Functionally annotating regulatory elements in the equine genome using histone mark chip-seq

N. B. Kingsley, Colin Kern, Catherine Creppe, Erin N. Hales, Huaijun Zhou, T. S. Kalbfleisch, James N. Macleod, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

One of the primary aims of the Functional Annotation of ANimal Genomes (FAANG) initiative is to characterize tissue-specific regulation within animal genomes. To this end, we used chromatin immunoprecipitation followed by sequencing (ChIP-Seq) to map four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) in eight prioritized tissues collected as part of the FAANG equine biobank from two thoroughbred mares. Data were generated according to optimized experimental parameters developed during quality control testing. To ensure that we obtained sufficient ChIP and successful peak-calling, data and peak-calls were assessed using six quality metrics, replicate comparisons, and site-specific evaluations. Tissue specificity was explored by identifying binding motifs within unique active regions, and motifs were further characterized by gene ontology (GO) and protein–protein interaction analyses. The histone marks identified in this study represent some of the first resources for tissue-specific regulation within the equine genome. As such, these publicly available annotation data can be used to advance equine studies investigating health, performance, reproduction, and other traits of economic interest in the horse.

Original languageEnglish
Article number3
JournalGenes
Volume11
Issue number1
DOIs
StatePublished - Jan 2020

Bibliographical note

Funding Information:
Funding: Funding for experimental materials, and other resources was provided by the Grayson Jockey Club Foundation, USDA NRSP-8 equine species coordinator funds, and the Center for Equine Health with funds provided by the State of California pari-mutuel fund and contributions by private donors. Support for N.B.K. was also provided by the Grayson Jockey Club Foundation, Morris Animal Foundation (D16-EQ-028), and a fellowship from the Center for Equine Health at the University of California—Davis. Support for C.J.F. was provided by the National Institutes of Health (NIH) (K01OD015134 and L40 TR001136).

Funding Information:
Funding for experimental materials, and other resources was provided by the Grayson Jockey Club Foundation, USDA NRSP-8 equine species coordinator funds, and the Center for Equine Health with funds provided by the State of California pari-mutuel fund and contributions by private donors. Support for N.B.K. was also provided by the Grayson Jockey Club Foundation, Morris Animal Foundation (D16-EQ-028), and a fellowship from the Center for Equine Health at the University of California?Davis. Support for C.J.F. was provided by the National Institutes of Health (NIH) (K01OD015134 and L40 TR001136).

Publisher Copyright:
© 2019 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

  • Annotation
  • Epigenetics
  • FAANG
  • Genome regulation
  • H3K27ac
  • H3K27me3
  • H3K4me1
  • H3K4me3
  • Horse
  • Tissue-specific

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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