Genome-wide identification of DNA-protein interaction to reconstruct bacterial transcription regulatory network

Abstract

The development and innovative use of next-generation sequencing technologies have opened the doors for genetic and epigenetic research at the next level. These technologies can be used to study gene expression regulation at the transcriptional and post-transcriptional levels in both prokaryotic and eukaryotic systems. In this review, we focused on the various tools and techniques for DNA-binding proteins such as RNA polymerase, sigma factors, nucleoid-associated proteins, and transcription factors in bacteria. Descriptions on series of Chromatin ImmunoPrecipitation (ChIP) technologies, including ChIP followed by microarray hybridization (ChIP-chip), ChIP followed by deep sequencing (ChIP-seq), and ChIP with exonuclease digestion and deep sequencing (ChIP-exo) has been given. Furthermore, recent investigations on transcriptional regulatory networks of a wide range of bacteria with ChIP technologies are discussed for the model bacteria Escherichia coli followed by pathogenic and other non-pathogenic bacteria. In conclusion, ChIP technologies have proven effective and efficient to reconstruct and to delineate transcriptional regulatory network in a variety of bacteria.