title: DeepCAGE and DeepSAGE with proliferating and differentiated C2C12 mouse myoblasts

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

summary: We use tag-based next generation sequencing analysis to quantify gene expression levels during myogenic differentiation and focused on the identifcation of novel 3' ends with DeepSAGE and novel 5' ends with DeepCAGE.

overall_design: Illumina DeepCAGE and DeepSAGE with C2C12 cells at time points T0 (proliferating) and T9 (differentiated) days of differentiation.

first: Matthew

last: Hestand


title: The role of nucleosome positioning in the evolution of gene regulation

status: Public on Jul 06 2010

city: Boston

first: Alex

middle: M

last: Tsankov

state: MA

address: 155 Bay State

country: USA

institute: MIT

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Lachancea waltii
Saccharomyces bayanus
Saccharomyces cerevisiae
Yarrowia lipolytica
Debaryomyces hansenii
Candida albicans
Nakaseomyces glabratus
Naumovozyma castellii
Saccharomyces paradoxus
Kluyveromyces lactis
Saccharomyces mikatae
Lachancea kluyveri NRRL Y-12651

overall_design: Refer to individual Series


title: H2A.Z Mapping During G0/G1 and Mitosis

status: Public on Jun 24 2010

city: Los Angeles

first: Benjamin

last: Berman

state: CA

department: USC Epigenome Center

institute: University of Southern California

summary: We report genome wide mapping of the histone variant H2A.Z during G0/G1 and mitosis in T24 bladder cancer cells.  The results show that the broad enrichment pattern of H2A.Z near transcription start sites of active genes is maintained during mitosis.  Furthermore, using H2A.Z localization to visualize nucleosome positioning near the start site, we see that the  +1 nucleosome of active genes shifts upstream to occupy the transcription start sites during mitosis and the nucleosome depleted region is shortened.  H2A.Z is also maintained on the -2 nucleosome which also shifts towrds the transcription start site during mitosis, further contributing to the shorteneing of the nucleosome depleted region.

overall_design: Examination of H2A.Z duing G0/G1 and mitosis in bladder cancer cells

first: Theresa

last: Kelly

last: Jones


title: Global identification of Arabidopsis thaliana ARGONAUTE1-associated small RNA.

status: Public on Jun 21 2010

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA from total RNA (input fraction) and immunoprecipitated HA-AGO1-complexes (IP fraction) were identified using high-throughput sequencing-by-synthesis.

overall_design: Two replicate input fraction samples were used as controls for two replicate IP fraction samples. Total RNA from input fractions and small RNA that co-immunoprecipitated with HA-AGO1 complexes were size fractionated by polyacrylamide gel electrophoresis to recover 18-24 nucleotide small RNA. 3' and then 5' adaptors were serially ligated on to each small RNA followed by PAGE purification. RT-PCR was used to convert RNA to DNA amplicons.  Amplicons were sequenced using the Illumina GAIIx platform. Resulting reads were parsed and mapped to the A. thaliana genome (TAIR9) using the CASHX pipeline.

first: Josh

middle: T

last: Cuperus

first: Alberto

last: Carbonell

first: Noah

last: Fahlgren

first: Hernan

last: Garcia-Ruiz

first: Russell

last: Burke

first: Atsushi

last: Takeda

first: Christopher

last: Sullivan

first: Sunny

middle: D

last: Gilbert

first: Taiowa

middle: A

last: Montgomery


title: Genome-wide Chromatin Maps Derived from Limited Numbers of Hematopoietic Progenitors

status: Public on Jul 01 2010

first: Jiang

last: Zhu

address: 185 Cambridge Street

institute: Massachusetts General Hospital, Harvard Medical School and Broad Institute

summary: Whole genome mapping of protein-DNA interactions can be performed by coupling chromatin immunoprecipitation (ChIP) with high-throughput sequencing (ChIP-Seq). However, current methods require large amounts of starting materials which precludes their application to rare cell types. Here, we combine a high-sensitivity ChIP assay with a novel library preparation procedure to map histone modifications in as few as 10,000 cells. We apply the technique to acquire genome-wide chromatin maps for an enriched population of hematopoietic progenitors, and thereby gain insight into their developmental program.

overall_design: An optimized ChIP protocol for small number of cells and a novel Librray preperation methods for high throughput sequencing of picograms amount of ChIP DNA.

first: Mazhar

last: Adli

first: Bradley

middle: E

last: Bernstein


title: Analysis of Geobacter sulfurreducens under multiple growth conditions

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

type: Expression profiling by high throughput sequencing


title: Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

city: St Lucia

first: Ryan

middle: J

last: Taft

state: QLD

address: 80 Carmody Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

summary: We have recently shown that transcription initiation RNAs (tiRNAs) are derived from sequences downstream of transcription start sites. Here we report the identification of a second class of nuclear-specific ~17-18 nucleotide small RNA whose 3’ ends map precisely to the splice donor site of internal exons in animals. These splice-site RNAs (spliRNAs) are associated with highly expressed genes, and show evidence of developmental stage- and region-specific expression. We also confirm that tiRNAs are nuclear localized, enriched at chromatin marks associated with transcription initiation, and possess a 3’ nucleotide bias. Additionally, we find that microRNA-offset RNAs (moRNAs), the oncogenic miR-15/16 cluster and most snoRNA-derived small RNAs (sdRNAs) are enriched in the nucleus, whereas most miRNAs and two H/ACA sdRNAs are cytoplasmically enriched. We propose that nuclear localized tiny RNAs are involved in epigenetic regulation of gene expression.

overall_design: Discovery and characterization of small RNA species through high-througput deep sequencing of nuclear, cytoplasmic and total small RNA fractions from THP-1 cells, a monocytic leukemia cell line. Additional files and information are available at http://matticklab.com/index.php?title=NuclearTinyRNAs

first: John

middle: S

last: Mattick


title: ATAC and Mediator coactivators form a stable complex and regulates a set of non-coding RNA genes

status: Public on Jun 25 2010

city: Illkirch

first: Laszlo

last: Tora

email: tora@igbmc.fr, krebs@igbmc.fr

address: 1, rue Laurent Fries

department: Functional Genomics

country: France

institute: IGBMC

summary: The ATAC histone acetyl-transferase (HAT) and the Mediator coactivator complexes regulate independent and distinct steps during transcription initiation and elongation. Here we report the identification of a new stable molecular assembly formed between the ATAC and the Mediator complex in mouse embryonic stem cells. Moreover, we identify LUZP1 as a subunit of this meta coactivator complex (MECO). Finally, we demonstrate that MECO regulates a subset of RNA polymerase II transcribed non-coding RNA genes. Our findings establish that transcription coactivator complexes can form stable sub-complexes in order to facilitate their combined actions on specific target genes.

overall_design: For ChIP-seq analysis, 300µg of chromatin (DNA) was incubated with GST (mock), LUZP1 and GCN5 antibodies. Retrieved purified DNA was sequenced using Illumina Genome Analyzer II following manufacturer recommendations. Illumina raw files were aligned against reference (mouse mm9) genome using the eland program allowing one mismatch. Enrichment clusters were detected using MACS (Zhang et al., 2008). The retrieved peaks were filtered (max size 1000bp, min size 100bp) and repeat masked, to establish the final binding sites lists. Peaks were annotated using the GPAT web server (Krebs et al., 2008) using ENSEMBL gene 57 database.

first: Arnaud

last: Krebs

first: Krishanpal

last: Karmodiya

first: László


title: Genome-wide analysis of snRNAs bound to Gemin5 upon protein synthesis inhibition

city: Philadelphia

first: Jeongsik

last: Yong

state: PA

address: 415 Curie Blvd.

department: Biochemistry and Biophysics

institute: University of Pennsylvania School of Medicine/HHMI

summary: Here, we report the genome-wide analysis of snRNAs that are bound to Gemin5 upon protein synthesis inhibition. Upon protein synthesis inhibition, the SMN complex that has a crucial role in the biogenesis of snRNPs dissociates into its subunits, leaving Gemin5 alone. The existence of these subunits was confirmed using a proteomics approach. As Gemin5 has been previously reported to be the RNA-binding protein of the SMN complex, we obtained the sequence of all Gemin5 immunoprecipitated snRNAs. We found that snRNAs that were accumulated on Gemin5 contained extra genomic sequences at the 3'-end. We were thus able to identify novel precursors of all the snRNAs that have not been identified previously. This study also provides a detailed method for the characterization of in vivo captured RNPs using a ribo-proteomics approach.

overall_design: Investigation of snRNAs specifically associated with Gemin5 upon protein synthesis inhibition

first: Mumtaz

last: Kasim

first: Jennifer

middle: L

last: Bachorik

first: Lili

last: Wan

first: Gideon

last: Dreyfuss


title: Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi

city: Worcester

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: A variety of small RNAs, including the Dicer-dependent miRNAs and the Dicer-independent Piwi-interacting RNAs, associate with Argonaute family proteins to regulate gene expression in diverse cellular processes.  These two species of small RNA have not been found in fungi. Here, by analyzing small RNA associated with the Neurospora Argonaute protein QDE-2, we show that diverse pathways generate miRNA-like small RNAs (milRNAs) and Dicer-independent small interfering RNAs (disiRNAs) in this filamentous fungus. Surprisingly, milRNAs are produced by at least four different mechanisms that use a distinct combination of factors, including Dicers, QDE-2, the exonuclease QIP and an RNAse III domain-containing protein MRPL3. In contrast, disiRNAs originate from loci producing overlapping sense and antisense transcripts, and do not require the known RNAi components for their production. Taken together, these results uncover several pathways for small RNA production in filamentous fungi, shedding light on the diversity and evolutionary origins of eukaryotic small RNAs.

overall_design: One small RNA library was generated using QDE-2 immunoprecipitate from Neurospora crassa.

first: Yi

last: Liu

first: Heng-Chi

last: Lee

first: Liande

last: Li

first: Weifeng

last: Gu


title: ChIP-Seq of H3K79me2 in Mouse Embryonic Fibroblasts

status: Public on Jun 15 2010

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: H3K79 dimethylation is a mark of transcriptional elongation.  To gain insight into the set of genes actively transcribed in MEFs, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the presence of H3K79me2 across the genome.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against H3K79me2.

