per genotype.

first: Ruslan

last: Medzhitov


title: Global variation of gene expression induced by constitutive activation of the NIK receptor in Arabidopsis

status: Public on Apr 21 2014

city: Viçosa

first: Otavio Jose

middle: Bernardes

last: Brustolini

state: MG

address: Av. PHRolfs, S/N

department: Bioquimica e Biologia Molecular

country: Brazil

institute: Universidade Federal de Viçosa

summary: Arabidopsis was transformed with the NIK receptor or the mutant T474D NIK receptor and infected with CaLCuV. The global variation of gene expression was analysed by RNA-seq at 10 days post inoculation and 20 days post inoculation and differential gene expression was determinated in comparison with mock inoculated Arabidopsis lines.

overall_design: Pairwise comparison between mock inoculated and infected genotypes (WT,NIK-expressing lines and T474D-expressing lines)  at 10 dpi and 20 dpi

first: Anésia

middle: A

last: Santos

first: Otávio

middle: J

first: Elizabeth

middle: P

last: Fontes


title: Analysis of chimeric reads from RNA-seq data

city: Stanford

first: Zhipeng

last: Lu

state: CA

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

summary: RNA-seq analysis of Drosophila pharate adults

overall_design: Total RNA extracted from four lines of Drosophila melanogaster pharate adults were depleted of ribosomal RNAs and sequenced.

first: A

middle: G

last: Matera


title: Genome-wide binding of Yki in S2 cells

city: Chicago

first: Jason

last: Grundstad

state: IL

address: 900 E 57th St

department: Division of Biological Sciences

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
The Hippo pathway regulates metazoan growth, acting through the transcriptional co-activators Yorkie (in Drosophila) and Yap and Taz (in vertebrates). Much attention has been focused on upstream regulators of Yorkie and its homologues. In contrast, the mechanisms by which they actually promote transcription have remained poorly understood. Genome-wide chromatin binding experiments support extensive functional overlap between Yorkie and GAF. Chromatin binding identifies thousands of Yorkie sites, the majority of which are associated with elevated transcription, based on genome-wide analysis of mRNA and histone H3K4Me3 modification. Our studies establish a molecular basis for transcriptional activation by Yorkie and implicate it as a global regulator of transcriptional activity in Drosophila.
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This dataset was generated in collaboration with Ken Irvine at HHMI/Rutgers University and Richard S. Mann at Columbia University.  It contains ChIP-seq data (Illumina) for multiple transcription factor antibodies in Drosophila embryos and larval wing imaginal discs.

overall_design: Yki in S2 cells

first: Matthew

last: Slattery

first: Hyangyee

last: Oh

first: Lijia

last: Ma

first: Kevin

last: White

first: Richard

last: Mann

first: Kenneth

last: Irvine


title: Comparative transcriptomic analysis of Rhodococcus erythropolis PR4 under hydrocarbon degrading conditions

city: Morahalom

first: Balazs

last: Horvath

address: Vallalkozok u. 7.

department: NGSP

country: Hungary

institute: SeqOmics Biotechnology Ltd.

summary: The marine bacterium Rhodococcus erythropolis PR4 was demonstrated to be able for assimilation/biodegradation of hydrocarbons. Not just the chromosome but two large plasmids provide versatile enzyme sets involved in many metabolic pathways. In order to identify the key elements involved in biodegradation of the model compound, hexadecane, and diesel oil, we performed whole transcriptome analysis on cells grown in the presence of n-hexadecane and diesel oil. Sodium acetate grown cells were used as control. The final goal of the project is a comparative transcriptomic analysis of Rhodococcus erythropolis PR4 cells grown on acetate, on the model compound: hexadecane and the real substrate: diesel oil.

overall_design: Comparative transcriptomics of Rhodococcus erythropolis PR4 grown on n-hexadecane, diesel oil, and sodium acetate.

first: Krisztián

last: Laczi

first: Ágnes

last: Kis

first: Gergely

last: Maróti

first: Balázs

last: Horváth

first: Katalin

last: Perei

first: Gábor

last: Rákhely


title: Validation of noise models for single-cell transcriptomics

status: Public on Apr 20 2014

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Single-cell transcriptomics has recently emerged as a powerful technology to explore gene expression heterogeneity amongst single cells. Here we identify two major sources of technical variability, sampling noise and global cell-to-cell variation in sequencing efficiency. We propose noise models to correct for this and after validation by single-molecule FISH experiments, we apply these models to demonstrate that growing mES cells in 2i instead of serum/LIF globally reduces gene expression variability.

overall_design: J1 mouse embryonic stem cells (mESCs) were cutured in 2i or in serum medium.  Cells were dissociated into a single cell suspension and picked under a stereomicroscope using a 30μm glass capillary and mouth pipette. Picked cells were deposited in the lid of an 0.5ml LoBind eppendorf tube and snap frozen in liquid nitrogen. For the pool and split controls, approximately 1 million cells were lysed, the amount of RNA was quantified on a bioanalyzer (Agilent) using the Eukaryote Total RNA pico kit. 20pg aliquots of total RNA were used for each pool and split control. Single cells and controls were processed using the previously described CEL-seq technique, with a few alterations. A 4bp random barcode as unique molecular identifier (UMI) was added to the primer in between the cell specific barcode and the poly T stretch. Libraries were sequenced on an Illumina HighSeq 2500 using 50bp paired end sequencing. For cells and controls, two libraries were sequenced on two lanes in total for each condition.

first: Lennart

last: Kester

first: Alexander

last: van Oudenaarden


title: Genome-wide transcriptome profiling of SK-Mel-28, UACC-62 and HCT-116 cells stably expressing scrambled shRNA and RAB7 shRNA

city: Madrid

first: Maria

middle: S

last: Soengas

address: Melchor Fernandez Almagro, 3

department: Molecular Pathology

country: Spain

institute: Spanish National Cancer Research Institute

summary:
Purpose: Asess the transcritpional changes induced upon RAB7 knock-down in melanoma (SK-Mel-28 and UACC-62) and in colon cancer (HCT-116) cell lines.
Methods: mRNA profiles of tumor cell lines (SK-Mel-28, UACC-62, HCT-116) stably expressing scrambled shRNA or RAB7 shRNA (harvested at day 3 after lentiviral infection) were generated by deep sequencing, using three biological replicates per condition. The sequence reads that passed quality filters were analyzed with TopHat and Cufflinks. Validation of induced / silenced genes was performed by western blot.
Results show a differential impact of RAB7 expression in the transcriptomic profile of melanoma vs non-melanoma cell lines, and support a lineage-specific role of this small GTPase in melanoma.

overall_design: Examination of the mRNA profiles RAB7-depleted vs wild type cells, performed in parallel in 3 different tumor cell lines (Melanomas: SK-Mel-28 and UACC-62, Non-melanoma: HCT-116) harvested at day 3 after lentiviral infection.

first: M

first: D

last: Alonso-Curbelo


title: Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

first: Xuebing

last: Wu

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

summary: The bacterial CRISPR-Cas9 system has been widely adapted for RNA-guided genome editing and gene regulation in diverse organisms yet its in vivo target specificity is poorly understood. Here we provide the first genome-wide binding maps of nuclease-deactivated Cas9 loaded with guide RNAs in mammalian cells. We find a 5-nucleotide seed region in the guide RNA targets Cas9 to thousands of sites in the genome. Chromatin accessibility limits binding to the other hundreds of thousands sites with matching seed sequences, and consequently 70% of off-target binding sites are associated with genes. U-rich seeds have low numbers of off-target sites limited by both low guide RNA abundance and scarcity of complimentary sites in accessible chromatin. Unexpectedly, off-target sites show little evidence of cleavage, supporting a two-state model reminiscent of eukaryotic RNAi machinery where a short seed match triggers binding but extensive pairing is required for cleavage.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq of HA-dCas9 loaded with 4 sgRNAs (Phc1-sg1, Phc1-sg2, Nanog-sg2, and Nanog-sg3) in mouse, and 2 sgRNAs in human (EMX1-sg1 and EMX1-sg3)

first: David

last: Scott

first: Andrea

last: Kriz

first: Anthony

middle: C

last: Chiu

first: Patrick

middle: D

last: Hsu

first: Daniel

middle: B

last: Dadon

first: Albert

middle: W

last: Cheng

first: Alexandro

middle: E

last: Trevino

first: Silvana

last: Konermann

first: Sidi

last: Chen

first: Rudolf

last: Jaenisch

first: Feng

last: Zhang

first: Phillip

last: Sharp


title: Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation [ChIP-seq]

city: Boston

last: Weinstock

state: MA

address: 450 Brookline Ave

institute: DFCI

summary: Children with Down syndrome (DS) have a 20-fold increased risk of developing B cell acute lymphoblastic leukemia (B-ALL). Polysomy 21 (i.e., extra copies of chr.21) is also the most frequent somatic aneuploidy among all B-ALLs. Additional B-ALLs harbor intrachromosomal amplifications of chr.21q22 (iAMP21). Yet, the mechanistic links between chr.21q22 triplication and B-ALL remain undefined. Here we show that germline triplication of only 31 genes orthologous to human chr.21q22 is sufficient to confer murine B cell self-renewal in vitro, B cell maturation defects in vivo, and B-ALL in concert with either BCR-ABL or CRLF2 with activated JAK2. Chr.21q22 triplication suppresses H3K27me3 in murine progenitor B cells and B-ALLs, and ÒbivalentÓ genes with both H3K27me3 and H3K4me3 at their promoters in wild-type progenitor B cells are preferentially overexpressed in triplicated cells. Strikingly, human B-ALLs with polysomy 21 are distinguished by their overexpression of genes known to be marked with H3K27me3 in multiple cell types. Finally, overexpression of HMGN1, a nucleosome remodeling protein encoded on chr.21q22, suppresses H3K27me3 and promotes both B cell proliferation in vitro and B-ALL in vivo. These data implicate HMGN1 overexpression and loss of H3K27me3 in progenitor B cell transformation and suggest strategies to target leukemias with polysomy 21.

