## Description

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 and chromatin modification profiles in many mouse (C57Bl/6) tissues and primary cells, including bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, mouse embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells.

In specific, the Ren lab examined RNA polymerase II (PolII), co-activator protein p300, the insulator protein CTCF, and two chromatin modification marks, H3K4me3 and H3K4me1, due to their demonstrated utilities in identifying promoters, enhancers and insulator elements (Barski et al., 2007; Blow et al., 2010; Heintzman et al., 2009; Kim et al., 2007; Kim et al., 2005a; Visel et al., 2009). Enrichment of H3K4me3 or PolII signals is a strong indicator of an active promoter, while the presence of p300 or H3K4me1 outside of promoter regions has been used as a mark for enhancers. CTCF binding sites are considered as a mark for potential insulator elements. 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 monoclonal, uniquely mapped tags.

## Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. This track contains the following views:

Peaks
  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 the point with the highest signal).
Signal
  Density graph (wiggle) of signal enrichment based on processed data.

## Methods

Cells were grown according to the approved ENCODE cell culture protocols.

Enrichment and Library Preparation
Chromatin immunoprecipitation was performed according to Ren Lab ChIP Protocol.

Library construction was performed according to 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 mm9 were performed using Illumina's RTA and Genome Analyzer Pipeline software. Alignment to the mouse genome was performed using ELAND or Bowtie (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.

## Credits

These data were generated and analyzed in Bing Ren's laboratory at the Ludwig Institute for Cancer Research.

Contact: Yin Shen

## References

Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. High-resolution profiling of histone methylations in the human genome. Cell 2007 May; 129(4): 823-837.

Blow, M.J., McCulley, D.J., Li, Z., Zhang, T., Akiyama, J.A., 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): 806-810.

Heintzman, N.D., Hon, G.C., Hawkins, R.D., Kheradpour, P., Stark, A., Harp, L.F., Ye, Z., Lee, L.K., Stuart, R.K., Ching, C.W., et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009 May; 459(7243): 108-112.

Kim, T.H., Abdullaev, Z.K., Smith, A.D., Ching, K.A., Loukinov, D.I., Green, R.D., Zhang, M.Q., Lobanenkov, V.V., and Ren, B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007 March; 128(6): 1231-1245.

Kim, T.H., Barrera, L.O., Qu, C., Van Calcar, S., Trinklein, N.D., Cooper, S.J., Luna, R.M., Glass, C.K., Rosenfeld, M.G., Myers, R.M., et al. Direct isolation and identification of promoters in the human genome. Genome Res 2005 June; 15(6): 830-839.

Langmead, B., Trapnell, C., Pop, M., and Salzberg, SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009 Mar; 10(3): R25.

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): 651-657.

Visel, A., Blow, M.J., Li, Z., Zhang, T., Akiyama, J.A., 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; 457(7231): 854-858.

## Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.