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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics, Breeding, and Animal Health Research » Research » Publications at this Location » Publication #314915

Research Project: Genetic and Biological Determinants Of Respiratory Diseases Of Ruminants

Location: Genetics, Breeding, and Animal Health Research

Title: Joint analysis of bacterial DNA methylation, predicted promoter and regulation motifs for biological significance

Author
item Harhay, Gregory
item Anton, Brian - New England Biolabs
item Smith, Timothy - Tim

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/26/2015
Publication Date: 6/1/2015
Citation: Harhay, G.P., Anton, B.P., Smith, T.P.L. [abstract]. 2015. Joint analysis of bacterial DNA methylation, predicted promoter and regulation motifs for biological significance. American Society for Microbiology 2015, 115th General Meeting, May 30-June 2, 2015, New Orleans, LA. Poster #3468.

Interpretive Summary:

Technical Abstract: Advances in long-read, single molecule real-time sequencing technology and analysis software over the last two years has enabled the efficient production of closed bacterial genome sequences. However, consistent annotation of these genomes has lagged behind the ability to create them, while the availability of closed genomes support analyses that were not previously possible and have yet to be fully developed. For example, the kinetics of single molecule real-time sequencing provides information on modified DNA bases present in the genomes of bacteria at the time of DNA isolation. This opens the possibility of co-analyzing the locations of modified DNA bases and annotated features such as genes and regulatory elements. Such analyses may help to uncover new modes of gene regulation that involve DNA methylation. Our approach is to develop genome-wide levels of statistical significance for motif discovery and to narrow this list of motifs down to putative regulatory and promoter regions, which in the genome of interest may be methylated or unmethylated. The statistics are sensitive to the completeness and quality of the assembly, and its annotation, and would be difficult to obtain without the high quality closed genomes that can now be produced. We applied this analysis to the 2.5 Mb bovine respiratory pathogen genome, Mannheimia haemolytica, to discover conserved, putative regulatory & promoter motifs, their coincidence with base modifications, and the biological significance of this coincidence.