overall_design: ChIP-seq in wild-type and Ts1Rhr B cell progenitors for H3K27ac and H3K4me3

first: Andrew

last: Lane

middle: M

first: Charles

middle: Y

last: Lin


title: Next Generation Sequencing of Wild-Type FVB/NJ Mouse Cardiac Polyadenylated RNA After 1 Week Pressure Overload

status: Public on Apr 18 2014

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary:
Purpose: Next-generation sequencing (NGS) provides for quantitation of RNA abundances and comparison of RNA abundances within tissues and cells in a manner not possible with previous microarray technologies.
5 female mice were subjected to a sham operation, and 5 female mice were subjected to transverse aortic constriction (TAC).
After 1 week, hearts were harvested and polyadenylated RNAs were profiled.  Analyzed data have been published in Hu et al., Proc Natl Acad Sci USA. 2012;109(48):19864-9, PMID: 23150554

overall_design: 10 cardiac polyA+-RNA profiles of 9 week-old FVB/NJ wild type (WT) mice (5 female sham, 5 female TAC) were generated on Illumina HiSeq 2000 instruments.

first: Gerald

last: Dorn


title: Genome-scale analysis in blood progenitor and mast cells reveals how lineage-affiliated transcription factors control distinct regulatory programs

status: Public on Apr 24 2014

city: Cambridge

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

country: United Kingdom

institute: Cambridge Institute for Medical Research

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

overall_design: Refer to individual Series


title: Ibf contributes to CP190 recruitment to chromatin [ChIP-seq]

city: Barcelona

first: M Lluisa

last: Espinas

address: Baldiri Reixac 10

institute: IBMB-CSIC

summary: ChIP-Seq peak calling of CP190 in wild-type and Ibf2 mutant Drosophila melanogaster third instar larvae

overall_design: Two  wild-type and two Ibf2 mutant Drosophila melanogaster third instar larvae were sequenced.

first: Maria

last: Espinàs

first: Sergi

last: Cuartero


title: Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation

first: David


title: The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Chromatin insulators are DNA-protein complexes situated throughout the genome that contribute to higher order organization and demarcation into distinct transcriptional domains.  Mounting evidence in different species implicates RNA and RNA-binding proteins as regulators of chromatin insulator activities.  Here we identify the Drosophila hnRNP M homolog Rumpelstiltskin (Rump) as an antagonist of gypsy chromatin insulator enhancer-blocking and barrier activities.  Despite ubiquitous expression of Rump, improvement of barrier activity is detected only in tissue outside of the central nervous system (CNS) when Rump levels are reduced.  Furthermore, rump mutants restore insulator complex localization in an otherwise compromised genetic background only in non-CNS tissues.  Rump associates physically with core gypsy insulator proteins, and ChIP-Seq analysis of Rump demonstrates extensive colocalization with a subset of gypsy insulator sites across the genome.  The genome-wide binding profile and tissue-specificity of Rump contrast with that of Shep, a recently identified RNA-binding protein that antagonizes gypsy insulator activity exclusively in the CNS.  Our findings indicate parallel roles for RNA-binding proteins in mediating tissue-specific regulation of chromatin insulator activity.

overall_design: ChIP-seq of Rump, Mod(mdg4)2.2, Shep, Su(Hw), and CP190 in Drosophila Kc167 cells

middle: K

first: Eliisa

last: Lei


title: Expression data from proximal, middle, and distal segments of E6.5 chicken cochlea

city: London

first: Michael

last: Lovett

state: London

address: Dovehouse St

department: NHLI

institute: Imperial College

summary: Precise frequency discrimination is a hallmark of auditory function in birds and mammals.  In the cochlea, tuning and spectral separation result from longitudinal differences in basilar membrane stiffness and numerous individual gradiations in sensory hair cell phenotypes, but it is unknown what patterns those phenotypes.  Hypothesizing that morphogen levels might differ along the longitudinal axis of the developing cochlea, we sequenced the transcriptomes of the proximal, middle, and distal thirds of the chicken cochlea at E6.5, when postmitotic hair cells first form.

overall_design: Embryonic day 6.5 chicken cochlea were dissected.  Three samples were collected from each cochlear duct by cutting the duct into three approximately equal sized pieces to produce proximal, middle, and distal pieces.  Each sample contained a portion of the future tegmentum vasculosum and the basilar papilla sensory epithelium.  The distal piece also contained the region fo the future lagena.

first: Benjamin

middle: R

last: Thiede

first: Zoe

middle: F

last: Mann

first: Weise

last: Chang

first: Yuan-Chieh

last: Ku

first: Yena

last: Son

first: Mattew

last: Kelley

first: Jeffrey

middle: T

last: Corwin


title: Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation [RNA-Seq]

last: Weinstock

summary: Down syndrome (DS) confers a 20-fold increased risk of B cell acute lymphoblastic leukemia (ALL), yet the mechanisms underlying this association are undefined.  We show that triplication of only 31 genes orthologous to the putative DS Critical Region (DSCR) on chr.21q22 is sufficient to promote B cell-autonomous self-renewal, in vivo maturation defects and leukemogenesis in concert with BCR-ABL.  DSCR triplication results in histone H3 lysine 27 (H3K27) hypomethylation at gene promoters and a transcriptional signature characterized by de-repression of genes targeted by polycomb repressor complex 2 (PRC2), which methylates H3K27.  The same signature is highly enriched among human DS-associated ALLs.  Pharmacologic inhibition of PRC2 function is sufficient to confer self-renewal in wild-type B cells while inhibition of H3K27me3 demethylases completely blocks self-renewal induced by DSCR triplication.  Finally, overexpression of the DSCR factor HMGN1, a nucleosome remodeling protein that suppresses H3K27me3, is necessary for self-renewal in B cells with DSCR triplication.

overall_design: Gene expression analysis of 6 samples, 3 wild-type and 3 Ts1Rhr proB cells at passage 1

first: Andrew

last: Lane


title: Argonaute and Trimmer generate Dicer-independent priRNAs and nucleate RNAi

city: Munich

first: Mario

last: Halic

address: Feodor-Lynenstr. 25

department: Department of Biochemistry

institute: Gene Center, University of Munich

summary: RNA interference is involved in silencing of transposable and repetitive elements.  How these elements are initially recognized by RNAi is a fundamental and unanswered question.  We previously identified a class of Dicer-independent small RNAs, called primal small RNAs (priRNAs), in fission yeast.  The mechanism by which Dicer-independent small RNAs are generated is not clear for any species.  Here we reconstitute priRNA biogenesis in vitro and demonstrate that priRNAs can nucleate RNAi in vivo.  We identify 3'-5' exonuclease Trimmer and show that Argonaute, loaded with longer RNA precursors, recruits Trimmer to generate the new 3' end.  Next, we show that antisense priRNAs accumulate in rrp6Δ cells and nucleate RNAi at subset of protein coding genes in a Trimmer- and priRNA-dependent manner.  Thus, Rrp6-mediated degradation of antisense transcripts and priRNA precursors protects the genome from spurious RNAi.  Our results suggest that Argonaute association with random RNA degradation products triggers RNAi in a process of transcriptome surveillance.

overall_design: small RNA profiling in wild type S. pombe cells and in mutant cells


title: Next Generation Sequencing of Wild-Type FVB/NJ Mouse Cardiac Small RNA, after 1 week pressure overload

first: Scot

last: Matkovich

summary:
Purpose: Next-generation sequencing (NGS) provides for quantitation of RNA abundances and comparison of RNA abundances within tissues and cells in a manner not possible with previous microarray technologies.
5 female mice were subjected to a sham operation, and 5 female mice were subjected to transverse aortic constriction (TAC).
After 1 week, hearts were harvested and small RNAs were profiled using Illumina small RNA TruSeq kits.  Analyzed data have been published in Hu et al., Proc Natl Acad Sci USA. 2012;109(48):19864-9, PMID: 23150554

overall_design: 10 cardiac small RNA (microRNA) profiles of 9 week-old FVB/NJ wild type (WT) mice (5 female sham, 5 female TAC) were generated on Illumina HiSeq 2000 instruments.

first: Gerald

last: Dorn


title: Ibf1 and Ibf2 are DNA-binding proteins required for insulator function in Drosophila [ChIP-seq]

first: M Lluisa

last: Espinas

summary: Here we report on the identification of two previously uncharacterized proteins as CP190 interacting proteins, that we have named Ibf1 and Ibf2. These proteins localize at insulator bodies and associate with chromatin at CP190-binding sites throughout the genome. We also show that Ibf1 and Ibf2 are DNAbinding proteins that form obligated hetero-oligomers that mediate CP190 binding to chromatin. Moreover, Ibf1 and Ibf2 are necessary for insulator activity in enhancerblocking assays. Taken together our data reveal a novel pathway of CP190 recruitment to chromatin that is required for insulator activity.

