title: CTCF controls HOXA cluster silencing and mediates PRC2-repressive higher-order chromatin structure in NT2/D1 cells.
abstract: HOX cluster genes are activated sequentially in their positional order along the chromosome during vertebrate development. This phenomenon, known as temporal colinearity, depends on transcriptional silencing of 5' HOX genes. Chromatin looping was recently identified as a conserved feature of silent HOX clusters, with CCCTC-binding factor (CTCF) binding sites located at the loop bases. However, the potential contribution of CTCF to HOX cluster silencing and the underlying mechanism have not been established. Here, we demonstrate that the HOXA locus is organized by CTCF into chromatin loops and that CTCF depletion causes significantly enhanced activation of HOXA3 to -A7, -A9 to -A11, and -A13 in response to retinoic acid, with the highest effect observed for HOXA9. Our subsequent analyses revealed that CTCF facilitates the stabilization of Polycomb repressive complex 2 (PRC2) and trimethylated lysine 27 of histone H3 (H3K27me3) at the human HOXA locus. Our results reveal that CTCF functions as a controller of HOXA cluster silencing and mediates PRC2-repressive higher-order chromatin structure.
authors.affiliation: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
authors.forename: Miao
authors.initials: M
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
authors.forename: Guang-Nian
authors.initials: GN
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Lv
authors.affiliation: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
authors.forename: Guoyou
authors.initials: G
authors.lastname: Liu
authors.affiliation: Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, People's Republic of China.
authors.forename: Lily Yan
authors.initials: LY
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
authors.forename: De-Long
authors.initials: DL
authors.lastname: Hao
authors.affiliation: Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China Center for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, People's Republic of China.
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China iudp@pumc.edu.cn.
authors.forename: De-Pei
authors.initials: DP
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
authors.forename: Chih-Chuan
authors.initials: CC
authors.lastname: Liang
mesh_terms: D001483:Base Sequence; D000076246:CCCTC-Binding Factor; D045744:Cell Line, Tumor; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D020868:Gene Silencing; D056426:Genetic Loci; D006657:Histones / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D006801:Humans; D008968:Molecular Conformation; D063151:Polycomb Repressive Complex 2 / Q000502:physiology*; D055550:Protein Stability; D012097:Repressor Proteins / Q000502:physiology*; D017384:Sequence Deletion; D014212:Tretinoin / Q000502:physiology
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D002843:Chromatin; D006657:Histones; D018398:Homeodomain Proteins; D012097:Repressor Proteins; C088144:HoxA protein; D014212:Tretinoin; D063151:Polycomb Repressive Complex 2