Zhongxian Xu, Tao Wang, Wei Zhu, Maosen Yang, Dong Leng, Ziyu Li, Jiaman Zhang, Pengliang Liu, Zhoulin Wu, Mengnan He, Yan Li, Hua Kui, Xue Bai, Bo Zeng, Yao Zhang, Qing Zhu, Xiaoling Zhao, Mingzhou Li, Diyan Li
{"title":"3D genomic alterations during development of skeletal muscle in chicken1","authors":"Zhongxian Xu, Tao Wang, Wei Zhu, Maosen Yang, Dong Leng, Ziyu Li, Jiaman Zhang, Pengliang Liu, Zhoulin Wu, Mengnan He, Yan Li, Hua Kui, Xue Bai, Bo Zeng, Yao Zhang, Qing Zhu, Xiaoling Zhao, Mingzhou Li, Diyan Li","doi":"10.1016/j.jia.2024.03.052","DOIUrl":null,"url":null,"abstract":"The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology, contractility, cell proliferation, differentiation, interactions, migration, and death. The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes. The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages. Hi-C was used to build a chromatin architectures during four representative stages. ChIP-seq was conducted to identify enhancers in these four stages, which are occupied by histone H3K27ac and H3K4me3 peaks. Results show that large-scale genome architecture changes are mostly unidirectional, and coupled by complex on/off dynamic patterns of gene expression. Specifically, we observed 258.30 Mb of the genome undergoing A/B compartment switching. Notable alterations (316.57 Mb) of interaction frequencies within TADs were observed. Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development. Some muscle-related gene promoters that interacted with active enhancers during development, and some myopathy/aging-associated genes that were activated in aging muscle were founded. These results provide key insights into skeletal muscle development in vivo, and offer a valuable resource that allows in-depth functional characterization of candidate genes.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":"30 1","pages":""},"PeriodicalIF":4.6000,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Integrative Agriculture","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1016/j.jia.2024.03.052","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRICULTURE, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
Abstract
The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology, contractility, cell proliferation, differentiation, interactions, migration, and death. The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes. The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages. Hi-C was used to build a chromatin architectures during four representative stages. ChIP-seq was conducted to identify enhancers in these four stages, which are occupied by histone H3K27ac and H3K4me3 peaks. Results show that large-scale genome architecture changes are mostly unidirectional, and coupled by complex on/off dynamic patterns of gene expression. Specifically, we observed 258.30 Mb of the genome undergoing A/B compartment switching. Notable alterations (316.57 Mb) of interaction frequencies within TADs were observed. Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development. Some muscle-related gene promoters that interacted with active enhancers during development, and some myopathy/aging-associated genes that were activated in aging muscle were founded. These results provide key insights into skeletal muscle development in vivo, and offer a valuable resource that allows in-depth functional characterization of candidate genes.
期刊介绍:
Journal of Integrative Agriculture publishes manuscripts in the categories of Commentary, Review, Research Article, Letter and Short Communication, focusing on the core subjects: Crop Genetics & Breeding, Germplasm Resources, Physiology, Biochemistry, Cultivation, Tillage, Plant Protection, Animal Science, Veterinary Science, Soil and Fertilization, Irrigation, Plant Nutrition, Agro-Environment & Ecology, Bio-material and Bio-energy, Food Science, Agricultural Economics and Management, Agricultural Information Science.