first: Steve

last: Bilodeau


title: Deciphering the cis-regulatory architecture of mammalian photoreceptors

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

country: Germany

institute: Institute of Human Genetics

summary: In order to define the genomic targets of Crx, we carried out Crx chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) of eight-week-old mouse retinas using the Solexa platform. Sequence reads were mapped to the genome and 'peaks' were identified.  These data were subjected to extensive bioinformatic analysis.  In addition, selected peaks were experimentally tested for cis-regulatory activity by electroporation as promoter-reporter fusions into living mouse retinas. Over 5,000 Crx-bound regions (CBRs) were identified throughout the mouse genome. Many of these clusters of CBRs occur specifically around photoreceptor genes. In fact, Crx directly regulates the majority of known photoreceptor transcription factors as well as most known photoreceptor disease genes.  Cis-regulatory analysis revealed that individual CBRs contribute in a combinatorial fashion to the overall activity of the gene they control.  In addition, multiple Crx-binding sites within CBRs cooperatively interact via precise spacing rules to generate optimal levels of transcription.

overall_design: Crx ChIP-Seq analysis of C57BL/6 and Nrl-/- retinas. IgG ChIP-Seq was performed as a control. 1-2 replicates each.

first: Joseph

last: Corbo


title: Genome-wide Analysis of Vitamin D Receptor Binding By ChIP-Seq

status: Public on Jun 22 2010

city: Oxford

first: Sreeram

last: Ramagopalan

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

summary: We used ChIP-Seq to identify the genomic locations bound by the vitamin D receptor (VDR) in two lymphoblastoid cell lines (LCLs) (CEPH individuals GM10855 and GM10861 from the International HapMap Project) before and after calcitriol treatment for 36 hours. Immunoprecipitated DNA was sequenced using the Illumina Genome Analyzer II. Sequence reads (35 bases; 10-19 million quality-filtered reads/sample) were aligned to the human genome (NCBI Build 36.3) using ELAND software. The number of unique alignments ranged from 7.73 million to 14.32 million. Peaks were called in the aligned sequence data using a model-based analysis of ChIP-Seq (MACS) and compared with sequenced sonicated and amplified input DNA. In the samples not treated with calcitriol, the number of peaks ranged from 468 to 4538 (median 975, mean 1587), while in the calcitriol-treated samples the number of peaks was between 2560 and 7244 (median 4546, mean 4560). 65-75% of peaks of untreated samples were in promoters, while only 24-50% of peaks of calcitirol-treated samples were in promoters. This study provides a comprehensive map of VDR binding in lymphoblastoid cell lines.

overall_design: The GM10855 and GM10861 cell lines were either stimulated for 36 hours with calcitriol or unstimulated, and crosslinked with formaldehyde to generate a snapshot of all protein-DNA interactions occurring in the nucleus at that particular point in time. Antibodies were then used to immunoprecipitate the VDR protein together with the crosslinked DNA fragments. Following reversal of crosslinks and digestion of protein, adaptors were ligated to immunoprecipitated DNA, and bridge PCR was used to generate clonally amplified amplicons before sequencing by synthesis using the Illumina Solexa Genome Analyzer.


title: Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei

city: Bern

first: Daniel

last: Nilsson

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

summary: Some organisms like the human and animal parasite Trypanosoma brucei add a leader sequence to their mRNAs through a reaction called trans-splicing. Until now the splice sites for most mRNAs were unknown in T. brucei. Using high throughput sequencing we have developed a method to identify the splice sites and at the same time measure the abundance of the corresponding mRNAs. Analyzing three different life cycle stages of the parasite we identified the vast majority of splice sites in the organism and, to our great surprise, uncovered more than 2500 alternative splicing events, many of which appeared to be specific for one of the life cycle stages. Alternative splicing is a result of the addition of the leader sequence to different positions on the mRNA, leading to mixed mRNA populations that can encode for proteins with varying properties. One of the most obvious changes caused by alternative splicing is the gain or loss of targeting signals, leading to differential localization of the corresponding proteins. Based on our findings we hypothesize that alternative splicing is a major mechanism to regulate gene expression in T. brucei and could contribute to protein diversity in the parasite.

overall_design: In total we sequenced three libraries from bloodstream form mRNA, (long slender and short stumpy, both Antat1.1 and monomorphic Lister 427), one from procyclic form mRNA (Antat1.1), 2x2 RNAi libraries (uninduced and induced), where each pair could be considered a biological replicate. Lastly we prepared and sequenced one conventional RNAseq library from procyclic mRNA (Antat1.1).

first: Kapila

last: Gunasekera

first: Jan

last: Mani

first: Magne

last: Osteras

first: Laurent

last: Farinelli

first: Loic

last: Baerlocher

first: Isabel

last: Roditi

first: Torsten

last: Ochsenreiter


title: RNA profiling in mouse haemopoiesis

first: Ryan

last: Taft

overall_design: RNA profiling of mouse haemopoetic lineages. For the isolation and sequencing of ouse granulocyte nuclei, bone marrow from C57BL/6J was harvested from the femur, tibia and spine using a mortar and pestle in PBS supplemented with 2% (v/v) FCS and mature granulocytes purified by flow cytometry as described previously. Purification was validated by reanalysis by flow cytometry and May-Grünwald Giemsa staining. Nuclear purification was carried out using the PARIS kit (Ambion). RNA was extracted from the nuclear fraction using Trizol before deep sequencing. Deep sequencing was performed by GeneWorks (Adelaide, Australia) on the Illumina GAII according to the manufacturer's instructions. For more details, see Supplementary Methods at the NSMB website. Additional files and resources can be found at http://matticklab.com/index.php?title=NuclearTinyRNAs

first: John

last: Rasko


title: modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data

status: Public on Aug 11 2010

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

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

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila simulans
Drosophila yakuba


title: [E-TABM-722] Transcription factor binding evolution in five vertebrates

status: Public on Jun 02 2010

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

summary:
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054.

ArrayExpress Submission Date: Apr 07 2010
ArrayExpress Release  Date: Apr 08 2010

Publication Author List: Dominic Schmidt; Michael D Wilson; Benoit Ballester; Petra C Schwalie; Gordon D Brown; Aileen Marshall; Claudia Kutter; Stephen Watt; Celia P Martinez-Jimenz; Sarah MacKay; Iannis Talianidis; Paul Flicek; Duncan T Odom
Publication Title: Transcription factor binding evolution in five vertebrates

Person Roles: submitter
Person Last Name: Flicek
Person First Name: Paul
Person Email: flicek@ebi.ac.uk
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Person Affiliation: EBI

sample_organism:
Gallus gallus
Homo sapiens
Canis lupus familiaris
Mus musculus
Monodelphis domestica

overall_design:
AEExperimentDisplayName: ChIP-seq of Canis familiaris, Gallus gallus, Mus musculus, Macaca mulatta, Monodelphis domestica to investigate CEBPA and HNF4a binding in five vertebrates
AEExperimentType: ChIP-seq
Experimental Design: binding_site_identification_design
Experimental Design: high_throughput_sequencing_design
Experimental Design: species_design

first: Paul

last: Flicek


title: Discrete Roles of STAT4 and STAT6 Transcription Factors in Tuning Epigenetic Modifications and Transcription during Helper T Cell Differentiation

status: Public on Jun 18 2010

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health


title: GEMINI (Gastric Encyclopedia of Molecular Interactions and Nodes for Intervention) : 37 unique Gastric cancer cell lines

status: Public on Jun 08 2010

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

institute: F. Hoffmann-La Roche Ltd.

summary:
Genome-wide mRNA expression profiles of 37 unique gastric cancer cell lines (GCCLs).
Keywords: gastric cancer, cell culture

overall_design:
Profiling of 37 unique Gastric Cancer Cell Lines on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. A total of 37 arrays.
21 of these Samples represent a re-analysis of CEL files initially submitted under Series GSE15455.

first: Iain

last: Tan

first: Patrick


title: Mouse MOV10L1 associates with Piwi proteins and is an essential component of the piRNA pathway

status: Public on Jun 13 2010

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: Piwi-interacting RNAs (piRNAs) are essential for silencing of transposable elements in the germline but their biogenesis is poorly understood. Here we demonstrate that MOV10L1, a germ cell-specific putative RNA helicase, is associated with Piwi proteins. Genetic disruption of the MOV10L1 RNA helicase domain in mice renders both MILI and MIWI2 devoid of piRNAs. Absence of a functional piRNA pathway in Mov10l1 mutant testes causes loss of DNA methylation and subsequent de-repression of retrotransposons in germ cells. The Mov10l1 mutant males are sterile due to complete meiotic arrest. This is the first mouse mutant that expresses Piwi proteins but lacks piRNAs, suggesting that MOV10L1 is required for piRNA biogenesis and/or loading to Piwi proteins.

overall_design: Examination of piRNAs in Mov10l IP and differences in total small RNA profiles in RNA helicase Mov10l+/- and Mov10l-/- mutants.

first: Ke

last: Zheng

first: Jordi

last: Xiol

first: Michael

last: Reuter

first: Sigrid

last: Eckardt

first: Adrian

last: Leu

last: McLaughlin

first: Alexander

last: Stark

first: Ravi

last: Sachidanandam

first: Jeremy

last: Wang


title: Whole Cell Extract for Mouse Embryonic Fibroblasts

first: Richard

last: Young

summary:
Mouse embryonic fibroblasts (MEFs) are an example of an early differentiated cell type.  The whole cell extract was prepared in order to have background information for additional ChIP-Seq experiments in MEFs.
The WCE data is a useful dataset that can be used as a background for many different analysis purposes.

overall_design: MEFs were sonicated, DNA was purified and prepared for solexa sequencing.

first: Steve

last: Bilodeau


title: A global network of transcription factors, involving E2A, EBF1 and FOXO1, that orchestrates the B cell fate

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: It is now established that the transcription factors E2A, EBF1 and Foxo 1 play critical roles in B cell development. Here we show that E2A and EBF1 bound regulatory elements present in the Foxo1 locus. E2A and EBF1 as well as E2A and Foxo1, in turn, were wired together by a vast spectrum of cis-regulatory codes. These associations were dynamic during developmental progression. Occupancy by the E2A isoform, E47, directly elevated the abundance as well as the pattern of histone H3K4 monomethylation across putative enhancer regions. Finally, the pro-B cell epigenome was divided into clusters of loci that show E2A, EBF and Foxo1 occupancy. From this analysis a global network consisting of transcriptional regulators, signaling and survival factors, was constructed that we propose orchestrates the B cell fate.