overall_design: ChIP-Seq peak calling of CP190, Ibf1 and Ibf2 against Input sample in Drosophila melanogaster S2 cells

first: Maria

middle: L


title: Ibf1 and Ibf2 are DNA-binding proteins required for insulator function in Drosophila


title: Chemical Inhibition of the RORγt-dependent Transcriptional Network in Th17 cells [RNA-Seq]

status: Public on Apr 17 2014

city: Berkeley

first: Nir

last: Yosef

address: Berkeley

department: EECS

institute: UC Berkeley

summary: RORγt is a transcription factor required for T helper 17 (Th17) cell development. We identified three RORγt-specific inhibitors that suppress Th17 cell responses including Th17 cell-mediated autoimmune disease. We systemically characterized RORγt binding data in the presence and absence of drug with corresponding whole-transcriptome sequencing for wild-type and RORγt-deficient cells. RORγt is central in a densely interconnected regulatory network, acting both as a direct activator of genes important for Th17 cell differentiation and as a direct repressor of genes from other T-cell lineages. The three inhibitors identified here reversed both of these modes of action, but to varying extents and through distinct mechanisms. Whereas one inhibitor displaced RORγt from its target-loci, the two more potent inhibitors affected transcription predominantly without removing DNA-binding. Our work illustrates the power of a system-scale analysis of transcriptional regulation to characterize potential therapeutic compounds that inhibit pathogenic Th17 cells and suppress autoimmunity.

overall_design: Transcriptional profiling of Th17 cells under chemical perturbations of RORγt, DMSO, and knockout of  RORγt

first: S

last: Xiao

first: N

first: J

last: Yang

first: Y

last: Wang

first: L

last: Zhou

first: C

last: Zhu

first: E

last: Baloglu

first: D

last: Schmidt

first: R

last: Ramesh

first: M

last: Lobera

last: Sundrud

first: P

last: Tsai

first: Z

last: Xiang

last: Xu

first: X

last: Lin

first: K

last: Kretschmer

last: Rahl

middle: A

last: Young

last: Zhong

last: Hafler

first: A

last: Regev

last: Ghosh

last: Marson

first: V

last: Kuchroo


title: Chemical Inhibition of the RORγt-dependent Transcriptional Network in Th17 cells [ChIP-Seq]

first: Nir

last: Yosef

overall_design: DNA binding of RORγt in WT Th17 cells  and under chemical perturbations of RORγt; Additional data is included for epitope-tagged exogenous RORγt in EL4 cells (a murine lymphoma cell line)

last: Xiao

last: Yang

last: Wang

last: Zhou

last: Zhu

last: Baloglu

last: Schmidt


title: Derivation and characterization of Dicer and microRNA deficient human cells

city: Durham

first: Adam

middle: Wesley

last: Whisnant

state: NC

address: 213 Research Drive 427 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University

summary: We have used genome editing to generate inactivating deletion mutations in all three copies of the dicer (hdcr) gene present in the human cell line 293T. As previously shown in murine ES cells lacking Dicer function, hDcr-deficient 293T cells are severely impaired for the production of mature microRNAs (miRNAs). Nevertheless, RNA-induced silencing complexes (RISCs) present in these hDcr-deficient cells are readily programmed by transfected, synthetic miRNA duplexes to repress mRNAs bearing either fully or partially complementary targets, including targets bearing incomplete seed homology to the introduced miRNA. Using these hDcr-deficient 293T cells, we demonstrate that human pre-miRNA processing can be effectively rescued by ectopic expression of the Drosophila Dicer 1 protein, but only in the presence of the PB isoform of Loquacious (Loqs-PB), the fly homolog of the hDcr co-factor TRBP. In contrast, Drosophila Dicer 2, even in the presence of its co-factors Loqs-PD and R2D2, was unable to support human pre-miRNA processing. Interestingly, although ectopic Drosophila Dicer 1/Loqs-PB or hDcr both rescued pre-miRNA processing effectively in these hDcr-deficient cells, there were significant differences in the ratio of the miRNA isoforms that were produced, especially in the case of miR-30 family members, and we also noted differences in the relative expression level of miRNAs versus passenger strands for a subset of human miRNAs. These data demonstrate that the mechanisms underlying the accurate processing of pre-miRNAs are largely, but not entirely, conserved between mammalian and insect cells.

overall_design: Series includes three datasets of total small RNA reads from wild type and Dicer negative 293T cells.  Also included are total small RNA reads of the Dicer-negative cell line NoDice(4-25) transfected with a vector expressing human Dicer, Drosophila Dicer1, or mock transfected.  RISC-associated small RNAs identified by ribonucleoprotein immunoprecipitation (RIP-Seq) in wild type 293T, Dicer-negative NoDice(4-25) line, and NoDice(4-25) transfected with either hsa-miR-155 or kshv-miR-K12-11 miRNA duplexes.  The final data series are PAR-CLIP libraries which identified microRNA targets in untransfected NoDice(4-25) cells and NoDice(4-25) cells transfected with either hsa-miR-92a, hsa-miR-155, kshv-miR-K12-11 miRNA duplexes

first: Hal

last: Bogerd

first: Edward

last: Kennedy

first: Omar

last: Flores

first: Bryan

last: Cullen


title: Chemical Inhibition of the RORγt-dependent Transcriptional Network in Th17 cells


title: Infection of apple by Apple stem grooving virus leads to extensive alterations in gene expression patterns but no disease symptoms

city: Beijing

first: Ting

last: Ye

address: No. 2, Yuanmingyuan West Road, Haidian District

department: Plant Pathology

country: China

institute: China Agricultural University

summary: To understand the molecular basis of viral diseases, transcriptome profiling has been widely used to correlate host gene expression change patterns with disease symptoms during viral infection in many plant hosts. We used infection of apple by Apple stem grooving virus (ASGV), which produces no disease symptoms, to assess the significance of host gene expression changes in disease development. We specifically asked the question whether such asymptomatic infection is attributed to limited changes in host gene expression. Using RNA-seq, we identified a total of 184 up-regulated and 136 down-regulated genes in apple shoot cultures permanently infected by ASGV in comparison with virus-free shoots cultures. As in most plant hosts showing disease symptoms during viral infection, these differentially expressed genes encode known or putative proteins involved in cell cycle, cell wall biogenesis, response to biotic and abiotic stress, development and fruit ripening, phytohormone function, metabolism, signal transduction, transcription regulation, translation, transport, and photosynthesis. Our data suggest that current approaches to correlate host gene expression changes under viral infection conditions to specific infection processes or disease symptom development, based on the interpretation of individual gene functions, have severe limitations. Integrative approaches that can take into account plant development stages, gene threshold levels as well as compensatory, synergistic and antagonistic effects may be necessary to develop a sound systems understanding of the biological significance of host gene expression changes during infection.

overall_design: Compare the transcript profiling of ASGV-infected asymptomatic apple planlets (AP-Vinfect) and virus-free apple plantlets (AP-Vfree) by deep sequencing using Illumina RNA-Seq to check whether lots of genes were modulated by ASGV infection.

first: Shanyi

last: Chen

first: Lu

last: Hao

first: Hui

first: Shaojie

first: Zaifeng

last: Fan

first: Liyun

last: Guo

first: Tao


title: Transcription factor cooperativity in early adipogenic hotspots and super-enhancers

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Here we have used a combination of advanced proteomics and genomics approaches to investigate the extent and mechanisms of transcription factor cross-talk at genomic hotspots. We identify ~12,000 transcription factor hotspots in the early phase of adipogenesis, and we find evidence of both simultaneous and sequential binding of transcription factors at these regions. We demonstrate for the first time that hotspots are highly enriched in large super-enhancer regions and that these drive the early adipogenic reprogramming of gene expression. Our results indicate that cooperativity between transcription factors at the level of hotspots as well as super-enhancers is very important for enhancer activity and transcriptional reprogramming. Thus, hotspots and super-enhancers constitute important regulatory hubs integrating external stimuli on chromatin.

overall_design: Genome-wide profiling of transcription factor and co-factor binding, epigenomic marks, and gene expression in 3T3-L1 pre-adipocytes.

first: Rasmus

last: Siersbæk

first: Atefeh

last: Rabiee

first: Ronni

last: Nielsen

first: Simone

last: Sidoli

first: Sofie

last: Traynor

first: Anne

last: Loft

first: Lars

last: Poulsen

first: Adelina

last: Rogowska-Wrzesinska

first: Ole

middle: N

last: Jensen


title: Chemical Inhibition of the RORγt-dependent Transcriptional Network in Th17 cells [RNA-Seq 2]

first: Nir

last: Yosef

overall_design: Transcriptional profiling of Th17 cells under chemical perturbations of RORγt, DMSO, and knockout of  RORγt. It includes repeats for all the data in GSE56018, plus one additional condition.

first: S

last: Xiao

first: N

first: J

last: Yang

first: Y

last: Wang

first: L

last: Zhou

first: C

last: Zhu

first: E

last: Baloglu

first: D

last: Schmidt

first: R

last: Ramesh

first: M

last: Lobera

last: Sundrud

first: P

last: Tsai

first: Z

last: Xiang

last: Xu

first: X

last: Lin

first: K

last: Kretschmer

last: Rahl

last: Young

last: Zhong

last: Hafler

first: A

last: Regev

last: Ghosh

last: Marson

first: V

last: Kuchroo


title: Whole transcriptome analysis of sinonasal sarcoma with translocation t(2;4)(q37.1;q31.3)

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: Conventioal cytogenetic on 2 sinonasal sarcoma (SNS) cases showed t(2;4)(q37.1;q31.3) translocation previously. The aim of this whole transcriptome analysis is to determine potential candidate genes involved in this translocation.

overall_design: Total RNA extracted from frozen cultured primary tumor cells from a SNS characterized at the cytogenetics level was subjected to Illumina whole transcriptome RNA-sequencing anslysis.

first: Andre

last: Oliveira

first: Xiaoki

last: Wang


title: Male and Female DNA and RNA sequencing in several nematode species

city: New York

first: Sarah

middle: Elizabeth

last: Albritton

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: New York University

summary: The overall goal of this investigation was to investigate X-content of sex-biased genes in several nematode species. The following species of nematode were investigated: *C. elegans, *N2; *C. brenneri, *PB2801; *C. briggsae, *AF16; *C. remanei*, PB4641; *P. **pacificus, *PS312*.*  Genomic DNA sequencing data was used to assign X and autosomal - linkage to unassembled sequencing contigs.  Male and female RNA seq data was then generated and used to determine sex-biased expression. For both DNA and RNA experiments,  50bp paired-end (DNA) or single-end (RNA) reads were generated on the Illumina HiSeq 2500. Sequencing lanes were multiplexed. Genomic DNA was isolated from 50-100 hand-picked young adult worms. At least two replicates for each sex were prepared. DNA was sheared via sonication and 350-500 bp sequencing libraries were prepared following the Illumina protocol. Total RNA was isolated from at least 1000 hand-picked L4/young adult worms (*C. **elegans, *N2) or J4/young adult worms (*P. pacificus, *PS312*). *PolyA beads were used to enrich for mRNA. Stranded RNAseq libraries were prepared via incorporation of dUTPs during cDNA synthesis, following the protocol detailed in Parkhomchuk et al, 2009. DNAseq and RNAseq reads were aligned to the appropriate WS228 reference genomes.

