Characterization of DNA Methylome in Bison Liver and Muscle Tissues Using Whole Genome Bisulfite Sequencing
Conference Year
January 2022
Abstract
American bison (Bison bison) are an iconic species believed to have covered over 30% of North America before undergoing a severe population bottleneck during the late 1800’s. Bison were mated with domestic cattle and significant amounts of genetic introgression have been confirmed in bison genomes. Epigenetics research captures environmental cues with specific genomic information and could further be used in the conservation of this species. To identify and characterize the bison methylome, we performed whole genome bisulfite sequencing (WGBS) in liver and muscle tissues from each of six male bison. WGBS generated approximately 1.2 billion paired-end reads (150 bp) for each of the liver and muscle sample groups of which approximately 69% mapped uniquely to the cattle reference genome (ARS-UCD1.2) at an average depth of 21x. Optimal parameters for mapping bison reads to the bovine genome were determined by first mapping reads to the bison reference genome (Bison_UMD1.0) and ascertaining the maximum number of mismatches allowed while maintained the integrity of the alignment. Globally, we found 64.73% and 61.76% methylation in CG sites in liver and muscle tissues, respectively. Surprisingly, we observed more than 2% methylation in non-CG sites in both these tissues. Previously, we have reported non-CG levels above 2% only in brain tissues of sheep and cattle. We further found that hypomethylated regions (HMRs) had a median size of 809 bp in liver and 668 bp in muscle tissues. Moreover, HMRs covered 3.4% and 3.1% of the liver and muscle genome, respectively. In both tissues, bovine autosomes 18, 19 and 25 contained the highest percent of HMRs after normalizing for chromosome size. The lowest percentage of HMRs in muscle were found on autosomes 1, 4, 6 and 9 while autosomes 6 and 9 contained the lowest percentage of HMRs in liver. This is the first study to characterize whole genome DNA methylation profiles in liver and muscle tissues of American bison.
Primary Faculty Mentor Name
Stephanie McKay
Status
Graduate
Student College
College of Agriculture and Life Sciences
Program/Major
Animal Science
Primary Research Category
Biological Sciences
Characterization of DNA Methylome in Bison Liver and Muscle Tissues Using Whole Genome Bisulfite Sequencing
American bison (Bison bison) are an iconic species believed to have covered over 30% of North America before undergoing a severe population bottleneck during the late 1800’s. Bison were mated with domestic cattle and significant amounts of genetic introgression have been confirmed in bison genomes. Epigenetics research captures environmental cues with specific genomic information and could further be used in the conservation of this species. To identify and characterize the bison methylome, we performed whole genome bisulfite sequencing (WGBS) in liver and muscle tissues from each of six male bison. WGBS generated approximately 1.2 billion paired-end reads (150 bp) for each of the liver and muscle sample groups of which approximately 69% mapped uniquely to the cattle reference genome (ARS-UCD1.2) at an average depth of 21x. Optimal parameters for mapping bison reads to the bovine genome were determined by first mapping reads to the bison reference genome (Bison_UMD1.0) and ascertaining the maximum number of mismatches allowed while maintained the integrity of the alignment. Globally, we found 64.73% and 61.76% methylation in CG sites in liver and muscle tissues, respectively. Surprisingly, we observed more than 2% methylation in non-CG sites in both these tissues. Previously, we have reported non-CG levels above 2% only in brain tissues of sheep and cattle. We further found that hypomethylated regions (HMRs) had a median size of 809 bp in liver and 668 bp in muscle tissues. Moreover, HMRs covered 3.4% and 3.1% of the liver and muscle genome, respectively. In both tissues, bovine autosomes 18, 19 and 25 contained the highest percent of HMRs after normalizing for chromosome size. The lowest percentage of HMRs in muscle were found on autosomes 1, 4, 6 and 9 while autosomes 6 and 9 contained the lowest percentage of HMRs in liver. This is the first study to characterize whole genome DNA methylation profiles in liver and muscle tissues of American bison.