overall_design: ChIP-Seq and gene expression profiling was performed in a variety of genetically modified primary B cell populations and cell lines approximating developmental stages of B cell development.

first: Yin

last: Lin

first: Suchit

last: Jhunjhunwala

first: Sven

last: Heinz

first: Eva

last: Welinder

first: Robert

last: Mansson

first: Mikael

last: Sigvardsson

first: James

last: Hagman

first: Celso

last: Espinoza

first: Janusz

last: Dutkowski

first: Trey

last: Ideker

middle: K

last: Glass

first: Cornelis

last: Murre


title: ChIP-Seq of Pol2 in Mouse Embryonic Fibroblasts

summary: RNA Polymerase II is the enzyme responsible for active transcription.  To gain insight into the genes occupied by RNA Polymerase II and actively transcribed in MEFS, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide binding targets of RNA Pol2.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against RNA Polymerase II.

first: Jamie

last: Newman


title: Relationship between nucleosome positioning and DNA methylation

status: Public on May 29 2010

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Arabidopsis thaliana
Homo sapiens

platform_organism:
Arabidopsis thaliana
Homo sapiens

overall_design: Refer to individual Series


title: Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis

status: Public on Jun 04 2010

city: Qingdao

first: Naihao

last: Ye

address: Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences, Qingdao, 266071, China

country: China

summary: This study provides a first large-scale cloning and characterization of Porphyra miRNAs and their predicted targets. These miRNAs belong to 224 conserved miRNA families and 7 are novel in Porphyra. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in the regulation of Porphyra yezoensis development.

overall_design: We constructed a small RNA library from Porphyra yezoensis.

first: Chengwei

last: Liang

first: Xiaowen

last: Zhang


title: CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.

status: Public on Jun 16 2010

city: Cleveland

first: Mike

middle: Paul

last: Schnetz

state: OH

address: 10900 Eulid Ave

department: Genetics

institute: Case Western Reserve University

summary:
Gene expression changes were measured between mouse ES cells of three genotypes: WT Chd7, Heterzygous Chd7 Null, Homozygous Chd7 Null.  The hypothesis being tested was that CHD7, a chromatin remodeling protein, functions as a transcriptional regulator.  This experiment was performed to detect gene targets of CHD7-mediated regulation.

We report the genome-wide binding profile of CHD7, the protein implicated in CHARGE syndrome, in mouse ES cells using ChIP-Seq technology. Combining these data with other genomic datasets, we discover CHD7 to colocalize with other transcription factors including Oct4, Nanog, Sox2, and p300 at gene enhancer elements to regulate ES cell specific gene expression.

overall_design:
Chd7 wildtype, heterozygous, and homozygous ES cells derived from preimplantation embryos were grown on feeder cells and total RNA was isolated using Trizol. The ratio of ES to feeder cells was estimated at 5:1.

ChIP sequencing of CHD7 and p300 in mouse ES cells

first: Michael

middle: P

first: Lusy

last: Handoko

first: Chia-Lin

last: Wei

first: Peter

last: Scacheri


title: The JMJD3-IRF4 axis regulates M2 macrophage polarization and host responses against helminth infection

status: Public on Aug 22 2010

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

country: Japan

institute: Kyoto University

summary:
Polarization of macrophages to M1 or M2 cells is important for mounting responses against bacterial and helminth infection respectively. Jumonji domain containing 3 (JMJD3), a histone 3 K27 demethylase, has been implicated in the activation of macrophages. Here we show that JMJD3 is essential for M2 macrophage polarization to helminth infection and chitin, though JMJD3 is dispensable for M1 responses. Furthermore, Jmjd3 is critical for proper bone marrow macrophage differentiation in a demethylase activity-dependent manner. Jmjd3 deficiency affected trimethylation of H3K27 in only a limited numbers of genes. Among them, we identified Irf4 as the target transcription factor critical for controlling M2 macrophage polarization. Collectively, these results show that JMJD3-mediated H3K27 demethylation is critical for regulating M2 macrophage development leading to anti-helminth host responses.

This SuperSeries is composed of the SubSeries listed below.


title: An effective approach for identification of in vivo protein–DNA binding sites from paired-end ChIP-Seq data

city: Shanghai

first: dabing

last: zhang

address: Dongchuan RD 800

institute: Shanghai Jiao Tong University

summary:
ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of protein–DNA interactions in-vivo in the genome. In general, current algorithms for ChIP-seq reads employ artificial estimation of the average length of DNA fragments for peak finding, leading to uncertain prediction of DNA-protein binding sites. Here, we present SIPeS (Site Identification from Paired-end Sequencing), a novel algorithm for precise identification of binding sites from short reads generated from paired-end Solexa ChIP-Seq technology. SIPeS uses a dynamic baseline directly via ‘piling up’ the corresponding fragments defined by the paired reads to efficiently find peaks corresponding to binding sites. The performance of SIPeS is demonstrated by analyzing the ChIP-Seq data of the Arabidopsis basic helix-loop-helix transcription factor ABORTED MICROSPORES (AMS). The robustness of SIPeS was demonstrated in higher sensitivity and spatial resolution in peak finding compared to three existing peak detection algorithms.

Keywords: transcription factors (protein-DNA interactions)

overall_design: Examination of protein-DNA interactions in buds of Arabidopsis anther cell

first: Congmao

last: Wang

first: Jie

last: Xu

first: Dasheng

first: Zoe

last: Wilson

first: Dabing


title: Regulation of microRNA Expression and Abundance during Lymphopoiesis

status: Public on Jun 07 2010

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

institute: NIH

summary: Although the cellular concentration of miRNAs is critical to their function, how miRNA expression and abundance are regulated during ontogeny is unclear. We used deep-sequencing to characterize the microRNome from most developing lymphocytes, various hematopoietic cell lineages, and representative mouse tissues. Epigenetic and transcriptome profiles were also compiled from selected T and B cell stages by ChIP-Seq and mRNA-Seq respectively. We show that lymphocyte-specific miRNAs are either tightly regulated during development by polycomb group-mediated H3K27me3, or maintained in a semi-activated state prior to full expression. Because of extensive miRNA biogenesis, the cellular concentration of mature miRNAs does not typically reflect transcriptional changes. However, we here uncovered a subset of miRNAs for which abundance is directly regulated by miRNA gene expression. Our data provides the most comprehensive view of the microRNome in the immune system and reveal underlying epigenetic and transcriptional forces that shape miRNA homeostasis.

overall_design:
small RNA expression profiles of 27 well defined cell types from the mouse immune system, hematopoietic progenitor cells, embryonic stem cells, as well as 12 tissues.  Biological and technical replicates for 3 of the cell types were included.

Regulation of MicroRNA Expression and Abundance during Lymphopoiesis
Immunity, Volume 32, Issue 6, 25 June 2010, Pages 828-839
doi:10.1016/j.immuni.2010.05.009

first: Stefan

last: Kuchen

first: Wolfgang

last: Resch

first: Arito

last: Yamane

last: Kuo

first: Zhiyu

last: Li

first: Tirtha

last: Chakraborty

first: Lai

first: Arian

last: Laurence

first: Tomoharu

last: Yasuda

first: Siying

last: Peng

first: Jane

last: Hu-Li

first: Kristina

last: Lu

first: Wendy

last: Dubois

first: Yoshiaki

last: Kitamura

first: Nicolas

last: Charles

first: Hong-wei

last: Sun

last: Muljo

first: Pamela

last: Schwartzberg

first: William

last: Paul

first: John

last: O'Shea

first: Klaus

last: Rajewsky

first: Rafael

last: Casellas


title: Small RNAs in transgenic TaNAM-RNAi wheat plants

city: Davis

first: Dario

last: Cantu

address: One Shields Ave

department: Plant Sciences

institute: UC Davis

summary: To explore the effect of stable RNAi on the small RNA (sRNA) population in wheat, we constructed a sRNA library from hexaploid wheat that expresses an RNAi construct under the 35S promoter that targets the endogenous NO APICAL MERISTEM (TaNAM) gene. The presence of this RNAi transgene causes a 40% reduction in expression of the target genes as measured by quantitative RT-PCR and significantly delays senescence and reduces remobilization of N, Fe, and Zn to the grain.

overall_design: RNA was extracted from flag-leaves of transgenic NAM-RNAi plants at 12 days post-anthesis. RNA was collected from a pool of flag-leaves from four plants.

first: Richard

last: Michelmore

first: Jorge

last: Dubcovsky


title: The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae

status: Public on May 28 2010

city: Lausanne

first: Jacques

last: Rougemont

address: Station 15

department: School of Life Sciences

institute: EPFL

summary: The majority of Saccharomyces cerevisiae snoRNA promoters contain an aRCCCTaa sequence motif located at the upstream border of a TATA-containing nucleosome-free region. Genome-wide ChIP-seq analysis showed that these motifs are bound in vivo by Tbf1, a telomere-binding protein known to recognize mammalian-like T2AG3 repeats at sub-telomeric regions. Tbf1 has over 100 additional promoter targets, including the TBF1 gene itself. Tbf1 is required for full snoRNA expression, yet it does not influence nucleosome positioning at snoRNA promoters.

overall_design: Analysis of Tbf1-binding sites in Saccharomyces cerevisiae by ChIP-seq of a Myc-tagged strain and a control untagged strain. 1 sample per strain, 1 lane per sample.

first: Felix

last: Naef

first: David

last: Shore

first: Giorgio

last: Dieci

first: Cyril

last: Ribeyre


title: Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations

first: Garrett

last: Frampton

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

summary: The presence of two active X chromosomes (XaXa) is a hallmark of the ground state of pluripotency specific to murine embryonic stem cells (ESCs). Human ESCs invariably exhibit signs of X chromosome inactivation (XCI) and are considered developmentally more advanced than their murine counterparts.  We describe the establishment of the first XaXa hESCs derived under physiological oxygen concentrations. Using these cell lines we demonstrate that (1) differentiation of hESCs induces random XCI in a manner similar to murine ESCs, (2) chronic exposure to atmospheric oxygen is sufficient to induce irreversible XCI with minor changes of the transcriptome, (3) the Xa exhibits heavy methylation of the XIST promoter region, and (4) XCI is associated with demethylation and transcriptional activation of XIST along with H3K27-me3 deposition across the Xi. These findings indicate that the human blastocyst contains pre-X-inactivation cells and that this state is preserved in vitro through culture under physiological oxygen.

