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Session: Small Ruminant Symposium: Current Status of Genomics Research in Sheep

378 - Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome

Monday, June 27, 2022

9:25 AM – 9:45 AM CT

Location: Oklahoma City Convention Center, 206 A/B

Presenting Author(s)

Brenda M. Murdoch, PhD

Associate Professor
Department of Animal, Veterinary and Food Sciences, University of Idaho
Moscow, Idaho

Author(s)

KD

Kimberly M. Davenport, M.S.

University of Idaho
Moscow, Idaho
SX

Shangqian Xie

University of Idaho
MS

Mazdak Salavati

The University of Edinburgh
EC

Emily Clark

The University of Edinburgh
AA

Alan Archibald

University of Edinburgh
SW

Stephen N. White

Washington State University
MM

Michelle R. Mousel

USDA Agricultural Research Service, Washington State University
USDA Agricultural Research Service, Washington State University
Pullman, Washington
KW

Kim Worley, Ph.D.

Baylor College of Medicine
Houston, Texas
SB

Suraj Bhattarai, n/a

PhD student
University of Vermont
Burlington, Vermont
Stephanie D. McKay, n/a

Professor
Department of Animal and Veterinary Sciences, University of Vermont, United States of America.
Vermont, VT
AC

Alex Caulton

University of Otago, New Zealand
SC

Shannon Clarke

University of Otago, New Zealand
RB

Rudiger Brauning

University of Otago, New Zealand
TH

Tracy Hadfield

Utah State University
BR

Benjamin D. Rosen, Ph.D.

Animal Genomics and Improvement Laboratory, USDA-ARS
Beltsville, Maryland
TS

Timothy P.L. Smith, Ph.D.

US Meat Animal Research Center, USDA-ARS
Clay Center, Nebraska
NC

Noelle Cockett, Ph.D.

President
Utah State University
Logan, Utah

Abstract: Characterizing the locations of genetic regulatory elements is critical for understanding the regulatory mechanisms of complex phenotypic traits related to production traits and health in livestock species. The Ovine Functional Annotation of Animal Genomes (FAANG) Project aims to characterize transcriptional regulatory elements across the sheep genome to facilitate a better understanding of the biological mechanisms influencing phenotypic traits in sheep. Assays including sequencing of messenger RNA (mRNA-seq), cap analysis of gene expression (CAGE), chromatin immunoprecipitation of histones (ChIP-seq), assay for transposase-accessible chromatin (ATAC-seq), whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) were performed on tissues collected from the Rambouillet ewe used to assemble the reference genome ARS-UI_Ramb_v2.0. Histone modifications were used to define nine chromatin states for tissues across the genome depicting promoters and enhancers (active, poised, and repressed) using ChromHMM. Chromatin states were overlayed with RNA-seq, ATAC-seq and DNA methylation. These data suggest that active promoter and enhancer states reside in open chromatin regions with a greater transcriptional activity and hypomethylated regions than other states. Further, poised and repressed enhancers did not primarily reside in open chromatin and had less transcriptional activity and more hypermethylated sites compared with active states. Collectively these data define transcriptional regulatory regions throughout the ovine genome which provides a valuable resource to better understand regulatory regions in the genome and how these influence economically important traits in sheep and other livestock species.