title: ChIP-Seq and the complexity of bacterial transcriptional regulation.
abstract: Transcription factors (TFs) play a central role in regulating gene expression in all bacteria. Yet, until recently, studies of TF binding were limited to a small number of factors at a few genomic locations. Chromatin immunoprecipitation followed by sequencing enables mapping of binding sites for TFs in a global and high-throughput fashion. The NIAID funded TB systems biology project                  http://www.broadinstitute.org/annotation/tbsysbio/home.html                                 aims to map the binding sites for every transcription factor in the genome of Mycobacterium tuberculosis (MTB), the causative agent of human TB. ChIP-Seq data already released through TBDB.org have provided new insight into the mechanisms of TB pathogenesis. But in addition, data from MTB are beginning to challenge many simplifying assumptions associated with gene regulation in all bacteria. In this chapter, we review the global aspects of TF binding in MTB and discuss the implications of these data for our understanding of bacterial gene regulation. We begin by reviewing the canonical model of bacterial transcriptional regulation using the lac operon as the standard paradigm. We then review the use of ChIP-Seq to map the binding sites of DNA-binding proteins and the application of this method to mapping TF binding sites in MTB. Finally, we discuss two aspects of the binding discovered by ChIP-Seq that were unexpected given the canonical model: the substantial binding outside the proximal promoter region and the large number of weak binding sites.
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA. jgalag@broadinstitute.org
authors.forename: James
authors.initials: J
authors.lastname: Galagan
authors.forename: Anna
authors.initials: A
authors.lastname: Lyubetskaya
authors.forename: Antonio
authors.initials: A
authors.lastname: Gomes
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D015964:Gene Expression Regulation, Bacterial; D007763:Lac Operon; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D017421:Sequence Analysis; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors