Decoding the Equine Genome: Lessons from ENCODE
The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to add...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/11/1707 |
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| author | Sichong Peng Jessica L. Petersen Rebecca R. Bellone Ted Kalbfleisch N. B. Kingsley Alexa M. Barber Eleonora Cappelletti Elena Giulotto Carrie J. Finno |
| author_facet | Sichong Peng Jessica L. Petersen Rebecca R. Bellone Ted Kalbfleisch N. B. Kingsley Alexa M. Barber Eleonora Cappelletti Elena Giulotto Carrie J. Finno |
| author_sort | Sichong Peng |
| collection | DOAJ |
| description | The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era. |
| first_indexed | 2024-03-10T05:28:14Z |
| format | Article |
| id | doaj.art-112ed98403814c90a5a8e52fd75e344b |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T05:28:14Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-112ed98403814c90a5a8e52fd75e344b2023-11-22T23:27:36ZengMDPI AGGenes2073-44252021-10-011211170710.3390/genes12111707Decoding the Equine Genome: Lessons from ENCODESichong Peng0Jessica L. Petersen1Rebecca R. Bellone2Ted Kalbfleisch3N. B. Kingsley4Alexa M. Barber5Eleonora Cappelletti6Elena Giulotto7Carrie J. Finno8Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USADepartment of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USADepartment of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USADepartment of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40503, USADepartment of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USADepartment of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USADepartment of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, ItalyDepartment of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, ItalyDepartment of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USAThe horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.https://www.mdpi.com/2073-4425/12/11/1707FAANGgene regulationhorsefunctional annotationtranscriptomeepigenetics |
| spellingShingle | Sichong Peng Jessica L. Petersen Rebecca R. Bellone Ted Kalbfleisch N. B. Kingsley Alexa M. Barber Eleonora Cappelletti Elena Giulotto Carrie J. Finno Decoding the Equine Genome: Lessons from ENCODE Genes FAANG gene regulation horse functional annotation transcriptome epigenetics |
| title | Decoding the Equine Genome: Lessons from ENCODE |
| title_full | Decoding the Equine Genome: Lessons from ENCODE |
| title_fullStr | Decoding the Equine Genome: Lessons from ENCODE |
| title_full_unstemmed | Decoding the Equine Genome: Lessons from ENCODE |
| title_short | Decoding the Equine Genome: Lessons from ENCODE |
| title_sort | decoding the equine genome lessons from encode |
| topic | FAANG gene regulation horse functional annotation transcriptome epigenetics |
| url | https://www.mdpi.com/2073-4425/12/11/1707 |
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