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A comprehensive allele specific expression resource for the equine transcriptome

by Peng, Sichong , Kalbfleisch, Theodore , Bellone, Rebecca R. , Finno, Carrie J. , Szmatola, Tomasz , Ryan, Stephanie , Heath, Harrison D. , Petersen, Jessica L.

in Alleles / Allelomorphism / Analysis / Animal genetics / Animal Genetics and Genomics / Animals / Annotations / Biomedical and Life Sciences / DNA methylation / Epigenetics / FAANG / Gene expression / Gene Expression Profiling / Gene sequencing / Genetic diversity / Genetic variance / Genetic variation / Genomes / Haplotype / Haplotypes / Histones / Horse / Horses / Horses - genetics / Life Sciences / Liver / Liver - metabolism / Methods / Microarrays / Microbial Genetics and Genomics / Plant Genetics and Genomics / Proteomics / Regulatory mechanisms (biology) / RNA sequencing / Software / Transcriptome / Transcriptomes

2025

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A comprehensive allele specific expression resource for the equine transcriptome

by Peng, Sichong , Kalbfleisch, Theodore , Bellone, Rebecca R. , Finno, Carrie J. , Szmatola, Tomasz , Ryan, Stephanie , Heath, Harrison D. , Petersen, Jessica L.

2025

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A comprehensive allele specific expression resource for the equine transcriptome

by Peng, Sichong , Kalbfleisch, Theodore , Bellone, Rebecca R. , Finno, Carrie J. , Szmatola, Tomasz , Ryan, Stephanie , Heath, Harrison D. , Petersen, Jessica L.

2025

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Journal Article

A comprehensive allele specific expression resource for the equine transcriptome

Peng, Sichong,

Kalbfleisch, Theodore,

Bellone, Rebecca R.,

Finno, Carrie J.,

Szmatola, Tomasz,

Ryan, Stephanie,

Heath, Harrison D.,

Petersen, Jessica L.

2025

Overview

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.

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Publisher

BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC

Subject

/ Animal Genetics and Genomics

/ Animals

/ Annotations