overall_design: Examination of 2 different histone modifications (H3K4me3 and H3K27me3) in 3 ES cell lines in 5% and 20% oxygen.

first: Christopher

last: Lengner

first: Jennifer

last: Erwin

first: Alexander

last: Gimelbrant

first: Albert

middle: W

last: Cheng

first: Matthew

middle: G

last: Guenther

first: G

last: Welstead

first: Raaji

last: Alagappan

first: Ping

last: Xu

first: Julien

last: Muffat

first: Doug

last: Powers

first: C

middle: B

last: Barrett

last: Young

first: Jeannie

last: Lee

first: Rudolf

last: Jaenisch

first: Maisam

last: Mitalipova


title: A large fraction of extragenic RNA Pol II transcription sites overlap enhancers (2)

status: Public on May 21 2010

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: Mammalian genomes are pervasively transcribed outside mapped protein-coding genes. One class of extragenic transcription products is represented by long non-coding RNAs (lncRNAs), some of which result from Pol_II transcription of bona-fide RNA genes. Whether all lncRNAs described insofar are products of RNA genes, however, is still unclear. Here we have characterized transcription sites located outside protein-coding genes in a highly regulated response, macrophage activation by endotoxin. Using chromatin signatures, we could unambiguously classify extragenic Pol_II transcription sites as belonging to either canonical RNA genes or transcribed enhancers. Unexpectedly, 70% of extragenic Pol_II peaks were associated with genomic regions with a canonical chromatin signature of enhancers. Enhancer-associated extragenic transcription was frequently adjacent to inducible inflammatory genes, was regulated in response to endotoxin stimulation and generated very low abundance transcripts. Moreover, transcribed enhancers were under purifying selection and contained binding sites for inflammatory transcription factors, thus suggesting their functionality. These data demonstrate that a large fraction of extragenic Pol_II transcription sites can be ascribed to cis-regulatory genomic regions rather than to autonomous RNA genes. Discrimination between lncRNAs generated by canonical RNA genes and products of transcribed enhancers will provide a framework for experimental approaches to lncRNAs and help complete the annotation of mammalian genomes.

overall_design: Chromatin immunoprecipitation of RNA polymerase II phosphorylated in ser5 followed by multiparallel sequencing was performed in bone marrow-derived macrophages. The experiment was also carried out in cells treated for 2hrs with lipopolysaccharide (LPS).

first: Francesca

last: De Santa

first: Flore

last: Mietton

first: Serena

last: Ghisletti

first: Sara

last: Polletti

first: Betsabeh

last: Tusi

first: Heiko

last: Muller

first: Jiannis

last: Ragoussis

first: Chia-Lin

last: Wei

first: Gioacchino

last: Natoli


title: Analysis of small RNAs in piRNA pathway mutant mouse testes

status: Public on May 27 2010

city: NewHaven

first: Toshiaki

last: Watanabe

state: CT

address: 10 Amistad

institute: Yale University

summary: Piwi-interacting RNAs are 25-32 nt small RNAs bound to Piwi proteins. To know the steps where factors involved in the piRNA biogenesis (MILI, MIWI2, ZUC (MitoPLD), MVH) work, we sequenced small RNAs from  mutant mouse testes and analyzed piRNAs.

overall_design: Examination of small RNAs in testes of mutant mouse

first: Shin-ichi

last: Tomizawa

first: Shinichiro

last: Chuma

first: Kohzoh

last: Mitsuya

first: Satomi

last: Kuramochi-Miyagawa

first: Naoko

last: Iida

first: Yuko

last: Hoki

first: Yasuhiro

last: Yamamoto

first: Patrick

last: Murphy

first: Yasushi

last: Totoki

first: Atsushi

last: Toyoda

first: Kengo

last: Gotoh

first: Asao

last: Fujiyama

first: Tatsuhiro

last: Shibata

first: Takashi

last: Sado

first: Toru

last: Nakano

first: Paul

last: Soloway

first: Hiroyuki

last: Sasaki


title: Diverse Targets of the Transcription Factor STAT3 Contribute to T Cell Pathogenicity and Homeostasis

status: Public on May 30 2010

first: Golnaz

last: Vahedi

summary:
STAT3, an essential transcription factor with pleiotropic functions, plays critical roles in the pathogenesis of autoimmunity. Despite recent data linking STAT3 with inflammatory bowel disease, exactly how it contributes to chronic intestinal inflammation is not known. Using a T cell transfer model of colitis we found that STAT3 expression in T cells was essential for the induction of both colitis and systemic inflammation. STAT3 was critical in modulating the balance of T helper 17 (Th17) and regulatory T (Treg) cells, as well as in promoting CD4+ T cell proliferation. We used chromatin immunoprecipitation and massive parallel sequencing (ChIP-Seq) to define the genome-wide targets of STAT3 in CD4+ T cells. We found that STAT3 bound to multiple genes involved in Th17 cell differentiation, cell activation, proliferation and survival, regulating both expression and epigenetic modifications.  Thus, STAT3 orchestrates multiple critical aspects of T cell function in inflammation and homeostasis.

This SuperSeries is composed of the SubSeries listed below.


title: ChIP-Seq of Oct4 in Human Embryonic stem cells.

status: Public on May 20 2010

city: Cambridge

first: Richard

last: Young

institute: Whitehead Institute for Biomedical Research

summary: Oct4, Sox2 and Nanog cooperate to form the transcriptional regulatory circuitry of embyronic stem cells.  To gain insight into the genes regulated by the core circuitry of transcription factors, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide binding targets of Oct4.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing.  ChIP was performed using an antibody against IgG as a background control.  ChIP was performed using an antibody against Oct4 in two biological replicates. The first replicate was sequenced twice (technical replicate 1 and technical replicate 2).

first: Alan

last: Mullen


title: Propagation of Adipogenic Signals through an Epigenomic Transition State

city: Philadelphia

first: David

last: Steger

address: 415 Curie Blvd

institute: University of Pennsylvania

summary: The transcriptional mechanisms by which temporary exposure to developmental signals instigates adipocyte differentiation are unknown. During early adipogenesis, we find transient enrichment of the glucocorticoid receptor (GR), CCAAT/enhancer binding protein b (CEBPb), p300, mediator subunit 1, and histone H3 acetylation near genes involved in cell proliferation, development and differentiation, including the gene encoding the master regulator of adipocyte differentiation, peroxisome proliferator activated receptor g2 (PPARg2). Occupancy and enhancer function are triggered by adipogenic signals, and diminish upon their removal. GR, which is required for adipogenesis but need not be active in the mature adipocyte, transiently functions with other enhancer proteins to propagate a new program of gene expression that includes induction of PPARg2, thereby providing a memory of the earlier adipogenic signal. Thus, the conversion of preadipocyte to adipocytes involves the formation of an epigenomic transition state that is not observed in cells at the beginning or end of the differentiation process.

overall_design: Genomic occupancy profiled by high throughput sequencing (ChIP-seq) from 3T3-L1 cells during differentiation for H3K9Ac, CEBPb and GR.

first: Mitchell

last: Lazar


title: A large fraction of extragenic RNA Pol II transcription sites overlap enhancers

first: Iros

last: Barozzi

overall_design: Analysis of nuclear RNA in bone marrow-derive macrophages.

first: Francesca

last: De Santa

first: Flore

last: Mietton

first: Serena

last: Ghisletti

first: Sara

last: Polletti

first: Betsabeh

last: Tusi

first: Heiko

last: Muller

first: Jiannis

last: Ragoussis

first: Chia-Lin

last: Wei

first: Gioacchino

last: Natoli


title: Dissecting the in vivo metabolic potential of two human gut acetogens.

status: Public on May 22 2010

city: Saint Louis

first: Jeremiah

last: Faith

address: Campus Box 8510

institute: Washington University in St. Louis

summary: Fermenting microbial communities generate hydrogen: its removal through production of acetate, methane, or hydrogen sulfide modulates the efficiency of energy extraction from available nutrients in many ecosystems. We noted that pathway components for acetogenesis are more abundantly and consistently represented in the gut microbiomes of monozygotic twins and their mothers than components for methanogenesis or sulfate reduction, and subsequently analyzed the metabolic potential of two sequenced human gut acetogens, Blautia hydrogenotrophica and Marvinbryantia formatexigens in vitro and in the intestines of gnotobiotic mice harboring a prominent saccharolytic bacterium. To do so, we developed a generally applicable method for multiplex sequencing of expressed microbial mRNAs, and together with mass spectrometry of metabolites, show that these organisms have distinct patterns of substrate utilization. B. hydrogenotrophica targets aliphatic and aromatic amino acids. It increases the efficiency of fermentation by consuming reducing equivalents, thereby maintaining a high NAD+/NADH ratio and boosting acetate production. In contrast, M. formatexigens consumes oligosaccharides, does not impact the redox state of the gut, and boosts the yield of succinate. These findings have strategic implications for those who wish to manipulate the hydrogen economy of gut microbial communities in ways that modulate energy harvest.

