Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.

By Tae Hoon Kim, Z. Abdullaev, Andrew D. Smith, K. Ching, D. Loukinov, Roland Green, Michael Q. Zhang, Victor V Lobanenkov, Bing Ren. Cell, 2007

1,100 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/79cffa655507760e869dbc80901b82ecca55e516

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Citations in the corpus

• Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes (2014, neutral): “…formation, insulator activity and transcriptional regulation (Bell et al., 1999; Denholtz et al., 2013; Felsenfeld et al., 2004; Handoko et al., 2011; Kim et al., 2007; Phillips and Corces, 2009; Schwartz et al., 2012; Sexton et al., 2012; Soshnikova et al., 2010; Valenzuela and Kamakaka, 2006).”
• High-resolution profiling of histone methylations in the human genome. (2007, background): “CTCF is a multi-zinc finger protein that binds the insulators in vertebrates (Gaszner and Felsenfeld, 2006; Kim et al., 2007).”
• Next-Generation Genomics: an Integrative Approach (2010, neutral): “, CCCTC-binding factor (CTCF) for insulator element”
• The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells. (2013, background): “The averaged H1 D regions, predicted active enhancers (as defined in Materials and Methods), the TS refGene), and CTCF binding sites (Kim et al., 2007).”
• Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules (2012, methodology): “For CTCF annotations, we used evolutionarily conserved CTCF binding motifs (Xie et al. 2007) that were bound in vivo in either HeLa cells (Kim et al. 2007) or CD4+ T-cells (Figs.”
• Widespread plasticity in CTCF occupancy linked to DNA methylation (2012, background): “T transitions at vertebrate-conserved binding sites (Kim et al. 2007), consistent with germline methylation.”
• DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning (2016, background): “17 of these annotated motifs were transcription factors with a known implication in DNA methylation [16, 44, 45], including CTCF [46], E2f [47] and members of the Sp/KLF family [48] — transcription factors and regulators of cell differentiation.”
• The Human Transcription Factors. (2018, neutral): “…under physiological conditions; the only clear example out of hundreds that have been examined by ChIP-seq is CTCF, which occupies most of the 14,000 matches to its 14-base motif in the human genome with most of the sites occupied across the tested cell types (Fu et al., 2008; Kim et al., 2007).”
• YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, neutral): “, 2006), but CTCF does not generally occupy these interacting elements (Cuddapah et al., 2009; Kim et al., 2007; Phillips-Cremins et al., 2013; Wendt et al., 2008).”