|Zhou, Yang - Northwest Agricultural & Forestry University|
|Xu, Lingyang - University Of Maryland|
|Hay, El Hamidi Abdel - Collaborator|
|Schroeder, Steven - Steve|
|Leeson, Alexander - Collaborator|
|Sonstegard, Tad - Former ARS Employee|
|Van Tassell, Curtis - Curt|
|Hong, Chen - Northwest Agriculture And Forestry University|
|Liu, Ge - George|
Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/23/2016
Publication Date: 10/6/2016
Citation: Zhou, Y., Xu, L., Bickhart, D.M., Hay, E., Schroeder, S.G., Connor, E.E., Leeson, A.J., Sonstegard, T., Van Tassell, C.P., Hong, C., Liu, G. 2016. Reduced representation bisulphite sequencing of the cattle genome reveals DNA methylation patterns. BMC Genomics. 17(1):779.
Interpretive Summary: DNA methylation has been widely recognized as a regulatory epigenetic mechanism that is crucial for cellular reprogramming, tissue differentiation and normal development. Using high-throughput sequencing, we obtained the first high resolution maps of bovine DNA methylation in ten somatic tissues. We then studied methylation patterns and their functions in bovine somatic tissues. Farmers, scientist, and policy planners who need to improve animal health and production based on genome-enabled animal selection will benefit from this study.
Technical Abstract: Using reduced representation bisulphite sequencing (RRBS), we obtained the first single-base-resolution maps of bovine DNA methylation in ten somatic tissues. In total, we observed 1,868,049 cytosines in the CG-enriched regions. Similar to the methylation patterns in other species, the CG context was predominantly methylated in cattle. However, the non-CG methylation was clearly detectable and mainly enriched at the lower level in somatic tissues than the pluripotent cells like oocytes. We did not detect the decreasing of non-CG methylation in either genic or CpG island regions. Correlation analysis among adjacent residues illustrated that methylation levels of CGs were highly correlated in a region. In contrast, weak or no correlation was found among non-CGs or between CGs and non-CGs. These results indicated that non-CG methylation in somatic tissues may be mediated by different mechanisms. We also detected 10,794 differently methylated cytosines (DMCs; 611 of them were in the non-CG context) and 836 differentially methylated CpG islands (DMIs). Combined with RNA-Seq, we discovered that several DMCs in the non-CGs context were highly correlated with gene expression, which suggested the potential function of non-CG methylation in somatic cells. These results provided initial information for DNA methylation patterns in bovine somatic tissues.