## Description

ChIP-seq is a new approach for investigating entire transcription factor-DNA interactomes. ChIP-seq is comprised of chromatin immunoprecipitation (ChIP) followed by single-molecule-based sequencing (seq). ChIP-seq avoids the complications of array hybridization.

This track shows 25mer sequence reads obtained via a ChIP-seq protocol from samples enriched for a variety of transcription factors and a companion control sample of the same fixed chromatin without immuno-enrichment. These sequence reads were later analyzed using a peak locator to identify transcription factor positive binding events.

## Methods

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Libraries were prepared from the ChIP DNA using the ligation mediated PCR Solexa protocol. The Solexa library construction protocol was modified to include a PCR preamplification following linker ligation and preceding gel electrophoresis. Reducing the size and narrowing the size range of DNAs collected from gel purification is intended to improve positional resolution of ChIP-seq. Reads which mapped to multiple genomic locations are not included. Up to two mismatches were allowed.

## Credits

Myers Group: David Johnson, Betsy Anton, Loan Nguyen, Cat Medina, Richard Myers.

Wold Group: Barbara Wold, Ali Mortazavi, Kenneth McCue.

Solexa/Illumina Sequencing: Gary Schroth.

## References

Fields S. Site-Seeing by Sequencing. Science 2007 June;316:1441-1442.

Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-Wide Mapping of in Vivo Protein-DNA Interactions. Science 2007 June;316:1497-1502.

Mortazavi A, Thompson EC, Garcia ST, Myers RM, Wold B. Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Res. 2006 Oct;16(10):1208-21.

Schoenherr CJ, Paquette AJ, Anderson DJ. Identification of potential target genes for the neuron-restrictive silencer factor. Proc. Natl. Acad. Sci.1996;93:9881-9886.

## Related Work

Mikkelsen TS et.al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 5 July 2007; 448(7149).