CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

By Ya Guo, Quan Xu, Daniele Canzio, Jia Shou, Jin-huan Li, David U. Gorkin, Inkyung Jung, Haiyang Wu, Yanan Zhai, Yuanxiao Tang and 8 more. Cell, 2015

905 citations recorded by the source corpus.

SUMMARY CTCF/cohesin play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. Inversion of CBS elements within the Pcdh enhancer reconfigures the topology of chromatin loops between the distal enhancer and target promoters, and alters gene-expression patterns. Thus, although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity. The findings reveal how 3D chromosome architecture can be encoded by genome sequence.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/dedfff413d395c99fbae55347745790deb41331a

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Citations in the corpus

Cohesin loss eliminates all loop domains (2017, background): “While there is clear agreement that deletion of individual CTCF binding sites can result in a loss of cohesin binding and can abolish loops and contact domains (Guo et al., 2015; Sanborn et al., 2015; de Wit et al., 2015), there have been conflicting reports about the effects of depleting cohesin or”
Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III (2020, background): “) [24, 25, 65-71], and noncoding RNAs have been implicated in organizing 3D genome structures, so the 3D genome may likely organize via a combinatory of many factors.”
CTCF Binding Polarity Determines Chromatin Looping. (2015, result): “Our data are in agreement with the recent demonstration that inversion of a kilobase-sized region carrying multiple CTCF/cohesin sites affects chromosome topology and expression (Guo et al., 2015).”
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks (2015, background): “Recent work has demonstrated that modulating CTCF binding at topologically associating domain boundaries can dramatically affect gene expression by altering the architecture of the genomic region (Lupiáñez et al. 2015; Guo et al. 2015).”
Predicting enhancer-promoter interaction from genomic sequence with deep neural networks (2016, background): “Distal regulatory enhancer elements in the genome can interact with proximal promoter regions to regulate the target gene’s expression, and mutations that change such interactions will cause the target gene to be dysregulated [6, 11, 34].”
YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, neutral): “CTCF proteins bound at enhancers and promoters can interact with one another and may thus facilitate enhancer-promoter interactions (Guo et al., 2015; Splinter et al., 2006), but CTCF does not generally occupy Cell.”
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. (2015, background): “Others have demonstrated deletion and inversion of DNA fragments containing CTCF/cohesin binding sites could disrupt the nearby TAD structure and alter associated gene transcription (Dowen et al., 2014; Guo et al., 2015).”
Regulation of disease-associated gene expression in the 3D genome (2016, neutral): “Alleles of SNPs are in linkage disequilibrium when their frequency of association in the population is not random, which indicates that they are physically and/or functionally linked. dysregulation (further discussed below) 91,92,98–100 .”
Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, background): “…of TAD Boundaries and CTCF-Mediated Loops Since TAD boundaries appear to restrict both enhancer function (Dowen et al., 2014; Flavahan et al., 2016; Guo et al., 2015; Lupiáñez et al., 2015) and spreading of chromatin marks (A) TADs appear to be highly conserved acrossmammals, therefore…”