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans
Caenorhabditis remanei
Pristionchus pacificus
Caenorhabditis brenneri

overall_design: DNA sequencing data (2-3 replicates) from male and female YA worms are included along with RNAseq data from C.elegans YA hermaphrodites and P.pacificus YA males and hermaphrodites.

first: Max

last: Kramer

first: Prashant

last: Rao

first: Sevinc

last: Ercan


title: rrp6l1-2 project

status: Public on Apr 16 2014

city: West Lafayette

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

type: Methylation profiling by high throughput sequencing

summary: 1, Using mRNA-Seq to get expression profiling of rrp6l1-2 mutant and Col-0 wild-type (WT); 2,Using MethylC-Seq to provide single-base resolution of DNA methylation status in rrp6l1-2 mutant; 3, Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of rrp6l1-2 and WT

overall_design: mRNA-Seq: 2 samples examined, WT and rrp6l1-2 mutant; MethylC-Seq: 1 sample examined, rrp6l1-2 mutant; small RNA-Seq: 2 samples examined, WT and rrp6l1-2 mutant

first: Huiming

last: Zhang

first: Kai

last: Tang


title: Novel PAX3-MAML3 Fusion in Biphenotypic Sinonasal Sarcoma

overall_design: Refer to individual Series

first: Xiaoke


title: Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary: During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults.

overall_design:
RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages;
embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes

first: Jimena

last: Giudice

first: Wei

last: Li

first: Thomas

last: Cooper


title: Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae

first: Meixia

last: Zhao

address: 915 W State Steet

department: Agronomy

summary: Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is effectively controlled by Rps genes in soybean. Rps genes are race-specific, yet the mechanism of resistance, as well as susceptibility, remains largely unclear. Taking advantage of RNA-seq technology, we sequenced the transcriptomes of 10 near isogenic lines (NIL), each with a unique Rps gene, and the recurrent susceptible parent ‘Williams’. A total of 4330 differentially expressed genes (DEGs) were identified in ‘Williams’ while 2075 to 5499 DEGs were identified in each NIL. Comparisons between the NILs and ‘Williams’ allowed classification of two major groups of DEGs of interest: incompatible reaction associated genes (IRAGs) and compatible reaction associated genes (CRAGs). Hierarchical cluster analysis divided NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6). Heatmap analysis, along with GO analysis suggested that the diversity of clusters for NILs were likely due to variation of the number of DEGs and the intensity of gene expression, rather than functional differentiation. Further analysis suggested that transcription factors might play pivotal role in determination of the cluster pattern, and that WRKY family were strongly associated with incompatible reactions. Analysis of IRAGs and CRAGs with putative functions suggested that the regulation of many phytohormone signaling pathways were associated with incompatible or compatible interactions with potential crosstalk between each other. As such, our study provides an in depth view of both incompatible and compatible interactions between soybean and P. sojae, which provides further insight into the mechanisms involved in host-pathogen interactions.

overall_design: 22 samples were sequenced, 11 inoculated with P. sojae, the other 11 were mock-inoculated

first: Feng

last: Lin

first: Douglas

last: Baumann

first: Jieqing

last: Ping

first: T

middle: S

last: Abney

first: Rebecca

last: Doerge

first: Teresa

middle: J

last: Hughes

first: Jianxin

last: Ma


title: Hes6 drives a critical AR transcriptional program to induce castration resistant prostate cancer through activation of an E2F1-mediated cell cycle network

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Castrate-resistant prostate cancer (CRPC) is poorly characterized and heterogeneous and while the androgen receptor (AR) is of singular importance, other factors such as c-Myc and the E2F family also play a role in later stage disease. Here we show that Hes6 is up-regulated in aggressive human prostate cancer and drives castration-resistant tumour growth in the absence of ligand binding by enhancing the transcriptional activity of the AR, which is preferentially directed to a regulatory network enriched for other transcription factors including E2F1. In the clinical setting, we have uncovered a Hes6-associated signature that predicts poor outcome in prostate cancer, which can be pharmacologically targeted with restoration of sensitivity to castration.

overall_design: AR and E2F1 ChIPseq from multiple simultaneous LNCaP cell replicates with and without bicalutamide

first: Antonio

last: Ramos-Montoya

first: Alastair

last: Lamb

first: Roslin

last: Russell

last: Carroll


title: Overexpression of GmDof4 from Soybean Significantly Enhances the Lipid Content of Chlorella ellipsoidea

first: Jin

last: Xu

state: Chaoyang District

address: No.7 Beitucheng West Road

institute: Beijing Institute of Genomics

summary: Here, we transferred GmDof4 from soybean (Glycine max), a transcription factor affecting content of lipid in Arabidopsis, into C. ellipsoidea and found that the expression of GmDof4 significantly enhanced the lipid content by maximum 57.21%, shifted the content of different fatty acids, but did not affect the growth of the host cells. Using the Solexa/Illumina-based RNA-Seq analysis, we found expression of GmDof4 significantly regulates 1,076 genes, of which 754 genes were up-regulated and 322 genes were down-regulated, under mixotrophic culture. This study provides a new way to improve the lipid of microalgae.

overall_design: The GmDof4 transgenic strain Dof4-1 and control (pCK transgenic line CK-1) were cultured in liquid antibiotic-free Endo medium at 25℃ under illumination (100 μmol photons m-2 s-1) for 120 h. Cells at a concentration of approximately 1× 10^7 cells/mL were collected for library construction and sequencing using Illumina GAIIx.

first: Jianhui

last: Zhang

first: Zanmin

last: Hu


title: RNA-Seq characterization of human H1-derived NPC differentiation timecourse

status: Public on Apr 15 2014

city: Baltimore

first: Loyal

last: Goff

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: High resolution transcriptional profiling of H1-derived human neuronal precursor cells over a timecourse of differentiation in vitro.

overall_design: Human NPC differentiation timecourse covers Days 0,1,2,4,5,11, and 18 after induction of neuronal differentiation as described in manuscript. Each time point was assayed in triplicate cultures with the exception of Day 5, in which one outlier culture has been removed.

first: Martin

last: Sauvageau

first: Simona

last: Lodato

first: Boyan

last: Bonev

first: Abigail

last: Groff

first: Chiara

last: Gerhardinger

first: Mavis

last: Swerdel

first: Michael

last: D'Ecclessis

first: Jennifer

middle: C

last: Moore

first: Manolis

last: Kellis

first: Ronald

middle: P

last: Hart

first: Paola

last: Arlotta

first: John

last: Rinn


title: Hes6 drives a network with therapeutic potential in castrate-resistant prostate cancer

first: Roslin

last: Russell

institute: Cambridge Research Institute, Cancer Research UK

summary:
Castrate-resistant prostate cancer (CRPC) is poorly characterized and heterogeneous and while the androgen receptor (AR) is of singular importance in early prostate cancer, other factors such as c-Myc and the E2F family also play a role in later stage disease. Hes6 is a transcription co-factor that has been associated with neurogenesis during gastrulation, a neuroendocrine phenotype in the prostate and metastasis in breast cancer but its role in prostate cancer remains uncertain. Here we show that Hes6 is controlled by c-Myc and AR and drives castration resistance in prostate cancer. Hes6 activates a cell-cycle enhancing transcriptional network that maintains tumour growth and nuclear AR localization in castrate conditions. We show aphysical interaction between E2F1 and both Hes6 and AR, and suggest a co-dependency of these transcription factors in castration-resistance. In the clinical setting, we have uncovered a Hes6-associated signature that predicts poor outcome in prostate cancer, which can be pharmacologically targeted. We have therefore shown for the first time the critical role of Hes6 in the development of CRPC and identified its potential in patient specific therapeutic strategies.

