title: Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression.
abstract: As a major epigenetic component, DNA methylation plays important functions in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in economically important animals like cattle.
  
  
  
  Using reduced representation bisulphite sequencing (RRBS), we obtained single-base-resolution maps of bovine DNA methylation from ten somatic tissues. In total, we evaluated 1,868,049 cytosines in CG-enriched regions. While we found slightly low methylation levels (29.87 to 38.06 %) in cattle, the methylation contexts (CGs and non-CGs) of cattle showed similar methylation patterns to other species. Non-CG methylation was detected but methylation levels in somatic tissues were significantly lower than in pluripotent cells. To study the potential function of the methylation, we detected 10,794 differentially methylated cytosines (DMCs) and 836 differentially methylated CG islands (DMIs). Further analyses in the same tissues revealed many DMCs (including non-CGs) and DMIs, which were highly correlated with the expression of genes involved in tissue development.
  
  
  
  In summary, our study provides a baseline dataset and essential information for DNA methylation profiles of cattle.
authors.affiliation: Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.|Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, People's Republic of China.
authors.forename: Lingyang
authors.initials: L
authors.lastname: Xu
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
authors.forename: Derek M
authors.initials: DM
authors.lastname: Bickhart
authors.affiliation: USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA.
authors.forename: El Hamidi
authors.initials: EH
authors.lastname: Abdel Hay
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
authors.forename: Steven G
authors.initials: SG
authors.lastname: Schroeder
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
authors.forename: Erin E
authors.initials: EE
authors.lastname: Connor
authors.affiliation: USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA.
authors.forename: Leeson J
authors.initials: LJ
authors.lastname: Alexander
authors.affiliation: Recombinetics, Inc., St. Paul, MN, 55108, USA.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
authors.forename: Curtis P
authors.initials: CP
authors.lastname: Van Tassell
authors.affiliation: Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China. chenhong1212@263.net.
authors.forename: Hong
authors.initials: H
authors.lastname: Chen
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA. George.Liu@ars.usda.gov.
authors.forename: George E
authors.initials: GE
authors.lastname: Liu
mesh_terms: D000818:Animals; D002417:Cattle; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D015870:Gene Expression; D009928:Organ Specificity / Q000235:genetics; D017422:Sequence Analysis, DNA
keywords: Cattle genome; DNA methylation; RRBS (reduced representation bisulphite sequencing); Somatic tissue