Yuan Zehu, Ge Ling, Zhang Weibo, Lv Xiaoyang, Wang Shanhe, Cao Xiukai, Sun Wei
Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China.
College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China.
Foods. 2022 Apr 7;11(8):1068. doi: 10.3390/foods11081068.
Tenderness is an important indicator of meat quality. Novel isoforms associated with meat tenderness and the role of the CCCTC-binding factor (CTCF) in regulating alternative splicing to produce isoforms in sheep are largely unknown. The current project studied six sheep from two crossbred populations (Dorper × Hu × Hu, DHH and Dorper × Dorper × Hu, DDH) with divergent meat tenderness. Pooled Iso-seq data were used to annotate the sheep genomes. Then, the updated genome annotation and six RNA-seq data were combined to identify differentially expressed isoforms (DEIs) in muscles between DHH and DDH. These data were also combined with peaks detected from CTCF ChIP-seq data to investigate the regulatory role of CTCF for the alternative splicing. As a result, a total of 624 DEIs were identified between DDH and DHH. For example, isoform 7.524.18 transcribed from may be associated with meat tenderness. In addition, a total of 86 genes were overlapped between genes with transcribed DEIs and genes in differential peaks identified by CTCF ChIP-seq. Among these overlapped genes, produces different isoforms which may be regulated by CTCF via methylation. As preliminary research, our results identified novel isoforms associated with meat tenderness and revealed the possible regulating mechanisms of alternative splicing to produce isoforms.
嫩度是肉质的一个重要指标。与肉嫩度相关的新型异构体以及CCCTC结合因子（CTCF）在调节绵羊可变剪接以产生异构体中的作用在很大程度上尚不清楚。当前项目研究了来自两个具有不同肉嫩度的杂交群体（杜泊×湖羊×湖羊，DHH和杜泊×杜泊×湖羊，DDH）的六只绵羊。汇集的Iso-seq数据用于注释绵羊基因组。然后，将更新后的基因组注释和六个RNA-seq数据相结合，以鉴定DHH和DDH之间肌肉中差异表达的异构体（DEIs）。这些数据还与从CTCF ChIP-seq数据中检测到的峰相结合，以研究CTCF对可变剪接的调控作用。结果，在DDH和DHH之间共鉴定出624个DEIs。例如，从 转录的异构体7.524.18可能与肉嫩度相关。此外，转录的DEIs基因与CTCF ChIP-seq鉴定的差异峰中的基因之间共有86个基因重叠。在这些重叠基因中， 产生不同的异构体，可能由CTCF通过甲基化进行调控。作为初步研究，我们的结果鉴定出了与肉嫩度相关的新型异构体，并揭示了可变剪接产生异构体的可能调控机制。