This SuperSeries is composed of the SubSeries listed below.


title: Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors

city: New Haven

first: Gerald

last: Goh

state: Connecticut

address: 1 Gilbert St TAC S355

institute: Yale University

summary: We performed mRNA-seq of a PRKACA-mutant adrenal tumor and demonstrated that the mutation is expressed at the mRNA level.

overall_design: Total RNA obtained from a cortisol-producing adrenal tumor with a PRKACA p.Leu206Arg mutation.

first: Richard

last: Lifton


title: Quantitation of microRNAs in seminal fluid from men with and without prostate cancer

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: The objective of this study was to determine whether prostate cancer-associated miRNAs are present in seminal fluid and, if so, evaluate their diagnostic potential.

overall_design: Small RNA sequencing was used to profile and compare miRNAs in the non-sperm cellular fraction of seminal fluid from men with biopsy-proven cancer (one pooled sample from 6 men) and men with elevated serum PSA but negative biopsy results (one pooled sample from 6 men).


title: Deep transcriptional sequencing of mucosal challenge compartment from rhesus macaques acutely infected with simian immunodeficiency virus implicates loss of cell adhesion preceding immune activation

city: Seattle

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Recent studies of nonhuman primates (NHPs) have suggested that during the acute phase of infection, antiviral mucosal immunity is restricting viral replication in the primary infection compartment. These studies imply that HIV achieves systemic infection as a consequence of a failure in host antiviral immunity. Here, we used high-dose intrarectal inoculation of rhesus macaques with SIVmac251 to examine how the mucosal immune system is overcome by SIV during acute infection. The host response in rectal mucosa was characterized by mRNA deep sequencing (mRNA-seq) at 3 and 12 days post inoculation (DPI) in 4 animals for each time point.

overall_design: The eight RMs were intrarectally challenged with SIVmac251 using 1 mL of a high-dose inoculum (6000 TCID50/mL). SIV inoculates were deposited at a rectal depth of 25 mm from the anus. Baseline rectal samples were obtained 14 days prior to viral challenge by pinch biopsy.

first: Fredrik

last: Barrenas

first: Robert

middle: E

last: Palermo

first: Brian

last: Agricola

middle: B

last: Agy

first: Lauri

last: Aicher

first: Victoria

last: Carter

first: Leon

last: Flanary

last: Green

first: Randy

last: McLain

first: Qingsheng

last: Li

first: Wuxun

last: Lu

last: Murnane

first: Xinxia

last: Peng

first: Matthew

last: Thomas

first: Jeffrey

last: Weiss

first: David

last: Anderson

middle: G


title: Nucleocytoplasmic shuttling of a GATA transcription factor functions as a development timer

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Biological oscillations are observed at many levels of cellular organization. In the social amoebae Dictyostelium discoideum, starvation-triggered multicellular development is organized by periodic cAMP waves, which provide both chemoattractant gradients and developmental signals. We report that GtaC, a GATA transcription factor, exhibits rapid nucleocytoplasmic shuttling in response to cAMP waves. This behavior requires coordinated action of a nuclear localization signal and reversible G protein-coupled receptor (GPCR)-mediated phosphorylation. While both are required for developmental gene expression, receptor occupancy promotes nuclear exit of GtaC, which leads to a transient burst of transcription at each cAMP cycle. We demonstrate that this biological circuit, like an “edge trigger”, filters out high frequency signals and counts those admitted, thereby enabling cells to modulate gene expression according to the dynamic pattern of the external stimuli.

overall_design: Transcriptional profiling during early development of wild-type, gtaC, GFP-GtaC/gtaC, and NLSex-GFP-GtaC/gtaC strains

first: Huaqing

last: Cai

first: Mariko

last: Katoh-Kurasawa

first: Tetsuya

last: Muramoto

first: Balaji

last: Santhanam

first: Yu

last: Long

first: Lei

first: Masahiro

last: Ueda

first: Pablo

last: Iglesias

first: Peter

last: Devreotes


title: Loss of Tet enzymes compromises proper differentiation of embryonic stem cells

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

summary: Tet enzymes (Tet1/2/3) catalyze the conversion of 5-methylcytosine (5mC) to 5-hydroxy-methylcytosine (5hmC) and are dynamically expressed in various embryonic and adult cell types. While loss of individual Tet enzymes or combined deficiency of Tet1/2 allows for embryogenesis, the effect of complete loss of Tet activity and 5hmC marks in development has not been established. To define the role of Tet enzymes and 5hmC in development we have generated Tet1, Tet2 and Tet3 triple knockout (TKO) mouse embryonic stem cells (ESCs) and examined their developmental potential in vitro and in vivo. Combined deficiency of all three Tet enzymes led to complete depletion of 5hmC and impaired ESC differentiation as seen in poorly differentiated TKO embryoid bodies and teratomas. Consistent with impaired differentiation, TKO ES cells exhibited limited contribution to the chimeric embryos and could not support embryonic development in tetraploid complementation assays. Gene expression profiles and genome wide methylome analyses of TKO embryoid bodies revealed promoter hypermethylation and deregulation of genes implicated in embryonic development and differentiation. These findings suggest a requirement for Tet and 5hmC-mediated DNA demethylation in proper regulation of gene expression during differentiation of embryonic stem cells and development.

overall_design: Methylation patterns in tissue samples from a series of wt and Tet1/Tet2 DKO embryos, neonates and adults were generated using ethylated DNA immunoprecipitation with antibodies against 5mC (MeDIP) and 5hmC (hMeDIP) followed by deep sequencing.

first: Frank

last: Lyko

first: Achim

last: Breiling

first: Meelad

middle: M

last: Dawlaty


title: Control of chitin and N-acetylglucosamine utilization in Saccharopolyspora erythraea

city: Brisbane

first: Cuauhtemoc

last: Licona-Cassani

state: Queensland

address: Crn College and Cooper rds

department: Australian Institute for Bioengineering and Nanotechnology

institute: The University of Queensland

summary: We report the effect of addition of N-acetylglucosamine in Saccharopolyspora erythraea reactor cultures on the transcription of genes related to dasR regulon

overall_design: Examination of one time-point after 45 minutes of the addition of N-acetylglucosamine in reactor cultures.

first: Esteban

last: Marcellin


title: Hormone and transcriptome profiling in aerial tissues derived from crown buds of glyphosate treated leafy spurge

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 ALBRECHT BLVD N

department: Sunflower and Plant Biology Research Unit

institute: United States Department of Agriculture, Agricultural Research Service

summary: Glyphosate is known to inhibit 5-enolpyruvylshikimate-3-phosphate synthase of the chorismate biosynthetic pathway, and chorismate is a precursor to aromatic amino acids, auxin, and many other secondary products. Although the perennial weed leafy spurge (Euphorbia esula L.) is considered glyphosate tolerant, glyphosate is often used as part of an integrated pest management program in non-cultivated ecosystems of North America. Part of its tolerance is attributed to escape through an abundance of underground adventitious buds (UABs). Sub-lethal concentrations of foliar applied glyphosate leads to new shoot growth from UABs that have a stunted and/or bushy phenotype after growth-inducing decapitation. To gain insights into glyphosate’s impact on molecular mechanisms associated with the stunted and bushy phenotype, we obtained global transcriptome abundance using RNAseq from a subsequent generation of aerial shoots derived from crown buds of glyphosate-treated and -untreated leafy spurge. We further correlated transcript abundance to accumulation of shikimate and phytohormones from the same samples to elucidate interactions. Abundance of shikimate was similar in subsequent generations of aerial shoots generated from crown buds of treated and untreated plants and is likely not a direct factor leading to the stunted and bushy phenotype. However, the results do suggest that transcripts involved in auxin transport and signaling and crosstalk with other phytohormones likely play a role in the bushy phenotype. The results of this study provide some insights for identifying new targets for manipulation of plant growth and development.

overall_design: Transcriptome and metabolite profiling are obtained for aerial tissues derived from crown buds of foliar glyphosate-treated and control (2.24 or 0 kg/ha active ingredient glyphosate + 0.25% v/v surfactant) leafy spurge plants. Each experiment included 4 biological replicates.

first: Michael

last: Foley

first: Alvaro

last: Hernandez

first: Radhika

last: Khetani

first: Christopher

last: Fields

first: Kathleen

last: Keating

first: Mark

last: Mikel

first: James

middle: V


title: Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm-mosquito interactions

city: Madison

first: Bruce

last: Christensen

state: WI

address: 1656 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary: Parasite biology, by its very nature, cannot be understood without integrating it with that of the host, nor can the host response be adequately explained without considering the activity of the parasite. However, due to experimental limitations, molecular studies of parasite-host systems have been predominantly one-sided investigations focusing on either of the partners. Here we conduct a joint dual RNA-seq time course analysis of filarial parasite and host mosquito to better understand the parasite processes underlying development in, and interaction with, the host tissue from the establishment of infection to the emergence of infective-stage larva. Using the Brugia malayi-Aedes aegypti system, we report the parasite gene transcription dynamics, which exhibit a highly ordered developmental program consisting of a series of cyclical and state-transitioning temporal patterns.  And, we contextualize these parasite data in relation to the concurrent dynamics of the host transcriptome. Comparative analyses using uninfected tissues and different host strains reveal the influence of parasite development on the host gene transcription as well as the influence of host environment on the parasite gene transcription. Furthermore, we critically evaluate the life-cycle transcriptome of B. malayi by comparing developmental stages in the mosquito relative to those in the mammalian host, providing insight into gene expression changes underpinning the mosquito-borne parasitic lifestyle of this heteroxenous parasite.

overall_design: Time-course mRNA profiles of filarial parasite Brugia malayi and host mosqutio Aedes aegypti were generated by deep sequencing using Illumina GAIIx.

