This track shows a comprehensive survey of cis-regulatory elements
in the mouse genome by using ChIP-seq (Robertson et al., 2007) to identify
transcription factor binding sites (TFBS) and chromatin modification
profiles in various mouse (C57BL/6) tissues, primary cells, and cell lines.
The Ren lab examined RNA polymerase II (PolII),
co-activator protein p300, the insulator protein CTCF, and
the following chromatin modification marks: H3K4me3 and H3K4me1,
H3K27ac, H3K36me3, H3K9me3, and H3K27me3 due to their
demonstrated utilities in identifying promoters, enhancers,
insulator elements, actively transcribed gene bodies, and
silent chromatin regions (Barski et al., 2007; Bernstein et al., 2006; Blow et al., 2010;
Creyghton et al., 2010; Francis et al., 2004; Hawkins et al., 2011; Heintzman et al., 2009; Kim et al., 2007; Kim et al., 2005; Krogan et al., 2003; Li et al., 2002; Peters et al., 2001; Rada-Iglesias et al., 2011; Schotta et al., 2002; Visel et al., 2009).
Enrichment of PolII signals is a strong indicator of
an active promoter and the presence of p300 outside of
promoter regions has been used as a mark for enhancers.
CTCF binding sites are considered as a mark for
potential insulator elements. H3K4me3 is an active mark
for promoters and H3K27ac is an active mark for both promoters
and enhancers. In the absence of H3K4me3, H3K4me1 serves as an
active mark for enhancers. H3K36me3 is normally found in actively
transcribed gene bodies whereas both H3K9me3 and H3K27me3 are common
repressive marks for transcriptionally silent chromatin regions.
For each transcription factor or chromatin mark in each tissue,
ChIP-seq was carried out with at least two biological
replicates. Each experiment produced 20-30 million uniquely-mapped monoclonal tags.
Display Conventions and Configuration
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- Regions of signal enrichment based on processed data
(normalized data from pooled replicates). Intensity is represented in
grayscale; darker shading shows higher intensity (a solid vertical line
in the peak region represents the point with the highest signal).
- Density graph (wiggle) of signal enrichment based on
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Cells were grown according to the approved
ENCODE cell culture protocols.
Enrichment and Library Preparation
Chromatin immunoprecipitation was performed according to the Ren Lab ChIP Protocol.
Library construction was performed according to the Ren Lab Library Protocol.
Sequencing and Analysis
Samples were sequenced on Illumina Genome Analyzer II,
Genome Analyzer IIx and HiSeq 2000 platforms
for 36 cycles. Image analysis, base calling and
alignment to the mouse genome version NCBI37/mm9 were performed
using Illumina's RTA and Genome Analyzer Pipeline software.
Alignment to the mouse genome was performed using ELAND or
(Langmead et al., 2009) with
a seed length of 25 and allowing up to two mismatches.
Only the sequences that mapped to one location were used
for further analysis. Of those sequences, clonal reads,
defined as having the same start position on the same
strand, were discarded. BED and wig files were
created using custom perl scripts.
This is Release 3 (August 2012). It contains a total of 58 ChIP-seq experiments on transcription factor binding. In this release, four controls (inputs) were dropped because they did not have accompanying TFBS experiments.
An error surrounding the metadata designation of replicates of the fastq and alignment files of Kidney PolII datasets has been fixed.
These data were generated and analyzed in
Bing Ren's laboratory
at the Ludwig Institute for Cancer Research (LICR).
Contact: Yin Shen
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K.
High-resolution profiling of histone methylations in the human genome.
Cell. 2007 May 18;129(4):823-37.
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K et al.
A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Cell. 2006 Apr 21;125(2):315-26.
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F et al.
ChIP-Seq identification of weakly conserved heart enhancers.
Nat Genet. 2010 Sep;42(9):806-10.
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA et al.
Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6.
Francis NJ, Kingston RE, Woodcock CL.
Chromatin compaction by a polycomb group protein complex.
Science. 2004 Nov 26;306(5701):1574-7.
Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z et al.
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.
Cell Res. 2011 Oct;21(10):1393-409.
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW et al.
Histone modifications at human enhancers reflect global cell-type-specific gene expression.
Nature. 2009 May 7;459(7243):108-12.
Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B.
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.
Cell. 2007 Mar 23;128(6):1231-45.
Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM et al.
Direct isolation and identification of promoters in the human genome.
Genome Res. 2005 Jun;15(6):830-9.
Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C et al.
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.
Mol Cell Biol. 2003 Jun;23(12):4207-18.
Langmead B, Trapnell C, Pop M, Salzberg SL.
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biol. 2009;10(3):R25.
Li J, Moazed D, Gygi SP.
Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation.
J Biol Chem. 2002 Dec 20;277(51):49383-8.
Peters AH, O'Carroll D, Scherthan H, Mechtler K, Sauer S, Schöfer C, Weipoltshammer K, Pagani M, Lachner M, Kohlmaier A et al.
Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability.
Cell. 2001 Nov 2;107(3):323-37.
Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J.
A unique chromatin signature uncovers early developmental enhancers in humans.
Nature. 2011 Feb 10;470(7333):279-83.
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A et al.
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
Nat Methods. 2007 Aug;4(8):651-7.
Schotta G, Ebert A, Krauss V, Fischer A, Hoffmann J, Rea S, Jenuwein T, Dorn R, Reuter G.
Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing.
EMBO J. 2002 Mar 1;21(5):1121-31.
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F et al.
ChIP-seq accurately predicts tissue-specific activity of enhancers.
Nature. 2009 Feb 12;457(7231):854-8.
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