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.

下一代测序技术的开发和创新使用为下一阶段的遗传和表观遗传学研究打开了大门。这些技术可用于在原核和真核系统中研究转录和转录后水平的基因表达调控。在这篇综述中，我们专注于DNA结合蛋白的各种工具和技术，例如细菌中的RNA聚合酶，σ因子，与核苷酸相关的蛋白和转录因子。已经给出了关于染色质免疫沉淀（ChIP）系列技术的说明，包括ChIP随后进行微阵列杂交（ChIP-chip），ChIP之后进行深度测序（ChIP-seq）以及具有核酸外切酶消化和深度测序的ChIP（ChIP-exo）。 。此外，大肠杆菌，其次是病原性细菌和其他非病原性细菌。总之，ChIP技术已被证明在多种细菌中重建和描绘转录调控网络的有效方法。