Bacterial Systems Biology: Genome, Transcriptome, Translatome, and Interactome

Friday, January 8, 2016 -
2:00pm to 3:00pm
Fung Auditorium | Powell-Focht Bioengineering Hall
Byung-Kwan Cho

Assistant Professor
Department of Biological Sciences
Korea Advanced Institute of Science and Technology

Bacterial Systems Biology: Genome, Transcriptome, Translatome, and Interactome


Over the past decade or so, dramatic developments in our ability to experimentally determine the contents and functions of genomes have taken place. In particular, high-throughput sequencing technologies are now inspiring a new understanding of the bacterial genome on a global scale. Bacterial genomes are organized by structural and functional elements, including promoters, transcription start and termination sites, open reading frames, regulatory noncoding regions, untranslated regions and transcription units. Thus, identification of those genomic elements is prerequisite for understanding the complete regulatory network of a bacterial cell. Here, we show the architecture of bacterial genome and gene expression patterns at transcriptional and translational level along with different developmental phases, by integrating genome-wide data of transcription start sites (TSSs), mRNA abundance and ribosome-protected mRNA fragment (RPF) abundance. Also, we disclosed the dynamics of transcription using ChIP-exo data with extremely high resolution of single base, together with ChIP-seq and RNA-seq data. The mobility of RNAP holoenzyme at transcription initiation was elucidated through genome-scale scanning for association of RNAP and sigma factor with genome. Thus, we offer comprehensive information on genome architecture, and transcriptional and translational gene expression patterns that allows better understanding of bacterial cells.


Byung-Kwan Cho is an assistant professor at the department of biological sciences of Korea Advanced Institute of Science and Technology (KAIST) since 2010, Korea. Before joining the KAIST, he has been a project scientist in the Palsson lab at the department of bioengineering of University of California San Diego. He completed his Ph.D. in the molecular biotechnology and biomaterials laboratory at the Seoul National University, Korea. His research has focused on the systems and synthetic biology of microorganisms, in particular he has contributed upon the understanding of transcriptional and translational regulatory networks at a genome-scale using high-throughput technologies. He is highly interested in the determination of bacterial metastructure, which consists of numerous cis- and trans-genetic elements such as transcription start sites, promoters, ribosome-binding sites, and non-coding RNAs. As of January 2016, he has published 70 scientific papers and gave about 300 presentations at the international conferences. He has appointed as a young scientist from World Economic Forum (WEF) 2012 and Korea Academy of Science and Technology (KAST) 2013.