Heath Harrison, Peng Sichong, Szmatola Tomasz, Ryan Stephanie, Bellone Rebecca, Kalbfleisch Theodore, Petersen Jessica, Finno Carrie
University of California, Davis.
University of Agriculture in Krakow.
Res Sq. 2024 Apr 4:rs.3.rs-4182812. doi: 10.21203/rs.3.rs-4182812/v1.
Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression.
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 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.
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.
等位基因特异性表达（ASE）分析为影响基因表达的顺式调控机制提供了一个细致入微的视角。
利用来自动物基因组功能注释（FAANG）项目的4匹健康纯种马（2匹母马和2匹种马）9个组织的整合Iso-seq和短读长RNA测序数据，进行了马的ASE分析。通过长读长数据的单倍型对等位基因表达进行定量，共比较了42,900个等位基因表达事件。在这些事件中，635个（1.48%）表现出ASE，其中肝脏组织中比例最高。ASE事件中的遗传变异有64.2%位于组蛋白修饰区域。使用来自多个品种的66份马肝脏样本对等位基因特异性变异进行验证，证实97%的变异表现出ASE。
这个宝贵的可公开获取的资源有望促进对马组织中调控变异的研究。我们的结果突出了马基因组中等位基因不平衡的组织特异性本质。
