Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell. 2007;128(6):1231–45.
Article
CAS
Google Scholar
Ong CT, Corces VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet. 2014;15(4):234–46.
Article
CAS
Google Scholar
Ren G, Zhao K. CTCF and cellular heterogeneity. Cell Biosci. 2019;9:83.
Article
Google Scholar
Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, Polotskaja AV, Goodwin GH. A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5′-flanking sequence of the chicken c-myc gene. Oncogene. 1990;5(12):1743–53.
CAS
PubMed
Google Scholar
Klenova EM, Nicolas RH, Paterson HF, Carne AF, Heath CM, Goodwin GH, Neiman PE, Lobanenkov VV. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol. 1993;13(12):7612–24.
Article
CAS
Google Scholar
Chung JH, Bell AC, Felsenfeld G. Characterization of the chicken beta-globin insulator. Proc Natl Acad Sci U S A. 1997;94(2):575–80.
Article
CAS
Google Scholar
Bell AC, Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature. 2000;405(6785):482–5.
Article
CAS
Google Scholar
Yusufzai TM, Tagami H, Nakatani Y, Felsenfeld G. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol Cell. 2004;13(2):291–8.
Article
CAS
Google Scholar
Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res. 2009;19(1):24–32.
Article
CAS
Google Scholar
Van Bortle K, Ramos E, Takenaka N, Yang J, Wahi JE, Corces VG. Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains. Genome Res. 2012;22(11):2176–87.
Article
Google Scholar
Taslim C, Chen Z, Huang K, Huang TH, Wang Q, Lin S. Integrated analysis identifies a class of androgen-responsive genes regulated by short combinatorial long-range mechanism facilitated by CTCF. Nucleic Acids Res. 2012;40(11):4754–64.
Article
CAS
Google Scholar
Bonora G, Plath K, Denholtz M. A mechanistic link between gene regulation and genome architecture in mammalian development. Curr Opin Genet Dev. 2014;27:92–101.
Article
CAS
Google Scholar
Rao SSP, Huang SC, Glenn SHB, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, et al. Cohesin loss eliminates all loop domains. Cell. 2017;171(2):305–20.e324.
Article
Google Scholar
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665–80.
Article
CAS
Google Scholar
Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, et al. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell. 2015;163(7):1611–27.
Article
CAS
Google Scholar
Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet. 2011;43(7):630–8.
Article
CAS
Google Scholar
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376–80.
Article
CAS
Google Scholar
Ren G, Jin W, Cui K, Rodrigez J, Hu G, Zhang Z, Larson DR, Zhao K. CTCF-mediated enhancer-promoter interaction is a critical regulator of cell-to-cell variation of gene expression. Mol Cell. 2017;67(6):1049–1058.e1046.
Article
CAS
Google Scholar
Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell. 2017;169(5):930–44 e922.
Article
CAS
Google Scholar
Zuin J, Dixon JR, van der Reijden MI, Ye Z, Kolovos P, Brouwer RW, van de Corput MP, van de Werken HJ, Knoch TA, van IJken WF, et al. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci U S A. 2014;111(3):996–1001.
Article
CAS
Google Scholar
Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, et al. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell. 2015;162(4):900–10.
Article
CAS
Google Scholar
Kang JY, Song SH, Yun J, Jeon MS, Kim HP, Han SW, Kim TY. Disruption of CTCF/cohesin-mediated high-order chromatin structures by DNA methylation downregulates PTGS2 expression. Oncogene. 2015;34(45):5677–84.
Article
CAS
Google Scholar
Lang F, Li X, Zheng W, Li Z, Lu D, Chen G, Gong D, Yang L, Fu J, Shi P, et al. CTCF prevents genomic instability by promoting homologous recombination-directed DNA double-strand break repair. Proc Natl Acad Sci U S A. 2017;114(41):10912–7.
Article
CAS
Google Scholar
Shin JO, Lee JJ, Kim M, Chung YW, Min H, Kim JY, Kim HP, Bok J. CTCF regulates Otic neurogenesis via histone modification in the Neurog1 locus. Mol Cell. 2018;41(7):695–702.
CAS
Google Scholar
Hirayama T, Tarusawa E, Yoshimura Y, Galjart N, Yagi T. CTCF is required for neural development and stochastic expression of clustered Pcdh genes in neurons. Cell Rep. 2012;2(2):345–57.
Article
CAS
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.
Article
CAS
Google Scholar
Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature. 2006;441(7095):840–6.
Article
CAS
Google Scholar
Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science. 2010;329(5991):533–8.
Article
CAS
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
Article
CAS
Google Scholar
Dobin A, Gingeras TR. Mapping RNA-seq reads with STAR. Curr Protoc Bioinformatics. 2015;51:11.14.1–11.14.19.
Article
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9.
Article
CAS
Google Scholar
Brennecke P, Anders S, Kim JK, Kolodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, et al. Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods. 2013;10(11):1093–5.
Article
CAS
Google Scholar
Jiao X, Sherman BT, Huang da W, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics. 2012;28(13):1805–6.
Article
CAS
Google Scholar
Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
Article
Google Scholar