Integrative ATAC-seq and RNA-seq analysis of myogenic differentiation of ovine skeletal muscle satellite cell

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics Pub Date : 2024-05-01 DOI:10.1016/j.ygeno.2024.110851

Yingxiao Su , Siqi He , Qian Chen , Hechun Zhang , Chang Huang , Qian Zhao , Yabin Pu , Xiaohong He , Lin Jiang , Yuehui Ma , Qianjun Zhao

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引用次数: 0

Abstract

Skeletal muscle satellite cells (SMSCs) play an important role in regulating muscle growth and regeneration. Chromatin accessibility allows physical interactions that synergistically regulate gene expression through enhancers, promoters, insulators, and chromatin binding factors. However, the chromatin accessibility altas and its regulatory role in ovine myoblast differentiation is still unclear. Therefore, ATAC-seq and RNA-seq analysis were performed on ovine SMSCs at the proliferation stage (SCG) and differentiation stage (SCD). 17,460 DARs (differential accessibility regions) and 3732 DEGs (differentially expressed genes) were identified. Based on joint analysis of ATAC-seq and RNA-seq, we revealed that PI3K-Akt, TGF-β and other signaling pathways regulated SMSCs differentiation. We identified two novel candidate genes, FZD5 and MAP2K6, which may affect the proliferation and differentiation of SMSCs. Our data identify potential cis regulatory elements of ovine SMSCs. This study can provide a reference for exploring the mechanisms of the differentiation and regeneration of SMSCs in the future.

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对绵羊骨骼肌卫星细胞成肌分化的 ATAC-seq 和 RNA-seq 整合分析

骨骼肌卫星细胞（SMSCs）在调节肌肉生长和再生方面发挥着重要作用。染色质可及性允许物理相互作用，通过增强子、启动子、绝缘体和染色质结合因子协同调控基因表达。然而，染色质可及性 Altas 及其在绵羊成肌细胞分化中的调控作用仍不清楚。因此，我们对处于增殖期（SCG）和分化期（SCD）的绵羊SMSCs进行了ATAC-seq和RNA-seq分析。结果发现了 17460 个 DARs（差异可及区域）和 3732 个 DEGs（差异表达基因）。基于ATAC-seq和RNA-seq的联合分析，我们发现PI3K-Akt、TGF-β和其他信号通路调控着SMSCs的分化。我们发现了两个可能影响 SMSCs 增殖和分化的候选基因 FZD5 和 MAP2K6。我们的数据确定了绵羊 SMSCs 的潜在顺式调控元件。这项研究可为今后探索 SMSCs 的分化和再生机制提供参考。

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来源期刊

Genomics 生物-生物工程与应用微生物

CiteScore

9.60

自引率

2.30%

发文量

260

审稿时长

60 days

期刊介绍： Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation. As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.