Abstract：
DNA methylation and microRNA (miRNA) expression are epigenetic mechanisms essential for regulating tissue-specific gene expression and metabolic processes. However, high-resolution transcriptome, methylome, or miRNAome data is only available for a few model organisms and selected tissues. Up to date, only a few studies have reported on gene expression, DNA methylation, or miRNA expression in adult equine tissues at the genome-wide level. In the present study, we used RNA-Seq, miRNA-seq, and reduced representation bisulfite sequencing (RRBS) data from the heart, lung, and liver tissues of healthy cold-blooded horses to identify differentially expressed genes (DEGs), differentially expressed miRNA (DE miRNA) and differentially methylated sites (DMSs) between three types of horse tissues. Additionally, based on integrative omics analysis, we described the observed interactions of epigenetic mechanisms with tissue-specific gene expression alterations. The obtained data allowed identification from 4067 to 6143 DMSs, 9733 to 11,263 mRNAs, and 155 to 185 microRNAs, differentially expressed between various tissues. We pointed out specific genes whose expression level displayed a negative correlation with the level of CpG methylation and miRNA expression and revealed biological processes that they enrich. Furthermore, we confirmed and validated the accuracy of the Next-Generation Sequencing (NGS) results with bisulfite sequencing PCR (BSP) and quantitative PCR (qPCR). This comprehensive analysis forms a strong foundation for exploring the epigenetic mechanisms involved in tissue differentiation, especially the growth and development of the equine heart, lungs, and liver.
摘要：
DNA甲基化和microRNA（miRNA）表达是调节组织特异性基因表达和代谢过程所必需的表观遗传机制。然而,高分辨率转录组，甲基化，或miRNAome数据仅适用于少数模型生物和选定的组织。到目前为止,只有少数研究报道了基因表达，DNA甲基化，或miRNA在成年马组织中的表达在全基因组水平。在本研究中,我们用RNA-Seq,miRNA-seq,并减少了来自心脏的代表亚硫酸氢盐测序（RRBS）数据，肺，和健康冷血马的肝脏组织，以鉴定差异表达基因（DEGs），三种马组织之间的差异表达miRNA（DEmiRNA）和差异甲基化位点（DMS）。此外,基于综合组学分析，我们描述了观察到的表观遗传机制与组织特异性基因表达改变的相互作用。获得的数据允许识别4067到6143个DMS，9733至11,263个mRNA，和155到185个microRNA，在各种组织之间差异表达。我们指出了表达水平与CpG甲基化水平和miRNA表达水平呈负相关的特定基因，并揭示了它们富集的生物学过程。此外，我们通过亚硫酸氢盐测序PCR(BSP)和定量PCR(qPCR)证实并验证了下一代测序(NGS)结果的准确性.这种综合分析为探索组织分化的表观遗传机制奠定了坚实的基础。尤其是马心的生长发育,肺,还有肝脏.