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

overall_design: 119 Samples consisting of Bacteroides thetaiotaomicron, Marvinbryantia formatexigens, and Blautia hydrogenotrophica cecal and fecal samples.   Please see the individual Sample descriptions for more information.

first: Federico

last: Rey


title: Genome-wide mapping of in vivo SCL/DNA interactions in erythroid cells

status: Public on May 18 2010

city: Oxford

first: Stephen

last: Taylor

address: Headington

institute: CBRG

summary: We have previously proposed two distinct molecular mechanisms by which SCL binds its targets in hematopoiesis; either by direct contact with specific DNA sequences or by indirect recruitment through interaction with other proteins.  We have established that direct DNA binding is the major non-redundant mechanism SCL exerts in red cells.  A DNA-binding mutant form of SCL (SCLRER) had detrimental effect on erythropoiesis in vivo. To extend these data to a molecular and mechanistic level, we have set out to identify the genomic sequences bound by SCL in vivo in erythroid precursors; we performed anti-SCL ChIP assays on immature, Ter119- erythroid cell populations isolated from day E12.5 wild-type (SCLWT/WT) fetal livers followed by ultra-throughput sequencing (ChIP-SEQ).  To compare SCL’s direct versus indirect DNA-binding activities and, thus, gain insight into its mechanisms of action, we also analysed material isolated from SCLRER/RER fetal livers.

overall_design: anti-SCL ChIP-enriched DNA from mouse fetal liver erythroblast chromatin was analysed by Solexa sequencing. Four samples were processed: chromatin from SCL wildtype erythroblasts (WT-SCL) and SCL mutant erythroblasts (RER-SCL) were ChIPed by anti-SCL antibody and sequenced with their respective 'no antibody' controls.

first: Mira

last: Kassouf

first: Catherine

last: Porcher


title: Pol II Ser7phospho ChIP-seq in mES cells

first: Richard

last: Young

summary: RNA Polymerase II transcribes protein-coding and many non-coding RNA genes in eukaryotes.  The largest subunit of RNA Polymerase II, Rpb1, contains a hepta-peptide repeat on its C-terminal tail with three potential phosphorylation sites (Serine 2, Serine 5 and Serine 7).  Mammalian Rpb1 contains 52 repeats.   The phosphorylation events are catalyzed by specific protein kinases where the phosphorylation of specific residues is coupled to the transcription cycle.  For example, the Cdk7 subunit of TFIIH phosphorylates both Serine 5 and Serine 7 during intiation and the Cdk9 subunit of P-TEFb phosphorylates Serine 2 during the transition into productive elongation.  The dataset presented here is the genome-wide distribution of RNA Pol II with Serine 7 of the CTD phosphorylated in murine embryonic stem cells.  This data, in addition to phospho-specific datasets generated in the same cell type in Rahl et al. Cell 2010 and Seila et al. Science 2008, represents the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II.

overall_design: An antibody specific to RNA Pol II Serine 7 phosphorylated CTD (gift of Dirk Eick; Chapman et al. Science 2008) was used to enrich for DNA fragments associated with this Pol II isoform in murine embryonic stem cells.  DNA was purified and prepared for Illumina/Solexa sequencing following their standard protocol.  This is a single dataset but together with datasets from Rahl et al. Cell 2010 and Seila et al. Science 2008, these datasets represent the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II.

first: Rahl

last: Peter


title: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data

city: New York

first: Markus

last: Hafner

state: NY

address: 1230 York Ave, Box 186

department: Laboratory of RNA Molecular Biology

institute: The Rockefeller University

summary: We applied 4-thiouridine to cultured cells expressing the FLAG/HA-tagged RNA-binding proteins (RBPs) followed by UV 365 nm irradiation. The crosslinked RNA-protein complexes were isolated by immunoprecipitation, and the covalently bound RNA was partially digested with RNase T1 and radiolabeled. The radiolabeled RNPs were subsequenctly separated by SDS-PAGE, the crosslinked RNA segments recovered and converted into a cDNA library and sequenced.

overall_design: RBPs were UV-crosslinked to their RNA targets containing 4-thiouridine. The RNA segments were recovered after immunoprecipitation and seqeunced by Solexa.


title: Relationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq

city: Los Angeles

first: matteo

last: Pellegrini

summary: Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes.  By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA.  These results suggest that nucleosome positioning strongly influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA.  We also observed similar trends in human nucleosomal DNA suggesting that the relationships between nucleosomes and DNA methyltransferases are conserved.  Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA Pol II was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity.  We also found that DNA methylation enriched on exons, consistent with the targeting of DNA methylation to nucleosomes.

overall_design: Genomic DNA  from Arabidopsis thaliana was MNase digested, size selected and sequenced.  Genomic DNA  associated with H3 was isolated using ChIP and sequenced.  Genomic DNA from human HSF1 embryonic stem cells was bisulfite converted and sequenced.

first: Ramakrishna

last: Chodavarapu

first: Suhua

last: Feng

first: Yana

last: Bernatavichute

first: Pao-Yang

last: Chen

first: Hume

last: Stroud

first: Yanchun

last: Yu

first: Jonathan

last: Hetzel

first: Frank

last: Kuo

first: Jin

last: Kim

first: Shawn

last: Cokus

first: David

last: Casero

first: Maria

last: Bernal

first: Peter

last: Huijser

first: Amander

last: Clark

first: Ute

last: Krämer

first: Sabeeha

last: Merchant

first: Xiaoyu

last: Zhang

first: Matteo

first: Steven

last: Jacobsen


title: Expression and ChIP-seq analyses of embryonic stem cells, extraembryonic endoderm stem cells, and trophoblast stem cells

status: Public on May 17 2010

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

summary: Bivalent histone domains have been proposed to contribute to pluripotency in embryonic stem cells, suggesting an epigenetic mechanism may regulate stem cell behavior in general. Here we compare histone modifications in two other stem cells derived from the blastocyst. We show that extraembryonic stem cells have little repressive lysine 27 trimethylation and few bivalent domains. Thus, bivalent domains are not a common mechanism for maintaining the undifferentiated state in blastocyst-derived stem cells and alternative mechanisms must mediate transcriptional repression in extraembryonic cells. We show that lysine 9 trimethylation, but not DNA methylation, is likely to fulfill this role. Intriguingly, although we do detect bivalent domains in pluripotent cells in the early mouse embryo, the epigenetic status of extraembryonic cells does not entirely reflect their in vitro stem cell counterparts. Therefore, differences in epigenetic regulation between lineage progenitors in vivo and in vitro may arise during selection for self-renewal in vitro.

overall_design:
Expression profiles [GSM388878-GSM388881] of three different stem cells (R1 embryonic stem cells, trophoblast stem cells, extraembryonic endoderm stem cells) were generated for comparison to CHIP-seq data [GSM392044-GSM392055] of the same three stem cell lines to observe correlations with Histone 3 K4 and K27 trimethylation patterns.

CHIP-seq details: R1 embryonic stem cells, trophoblast stem cells or extraembryonic endoderm stem cells were grown, lysed and chromatin purified. The chromatin was immunoprecipitated for either histone 3 K4 trimethylation or histone 3 K27 trimethylation and the immunoprecipitate was subjected to purification and high-throughput Illumina-based sequencing.

last: Rugg-Gunn

first: Janet

last: Rossant


title: Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa

status: Public on May 16 2010

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

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

overall_design: Refer to individual Series


title: An Integrated Network of Androgen Receptor and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression (II)

city: Chicago

first: Jindan

last: Yu

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

summary: Androgen receptor (AR) is a transcription factor that plays a central role in the growth and development of the normal prostate and its malignant transformation.  More recently, a majority of prostate cancers have been shown to harbor recurrent gene fusions of the androgen-regulated gene, TMPRSS2, to the oncogenic ETS transcription factor ERG.  Here we employed chromatin immunoprecipitation coupled to massively parallel sequencing (ChIP-Seq) to explore the genome-wide localization of these transcription factors in human prostate cancer cell lines as well as tissues.  Unexpectedly, transcriptional networks emanating from AR and ERG were found to be highly overlapping.  Furthermore, AR was found to regulate known 5’ fusion partners in prostate cancer including TMPRSS2, as well as negatively regulating its own expression.  While induced by androgen through fusion to TMPRSS2, ERG itself was shown to inhibit AR expression and positively regulate the genomic locus of wild-type ERG, thus revealing multiple levels of molecular cross-talk between AR and ERG.  Importantly, androgen-sensitive prostate cancer cells in which ERG is overexpressed are able to proliferate and invade in the absence of androgen.  Thus, we dissected the intertwined genomic landscape of two master transcriptional regulators of prostate cancer and suggest a role for ERG in maintaining transcriptional networks necessary for androgen-independent prostate cancer growth.  These studies may suggest that future therapies against prostate cancer should target both AR and ERG, rather than AR alone, in order to achieve maximum effectiveness.

overall_design:
ChIP_Seq examination of histone modifications and key transcription factors in LNCaP and VCaP prostate cancer cell lines in un-treated, vehicle treated or 10nM R1881 treated conditions.
LNCaP ChIP-Seq experiments include samples GSM353609-GSM353618, GSM353625-GSM353628, GSM353633-GSM353635, GSM353641-GSM353644, and GSM353648.
VCaP ChIP-Seq experiments include samples GSM353601-GSM353608, GSM353619-GSM353624, GSM353629-GSM353632, and GSM353645-GSM353647.
In addition, we performed re-ChIP of AR and ERG in VCaP cells (GSM356767), and examined the effect of ERG knockdown on AR and ERG binding (samples GSM353636-GSM353639).
To study ectopic ERG binding we performed ERG ChIP-Seq in stable RWPE+ERG or control cells (samples GSM353649-GSM353650).
AR ChIP-Seq was also done in the AR-positive but ETS fusion-negative 22RV1 cells (GSM353640).

To further study transcription factor binding and chromatin state we performed ChIP-Seq of AR, ERG, H3K4me3, H3K9me3, H3K27me3 and RNA Pol II in a metastatic prostate tumor tissue (samples GSM353651-GSM353656).

To couple  the ChIP-Seq experiments with gene expression, we have also done Illumian SAGE-tag profiling in LNCaP cells following androgen treatment for 0, 24 and 48hrs. These DGE experiments correspond to samples GSM353657-GSM353659.

first: Arul

middle: M

last: Chinnaiyan


title: An Integrated Network of Androgen Receptor and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression


title: Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa (Illumina)

summary: In higher eukaryotes, histone methylation is involved in the maintenance of cellular identity during somatic development. During spermatogenesis, Since most nucleosomes are replaced by protamines during spermatogenesis . Iit is therefore unclear whether if histone modifications function in paternal transmission of epigenetic information. Here we show that H3K4 di-methylation (H3K4me2) and H3K27 tri-methylation (H3K27me3), two modifications important for Trithorax and Polycomb-mediated gene regulation, display methylation-specific distributions at regulatory regions in human spermatozoa. H3K4 dimethylation H3K4me2-marksed promoters of genes relevant control gene functions in spermatogenesis and cellular homeostasis suggesting that this mark reflects germline transcription. In contrast, H3K27 trimethylation (H3K27me3) marks promoters of key developmental regulators in sperm like in somatic cells. Promoters of orthologous genes are similarly modified in mouse spermatozoa.  Further, particularly genes with extensive H3K27me3 coverage around transcriptional start sites are never expressed during male and female gametogenesis, nor in pre-implantation embryos. These data are compatible with a function for Polycomb in repressing somatic determinants across generations. Importantly, however, we observe only modest selective retention of nucleosomes at regulatory regions in human sperm suggesting that paternal transmission of H3K27me3-encoded epigenetic information may be subjected to variegation.

