Biotechnology and Bioprocess Engineering 2020; 25(6): 944-954  
Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network
Joon Young Park, Hemraj Rimal, Ina Bang, Linh Khanh Nong, and Donghyuk Kim
Joon Young Park, Hemraj Rimal, Ina Bang, Linh Khanh Nong, Donghyuk Kim*
Schools of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
Tel: +82-52-217-2945
E-mail: dkim@unist.ac.kr
Donghyuk Kim
Schools of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
These authors contributed equally.
Received: January 29, 2020; Revised: April 6, 2020; Accepted: April 8, 2020; Published online: December 31, 2020.
© The Korean Society for Biotechnology and Bioengineering. All rights reserved.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
The development and innovative use of nextgeneration 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, nucleoidassociated 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.
Keywords: transcription regulation, ChIP-chip, ChIP-seq, ChIP-exo, DNA-binding protein, binding site, genome-wide identification


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