猪骨骼肌 27 个发育阶段的转座元件表达图谱分析：揭示猪肉生产特性的分子见解,Animals

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猪骨骼肌 27 个发育阶段的转座元件表达图谱分析：揭示猪肉生产特性的分子见解
Animals ( IF 2.7 ) Pub Date : 2023-11-20 , DOI: 10.3390/ani13223581
Chao Wang _{1,

2,

3} , Bowen Lei _{1,

2,

3} , Yuwen Liu _{1,

2,

3,

4}

Affiliation

猪骨骼肌的发育和生长决定猪肉的品质和产量。虽然使用各种组学数据对猪骨骼肌发育的遗传调控进行了广泛的研究，但转座元件（TE）在这方面的作用却很少被探索。为了弥补这一差距，我们构建了猪骨骼肌整个发育阶段的 TE 表达综合图谱。这是通过将猪 TE 基因组坐标与 27 个发育阶段的全转录组 RNA-Seq 数据整合来实现的。我们发现，在猪骨骼肌中，活跃的 Tes 与活跃的表观基因组标记密切相关，包括低水平的 DNA 甲基化、高水平的染色质可及性和活跃的组蛋白修饰。此外，这些 TE 包括 6074 个自我表达的 TE，它们在肌肉细胞发育和肌原纤维组装方面显着丰富。利用TE表达数据，我们进行了加权基因共表达网络分析（WGCNA）并鉴定了与肌肉组织发育显着相关的模块以及猪肉和胴体信号的全基因组关联研究（GWAS）特征。在这个模块中，我们通过采用独特的多组学整合方法构建了 TE 介导的基因调控网络。该网络突出显示了与肌肉相关性状相关的几个已确定的候选基因，包括 HES6、CHRNG、ACTC1、CHRND、MAMSTR 和 PER2，以及 ENSSSCG00000005518、ENSSSCG00000033601 和 PIEZO2 等新基因。这些新基因有望调节猪的肌肉相关性状。总之，我们的研究不仅增强了以 TE 为中心对猪肉生产性状遗传基础的剖析，而且还提供了构建 TE 介导的调控网络以研究复杂性状或疾病的通用方法。

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An Analysis of a Transposable Element Expression Atlas during 27 Developmental Stages in Porcine Skeletal Muscle: Unveiling Molecular Insights into Pork Production Traits

The development and growth of porcine skeletal muscle determine pork quality and yield. While genetic regulation of porcine skeletal muscle development has been extensively studied using various omics data, the role of transposable elements (TEs) in this context has been less explored. To bridge this gap, we constructed a comprehensive atlas of TE expression throughout the developmental stages of porcine skeletal muscle. This was achieved by integrating porcine TE genomic coordinates with whole-transcriptome RNA-Seq data from 27 developmental stages. We discovered that in pig skeletal muscle, active Tes are closely associated with active epigenomic marks, including low levels of DNA methylation, high levels of chromatin accessibility, and active histone modifications. Moreover, these TEs include 6074 self-expressed TEs that are significantly enriched in terms of muscle cell development and myofibril assembly. Using the TE expression data, we conducted a weighted gene co-expression network analysis (WGCNA) and identified a module that is significantly associated with muscle tissue development as well as genome-wide association studies (GWAS) of the signals of pig meat and carcass traits. Within this module, we constructed a TE-mediated gene regulatory network by adopting a unique multi-omics integration approach. This network highlighted several established candidate genes associated with muscle-relevant traits, including HES6, CHRNG, ACTC1, CHRND, MAMSTR, and PER2, as well as novel genes like ENSSSCG00000005518, ENSSSCG00000033601, and PIEZO2. These novel genes hold promise for regulating muscle-related traits in pigs. In summary, our research not only enhances the TE-centered dissection of the genetic basis underlying pork production traits, but also offers a general approach for constructing TE-mediated regulatory networks to study complex traits or diseases.

更新日期：2023-11-20

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