Repressor elements provide insights into tissue development and phenotypes in pigs  

作　　者：Yue-Dong Zhang Chao Guo Hang Liu Yun Gao Yongjun Tan Longjian Niu Ligang Wang Lixian Wang David MIrwin Chunhui Hou Zhong-Yin Zhou Ya-Ping Zhang 

机构地区：[1]Key Laboratory of Genetic Evolution&Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming,Yunnan 650223,China [2]Kunming College of Life Science,University of Chinese Academy of Sciences,Kunming,Yunnan 650204,China [3]State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan,Yunnan University,Kunming,Yunnan 650091,China [4]School of Life Science,Yunnan University,Kunming,Yunnan 650091,China [5]School of Life Sciences,Division of Life Sciences and Medicine,University of Science and Technology of China,Hefei,Anhui 230026,China [6]State Key Laboratory of Hybrid Rice,Hunan Hybrid Rice Research Center,Hunan Academy of Agricultural Sciences,Changsha,Hunan 410125,China [7]School of Public Health and Emergency Management,Southern University of Science and Technology,Shenzhen,Guangdong 518055,China [8]Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine,Southern University of Science and Technology,Shenzhen,Guangdong 518055,China [9]Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture,Institute of Animal Science,Chinese Academy of Agricultural Sciences,Beijing 100081,China [10]Department of Laboratory Medicine and Pathobiology,University of Toronto,Toronto M5S 1A8,Canada [11]Yunnan Key Laboratory of Biodiversity Information KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming,Yunnan 650223,China [12]Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences,Kunming,Yunnan 650223,China

出　　处：《Zoological Research》2024年第6期1313-1326,共14页动物学研究（英文）

基　　金：supported by the Science&Technology Department of Yunnan Province (202102AE090039);National Natural Science Foundation of China (32100502);Yunnan Revitalization Talent Support Program Young Talent Project;CAS “Light of West China”Program;Spring City Plan:High-level Talent Promotion and Training Project of Kunming (2022SCP001);CAS Key Technology Talent Program to Y.G。

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 2034 super repressor elements(SREs) and 22223 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.

关 键 词：Repressor elements Super repressor elements SILENCER Regulatory model Tissue development KLF4 Pig 

分 类 号：S828[农业科学—畜牧学]