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Repressor elements provide insights into tissue development and phenotypes in pigs

文献类型： 外文期刊

作者： Zhang, Yue-Dong 1 ; Guo, Chao 1 ; Liu, Hang 1 ; Gao, Yun 1 ; Tan, Yongjun 7 ; Niu, Longjian 8 ; Wang, Ligang 10 ; Wang, Lixian 10 ; Irwin, David M. 1 ; Hou, Chunhui 1 ; Zhou, Zhong-Yin 1 ; Zhang, Ya-Ping 1 ;

作者机构： 1.Chinese Acad Sci, Kunming Inst Zool, Key Lab Genet Evolut & Anim Models, Kunming 650223, Yunnan, Peoples R China

2.Chinese Acad Sci, Kunming Inst Zool, Yunnan Key Lab Mol Biol Domest Anim, Kunming 650223, Yunnan, Peoples R China

3.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650204, Yunnan, Peoples R China

4.Yunnan Univ, State Key Lab Conservat & Utilizat Bioresources Yu, Kunming 650091, Yunnan, Peoples R China

5.Yunnan Univ, Sch Life Sci, Kunming 650091, Yunnan, Peoples R China

6.Univ Sci & Technol China, Sch Life Sci, Div Life Sci & Med, Hefei 230026, Anhui, Peoples R China

7.Hunan Acad Agr Sci, Hunan Hybrid Rice Res Ctr, State Key Lab Hybrid Rice, Changsha 410125, Hunan, Peoples R China

8.Southern Univ Sci & Technol, Sch Publ Hlth & Emergency Management, Shenzhen 518055, Guangdong, Peoples R China

9.Southern Univ Sci & Technol, Shenzhen Key Lab Cardiovasc Hlth & Precis Med, Shenzhen 518055, Guangdong, Peoples R China

10.Chinese Acad Agr Sci, Inst Anim Sci, Key Lab Farm Anim Genet Resources & Germplasm Inno, Minist Agr, Beijing, Peoples R China

11.Univ Toronto, Dept Lab Med & Pathobiol, Toronto, ON M5S 1A8, Canada

12.Chinese Acad Sci, Kunming Inst Zool, Yunnan Key Lab Biodivers Informat, KIZ CUHK Joint Lab Bioresources & Mol Res Common D, Kunming 650223, Yunnan, Peoples R China

13.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China

关键词： Repressor elements; Super repressor elements; Silencer; Regulatory model; Tissue development; KLF4; Pig

期刊名称：ZOOLOGICAL RESEARCH （ 影响因子：4.7； 五年影响因子：4.7 ）

ISSN： 2095-8137

年卷期： 2024 年 45 卷 6 期

页码：

收录情况： SCI

摘要： Repressor elements significantly influence economically relevant phenotypes in pigs; however, their precise roles and characteristics are inadequately understood. In the present study, we employed H3K27me3 profiling, assay for transposase-accessible chromatin with highthroughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq) data across six tissues derived from three embryonic layers to identify and map 2 034 super repressor elements (SREs) and 22 223 typical repressor elements (TREs) in the pig genome. Notably, many repressor elements were conserved across mesodermal and ectodermal tissues. SREs exhibited tight regulation of their target genes, affecting a limited number of genes within a specific genomic region with pronounced effects, while TREs exerted broader but weaker regulation over a wider range of target genes. Furthermore, in neuronal tissues, genes regulated by repressor elements started to be repressed during the differentiation of stem cells into progenitor cells. Notably, analysis showed that many repressor elements exhibited cooperative and additive effects on the modulation of KLF4 expression. This research provides the first comprehensive map of pig repressor elements, serving as an essential reference for future studies on repressor elements.

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