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Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network

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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.

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Acknowledgements

This work was funded by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded from the Ministry of Education (NRF-2017R1C1B2002441), from the Strategic Initiative for Microbiomes in Agriculture and Food, MAFRA, Republic of Korea as part of the (multi-ministerial) Genome Technology to Business Translation Program (918020-4).

The authors declare no conflict of interest.

Neither ethical approval nor informed consent was required for this study.

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  1. Schools of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea

    Joon Young Park, Hemraj Rimal, Ina Bang, Linh Khanh Nong & Donghyuk Kim

  2. Schools of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea

    Donghyuk Kim

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Park, J.Y., Rimal, H., Bang, I. et al. Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network. Biotechnol Bioproc E 25, 944–954 (2020). https://doi.org/10.1007/s12257-020-0030-9

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