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PLoS genetics2023; 19(3); e1010468; doi: 10.1371/journal.pgen.1010468

Functional annotation of the animal genomes: An integrated annotation resource for the horse.

Abstract: The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Due to the limited availability of functional data for the equine genome, as well as the technical limitations of short-read RNA-seq, existing annotation of the equine genome contains limited information about important aspects of gene regulation, such as alternate isoforms and regulatory elements, which are either not transcribed or transcribed at a very low level. To solve above problems, the Functional Annotation of the Animal Genomes (FAANG) project proposed a systemic approach to tissue collection, phenotyping, and data generation, adopting the blueprint laid out by the Encyclopedia of DNA Elements (ENCODE) project. Here we detail the first comprehensive overview of gene expression and regulation in the horse, presenting 39,625 novel transcripts, 84,613 candidate cis-regulatory elements (CRE) and their target genes, 332,115 open chromatin regions genome wide across a diverse set of tissues. We showed substantial concordance between chromatin accessibility, chromatin states in different genic features and gene expression. This comprehensive and expanded set of genomics resources will provide the equine research community ample opportunities for studies of complex traits in the horse.
Copyright: © 2023 Peng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Publication Date: 2023-03-02 PubMed ID: 36862752PubMed Central: PMC10013926DOI: 10.1371/journal.pgen.1010468Google Scholar: Lookup
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  • Review
  • Journal Article
  • Research Support
  • U.S. Gov't
  • Non-P.H.S.
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article is about a comprehensive study done on the horse genome, presenting new findings about gene expression and regulation, which were achieved using a systemic approach proposed by the Functional Annotation of the Animal Genomes (FAANG) project.

Introduction

  • The research focuses on the thorough annotation of the horse genome. While the entire genomic sequence of the horse has been known since 2009, understanding the full implications of its genetic variants has been a challenge due to limited functional data.
  • Solving this deficit in information requires the detailed annotation of the horse genome, particularly understanding gene regulation aspects such as alternate isoforms and regulatory elements – something that traditional methods were not able to achieve.

The FAANG Project

  • To address these limitations, this research incorporated the methodologies from the Functional Annotation of the Animal Genomes (FAANG) project, a system that presents a new way of tissue collection, phenotyping, and data generation.
  • The FAANG approach was inspired by the Encyclopedia of DNA Elements (ENCODE) project, showing its solid foundation in recognized research.

Results

  • As a result of this research, for the first time, a comprehensive overview of gene expression and regulation in the horse is presented. This includes the discovery of 39,625 novel transcripts, which are unique sequences of RNA molecules that indicate the presence of genetic information.
  • A major highlight of the study is the identification of 84,613 candidate cis-regulatory elements (CRE) and their target genes, which play a critical role in controlling the transcription of nearby genes.
  • The study also identified 332,115 open chromatin regions across various tissues. The openness or closeness of these chromatin regions usually affects gene regulation, providing essential clues about the genomic functioning.
  • The research also established significant concordance between chromatin accessibility, chromatin states in different genic features, and gene expression, offering a deep dive into genomic analysis previously not available for the horse.

Conclusion

  • The findings from this research provide a comprehensive and expanded set of genomics resources. These resources will indeed serve as a significant contribution to ongoing and future research, allowing for in-depth studies of complex traits in horses.

Cite This Article

APA
Peng S, Dahlgren AR, Donnelly CG, Hales EN, Petersen JL, Bellone RR, Kalbfleisch T, Finno CJ. (2023). Functional annotation of the animal genomes: An integrated annotation resource for the horse. PLoS Genet, 19(3), e1010468. https://doi.org/10.1371/journal.pgen.1010468

Publication

PLoS genetics
ISSN: 1553-7404
NlmUniqueID: 101239074
Country: United States
Language: English
Volume: 19
Issue: 3
Pages: e1010468
PII: e1010468

Researcher Affiliations

Peng, Sichong
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Dahlgren, Anna R
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Donnelly, Callum G
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Hales, Erin N
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.
Bellone, Rebecca R
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Kalbfleisch, Ted
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, United States of America.
Finno, Carrie J
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.

MeSH Terms

  • Horses / genetics
  • Animals
  • Transcriptome
  • Molecular Sequence Annotation
  • Organ Specificity
  • Chromatin
  • Regulatory Elements, Transcriptional
  • Genome
  • Transcription Initiation Site
  • Sequence Analysis, RNA
  • Gene Expression Regulation

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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Citations

This article has been cited 1 times.
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