overall_design: Identification of nucleosome containing regions in 6 human sperm samples

first: Mizue

last: Hisano

first: Serap

last: Erkek

first: Michael

last: Stadler

middle: H


title: Endogenous, tissue-specific short-interfering RNAs silence the chalcone synthase gene family in Glycine max seed coats

status: Public on May 14 2010

city: Urbana

first: Lila

middle: O.

last: Vodkin

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: We present results from deep sequencing of small RNA populations from several genotypes of soybean and demonstrate that the CHS siRNAs accumulated only in the seed coats of the yellow varieties having either the dominant I or i-i alleles and not in the pigmented seed coats with homozygous recessive i genotypes. However, the diagnostic CHS siRNAs did not accumulate in the cotyledons of genotypes with the dominant I or i-i alleles thus demonstrating the novelty of an endogenous inverted repeat region of CHS genes driving RNA silencing in trans of non-linked CHS family members in a tissue-specific manner.  The phenomenon results in inhibition of a metabolic pathway by siRNAs in one tissue allowing expression of the flavonoid pathway and synthesis of secondary metabolites in other organs as the chalcone synthase small RNAs are found in the seed coats of yellow seeded soybean varieties but not in the cotyledons of the same genotype.

overall_design: In order to compare the population of chalcone synthase related small RNAs, we sequenced 3 to 6 million small RNAs using the Illumina Genome Analyzer from the following four soybean cultivars and tissues with specific genotypes at the I locus: Richland immature seed coats (homozygous for the dominant I allele that specifies yellow seed coat); Williams immature seed coats (homozygous for the dominant i-i allele that specifies yellow seed coat with pigmented hilum) Williams (i-i/i-i yellow) immature cotyledons (homozygous for the dominant i-i allele that specifies yellow seed coat with pigmented hilum); Williams 55 immature seed coats (a Williams isogenic line homozygous for the recessive i allele that specifics pigmented seed coats. All seed coats and cotyledons were dissected from green stage immature seeds within the fresh weight range of 50-75 mg.

first: Jigyasa

last: Tuteja

first: Gracia

last: Zabala

first: Kranthi

last: Varala

first: Matthew

last: Hudson

middle: O


title: MIRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana

first: James

middle: C

last: Carrington

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata
Capsella rubella


title: Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood (seq data)

status: Public on May 13 2010

city: New Delhi

first: Alok

last: Bhattacharya

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: MicroRNAs are a class of small non-coding RNAs that regulate mRNA expression at the post-transcriptional level and thereby many fundamental biological processes. A number of methods, such as multiplex polymerase chain reaction, microarrays have been developed for profiling levels of known miRNAs. These methods lack ability to identify novel miRNAs and accurately determine expression at a range of concentration. Deep or massively parallel sequencing methods are providing suitable platforms for genome wide transcriptome analysis and have the ability to identify novel transcripts. The results of analysis of small RNA sequences obtained by Solexa technology of normal peripheral blood mononuclear cells, tumor cell lines K562 (chronic myelogenous leukemia) and HL60 (acute promyelogenous leukemia) are presented. Custom computation pipelines were used to generate expression profiles of known and for identification of novel miRNAs. Some of the highly expressed miRNAs in the leukocytes include several members of the let 7 family, mir-21, 103, 185, 191 and 320a. Comparison of the miRNA profiles of normal versus K562 cells or HL60 revealed a specific set of differentially expressed molecules. Correlation of the miRNA with that of mRNA expression profiles, obtained by microarray, revealed a set of target genes showing inverse correlation with miRNA levels. Our computational pipeline also predicted a number of novel miRNAs. Some of the predictions were validated by realtime RT-PCR and or RNAase protection assay.

overall_design: The small RNA population from four samples - Two Normal Peripheral blood mononuclear cells (PBMC) samples, K562 cell line (This cell line is used as a model to study Chronic Myelogenous Leukemia), HL60 (This cell line is used to study acute promyelogenous leukemia) was sequenced using Solexa technology.

first: Candida

last: Vaz


title: Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood


title: A quantitative model of transcription regulation reveals the role of non-conserved enhancers

first: Kenzie

last: MacIsaac

address: 77 Massachusetts Ave.

institute: MIT

summary: We identify sites of combinatorial control by performing high throughput ChIP experiments on p300, CREB-binding protein (CBP), the deacetylase SIRT1 and on multiple DNA-binding transcription factors in three different tissues.  We present a quantitative model of transcriptional regulation that reveals the contribution of each binding site to tissue-specific gene expression in several mouse cell types. Binding to both evolutionarily conserved and non-conserved sequences is found to contribute significantly to transcriptional regulation. We demonstrate that binding location strongly predicts the expression level of nearby genes.

overall_design: Liver hepatocytes and cerebellum tissue were harvested from male C57BL/6J mice. RNA was extracted and hybridized to Affymetrix arrays. Examination of transcriptional regulator binding in three mouse tissues by ChIP-IP using tiling arrays. Examination of CBP binding in mouse liver and cerebellum by ChIP-seq.

first: Ernest

last: Fraenkel


title: Genome wide analysis of ER beta in U2OS cells

status: Public on May 12 2010

city: Emeryville

first: Xiaoyue

last: Zhao

address: 5858 Horton St

institute: Bionovo Inc.


title: Genome-wide maps of ERbeta binding sites in U2OS cells

summary: Estrogen receptor beta (ERbeta) has potent anti-proliferative and anti-inflammatory properties, suggesting that ER beta-selective agonists might be a new class of therapeutic and chemopreventative agents. To understand how ER beta regulates genes, we identified genes regulated by the unliganded and liganded forms of ER alpha and ER beta in U2OS cells. Microarray data demonstrated that virtually no gene regulation occurred with unliganded ER alpha, whereas many genes were regulated by estradiol (E2). These results demonstrate ER alpha requires a ligand to regulate a single class of genes. In contrast, ER beta regulated three classes of genes. Class I genes were regulated primarily by unliganded ER beta. Class II genes were regulated only with E2, whereas Class III genes were regulated by both unliganded ER beta and E2. There were 453 Class I genes, 258 Class II genes and 83 Class III genes. To explore the mechanism whereby ER beta regulates different classes of genes ChIP-seq was performed to identify ER beta binding sites and adjacent transcription factor motifs in regulated genes. AP1 binding sites were more enriched in Class I genes, whereas ERE, NFKB1 and SP1 sites were more enriched in class II genes. ER beta bound to all three classes of genes demonstrating that ER beta binding is not responsible for differential regulation of genes by unliganded and liganded ER beta. The coactivator, NCOA2 was differentially recruited to several target genes. Our findings indicate that the unliganded and liganded forms of ER beta regulate three classes of genes by interacting with different transcription factors and coactivators.

overall_design: Examination of ER beta binding sites in U2OS cells with or without E2 treatment


title: Small RNA profile in E18.5 fetal liver from wild type and Ago2 catalytically inactive mutant mice

status: Public on May 06 2010

city: cold spring harbor

first: sihem

last: cheloufi

address: 1 bungtown road

institute: Cold spring harbor laboratory

summary: Examination of miRNAs in fetal liver revealed a loss of miR-451, a small RNA important for erythropoiesis.

overall_design: Total RNA was isolated and size-fractionated by PAGE into 19-30nt. These were processed and sequenced on Illumina GA2 platform.

first: Sihem

last: Cheloufi

first: Camila

last: DosSantos

first: Mark

last: Chong

first: Gregory

last: Hannon


title: Genome-wide mapping of EBF1 binding sites in murine pre B-cells

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

institute: University of Chicago

summary: Early B cell factor-1 (Ebf1), a transcription factor expressed in B cells, adipocytes and neuronal cells, has been identified as a determinant in the specification of the B cell lineage in which Ebf1 acts in a regulatory network with the transcription factors E2A and Pax5.  To gain insight into the molecular basis of Ebf1 function in early stage B cells, we compared the data set of a genome-wide ChIP sequencing analysis with gain- and loss-of-function transcriptome analyses.

overall_design: Identification of genetic loci enriched by chromatin-immunoprecipitation using antibodies against EBF1.

first: T

last: Treiber

first: R

last: Grosschedl


title: MIRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana: Illumina sequencing

summary: Deep sequencing of small RNA from three closely related brassicaceae A. thaliana, A. lyrata and Capsella rubella was done to systematically analyze the evolution of MIRNA genes and their targets.

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata

platform_organism:
Arabidopsis thaliana
Arabidopsis lyrata

overall_design:
Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR.  DNA amplicons were sequenced using an Ilumina Genome Analyzer.  Resulting sequences were computationally trimmed to remove 3' adaptor sequences.
Raw data files (fastq) are unavailable for two of the samples (A.lyrata_flowers-stage1-12_rep1 and A.lyrata_flowers-stage1-12_rep2).

first: Noah

last: Fahlgren

first: Sanjuro

last: Jogdeo

first: Kristin

middle: D

last: Kasschau

first: Christopher

last: Sullivan

first: Elisabeth

last: Chapman

first: Sascha

last: Laubinger

first: Lisa

last: Smith

last: Dasenko

first: Scott

middle: A

last: Givan

first: Detlef

last: Weigel


title: Transcriptome changes in soybean seeds resulting from RNAi suppression of seed storage proteins

status: Public on May 01 2010

city: St. Louis

first: Eliot

middle: Mark

last: Herman

address: 975 N. Warson Rd

department: Plant Genetics  Research

institute: USDA/ARS

summary: We report the changes in transcriptome that results from RNAi suppression of 7S and 11S storage protein synthesis in soybean seeds, Proteomic results show that other proteins compensate for the storage protein shortfall. The transcriptome analysis show numerous changes result from suppressing storage proteins but compensating proteins are accumulated without parallel changes in the protein's transcription.

overall_design: Total RNA samples prepared from midmaturation wildtype and storage protein RNAi (SP-) soybeans were used to produce cDNA that was subjected to Illumina sequencing. The resulting sequences were assembled and analyzed to characterize the changes in transcriptome that results from suppressing storage protein synthesis/accumulation.

first: Monica

last: Schmidt


title: Transcriptome-wide identification of small RNA targets in rice

status: Public on May 04 2010

city: Stillwater

first: Ramanjulu

last: Sunkar

address: 246 Noble Research center

department: Biochemistry and Molecular biology

institute: Oklahoma State University

summary:
MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. Most miRNA targets in Arabidopsis are validated, but those in rice are yet to be characterized. To identify transcriptome-wide small RNA targets in rice, we generated 20-nt small cDNA library and obtained nearly 40 million reads. Sequence analysis yielded 11,552,007 unique reads that can be perfectly mapped to the rice genome. Sequence analysis not only found homologous targets for conserved miRNAs but also many novel targets. Besides miRNA atregts, the rice degradome contained fragments derived from MIRNA precursors. A closer inspection of these fragments revealed a unique pattern distinct from siRNA producing loci. This attribute can serve as one of the ancillary criteria for separating miRNAs from siRNAs in plants.

