Abstract：
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 CAPN3 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, ANKRD23 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.
摘要：
嫩度是肉品质的重要指标。与肉嫩度相关的新型同工型以及CCCTC结合因子（CTCF）在调节绵羊选择性剪接以产生同工型中的作用在很大程度上是未知的。当前项目研究了来自两个杂交种群（Dorper×Hu×Hu，DHH和Dorper×Dorper×Hu，DDH）具有不同的肉嫩度。汇集的Iso-seq数据用于注释绵羊基因组。然后，将更新的基因组注释和6个RNA-seq数据结合起来,以鉴定DHH和DDH之间肌肉中差异表达的同工型(DEI).还将这些数据与从CTCFChIP-seq数据检测到的峰组合以研究CTCF对选择性剪接的调节作用。因此,在DDH和DHH之间共鉴定出624个DEI。例如,从CAPN3转录的同工型7.524.18可能与肉的嫩度有关。此外,在具有转录DEI的基因和通过CTCFChIP-seq鉴定的差异峰的基因之间，共有86个基因重叠。在这些重叠的基因中，ANKRD23产生不同的同工型,其可通过甲基化被CTCF调节。作为初步研究,我们的研究结果发现了与肉嫩度相关的新型同工型，并揭示了选择性剪接产生同工型的可能调控机制。
