CTCF: Master Weaver of the Genome

By Jennifer Phillips, V. Corces. Cell, 2009

1,575 citations recorded by the source corpus.

CTCF is a highly conserved zinc finger protein implicated in diverse genomic regulatory functions, including transcriptional activation/repression, insulation, imprinting, and X-chromosome inactivation. Here we re-evaluate data supporting these roles in the context of mechanistic insights provided by recent genome-wide studies and highlight evidence for CTCF-mediated intra- and inter-chromosomal contacts at several developmentally regulated genomic loci. These analyses support a primary role for CTCF in the global organization of chromatin architecture and suggest that CTCF may be a heritable component of an epigenetic system regulating the interplay between DNA methylation, higher-order chromatin structure, and lineage-specific gene expression.

Subfields: Genetics, Molecular Biology, Pediatrics, Perinatology and Child Health

View Paper: https://www.semanticscholar.org/paper/edc65153cc31e8390863f2f87302f95edde6a614

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In Genetics

In Molecular Biology

In Pediatrics, Perinatology and Child Health

Citations in the corpus

Charting histone modifications and the functional organization of mammalian genomes (2011, background): “Insulators are DNA elements that block enhancer activitie”
Transcriptional Regulation and its Misregulation in Disease (2013, neutral): “Thus, cohesin is thought to have roles in transcription activation at some genes and in silencing at others (Dorsett, 2011; Hadjur et al., 2009; Parelho et al. 2008; Phillips and Corces, 2009; Schmidt et al., 2010; Seitan and Merkenschlager, 2012; Wendt et al. 2008).”
Comprehensive Genome-wide Protein-DNA Interactions Detected at Single Nucleotide Resolution (2011, background): “CTCF is a sequence-specific DNA-binding protein that plays important roles in metazoan gene regulation and three-dimensional chromatin organization in a wide variety of cell types (Ohlsson et al., 2010; Phillips and Corces, 2009).”
Functional and mechanistic diversity of distal transcription enhancers (2011, neutral): “Notably, CTCF binding to insulator elements can block enhancer-mediated gene activation when such elements are located between an enhancer and promoter (Phillips and Corces, 2009).”
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture (2011, background): “Asymmetric contacts around CTCF binding sites CTCF binding sites are studied extensively in the context of insulation of chromosomal domains and are hypothesized to provide chromosomes with a grid of highly organized anchor points facilitating domain demarcation and looping interaction”
Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. (2012, background): “To determine whether Ctcf interfered with reprogramming, we overexpressed Ctcf in NGFP2 MEFs (Figure S4D).”
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing (2011, neutral): “CTCF is an 11 zinc-finger DNA-binding protein with multiple nuclear functions, largely grouped into two categories: insulating inactive regions of the genome from active regions and promoting long-range interactions between distal regions of the genom”
Insights into hominid evolution from the gorilla genome sequence (2012, background): “We further investigated great ape regulatory evolution by comparing the binding in human and gorilla of CTCF, a protein essential to vertebrate development that is involved in transcriptional regulation, chromatin loop formation and protein scaffolding 36 .”