Annotating Gene Expression and Regulatory Elements in Tissues from Healthy Thoroughbred Horses and Identifying Candidate Mutations Associated with Perosomus elumbis in an Angus Calf

Authors

• Alexa McKenna Barber, University of Nebraska-LincolnFollow

First Advisor

Jessica Lynn Petersen

Committee Members

Daniel C. Ciobanu, Audrey L. Atkin

Date of this Version

4-2022

Document Type

Thesis

Citation

A thesis presented to the faculty of the Graduate College at the University of Nebraska in partial fulfillment of requirements for the degree of Master of Science

Major: Animal Science

Under the supervision of Professor Jessica Lynn Petersen

Lincoln, Nebraska, April 2022

Comments

Copyright © 2022, Alexa McKenna Barber, Used by permission

Abstract

Genome annotation has a direct impact on the success of genomic studies. Transcriptome analyses and chromatin immunoprecipitation and sequencing (ChIP-seq) have been used to functionally annotate genomes. These methods can identify protein-coding genes, non-coding transcripts, and cis-regulatory elements across the genome. The primary objective of the first study was to functionally annotate the equine genome through the assessment of nine tissues: adipose, brain, heart, lamina, liver, lung, skeletal, muscle, testis, and ovary. In the first project, 150 bp, paired-end RNA sequencing (RNA-seq) libraries were generated in stallion tissues and compared to previously generated mare RNA-seq libraries to quantify variation in gene expression due to sex and tissue type. On average, each tissue expressed (> 10 transcripts per million) over 8,000 genes, and adipose, liver, and skeletal muscle each had over 900 genes differentially expressed due to sex (P adj < 0.05). In the second study, the peaks of four histone marks, H3K27ac, H3K4me1, H3K4me3, and H3K27me3, were examined to identify activated regions, enhancers, promoters, and silencers, respectively. Fifty base pair, paired-end ChIP-seq libraries were created for each histone mark in stallion tissues and compared to data from 50 bp single-end ChIP-seq libraries from mare tissues. On average, 77,000 activated regions, 120,000 enhancers, 34,000 promoters, and 32,000 silenced regions were detected in each stallion tissue. Due to high correlations among sequencing depth, total peaks called, and tissue-unique peaks, regulatory elements unique to tissue types and sexes could not be well characterized.

The third study examined genomic variation associated with a congenital defect, perosomus elumbis, (PE) in Angus cattle. The affected calf was still-born, displaying lumbar aplasia, and arthrogryposis. Whole-genome sequencing of 31 Angus cattle identified a frameshift mutation in PTK7 as a candidate variant for the development of PE in an Angus calf. Despite the implication of PTK7 in similar phenotypes, additional research is needed to verify the etiology of PE in Angus cattle.

Advisor: Jessica Lynn Petersen