Identification of 5-hydroxymethylcytosine markers in the cattle brain
Conference Year
January 2020
Abstract
Epigenetic variation plays an important role in phenotypic variability. DNA methylation is a dynamic epigenetic marker that can be added and removed from DNA nucleotides. The removal pathway begins when 5-methylcytosine (5-mC) is oxidized to 5-hydroxymethylcytosine (5-hmC). Both 5-mC and 5-hmC are stable epigenetic markers that influence transcription. 5-mC is thought to inhibit transcription, whereas 5-hmC is thought to promote transcription. It is important to distinguish between these stable epigenetic markers to gain a clear understanding of how epigenetics is influencing transcription. However, traditional whole genome bisulfite sequencing methods do not differentiate between these markers. Because of this, 5-hmC is often misrepresented as 5-mC. The grouping of these two distinct markers during data collection could lead to misinformation on the impact of DNA methylation markers on transcription and phenotype. The McKay laboratory has previously studied the relationship between DNA methylation and docility using standard whole genome bisulfite sequencing on select brain tissues. Differentiating between markers is especially significant in the brain, where there is an increase in the presence of 5-hmC. We now present work to differentiate between 5-hmC and 5-mC in this research. Brain tissues in the limbic system of 8 Red Angus x Simmental steers underwent reduced representation oxidative bisulfite sequencing to identify hydroxymethylated cytosines. Fastq sequencing files were trimmed with Trim Galore. Bismark was then used for alignment to a bovine reference index and to call methylation. These data show the presence of 5-hmC in the brain, which emphasizes the need to differentiate between 5-hmC and 5-mC.
Primary Faculty Mentor Name
Dr. Stephanie McKay
Faculty/Staff Collaborators
Bonnie Cantrell, Shuli Liu, Nathan Jebbett, Robert C. Switzer III, Eugene Delay, Steven Zinn, Sharon Aborn, Jane O’Neil, Julia Sjoquist, Joseph Waksman, Hannah Lachance, Brenda Murdoch, Rick Funston, Robert Weaber, George Liu, Stephanie McKay
Status
Graduate
Student College
College of Agriculture and Life Sciences
Program/Major
Cellular, Molecular and Biomedical Sciences
Primary Research Category
Biological Sciences
Identification of 5-hydroxymethylcytosine markers in the cattle brain
Epigenetic variation plays an important role in phenotypic variability. DNA methylation is a dynamic epigenetic marker that can be added and removed from DNA nucleotides. The removal pathway begins when 5-methylcytosine (5-mC) is oxidized to 5-hydroxymethylcytosine (5-hmC). Both 5-mC and 5-hmC are stable epigenetic markers that influence transcription. 5-mC is thought to inhibit transcription, whereas 5-hmC is thought to promote transcription. It is important to distinguish between these stable epigenetic markers to gain a clear understanding of how epigenetics is influencing transcription. However, traditional whole genome bisulfite sequencing methods do not differentiate between these markers. Because of this, 5-hmC is often misrepresented as 5-mC. The grouping of these two distinct markers during data collection could lead to misinformation on the impact of DNA methylation markers on transcription and phenotype. The McKay laboratory has previously studied the relationship between DNA methylation and docility using standard whole genome bisulfite sequencing on select brain tissues. Differentiating between markers is especially significant in the brain, where there is an increase in the presence of 5-hmC. We now present work to differentiate between 5-hmC and 5-mC in this research. Brain tissues in the limbic system of 8 Red Angus x Simmental steers underwent reduced representation oxidative bisulfite sequencing to identify hydroxymethylated cytosines. Fastq sequencing files were trimmed with Trim Galore. Bismark was then used for alignment to a bovine reference index and to call methylation. These data show the presence of 5-hmC in the brain, which emphasizes the need to differentiate between 5-hmC and 5-mC.