Computational Biology Branch (CBB) is the research branch of the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH).

We hold weekly seminars by CBB members each Tuesday at 11 AM in the Building 38A B2 NCBI Library. Visitors' presentations usually take place in the same room, but are scheduled on a different day of the week. If scheduling a visitor's presentation, please don't forget to book a seminar room.

To schedule a seminar, please click on the appropriate date in the calendar.

Contact Ivan Ovcharenko with questions or if you need help in scheduling a seminar.

About CBB

Genome-wide Regulatory Roles of Non-B DNA Structure in Escherichia coli
“Usually DNA exists as standard right-handed B form, which is double helix with Watson-Crick base pairing. But several other non-B DNA structures can also be formed and sequence signatures compatible with formation of such alternative structures are abundant in all species. Non-B DNA structures include tetraplexes (G-quadruplex), left-handed Z-DNA (Z-DNA), stress-induced DNA duplex destabilization (SIDD), cruciform (Cruciform), triplex (H-DNA) and slipped structure (S-DNA). Most of those non-B DNA structures are postulated to be formed in part during transcription or protein binding, and play important roles in regulation. Otherwise, the non-B DNA structures are believed to be involved in genetic instability and thus strongly associated with human diseases. Currently, with few notable exceptions, most evidences regarding the roles of non-B DNA structures are computational and indirect. Such analyses are mainly in eukaryote, and typically look for enrichment of characteristic sequence signatures in regulatory regions based on individual genes. In prokaryote, functionally related genes are grouped as operon and transcribed together, which gives us a unique opportunity to test the hypothesis about regulatory roles of non-B DNA structures: if they paly a role in regulation, the distribution of such structures should be different in regulatory regions of the operon as compared to the middle genes of the operon. In this study, for the first time, we sought to systematically investigate the regulatory roles of non-B DNA structures in E. coli based on operon. We found that there is indeed a significant enrichment (SIDD, Cruciform, H-DNA and S-DNA) or avoidance (G-quadruplex and Z-DNA) of non-B DNA structures in the promoter region of operon compared to the upstream region of middle genes. Additionally, we found that, after correction for Rho-independent terminator, cruciform is still highly enriched in downstream of operon compared to middle genes. Also, non-B DNA structures are enriched in intergenic regions separating either divergently oriented operons (SIDD, H-DNA and S-DNA) or convergent oriented operons (Cruciform). Above all, all the results are consistent with the hypothesis that non-B DNA structures play important regulatory roles in the activity of operon. The enrichment of cruciform downstream even after correction for standard Rho-independent terminator indicates that role of cruciform in regulation of termination has been underappreciated in E. coli.“

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