first: Young-Jun

last: Choi

first: George

middle: F

last: Mayhew

first: Sara

last: Erickson

first: Matthew

last: Aliota


title: Expanding the Catalog of Enhancer Marks In Vivo

city: Berkeley

middle: James

last: Blow

state: CA

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

summary: While the majority of protein-coding genes in the human genome have been identified, the location of the regulatory sequences that control their expression in time and space remains poorly defined. The importance of identifying these elements is underscored by a growing number of studies (such as GWAS) supporting a relationship between variation in non-coding sequences and human disease. We previously demonstrated that ChIP-Seq with p300 directly on human or mouse tissues represents a powerful method to identify the location and tissue-specific activity pattern of enhancers in the genome. While p300 is a highly specific chromatin mark for the prediction of in vivo enhancers, it is not without limitations. In particular, comparison of p300-bound regions with previously generated enhancer sets shows that the majority of enhancers are activated independently of p300. To attempt to identify a larger proportion of enhancers in vivo, we have focused on several additional transcriptional coactivators that are hypothesized to be associated with active tissue-specific enhancers. To overcome the limited availability of ChIP-seq grade antibodies for these coactivators, FLAG-tag knock-in mice were generated and ChIP-seq using a FLAG antibody was performed on various tissues from e11.5 mouse embryos. Indeed, as these mouse lines have become available we have validated their valuable role as marks for transcriptional enhancers in vivo. These ongoing studies are expected to further expand the catalogue of in vivo functional enhancers, which will aid in the decoding of the regulatory genome and provide new insights into the role of gene regulation in human biology and disease. In addition to FLAG data, this accession includes histone acetylation / methylation ChIP-seq data from e11.5 mouse embryonic tissues. Histone ChIP-seq data was used in combination with FLAG data for various computational analyses.

overall_design: Examination of FLAG-labeled transcriptional coactivator binding in mouse embryonic stage 11.5 and embryonic stem cells.

first: Alexander

last: Nord

first: Len

last: Pennacchio

first: Catia

last: Attanasio


title: The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by genome tiling array

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

first: Peter

last: Skene

first: Aaron

last: Groudine

first: Steven


title: Origins and functional evolution of Y chromosome gene repertoires across the class Mammalia

city: Lausanne

first: Diego

last: Cortez

address: Rue de Lausanne

country: Switzerland

institute: Univerity of Lausanne - CIG

summary:
We collected (Illumina) RNA-seq data (polyadenylated RNA fraction) for a number of tissue samples from common marmoset and elephant. We developed a subtraction approach based on male/female RNA-seq data, Illumina genomic data and available genomes to identify and assemble Y transcripts.
For marmoset samples, we added Y coding genes and noncoding sequences to the reference genomes in order to assess their expression levels. We then mapped all RNA-seq reads with TopHat 1.4.0 and used Cufflinks 2.0.0 (all mapped reads, embedded multi-read and fragment bias correction) to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all genes in the genomes with our refined annotations.

sample_organism:
Notamacropus eugenii
Callithrix jacchus
Loxodonta africana
Rattus norvegicus

overall_design: Sequence and expression levels of reconstructed Y-linked genes

first: Ray

last: Marin

first: Laure

last: Froidevaux

first: Angélica

last: Liechti

first: Paul

middle: D

last: Waters

first: Frank

last: Grützner

first: Henrik

last: Kaessmann


title: The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1 [HiSeq]

summary: We use a metabolic labeling strategy for directly measuring nucleosome turnover to determine the role of chromatin remodeler Chd1 on chromatin dynamics in mouse embryonic fibroblasts expressing with wildtype-Chd1 and dominant negative K510R-Chd1. We find that expression of K5 10R-Chd1 decreases nucleosome turnover at the promoter and increases turnover within the gene body.

overall_design: 10 Illumina sequencing samples and 4 Nimblegen array samples

last: Hernandez

first: Mark


title: Genomewide analysis of QKI-dependent alternative splicing

status: Public on Apr 14 2014

city: Shanghai

first: Jingyi

last: Hui

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary: To identify QKI targets, we performed QKI knockdown in BEAS2B cells and analyzed alternative splicing patterns by high-throughput RNA sequencing.

overall_design: The mRNA profiles of control- and QKI-knockdown BEAS2B cells were generated by deep sequencing using Illumina GAIIx sequencer.

first: Xing

last: Fu

first: Feng-Yang

last: Zong


title: Genome-wide analysis of SPL7 regulated genes in Arabidopsis

city: Charlottesville

first: xin

last: zhao

state: VA

address: Department of Biology, 229 Gilmer Hall

institute: University of Virginia

summary: To study the genes regulated by transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 (SPL7) in Arabidopsis thaliana, we conducted chromatin immunoprecipitation-based sequencing (ChIP-seq) in 35S:FALG-SPL7 transgenic plant and spl7 mutant, and genome-wide sequencing-based transcript profiling of Arabidopsis thaliana wild-type plants and of spl7 mutant under MS medium and MS supplement with 5µM CuSO4. These experiments led to the identification of genes that are direct target of SPL7 and genes differentially expressed in an SPL7-dependent or Cu-dependent manner. This study provides a framework for the identification of SPL7 regulated genes towards characterization of SPL7 in copper homeostasis.

overall_design:
ChIP-Seq: Chromatin isolation was performed with 7-day-old whole seedlings of spl7 mutant (negative control) and 35S:FALG-SPL7 transgene (sample) grown on standard MS medium under continuous white light according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor set at high intensity for 10 min (30 s on, 30 s off intervals). The DNA was sheared to an average size of approximately 500 bp. Chromatin was immunoprecipitated with FLAG antibody (Sigma) according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3. Reverse cross-linked DNA was purified and used for sequencing libraries construction following the manufacture’s protocol (Illumina).
RNA-Seq: DNase I-treated total RNA was prepared from 7-day-old whole seedlings of wild type (Col-0) and spl7 mutant grown on standard MS medium and MS supplement with 5µM CuSO4 under continuous white light (WL). First- and second-strand cDNA were generated using SuperScript II and random hexamer primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the manufacturer’s protocol (Illumina). Tophat was used to map the sequence reads to the Arabidopsis genome and only uniquely mapped reads were used in subsequent analyses. mRNA profiles of 7-day-old whole seedlings of wild type (Col-0) or spl7 mutant grown on standard MS medium and MS supplement with 5µM CuSO4 under continuous white light (WL) were generated by deep sequencing using illumine HiSeq2000.

first: Huiyong

last: Zhang

first: Xin

last: Zhao

first: Lei

last: Li


title: Peripheral blood mononuclear cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)

city: Bronx

first: Deepa

last: Rastogi

address: 3415 Bainbridge Ave

institute: Albert Einstein College of Medicine

summary: Obesity-associated asthma is recognized as a distinct entity with non-atopic T-helper 1 polarized systemic inflammation. DNA methylation is linked with T helper cell maturation and is associated with inflammatory patterns in asthma and obesity. However, it is unknown whether pathologic dysregulation of DNA methylation patterns occurs in obesity-associated asthma.   Using HELP-tagging, we studied epigenome wide DNA methylation in peripheral blood mononuclear cells in 8 urban minority obese asthmatic pre-adolescent children and compared it to methylation in groups of 8 children with asthma alone, obesity alone and healthy controls. Ingenuity Pathway Analysis was used to identify biological pathways that were differentially targeted by methylation dysregulation.  We found that obese asthmatics had distinct epigenome wide methylation patterns associated with decreased promoter methylation of a subset of genes, including RANTES, IL-12R and TBX21 and increased promoter methylation of CD23, a low affinity receptor for IgE and of TGFβ, inhibitor of Th cell activation. T cell signaling and macrophage activation were the two primary pathways that were selectively hypomethylated in obese asthmatics. These methylation patterns suggest that methylation is associated with non-atopic inflammation observed in obese asthmatic children compared to children with asthma alone and obesity alone.   Our findings suggest a role of DNA methylation in the observed inflammatory patterns in pediatric obesity-associated asthma in minorities.

overall_design: 32 HpaII test

first: Masako

last: Suzuki

first: John

last: Greally


title: Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine in rice

city: Beijing

first: Shuhui

last: Song

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

summary: We generated a genome-wide map of 5hmC in rice panicle using a sensitive chemical labeling method to capture DNA fragments with 5hmC modification, followed by NGS sequencing. We showed that the 5hmC peaks distribution is non-random, about 52% 5hmC was located in gene bodies, 25% in intergenic regions, 11% in promoters, and 12% in immediate downstream. It was significantly enriched in heterochromatic regions of chromosomes 4 and 10, and especially located around TE genes. Combined with RNA-seq transcriptome data, we found that the gene-specific alterations of 5hmC can result in gene activation or repression, suggesting a potential role for 5hmC in gene regulation. From the compared distribution analysis among super-hybrid rice cultivars LYP9, and its parental lines 93-11 and PA64s, we investigated the cultivar-specificity of both the global levels and locus-specific distribution of 5hmC. Our data provided an overview of the genomic distribution of 5hmC in rice panicle. This will set the stage for further functional characterization of this novel DNA modification and its biosynthesis in rice.

overall_design:
Examination of 5hmC modifications in rice panicle

This submission represents ChIP-Seq component of study.

first: Shu-hui


title: Caligus rogercresseyi transcriptome

status: Public on Apr 12 2014

city: Victoria

first: Ben

last: Koop

state: BC

address: PO Box 3020 STN CSC

country: Canada

institute: The University of Victoria

summary: RNA-seq expression data from 6 libraries in Caligus rogercresseyi

overall_design: RNA from pooled samples from farmed Atlantic salmon was extracted by mixer-mill (Retsch) homogenization in Trizol (Invitrogen), followed by column clean-up using the RNeasy kit (QIAGEN)

first: Jong

last: Leong


title: mRNA expression in C-33A cells expressing HPV1 E2

city: Bethesda

first: Kui

last: Shen

address: Room 3B62, 31 Center Drive

institute: National Institute of Allergy and Infectious Diseases, NIH

summary: Profile of RNA expression in a C-33A cell line derived from an HPV negative cervical carcinoma in the presence or absence of HPV1 E2 expression.