Keywords: high throughout sequencing of rice degradome

overall_design: Identify transcriptome-wide small RNA targets in rice

first: Yong-Fang

last: Li

first: Yun

last: Zheng

first: Charles

last: Addo-Quaye

first: Li

last: Zhang

first: Ajay

last: Saini

first: Guru

last: Jagadeeswaran

first: Michael

last: Axtell

first: Weixiong


title: Identification of Genes Preferentially Required for Growth of p53-Deficient Human Cancer Cells

city: Worcester

middle: R.

last: Green

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary:
We describe a synthetic interaction screen to identify genes preferentially required for proliferation of p53-deficient human cancer cells.  An isogenic pair of p53+/+ and p53-/- human colorectal HCT116 cell lines was stably transduced with a short hairpin RNA (shRNA) library encoded by lentiviruses that integrate in the genomic DNA of the host.  Comparison of the frequency of  each  type of integrated lentivirus in the 2 cell types at an early time point (40hrs) and after about 12 mitotic cycles (10days), reveals genes whose knockdown preferentially impaired growth of p53-/- or p53+/+ HCT116 cells.

Keywords: Functional Genomics

overall_design: The region of the integrated lentiviruses is  PCR amplified from  genomic DNA of the two  transduced cell populations at an early and a late time point.

last: Xie

first: Claude

last: Gazin

first: Lihua

middle: J

last: Zhu

first: Marie-anne

last: Debily

first: Ellen

middle: L

last: Kittler

first: Maria

last: Zapp

first: David

last: Lapointe

first: Stephane

last: Gobeil

first: Ching-Man

last: Virbasius

middle: R


title: Effect of s100b on lan5 cells

status: Public on May 31 2010

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

country: Italy

institute: UCSC

summary: The human neuroblastoma cell line Lan5 cells were cultured in complete DMEM till 80% confluence, then placed at 60000 cells per squared cm. Cells were then plated in 24-well plates for cell viability assay and in T75 flasks for RNA isolation. Medium was replaced with serum-free fresh medium for 12 hours prior to s100b treatment. Gene expression patterns were then analysed using the Human Focus Genechip array.

overall_design:
In this study we analyze gene expression patterns in Lan5 cells treated with s100b protein. We utilized control cells (untreated) and two different concentrations (0.5 nM and 5 uM) of s100b.
We used three biological replicates, for the three concentration tested, according to MIAME guidelines (total 9 chips were used in this study).

first: Camilla

last: Bernardini

first: Wanda

last: Lattanzi


title: mRNA-seq with Agnostic Splice Site Discovery for CNS Transcriptomics Tested in Chronic Pain

status: Public on May 02 2010

city: Wildau

first: Peter

last: Beyerlein

state: Brandenburg

address: Bahnhofstraße 1

department: Bioinformatics

institute: Technische Hochschule Wildau

summary: The study pursued dual goals: To advance mRNA-seq bioinformatics towards unbiased transcriptome capture and to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We found that 12.4% of known genes were induced and 7% were suppressed in the dysfunctional (but anatomically intact) L4 dorsal root ganglion (DRG) 2 weeks after L5 spinal Nerve Ligation (SNL). A new algorithm for agnostic mapping of pre-mRNA splice junctions (SJ) achieved a precision of 97%.

overall_design:
mRNA-seq of L4 DRG 2 weeks and 2 months after L5 spinal nerve ligation.

CONTROL and SNL were used to identify differential gene expression between chronic pain and standard conditions in Rattus norvegicus.

CONTROL and SNL and PILOT were used to perform 'agnostic splice site discovery' in the nervous system transcriptome in Rattus norvegicus

first: Paul

last: Hammer

first: Michaela

middle: S

last: Banck

first: Ronny

last: Amberg

first: Cheng

last: Wang

first: Gabriele

last: Petznick

first: Shujun

last: Luo

first: Irina

last: Khrebtukova

first: Gary

middle: P

last: Schroth

first: Andreas

last: Beutler


title: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

status: Public on Apr 29 2010

first: Markus

last: Hafner


title: The effect of bound RSC/nucleosome complex on chromatin architecture and gene expression at the GAL genes of yeast

city: Cold Spring Harbor

first: Jude

last: Kendall

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: How is chromatin architecture established and what role does it play in activation of transcription?  We show that a regulatory locus in yeast (the UASg) bears, in addition to binding sites for the activator Gal4, sites bound by the protein RSC.  RSC tightly positions a nucleosome, evidently partially unwound, in a structure that facilitates Gal4 binding to its sites.  The complex comprises a barrier that suffices to impose characteristic features of chromatin architecture.  Removal of RSC allows ordinary nucleosomes to form more broadly over the UASg, and these nucleosomes compete with (but do not exclude) Gal4 binding to its sites.  Taken with our previous work, the results show that both prior to and following induction specific DNA binding proteins are the predominant determinants of chromatin architecture at the GAL1/10 genes. RSC/nucleosome complexes are found scattered throughout the yeast genome.  We surmise, also, that Gal4 works in higher eukaryotes despite whatever obstacle broadly positioned nucleosomes present.

overall_design: Chromatin was digested under conditions that yielded primarily mononucleosomes, and RSC-bearing fragments were recovered on IgG-beads.  Fragments (of size ca. 50-200 bp) were analyzed by paired-end high throughput DNA sequencing (Illumina).  This technique determines the sequences found at both ends of each fragment, thus revealing the sizes and genomic origin of these fragments.

first: Monique

last: Floer

first: Xin

first: Vidya

last: Prabhu

first: Georgina

last: Berrozpe

first: Santosh

last: Narayan

first: Dan

last: Spagna

first: David

last: Alvarez

first: Alexander

last: Krasnitz

first: Asya

last: Stepansky

first: James

last: Hicks

first: Gene

last: Bryant

first: Mark

last: Ptashne


title: ChIP-Seq of TBP in Mouse Embryonic Stem Cells

status: Public on Jun 15 2010

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The TATA binding protein (TBP) is a transcription factor that binds specifically to a DNA sequence called the TATA box upstream of the transcription start site. To gain insight into the genes occupied by TBP, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide binding targets.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against TBP.

first: Steve

last: Bilodeau

first: Rahl

last: Peter


title: microRNA-target RNA pairs revealed by Parallel analysis of RNA ends in Vitis vinifera

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

institute: University of East Anglia

summary: Vitis vinifera RNA degradome

overall_design: Isolated polyadenylated RNA from total RNA extracts of  Vitis vinifera leaves, were ligated to 5'-adapter that include san MmeI recognition site. The ligated products were purified again, reverse transcribed and cleaved with MmeI. The 5' fragments were purified from gel and to a 3'- dsDNA adapter and PCR amplified. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

first: Vitantonio

last: Pantaleo

first: Gyorgy

last: Szittya

first: Laura

last: Miozzi

first: Tamas

last: Dalmay

first: József

last: Burgyán


title: High-throughput sequencing of small RNAs in Vitis vinifera

summary: Vitis vinifera endogenous small RNAs

overall_design: Size fractionated small RNA from total RNA extracts of Vitis vinifera leaves, inflorescences, tendrils and small berries were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.


title: ChIP-seq of PHF8 and H3K4me3

status: Public on Apr 27 2010

city: Barcelona

first: Klaus

last: Fortschegger

address: C/ Dr. Aiguader 88

department: Gene Regulation

country: Spain

institute: Center for Genomic Regulation

summary: PHF8 is an H3K9me2 demethylase, interacts with H3K4me3 and RNA Polymerase II, is enriched at thousands of transcription start sites and can act as a transcriptional co-activator.

overall_design: ChIP-seq of PHF8 in HeLa, 293T and Hs68 cells, and of H3K4me3 in Hs68 fibroblasts was performed. Normal IgG-IP or input DNA served as negative controls.

first: Ramin

last: Shiekhattar


title: Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumors and matched controls

status: Public on Apr 28 2010

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: We prepared small RNA libraries from 29 tumor/normal pairs of human cervical tissue samples. Analysis of the resulting sequences (42 million in total) defined 64 new human microRNA (miRNA) genes. Both arms of the hairpin precursor were observed in twenty-three of the newly identified miRNA candidates. We tested several computational approaches for analysis of class differences between high throughput sequencing datasets, and describe a novel application of log linear model that has provided the most datasets, and describe a novel application of log linear model that has provided the most effective analysis for this data. This method resulted in the identification of 67 miRNAs that were differentially-expressed between the tumor and normal samples at a false discovery rate less than 0.001.

overall_design: A total of 29 tumor/normal pairs of human cervical tissue samples were analyzed. Two samples (G699N_2 and G761T_2) were performed in duplicates. No Fastq files for GSM532871 to GSM532889, GSM532929, and GSM532930. Sequence files are provided as text files for these 22 Sample records in GSE20592_RAW.tar.  38 samples with quality scores are available from SRA as SRP002/SRP002326 (see Supplementary file below).

first: Daniela

last: Witten

first: Robert

last: Tibshirani

middle: G

first: Andrew

last: Fire

first: Weng-Onn

last: Lui


title: Endogenous short RNAs in Mucor circinelloides sequenced on the Illumina platform (Solexa)

summary: We sequenced Endogenous short RNAs in Mucor circinelloides fungus grown in standard liquid culture. Short RNAs were profiled in wild type, Dicer-like 1 mutant (dcl1-), Dicer-like 2 mutant (dcl2-) and double Dicer mutant (dcl1-/dcl2-) strains. We identified many loci that produced less short RNAs in the dcl2- strain suggesting that DCL2 is the major protein generating short RNAs in Mucor circinelloides.

overall_design: Endogenous short RNAs were profiled in wild type, single and double dcl mutant strains.

