Modeling the integration of bacterial rRNA fragments into the human cancer genome

BMC Bioinformatics

Research Article

Karsten B. Sieber¹  Pawel Gajer²  Julie C. Dunning Hotopp³ 

[1] Institute for Genome Science, University of Maryland School of Medicine, 21201, Baltimore, MD, USA;Institute for Genome Science, University of Maryland School of Medicine, 21201, Baltimore, MD, USA;Department of Microbiology and Immunology, University of Maryland School of Medicine, 21201, Baltimore, MD, USA;Institute for Genome Science, University of Maryland School of Medicine, 21201, Baltimore, MD, USA;Department of Microbiology and Immunology, University of Maryland School of Medicine, 21201, Baltimore, MD, USA;Greenebaum Cancer Center, University of Maryland School of Medicine, 21201, Baltimore, MD, USA;

关键词: DNA integration;    Somatic genome;    Genome variation;    Cancer genomics;    Host-bacteria interactions;   

DOI  :  10.1186/s12859-016-0982-0

 received in 2015-08-25, accepted in 2016-03-09,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundCancer is a disease driven by the accumulation of genomic alterations, including the integration of exogenous DNA into the human somatic genome. We previously identified in silico evidence of DNA fragments from a Pseudomonas-like bacteria integrating into the 5′-UTR of four proto-oncogenes in stomach cancer sequencing data. The functional and biological consequences of these bacterial DNA integrations remain unknown.ResultsModeling of these integrations suggests that the previously identified sequences cover most of the sequence flanking the junction between the bacterial and human DNA. Further examination of these reads reveals that these integrations are rich in guanine nucleotides and the integrated bacterial DNA may have complex transcript secondary structures.ConclusionsThe models presented here lay the foundation for future experiments to test if bacterial DNA integrations alter the transcription of the human genes.

【 授权许可】

CC BY   
© Sieber et al. 2016

【 图 表 】

Fig. 6