overall_design: mRNA profiles of C-33A cells in presence or absence of HPV1 E2 expression were generated by deep sequencing using Illumina GAIIx. Two samples (no replicates). One control and one experimental.

first: McBride

middle: A

last: Alison

first: Moon

middle: K

last: Jang

first: Shen

last: Kui


title: Multiscale representation of genomic signals

status: Public on Apr 13 2014

first: Theo

last: Knijnenburg

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary: Genomic information is encoded on a wide range of distance scales, ranging from tens of base pairs to megabases. We developed a multiscale framework to analyze and visualize the information content of genomic signals. Different types of signals, such as GC content or DNA methylation, are characterized by distinct patterns of signal enrichment or depletion across scales spanning several orders of magnitude. These patterns are associated with a variety of genomic annotations, including genes, nuclear lamina associated domains, and repeat elements. By integrating the information across all scales, as compared to using any single scale, we demonstrate improved prediction of gene expression from Polymerase II ChIP-seq measurements and we observed that gene expression differences in colorectal cancer are not most strongly related to gene body methylation, but rather to methylation patterns that extend beyond the single-gene scale.

overall_design: ChIP-seq data of six proteins in primary murine bone marrow macrophage cells (BMMs) under unstimulated and lipopolysaccharide (LPS) stimulated conditions. The BMMs were cultured from female C57BL/6 mice (age 8-12 weeks). Amongst these six proteins were three transcription factors (TFs), ATF340, NFκB/p50 and NFκB/p65, all of which are involved in regulating macrophage activation by microbial molecular components such as LPS. The other three ChIP-seq targets were RNA polymerase II (Pol II), and two chromatin modification marks: acetylation of histone H4 (H4ac) and tri-methylation of histone H3 lysine 27 (H3K27me3).

first: Stephen

last: Ramsey

first: Kathleen

last: Kennedy

first: Alan

last: Aderem

first: Ilya

last: Shmulevich


title: mRNA-seq data from embryonic autopods of the common bent-wing bat (Miniopterus schreibersii)

first: Zhe

last: Wang

address: 3663 N. Zhongshan Rd.

institute: East China Normal University

summary: The only freely flying mammals, bats, develop a pair of dramatically elongated hands and broad wing membranes. It is hypothesized that alterations of many gene expressions result in the bat wing formation. However, it remains to be proved. Here, by mRNA-seq, we found that hundreds of genes are significantly high expressed in the elongating forelimb digits.

overall_design: mRNA-seq data of 14 autopod samples from embryonic bats (Miniopterus schreibersii) were obtained by Illumina HiSeq 2000.

first: Shuyi

last: Zhang


title: Sumoylation Pathway Is Required to Maintain the Basal Breast Cancer Subtype

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: This study is an attempt to characterize the molecular basis for the functional differences between TFAP2A and TFAP2C. Recent findings have highlighted a critical role for the TFAP2C (AP-2γ) transcription factor in maintaining the luminal phenotype through the regulation of luminal-associated genes.  Of particular interest is that the highly homologous AP-2 family member, TFAP2A (AP-2α), is expressed in luminal breast cancer but appears to have a functionally distinct role in gene regulation.  There is 83% similarity between TFAP2A and TFAP2C with 76% identity in the carboxyl-half of the proteins containing the DNA binding and dimerization domains.  Although the two family members appear to have complementary and overlapping roles in regulating neural crest development, they have clear functional differences with regard to regulation of ERα expression. The global genomic binding pattern for TFAP2A and TFAP2C is highly similar. Genomic binding for TFAP2A and TFAP2C in the regulatory region for luminal-associated genes further demonstrated co-localization of the two factors.  On the other hand, clear functional differences exist when comparing the effect on the pattern of gene expression following knockdown of TFAP2A vs. TFAP2C.  In each case, knockdown of TFAP2C resulted in an abrogation of expression (RNA and protein) of the luminal-associated gene, whereas, knockdown of TFAP2A had minimal or no effect.  By contrast, a known TFAP2A target gene, CDKN1A, was responsive to TFAP2A only.

overall_design: 1 ChIP-Seq data for TFAP2A in human breast carcinoma cell line MCF-7. See associated publication.

first: Mikhail

last: Kulak

first: Ronald

last: Weigel


title: Inflammation induced repression of Foxp3-bound chromatin in regulatory T cells

city: New York

first: Aaron

last: Arvey

state: NY

institute: Memorial Sloan-Kettering Cancer Center

overall_design: Refer to individual Series


title: Inflammation induced repression of Foxp3-bound chromatin in regulatory T cells [sequencing]

summary:
The transcription factor Foxp3 is indispensable for the ability of regulatory T (Treg) cells to suppress fatal inflammation. Here, we characterized the role of Foxp3 in chromatin remodeling and regulation of gene expression in actively suppressing Treg cells in an inflammatory setting. Although genome-wide Foxp3 occupancy of DNA regulatory elements was similar in resting and in vivo activated Treg cells, Foxp3-bound enhancers were poised for repression only in activated Treg cells. Following activation, Foxp3-bound sites showed reduced chromatin accessibility and selective H3K27 tri-methylation, which was associated with Ezh2 recruitment and downregulation of nearby gene expression. Thus, Foxp3 poises its targets for repression by facilitating formation of repressive chromatin in regulatory T cells upon their activation in response to inflammatory cues.
The supplementary file foxp3_rest_act_table.txt includes Foxp3 ChIP data that is co-normalized with data from Foxp3 ChIP data from GSE40684.

overall_design: Foxp3 ChIP-seq, H3K27me3 ChIP-seq, and DNase-seq, were integrated with array expression data to find that Foxp3 is required for formation of repressive chromatin

first: Joris

last: van der Veeken

first: Robert

last: Samstein

first: Alexander

middle: Y

last: Rudensky


title: MOV10 Is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3'UTRs (expression)

status: Public on Apr 11 2014

city: Berlin

first: Markus

last: Landthaler

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrück-Center for Molecular Medicine

summary: RNA helicases are important regulators of gene expression that act by remodeling RNA secondary structures and as RNA-protein interactions. Here, we demonstrate that MOV10 has an ATP-dependent 5' to 3' in vitro RNA unwinding activity and determine the RNA-binding sites of MOV10 and its helicase mutants using PAR-CLIP. We find that MOV10 predominantly binds to 3' UTRs upstream of regions predicted to form local secondary structures and provide evidence that MOV10 helicase mutants are impaired in their ability to translocate 5' to 3' on their mRNA targets. MOV10 interacts with UPF1, the key component of the nonsense-mediated mRNA decay pathway. PAR-CLIP of UPF1 reveals that MOV10 and UPF1 bind to RNA in close proximity. Knockdown of MOV10 resulted in increased mRNA half-lives of MOV10-bound as well as UPF1-regulated transcripts, suggesting that MOV10 functions in UPF1-mediated mRNA degradation as an RNA clearance factor to resolve structures and displace proteins from 3' UTRs.

overall_design: Flp-In T-REx HEK293 cells expressing FLAG/HA-tagged MOV10 WT, MOV10 K530A, MOV10 D645N and UPF1 were used to determine the protein-RNA interaction sites of RNA helicases MOV10 and UPF1 as well as MOV10 inactive variants using PAR-CLIP in combination with next generation sequencing. mRNA half-life changes of MOV10-targeted mRNA were determined by measuring mRNA half-lives by mRNA sequencing of mock and MOV10-depleted HEK293 cells.


title: Genome wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress [ChIP-Seq]

city: Belfast

first: Simon

last: McDade

address: 97 Lisburn Road

department: CCRCB

institute: Queen's University Belfast

summary: In response to genotoxic stress the TP53 tumour suppressor activates target gene expression to induce cell cycle arrest or apoptosis depending on the extent of DNA damage.  These canonical activities can be repressed by TP63 in normal stratifying epithelia to maintain proliferative capacity or drive proliferation of squamous cell carcinomas, where TP63 is frequently overexpressed/amplified.  Here we use ChIP-sequencing, integrated with microarray analysis, to define the genome wide interplay between TP53 and TP63 in response to genotoxic stress in normal cells.  We reveal that TP53 and TP63 bind to overlapping, but distinct cistromes of sites through utilization of distinctive consensus motifs and that TP53 is constitutively bound to a number of sites.  We demonstrate that cisplatin and adriamycin elicit distinct effects on TP53 and TP63 binding events, through which TP53 can induce or repress transcription of an extensive network of genes by direct binding and/or modulation of TP63 activity.  Collectively, this results in a global TP53 dependent repression of cell cycle progression, mitosis and DNA damage repair concomitant with activation of anti-proliferative and pro-apoptotic canonical target genes. Further analyses reveals that in the absence of genotoxic stress TP63 plays an important role in maintaining expression of DNA repair genes, loss of which results in defective repair

overall_design: Examination of p63 and p53 binding sites in neonatal foreskin keratinocytes in response to adriamycin or cisplatin treatment

first: Dennis

last: McCancer


title: seq-UP07329_H4K16ac:DAM1687546_N2_Eemb

status: Public on Apr 10 2014

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Strain N2; Antibody MP07-329-H4K16ac (target is h4K16ac)

first: Thea

last: Egelhofer

first: Andreas

last: Rechtsteiner


title: The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo

city: Seattle

first: Jorja

last: Henikoff

summary: High resolution ChIP-seq mapping, supported by in vitro reconstitution studies, suggests that the Cse4 nucleosome is a hemisome that occupies the ~80-bp AT-rich CDEII sequence.

