Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors英文文献.pdfVIP

Chapter 11 Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors Kenzie D. MacIsaac and Ernest Fraenkel Abstract Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome. Subsequent analysis of the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experi- ments without sequence analysis and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we review the tools, workflow, and common pitfalls of such anal- yses and recommend strategies for effective motif discovery from these data. Key words: Motif discovery, sequence motifs, chromatin immunoprecipitation, ChIP-seq, ChIP-chip, transcriptional regulation. 1. Introduction The regulatory programs enacted by transcription factors in response to developmental or environmental cues depend on spe- cific interactions between these proteins and the genes whose expression they regulate. This specificity is provided, in large part, by short DNA sequences that are recognized and bound by tran- scription factors, thereby localizing them to their targets (1). In general, different transcription factors recognize different bind- ing sites. The varying sequence specificities of these regulators and the genomic location of the sites they bind form a regulatory code whose decipherment has been an important area of researc