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ARS Home » Pacific West Area » Pullman, Washington » Animal Disease Research » Research » Publications at this Location » Publication #379974
Research Project: Identification of Host Factors and Immunopathogenesis of Pneumonia in Domestic and Bighorn Sheep

Location: Animal Disease Research

Title: Characterizing genetic regulatory elements in ovine tissues

Author
item DAVENPORT, KIMBERLY - University Of Idaho
item MASSA, ALISHA - Washington State University
item BHATTARAI, SURAJ - University Of Vermont
item MCKAY, STEPHANIE - University Of Vermont
item Mousel, Michelle
item HERNDON, MARIA - Washington State University
item White, Stephen
item COCKETT, NOELLE - Utah State University
item Smith, Timothy - Tim
item MURDOCH, BRENDA - University Of Idaho

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2021
Publication Date: 5/20/2021
Citation: Davenport, K.M., Massa, A.T., Bhattarai, S., McKay, S.D., Mousel, M.R., Herndon, M.K., White, S.N., Cockett, N.E., Smith, T.P., Murdoch, B.M. 2021. Characterizing genetic regulatory elements in ovine tissues. Frontiers in Genetics. 12. Article 628849. https://doi.org/10.3389/fgene.2021.628849.
DOI: https://doi.org/10.3389/fgene.2021.628849

Interpretive Summary: Domestic sheep production for food and fiber is an important global agricultural industry. Identifying regions of the genome that affect health and production traits is a priority but greater than 90% of causal mutations are outside gene boundaries. This work defined regulatory elements in sheep liver, spleen, and brain. Approximately 22% of the genome was assigned a regulatory function. In addition, areas of methylation (gene silencing) were characterized in the three tissues. In summary, this study has identified regulatory regions of genes in three tissues that play key roles in defining health and economically important traits and has set the precedent for the characterization of regulatory elements in sheep tissues using the Rambouillet reference genome.

Technical Abstract: The Ovine Functional Annotation of Animal Genomes (FAANG) project, part of the broader livestock species FAANG initiative, aims to identify and characterize gene regulatory elements in domestic sheep. Regulatory element annotation is essential for elucidating the genetic mechanisms that affect health and economically important traits in this important agricultural species, as greater than 90% of causal mutations are estimated to be outside of gene boundaries. Histone modifications that distinguish active or repressed chromatin states, CTCF, and DNA methylation were used to characterize regulatory elements in liver, spleen, and cerebellum tissues from four yearling sheep. Chromatin immunoprecipitation with sequencing (ChIP-seq) was performed for H3K4me3, H3K27ac, H3K4me1, H3K27me3, and CTCF. Nine chromatin states including active promoters, active enhancers, poised enhancers, repressed enhancers, and insulators were characterized in each tissue using ChromHMM. Whole genome bisulfite sequencing (WGBS) was performed, to determine the complement of whole genome DNA methylation with the ChIP-seq data. Hypermethylated and hypomethylated regions were identified across tissues and these locations were compared with chromatin states to better distinguish and validate regulatory elements in these tissues. Interestingly, chromatin states with the poised enhancer mark H3K4me1 in spleen and cerebellum, and CTCF in liver displayed the greatest number of hypermethylated sites. Not surprisingly, active enhancers in liver and spleen, and promoters in cerebellum, displayed the greatest number of hypomethylated sites. Overall, chromatin states defined by histone marks and CTCF occupied approximately 22% of the genome in all three tissues. Further, liver and spleen displayed the greatest percent of active promoter (65%) active enhancer (81%) states in common, and liver and cerebellum displayed the greatest percent of poised enhancer (53%), repressed enhancer (68%), hypermethylated sites (75%), and hypomethylated sites (73%) in common. In addition, both known and de novo CTCF binding motifs were identified in all three tissues, with the highest number of unique motifs identified in cerebellum. In summary, this study has identified the regulatory regions of genes in three tissues that play key roles in defining health and economically important traits and has set the precedent for the characterization of regulatory elements in ovine tissues using the Rambouillet reference genome.