Virus Infection Induces Immune Gene Activation with CTCF-anchored Enhancers and Chromatin Interactions in Pig Genome  

作　　者：Jianhua Cao Ruimin Ren Xiaolong Li Xiaoqian Zhang Yan Sun Xiaohuan Tian Ru Liu Xiangdong Liu Yijun Ruan Guoliang Li Shuhong Zhao 

机构地区：[1]Key Laboratory of Agricultural Animal Genetics,Breeding and Reproduction,Ministry of Education,College of Animal Science and Technology,Huazhong Agricultural University,Wuhan 430070,China [2]Key Laboratory of Swine Genetics and Breeding,Ministry of Agriculture and Rural Affairs,Huazhong Agricultural University,Wuhan 430070,China [3]Life Sciences Institute,Zhejiang University,Hangzhou 310058,China [4]Key Laboratory of Smart Farming for Agricultural Animals,College of Informatics,Huazhong Agricultural University,Wuhan 430070,China [5]Engineering Research Center of Intelligent Technology for Agriculture,Ministry of Education,Huazhong Agricultural University,Wuhan 430070,China [6]National Key Laboratory of Crop Genetic Improvement,Hubei Hongshan Laboratory,Huazhong Agricultural University,Wuhan 430070,China

出　　处：《Genomics, Proteomics & Bioinformatics》2024年第5期109-120,共12页基因组蛋白质组与生物信息学报(英文版)

基　　金：supported by the National Key R&D Program of China(Grant No.2021YFF1000601);the Hubei Provincial Natural Science Foundation(Grant No.2023AFB1085);the Wuhan Science and Technology Major Project on Key Techniques of Biological Breeding and Breeding of New Varieties(Grant No.2022021302024853);the National Natural Science Foundation of China(Grant Nos.31772563,31790414,and 31771402);the Fundamental Research Funds for the Central Universities(Grant No.2662014PY067).

摘　　要：Chromatin organization is important for gene transcription in pig genome.However,its three-dimensional(3D)structure and dynamics are much less investigated than those in human.Here,we applied the long-read chromatin interaction analysis by paired-end tag sequencing(ChIA-PET)method to map the whole-genome chromatin interactions mediated by CCCTC-binding factor(CTCF)and RNA polymerase II(RNAPII)in porcine macrophage cells before and after polyinosinic-polycytidylic acid[Poly(I:C)]induction.Our results reveal that Poly(I:C)induction impacts the 3D genome organization in the 3D4/21 cells at the fine-scale chromatin loop level rather than at the large-scale domain level.Furthermore,our findings underscore the pivotal role of CTCF-anchored chromatin interactions in reshaping chromatin architecture during immune responses.Knockout of the CTCF-binding locus further confirms that the CTCF-anchored enhancers are associated with the activation of immune genes via long-range interactions.Notably,the ChIA-PET data also support the spatial relationship between single nucleotide polymorphisms(SNPs)and related gene transcription in 3D genome aspect.Our findings in this study provide new clues and potential targets to explore key elements related to diseases in pigs and are also likely to shed light on elucidating chromatin organization and dynamics underlying the process of mammalian infectious diseases.

关 键 词：CTCF ChIA-PET CHROMATIN Immunity PIG 

分 类 号：Q78[生物学—分子生物学]