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. 2025 Jan 30;26(1):88.
doi: 10.1186/s12864-025-11240-6.

A comprehensive allele specific expression resource for the equine transcriptome

Harrison D Heath  1 , Sichong Peng  1   2 , Tomasz Szmatola  1   3 , Stephanie Ryan  1 , Rebecca R Bellone  1   4 , Theodore Kalbfleisch  5 , Jessica L Petersen  6 , Carrie J Finno  7
Affiliations

A comprehensive allele specific expression resource for the equine transcriptome

Harrison D Heath et al. BMC Genomics. .

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.

Keywords: Epigenetics; FAANG; Haplotype; Horse; RNA-sequencing.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: All protocols were approved by the University of California Davis Institutional Animal Care and Use Committee (Protocol #19037). Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
ASDEGs Comparisons Across Tissues. The scatter plots display the absolute log2-fold change in allele expression for identified ASDEGs across various tissues. Each gene featured has at least 2 identified ASE events across all horses and tissues. ASDEGs are graphed in alphabetical order. Each dot represents the expression fold change for a gene in a specific tissue, plotted against the gene symbol on the x-axis and the absolute log2-fold change on the y-axis. The dotted line indicates the significance threshold of a twofold change. The color coding corresponds to different tissues, as indicated in the legend
Fig. 2
Fig. 2
Histone Modified Regions Overlapping Variants of ASE Events. Upset plot representing the distribution and overlap of histone modifications across heterozygous loci associated with allele-specific differentially expressed genes (ASDEGs). Each circle corresponds to a specific histone modification as indicated by the legend (H3K27ac, H3K4me1, H3K27me3, H3K4me3). Circles, and their respective frequency bars, denote the count of SNP regions that exhibit the corresponding histone modifications
Fig. 3
Fig. 3
ASDEG enrichment analysis. Bar chart depicting the number of ASDEGs (Allele Specific Differentially Expressed Genes) present within significantly enriched pathways identified in each tissue type from KOBAS enrichment analysis. Tissues analyzed include Liver, Ovary, Testis, Lamina, Heart, Parietal Cortex, and Adipose
Fig. 4
Fig. 4
Validation of ASE in Heterozygous Loci in Liver Tissue from Independent Dataset. Distribution of absolute log-fold changes at heterozygous loci identified within allele-specific expression (ASE) events in liver tissue, and their overlay with a validation set of short-read RNA-seq data. Two categories are presented: non-significant events (blue) and significant events (orange) that exhibit ASE. The dashed red line indicates the significance threshold, with the loci to the right deemed to show significant ASE
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