A comprehensive allele specific expression resource for the equine transcriptome

Area of Science:

• Genomics
• Molecular Biology
• Animal Science

Background:

• Allele-specific expression (ASE) analysis offers detailed insights into cis-regulatory mechanisms governing gene expression.
• Understanding ASE is crucial for deciphering gene regulation complexities.

Purpose of the Study:

• To conduct a comprehensive allele-specific expression analysis in equine tissues.
• To identify and characterize allele expression events in horses.
• To investigate the tissue-specific patterns of allelic imbalance.

Main Methods:

• Integrated analysis of Iso-seq and short-read RNA sequencing data from four Thoroughbred horses across nine tissues.
• Quantification of allele expression using haplotypes derived from long-read sequencing data.
• Validation of identified allele-specific variants in a larger cohort of equine liver samples.

Main Results:

• Comparison of 42,900 allele expression events revealed 635 (1.48%) instances of ASE.
• Liver tissue exhibited the highest proportion of ASE events.
• Genetic variants associated with ASE were frequently located within histone-modified regions (64.2%).
• Validation confirmed ASE in 97% of tested allele-specific variants.

Conclusions:

• The study generated a valuable, publicly accessible resource for equine gene regulation research.
• Results underscore the significant tissue-specific nature of allelic imbalance in the equine genome.
• This work facilitates future investigations into regulatory variation within equine tissues.