School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.
National Council for Scientific and Technological Development (CNPq), Brasilia, DF, Brazil.
Sci Rep. 2020 Sep 7;10(1):14701. doi: 10.1038/s41598-020-71783-4.
Transcript data obtained by RNA-Seq were used to identify differentially expressed alternatively spliced genes in ribeye muscle tissue between Nelore cattle that differed in their ribeye area (REA) or intramuscular fat content (IF). A total of 166 alternatively spliced transcripts from 125 genes were significantly differentially expressed in ribeye muscle between the highest and lowest REA groups (p ≤ 0.05). For animals selected on their IF content, 269 alternatively spliced transcripts from 219 genes were differentially expressed in ribeye muscle between the highest and lowest IF animals. Cassette exons and alternative 3' splice sites were the most frequently found alternatively spliced transcripts for REA and IF content. For both traits, some differentially expressed alternatively spliced transcripts belonged to myosin and myotilin gene families. The hub transcripts were identified for REA (LRRFIP1, RCAN1 and RHOBTB1) and IF (TRIP12, HSPE1 and MAP2K6) have an important role to play in muscle cell degradation, development and motility. In general, transcripts were found for both traits with biological process GO terms that were involved in pathways related to protein ubiquitination, muscle differentiation, lipids and hormonal systems. Our results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the whole cell muscle mRNA of Nelore cattle.
通过 RNA-Seq 获得的转录本数据用于鉴定在 REA（眼肌面积）或 IF（肌内脂肪含量）不同的尼洛拉牛的眼肌组织中差异表达的可变剪接基因。在最高和最低 REA 组之间的眼肌中，有 125 个基因的 166 个可变剪接转录本显著差异表达（p≤0.05）。对于根据 IF 含量选择的动物，在最高和最低 IF 动物之间的眼肌中，有 219 个基因的 269 个可变剪接转录本差异表达。盒外显子和替代 3' 剪接位点是与 REA 和 IF 含量最相关的可变剪接转录本。对于这两个特征，一些差异表达的可变剪接转录本属于肌球蛋白和肌联蛋白基因家族。对于 REA（LRRFIP1、RCAN1 和 RHOBTB1）和 IF（TRIP12、HSPE1 和 MAP2K6），枢纽转录本在肌肉细胞降解、发育和运动中起着重要作用。一般来说，对于这两个特征，都发现了与蛋白质泛素化、肌肉分化、脂质和激素系统相关途径有关的生物过程 GO 术语的转录本。我们的结果不仅强调了这些已知过程的生物学重要性，而且还揭示了尼洛拉牛整个肌肉 mRNA 细胞复杂性的新见解。
