整合 ATAC-Seq 和 RNA-Seq 分析鉴定天竺白牦牛背长肌发育的关键基因

IF 4.9 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Jingsheng Li, Zongchang Chen, Yan-qing Bai, Yali Wei, Dashan Guo, Zhanxin Liu, Yanmei Niu, Bingang Shi, Xiaolan Zhang, Yuan Cai, Zhidong Zhao, Jiang Hu, Jiqing Wang, Xiu Liu, Shaobin Li, Fangfang Zhao
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引用次数: 0

摘要

在出生后阶段,骨骼肌的发育经历了一系列精心调控的基因表达变化。然而,利用染色质可及性来揭示牦牛肌肉发育潜在分子机制的研究还很有限。因此,我们对基因表达水平和染色质可及性进行了分析,以全面描述天竺白牦牛肌肉生长发育过程中全基因组染色质可及性的动态特征,从而阐明整个过程中染色质可及区域的特征。首先,我们比较了两组牦牛染色质可及性的差异,观察到犊牛的染色质可及性水平高于成年牛,尤其是在转录起始位点(TSS)±2 kb范围内。为了研究染色质可及性区域的改变与基因表达水平变化之间的相关性,我们结合使用了 ATAC-seq 和 RNA-seq 技术,从而鉴定出 18 个中心转录因子 (TF) 和 110 个有显著影响的关键基因。通过进一步分析,我们成功鉴定了包括 Sp1、YY1、MyoG、MEF2A 和 MEF2C 在内的多个 TFs,以及一些可能与肌肉生长发育密切相关的候选基因(ANKRD2、ANKRD1、BTG2 和 LMOD3)。此外,我们还构建了一个互动网络程序,其中包括与肌肉生长和发育相关的枢纽 TF 和关键基因。这一创新方法为天竺白牦牛产后骨骼肌发育的分子机制提供了有价值的见解,同时也为今后牦牛肌肉发育的研究奠定了坚实的理论基础。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (ANKRD2, ANKRD1, BTG2 and LMOD3) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development.
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来源期刊
International Journal of Molecular Sciences
International Journal of Molecular Sciences Chemistry-Organic Chemistry
CiteScore
8.10
自引率
10.70%
发文量
13472
审稿时长
17.49 days
期刊介绍: The International Journal of Molecular Sciences (ISSN 1422-0067) provides an advanced forum for chemistry, molecular physics (chemical physics and physical chemistry) and molecular biology. It publishes research articles, reviews, communications and short notes. Our aim is to encourage scientists to publish their theoretical and experimental results in as much detail as possible. Therefore, there is no restriction on the length of the papers or the number of electronics supplementary files. For articles with computational results, the full experimental details must be provided so that the results can be reproduced. Electronic files regarding the full details of the calculation and experimental procedure, if unable to be published in a normal way, can be deposited as supplementary material (including animated pictures, videos, interactive Excel sheets, software executables and others).
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