A comprehensive allele specific expression resource for the equine transcriptome
Abstract Background Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stall...
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2025-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11240-6 |
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| author | Harrison D. Heath Sichong Peng Tomasz Szmatola Stephanie Ryan Rebecca R. Bellone Theodore Kalbfleisch Jessica L. Petersen Carrie J. Finno |
| author_facet | Harrison D. Heath Sichong Peng Tomasz Szmatola Stephanie Ryan Rebecca R. Bellone Theodore Kalbfleisch Jessica L. Petersen Carrie J. Finno |
| author_sort | Harrison D. Heath |
| collection | DOAJ |
| description | Abstract Background Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic variants within ASE events were located in histone modified regions 64.2% of the time. Validation of allele-specific variants, using a set of 66 equine liver samples from multiple breeds, confirmed that 97% of variants demonstrated ASE. Conclusions This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues. Our results highlight the tissue-specific nature of allelic imbalance in the equine genome. |
| format | Article |
| id | doaj-art-71358a53d7a9448fb115be59a6182de9 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-71358a53d7a9448fb115be59a6182de92025-02-02T12:10:15ZengBMCBMC Genomics1471-21642025-01-0126111110.1186/s12864-025-11240-6A comprehensive allele specific expression resource for the equine transcriptomeHarrison D. Heath0Sichong Peng1Tomasz Szmatola2Stephanie Ryan3Rebecca R. Bellone4Theodore Kalbfleisch5Jessica L. Petersen6Carrie J. Finno7Department of Population Health and Reproduction, Davis School of Veterinary Medicine, University of CaliforniaDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of CaliforniaDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of CaliforniaDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of CaliforniaDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of CaliforniaMaxwell H. Gluck Equine Research Center, University of KentuckyDepartment of Animal Science, University of Nebraska-LincolnDepartment of Population Health and Reproduction, Davis School of Veterinary Medicine, University of CaliforniaAbstract Background Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic variants within ASE events were located in histone modified regions 64.2% of the time. Validation of allele-specific variants, using a set of 66 equine liver samples from multiple breeds, confirmed that 97% of variants demonstrated ASE. Conclusions This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues. Our results highlight the tissue-specific nature of allelic imbalance in the equine genome.https://doi.org/10.1186/s12864-025-11240-6EpigeneticsFAANGHaplotypeHorseRNA-sequencing |
| spellingShingle | Harrison D. Heath Sichong Peng Tomasz Szmatola Stephanie Ryan Rebecca R. Bellone Theodore Kalbfleisch Jessica L. Petersen Carrie J. Finno A comprehensive allele specific expression resource for the equine transcriptome BMC Genomics Epigenetics FAANG Haplotype Horse RNA-sequencing |
| title | A comprehensive allele specific expression resource for the equine transcriptome |
| title_full | A comprehensive allele specific expression resource for the equine transcriptome |
| title_fullStr | A comprehensive allele specific expression resource for the equine transcriptome |
| title_full_unstemmed | A comprehensive allele specific expression resource for the equine transcriptome |
| title_short | A comprehensive allele specific expression resource for the equine transcriptome |
| title_sort | comprehensive allele specific expression resource for the equine transcriptome |
| topic | Epigenetics FAANG Haplotype Horse RNA-sequencing |
| url | https://doi.org/10.1186/s12864-025-11240-6 |
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