first: Francisco

middle: E

last: Nicolas

first: Rosa

last: Ruiz-Vázquez


title: CpG islands recruit a histone H3 lysine 36 demethylase

city: Boston

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Mammalian microRNAs: Experimental evaluation of novel and previously annotated genes

status: Public on Apr 26 2010

first: H. Rosaria

last: Chiang

institute: MIT/Whitehad Institute

summary: MicroRNAs (miRNAs) are small regulatory RNAs that derive from distinctive hairpin transcripts. To learn more about the miRNAs of mammals, we sequenced 60 million small RNAs from mouse brain, ovary, testes, embryonic stem cells, three embryonic stages, and whole newborns. Analysis of these sequences confirmed 387 annotated miRNA genes and identified 110 novel miRNA genes. Over 150 previously annotated miRNAs and hundreds of candidates failed to yield sequenced RNAs with miRNA-like features. Ectopically expressing these previously proposed miRNA hairpins also did not yield small RNAs, whereas ectopically expressing the confirmed and newly identified hairpins usually did yield small RNAs with the classical miRNA features, including dependence on the Drosha endonuclease for processing. These experiments, which suggest that previous estimates of conserved mammalian miRNAs were inflated, provide a substantially revised list of confidently identified mammalian miRNAs from which to infer the general features of mammalian miRNAs. Our analyses also revealed new aspects of miRNA biogenesis and modification, including tissue-specific strand preferences, sequential Dicer cleavage of a metazoan pre-miRNA, newly identified instances of miRNA editing, and evidence for widespread Lin28-like miRNA regulation.

overall_design: For miRNA discovery, small RNAs were sequenced from mouse brain, ovary, testes, three embryonic stages, and whole newborns; for ectopic over-expression assays, pre-miRNA hairpins and the surrounding regions were transfected into HEK293T, and the small RNA were sequenced from the transfected cells 39-48 hours after transfection.

first: H

first: Lori

middle: W

last: Schoenfeld

first: J

last: Ruby

first: Vincent

last: Auyeung

first: Noah

last: Spies

first: Daehyun

last: Baek

first: Wendy

middle: K

last: Johnston

first: Carsten

last: Russ

first: Shujun

last: Luo

first: Joshua

last: Babiarz

last: Blelloch

first: Gary

last: Schroth

first: Chad

last: Nusbaum

first: David

last: Bartel


title: PHF8 targets histone methylation and RNA polymerase II to activate transcription

first: Klaus

last: Fortschegger

summary:
Mutations in PHF8 are associated with X-linked mental retardationand cleft lip/cleft palate. PHF8 contains a plant homeodomain(PHD) in its N-terminus and is member of a family of JmjC-domaincontaining proteins. While PHDs can act as methyl lysine recognitionmotifs, JmjC-domains can catalyze lysine demethylation. Here,we show that PHF8 is a histone demethylase that removes repressivehistone H3 dimethyl lysine 9 marks. Our biochemical analysisrevealed specific association of the PHF8 PHD domain with histoneH3 trimethylated at lysine 4 (H3K4me3). Chromatin-immunoprecipitationfollowed by high throughput sequencing indicated that PHF8 isenriched at transcription start sites of many active or poisedgenes, mirroring the presence of RNA polymerase II (RNAPII)and of H3K4me3-bearing nucleosomes. We show that PHF8 can actas a transcriptional co-activator and its activation functionlargely depends on binding of the PHD to H3K4me3. Furthermore,we present evidence for  direct interaction of PHF8 with theC-terminal domain of RNAPII. Importantly, a PHF8 disease mutantis defective in demethylation and in co-activation. This isthe first demonstration of a chromatin-modifying enzyme whichis globally recruited to promoters through its association withH3K4me3 and RNAPII.

This SuperSeries is composed of the SubSeries listed below.

first: Ramin

last: Shiekhattar


title: Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes

status: Public on Apr 25 2010

city: Cincinnati

first: Iouri

last: Chepelev

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center


title: Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq

summary: Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understanding of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously. To gain a better understanding of cellular differentiation in gonads, we analyzed mRNA profiles from Drosophila testes and ovaries using RNA-seq. We identified a set of genes that have sex-specific isoforms in wild-type (WT) gonads, including several transcription factors. We found that differentiation of sperms from undifferentiated germ cells induced a dramatic downregulation of RNA splicing factors. Our data confirmed that RNA splicing events are significantly more frequent in the undifferentiated cell-enriched bag of marbles (bam) mutant testis, but downregulated upon differentiation in WT testis. Consistent with this, we showed that genes required for meiosis and terminal differentiation in WT testis were mainly regulated at the transcriptional level, but not by alternative splicing. Unexpectedly, we observed an increase in expression of all families of chromatin remodeling factors and histone modifying enzymes in the undifferentiated cell-enriched bam testis. More interestingly, chromatin regulators and histone modifying enzymes with opposite enzymatic activities are coenriched in undifferentiated cells in testis, suggesting that these cells may possess dynamic chromatin architecture. Finally, our data revealed many new features of the Drosophila gonadal transcriptomes, and will lead to a more comprehensive understanding of how differential gene expression and splicing regulate gametogenesis in Drosophila. Our data provided a foundation for the systematic study of gene expression and alternative splicing in many interesting areas of germ cell biology in Drosophila, such as the molecular basis for sexual dimorphism and the regulation of the proliferation vs terminal differentiation programs in germline stem cell lineages.

overall_design: RNA-Seq experiments for four Drosophila melanogaster samples: (1) bam mutant testes, (2) wild-type testes, (3) bam mutant ovaries, (4) wild-type ovaries

first: Qiang

last: Gan

first: Gang

last: Wei

first: Lama

last: Tarayrah

first: Kairong

last: Cui

first: Keji

last: Zhao

first: Xin

last: Chen


title: Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (II)

summary: Epigenetic control is an important aspect of gene regulation.  Despite detailed understanding of many examples, the transcription of non-coding RNA genes by RNA polymerase (pol) III is less well characterized.  Here we profile the epigenetic features of pol III target genes  throughout the human genome.  This reveals that the chromatin landscape of pol III-transcribed genes resembles that of pol II templates in many ways, although there are also clear differences.  Our analysis also discovered an entirely unexpected phenomenon, namely that pol II co-localizes with the majority of genomic loci that are bound by pol III.

overall_design: RNA-seq experiment for total RNA in CD4+ cells.

first: Artem

last: Barski

first: Joanna

last: Birch

first: Suresh

last: Cuddapah

first: Alastair

last: Fleming

first: Dritan

last: Liko

first: Robert

last: White


title: Genome-wide mapping of Nuclear Factor I binding sites using ChIP-Seq in WT and NFI-C knock-out MEFs

status: Public on Apr 24 2010

city: Lausanne

first: Milos

last: Pjanic

state: VD

address: EPFL CH B1 426 Station 6

department: Institute of Biotechnology

institute: Faculty of Biology and Medicine, University of Lausanne

summary:
The Nuclear Factor I (NFI) family of DNA binding proteins (also called CAAT box transcription factors or CTF) is involved both in replication of adenoviral DNA and in regulation of gene expression. Using chromatin immuno-precipitation and high throughput sequencing (method termed ChIP-Seq) we performed genome-wide mapping of Nuclear Factor I DNA binding sites in mouse embryonic fibroblasts. We found that in vivo and in vitro NFI binding specificities are identical, since previously established position weight matrix was found to accurately predict binding sites for NFI group of proteins. Positional correlation between + and - strand ChIP-Seq tags revealed that NFI is a nucleosome-binding protein, unlike some other transcription factors. We further found that NFI binding correlates with the specific histone modification H3K4me3, the marker of transcribed promoters. Combining ChIP-Seq with the microarray expression data, we found that NFI associates with promoters with higher transcription level. We estimate that transcribed promoters may be more accessible to transcription factor binding than their nearby regions since NFI preferentially bind their DNA target sites located around transcription start sites. Knocking-out one of the NFI proteins (NFI-C), reduced the occupancy of predicted sites, however at the same time indicating that cells could compensate the missing protein with the other members of the family.

Keywords: ChIP-Seq (chromatin immunoprecipitation and high throughput sequencing)

overall_design: ChIP-Seq (chromatin immunoprecipitation and high throughput sequencing) using antibody against NFI family of transcription factors in two cell types (wild type and NFI-C knock-out mouse embryonic fibroblasts MEFs)

first: Christoph

last: Schmid

first: Giovanna

last: Ambrosini

first: Philipp

last: Bucher

first: Nicolas

last: Mermod


title: Arabidopsis thaliana and Arabidopsis lyrata degradomes

status: Public on Apr 22 2010

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

institute: Pennsylvania State University

summary: Deep sequencing of the 5' ends of uncapped, polyA-enriched mRNA from two biological replicate samples from Arabidopsis thaliana inflorescences, as well as two biological replicates of Arabidopsis lyrata inflorescences.  These data were used to experimentally identify sliced microRNA targets from the two species.

overall_design: Two biological replicate samples of the 5' ends of uncapped, polyA+ RNAs from both A. thaliana and A. lyrata

first: Zhaorong

last: Ma

first: Ceyda

last: Coruh


title: Chromatin and Sequence Features that Define the Fine and Gross Structure of Genomics Methylation Patterns

status: Public on Apr 16 2010

first: John

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

summary: We report a new method for genome-wide methylation profiling that is able to probe methylation status in both single-copy DNA and interspersed repeats.  This method, MethylMAPS, uses methylation-sensitive and -dependent enzymes to fractionate the genome according to methylation state.  Methylated and unmethylated fragments are then sequenced with Next-Gen sequencing to map methylated and unmethylated CpG sites in the genome. We have used this method to determine the methylation status of >275 million CpG sites in human and mouse DNA from breast and brain tissues. We conclude that methylation is the default state of most CpG dinucleotides and that a combination of local dinucleotide frequencies, the interaction of repeated sequences, and the presence or absence of histone variants or modifications shields a population of CpG sites (most of which are in and around promoters) from DNA methyltransferases that lack intrinsic sequence specificity.

overall_design: Genome-wide methylation mapping in two normal human breast tissues, human brain tissue and mouse brain tissue.

first: Timothy

middle: H

last: Bestor


title: Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (I)

first: Iouri

last: Chepelev

overall_design: Chip-Seq experiments for six samples: Pol III, TFIIIB, TFIIIC, H3K4me3 in HeLa cells and Pol III, S2 phos Pol II in CD4+ cells.

first: Kairong

last: Cui

first: Keji

last: Zhao