Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

By J. Zuin, Jesse R. Dixon, Michael van der Reijden, Z. Ye, Petros Kolovos, R. Brouwer, M. V. D. van de Corput, H. V. D. van de Werken, T. Knoch, W. V. van Ijcken and 3 more. Proceedings of the National Academy of Sciences of the United States of America, 2013

801 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/1ced886f74cde8bf49fea8917e2c84b8a8db993c

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Citations in the corpus

Gene-specific H1 eviction through a transcriptional activator-p300-NAP1-H1 pathway (2019, result): “The results also are consistent with recent reports that CTCF degradation has minimal immediate effect on transcription (Rao et al., 2017; Zuin et al., 2014) and that H1 loss can have significant effects on chromosome organization without major transcriptional changes (Geeven et al.”
Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, background): “Interestingly, neighboring topological domains do not completely collapse or merge upon deletion of domain boundary regions nor when cohesin is depleted in non-cycling cells (Seitan et al., 2013; Sofueva et al., 2013; Zuin et al., 2014).”
Formation of Chromosomal Domains by Loop Extrusion (2015, background): “, 2014), and its depletion makes TADs less prominent (Sofueva et al., 2013; Zuin et al., 2014).”
Genome-wide mapping and analysis of chromosome architecture (2016, background): “A substantial, although variable (~7–50%), proportion of Hi-C contacts detected in mammals using the original Hi-C protocol originate from inter-chromosomal (‘ trans ’) ligation events 6,19,22,28,62–68 .”
Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture (2015, positive): “, 2012), and knockout experiments have suggested a quantitative link between loss of chromosomal looping structure and loss of the CTCF/cohesin binding landscapes (Sofueva et al., 2013; Zuin et al., 2014; Seitan et al., 2013).”
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes (2014, positive): “Gene loops and other structures within TADs are thought to reflect the activities of transcription factors (TFs), cohesin and CTCF (Baranello et al., 2014; Gorkin et al., 2014; Phillips-Cremins et al., 2013; Seitan et al., 2013; Zuin et al., 2014).”
A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome (2016, neutral): “…architecture in mammalian cells indicated that loss of Cohesin results in a reduction of interaction frequency within TADs (“intra-TAD”), while knockdown of CTCF results in both loss of intra-TAD contact frequency accompanied by an increase in inter-TAD contact frequency (Zuin et al., 2014).”
Cohesin loss eliminates all loop domains (2017, background): “However, initial, low-resolution experiments examining genome-wide depletion of CTCF and cohesin observed only limited effects, reporting that compartments and contact domains still appear to be present (Seitan et al., 2013; Sofueva et al., 2013; Zuin et al., 2014).”
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function (2015, positive): “, 2012); however, CBSs are enriched at constitutive boundaries of topologically associated domains (TADs) (Dixon et al., 2012; Gibcus and Dekker, 2013; Zuin et al., 2014).”
Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization (2017, positive): “In line with earlier less impactful (Figure S3M) RNAi-mediated CTCF depletion (Zuin et al., 2014) we detected fewer intra-TAD contacts upon loss of CTCF by Hi-C, while FISH did not detect changes in intra-TAD compaction (Figure 3C-F).”