overall_design: H4S47C-anchored cleavage mapping of S. cerevisiae centromeres

first: Steven

first: Srinivas

last: Ramachandran

first: Kristina

last: Krassovsky

first: Terri

last: Bryson

first: Kristin

last: Brogaard

first: Jonathan

last: Widom

first: Ji-ping


title: Implication of small sperm RNAs in the inheritance of the effect of early traumatic stress in mice

city: Zürich

first: Katharina

last: Gapp

address: Winterthurerstrasse 190

department: Health Science and Technology

institute: Swiss Federal Institue of Technology

summary: Small non-coding RNAs (sncRNAs) have been proposed as potential vectors of the interface between genes and environment. Here, we report that environmental conditions involving traumatic stress in early life, alter miRNA and piRNA composition in sperm of adult males in mice.

overall_design: Examination of small RNA content of sperm from males, that experienced early chronic stress during their first two weeks of life versus small RNA content of sperm from control males.

first: Peter

last: Sarkies

first: Laurent

last: Farinelli

first: Eric

last: Miska

first: Isabelle

last: Mansuy

first: Julien

last: Prados


title: Alternative poladenylation of tumor suppressor genes in small intestinal neuroendocrine tumors

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

institute: MDC-Berlin

summary:
The tumorigenesis of small intestinal neuroendocrine tumors (NETs) is poorly understood. Recent studies have associated alternative polyadenylation with proliferation, cell transformation and cancer. Polyadenylation is the process in which the pre-mRNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo alternative polyadenylation. This produces two or more distinct mRNA isoforms with different 3’ untranslated regions. Additionally, alternative polyadenylation can also produce mRNAs containing different 3’-terminal coding regions. Therefore, alternative polyadenylation alters both the repertoire and the expression level of proteins.
Here we used high-throughput sequencing data to map polyA sites and characterize polyadenylation genome-wide in three small intestinal neuroendocrine tumors and a reference sample. In the tumors sixteen genes showed significant changes of alternative polyadenylation pattern, which lead to either the 3’ truncation of mRNA coding regions or 3’ untranslated regions. Among these, 11 genes had been previously associated with cancer, with 4 genes being known tumor suppressors: DCC, PDZD2, MAGI1 and DACT2. We validated the alternative polyadenylation in 3 out of 3 cases with Q-RT-PCR.
Our findings suggest that changes of alternative polyadenylation pattern in these 16 genes could be involved in the tumorigenesis of small intestinal neuroendocrine tumors. Furthermore, they also point to alternative polyadenylation as a new target for both diagnostic and treatment of small intestinal neuroendocrine tumors. The identified genes with alternative polyadenylation specific to the small intestinal neuroendocrine tumors could be further tested as diagnostic markers and drug targets for disease prevention and treatment.

overall_design: PolyA-seq profiling of 3 human neuroendocrine tumors compared and pituitary using Direct RNA Sequencing from Helicos Biosciences Technology

first: Anders

last: Rehfeld

last: Døssing

first: Ulrich

last: Knigge

last: Kjaer

last: Krogh

first: Lennart

last: Friis-Hansen


title: Identification of Transcription Factor EFL-1::GFP Binding Regions in L1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3211
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: YL418(official name : YL418 genotype : unc-119(ed3) III; vrIs65[pGES-1::EFL-1::GFP FLAG:EFL-1 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The EFL-1::GFP fusion protein is driven by the ges-1 promoter and expressed in the instestine. made_by : Michelle Kudron (Valerie Reinke's lab) ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs65[pGES-1::EFL-1::GFP FLAG:EFL-1 3'-UTR; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene efl-1; Strain YL418(official name : YL418 genotype : unc-119(ed3) III; vrIs65[pGES-1::EFL-1::GFP FLAG:EFL-1 3'-UTR genotype : unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : The EFL-1::GFP fusion protein is driven by the ges-1 promoter and expressed in the instestine. made_by : Michelle Kudron (Valerie Reinke's lab) ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Human nuclear Dicer restricts the deleterious accumulation of endogenous double strand RNA

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: Dicer is a central enzymatic player in RNA interference (RNAi) pathways that acts to regulate gene expression in nearly all eukaryotes. Although the cytoplasmic function of Dicer is well documented in mammals, there is little known about any possible nuclear function.  Here we show that Dicer is present in both the nucleus and cytoplasm, but that its nuclear levels are tightly regulated. In its nuclear manifestation Dicer interacts with RNA polymerase II (Pol II) at actively-transcribed gene loci. Loss of Dicer causes the appearance of endogenous dsRNA, leading to induction of the interferon response pathway and consequent cell death. Our results suggest that Pol II-associated Dicer restricts endogenous dsRNA formation from overlapping non-coding RNA transcription units. Failure to do so has catastrophic effects on cell function. Taken together, we present here a micro (mi)RNA independent role for human nuclear Dicer.

overall_design: DICER ChIP-seq profile in wt 293 HEK cells, and dsRNA-seq profile in wt and DICER-depleted 293 HEK cells

first: Eleanor

last: White

first: Margarita

last: Schlackow

first: Nicholas

last: Proudfoot

first: Monika

last: Gullerova


title: RNAseq Analysis of Formalin-Fixed Paraffin-Embedded Prostate Cancer Tissues

city: Atlanta

first: Carlos

last: Moreno

state: Georgia

address: 615 Michael St

department: Department of Pathology & Laboratory Medicine

institute: Emory University

summary: In an effort to identify biomarkers of recurrence, we have performed global RNA-sequencing on 106 formalin-fixed, paraffin-embedded (FFPE) prostatectomy samples from 100 patients at three independent sites, and identified a new set of biomarkers of biochemical recurrence composed of a 24-gene panel. We validated this 24-gene panel on an independent publicly available dataset of 140 patients and this new panel outperformed previously published markers based on cell proliferation gene sets in terms of prediction of biochemical recurrence (BCR).  In addition we identified differences in gene expression between Gleason Pattern 4+3 and Gleason Pattern 3+4 tumors.

overall_design: 106 samples from 100 patients were sequenced.  Six samples were sequenced from two independent RNA preps and libraries.  All samples were taken from FFPE Radical Prostatectomies.  Samples were obtained from Atlanta VA Medical Center, U. Toronto Sunnybrook Research Centre, and Moffitt Cancer Center.


title: MOV10 is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation Along 3' UTRs (PAR-CLIP)

first: Markus

last: Landthaler

overall_design:
Flp-In T-REx HEK293 cells expressing FLAG/HA-tagged MOV10 WT, MOV10 K530A, MOV10 D645N and UPF1 were sequenced.
mRNA half-life data under GSE56751.

first: Lea

middle: H

last: Gregersen

first: Mathias

last: Munschauer

last: Schueler

first: Chistoph

last: Dieterich


title: Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) Analysis Uncovers Broad Changes in Chromatin Structure Resulting from Hexavalent Chromium Exposure

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 ability of chromatin to switch back and forth from open euchromatin to closed heterochromatin is vital for transcriptional regulation and genomic stability, and subject to disruption by exposure to environmental agents such as hexavalent chromium. Cr(VI) exposure can cause chromosomal disruption through formation of Cr-DNA adducts, free radical-induced DNA damage, and DNA-Cr-protein and DNA-Cr-DNA cross-links, all of which may disrupt chromatin remodeling mechanisms responsible for maintenance or controlled modification of epigenetic homeostasis. In addition, dose-response analyses have shown that acute exposures to high-concentrations of Cr(VI) and chronic exposures to low-concentrations of the same agent lead to significantly different transcriptomic and genomic stability outcomes.  To investigate how transcriptional responses to chromium exposure might correlate to structural changes in chromatin, we have used whole genome Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) analysis coupled with deep sequencing to identify regions of the genome that switch from open to closed chromatin or vice versa in response to exposure to varying Cr(VI) concentrations.  We find that the switch affects gene expression levels in the target areas that vary depending on Cr(VI) concentration.  At either Cr(VI) concentration, chromatin domains surrounding binding sites for AP-1 transcription factors become significantly open, treatment whereas BACH2 and CTCF binding sites are open solely at the low and high concentrations, respectively.  Our results suggest that FAIRE may be a useful technique to map chromatin elements targeted by DNA damaging agents for which there is no prior knowledge of their specificity, and to identify subsequent transcriptomic changes induced by those agents.

overall_design: Cr25 treatment and control samples are in duplicate for RNA-seq, and no replicate for FAIRE-seq. Cr0.5 treatment and control samples are in duplicate for RNA-seq, and no replicate for FAIRE-seq.

first: Jerald

middle: L

last: Ovesen

first: Yunxia

last: Fan

first: Xiang

last: Zhang

first: Jing

last: Chen

first: Ying

last: Xia

first: Alvaro

last: Puga


title: seq-UP07329_H4K16ac:JBC1888188_N2_L3

city: Cambridge

first: Przemyslaw

middle: Aleksander

last: Stempor

state: United Kingdom

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

summary:
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population. EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20 degree Celsius; Strain N2; Antibody UP07329 H4K16ac:JBC1888188 (target is H4K16ac).

first: Julie

last: Ahringer

first: Alex

last: Appert


title: Esox lucius transcriptome

first: Ben

last: Koop

department: Biology

summary: Expression data from 13 tissues in Esox lucius using RNA-seq

overall_design: All tissues for RNA-seq were extracted from a single, juvenile, male pike caught November 1, 2011 in the Portage Diversion/Assiniboine River Floodway near Portage la Prairie, MB, Canada (N50.00747 W98.38181). The animal was euthanized and then frozen on dry ice until sampling, and subsequently at -80°C. Tissues were extracted by mixer-mill (Retsch) homogenization in Trizol (Invitrogen), followed by column clean-up using the RNeasy kit (QIAGEN).

first: Jong

middle: S

last: Leong

first: Eric

last: Rondeau