Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

By Adrian L. Sanborn, Suhas S. P. Rao, Su-Chen Huang, Neva C. Durand, Miriam H. Huntley, A. Jewett, Ivan D. Bochkov, D. Chinnappan, Ashok Cutkosky, Jian Li and 7 more. Proceedings of the National Academy of Sciences of the United States of America, 2015

1,602 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dd21b98d33edbefa9ff877c77dae0c309e17a361

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Citations in the corpus

Genome-wide mapping and analysis of chromosome architecture (2016, methodology): “In Capture-HiC, sequences of interest can be enriched from a Hi-C DNA library to obtain highly multiplexed, targeted interaction profiles 29,53–60 .”
Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization (2017, neutral): “Our observations are compatible with mechanistic models where domain-wide enrichment of chromosomal contact is the result of a process that accumulates chromatin loops between CTCF-bound boundary elements (Fudenberg et al., 2016; Sanborn et al., 2015) (Figure 7D).”
Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data (2017, neutral): “…variety of contact mapping experiments, such as dilution Hi-C (Lieberman-Aiden et al., 2009), in situ Hi-C (Rao et al., 2014), single-cell Hi-C (Nagano et al., 2013), Hi-C 2 (Sanborn et al., 2015), ChIA-PET (Fullwood et al., 2009), HiChIP (Mumbach et al., 2016), and SPRITE (Quinodoz et al., 2017).”
Regulation of disease-associated gene expression in the 3D genome (2016, neutral): “On the basis of these findings, it has now been suggested that loop extrusion 95 underlies TAD formation 93,96 (reviewed in REF.”
Cohesin loss eliminates all loop domains (2017, methodology): “…simulations integrating extrusion and compartmentalization can recapitulate Hi-C experimental results To test the hypothesis that the Hi-C contact maps we observed are consistent with the presence of two distinct folding mechanisms, we modeled a 2.1 Mb region on chromosome 3 (Sanborn et al., 2015).”
Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus (2018, background): “Finally, at 25kb resolution, we observe specific “looping” interactions that connect local regions that contain the expected convergent CTCF motif orientation previously described for loop structures (Figure 1E, Figure S1J) (Sanborn et al., 2015).”
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells (2018, background): “The loop extrusion model (22, 40), in which cohesin complexes extrude DNA until stopped by a pair of CTCF motifs, has been proposed to explain the formation of TADs and sub-TADs at the population level (22, 25, 40, 41).”
Chromatin organization by an interplay of loop extrusion and compartmental segregation (2017, background): “Active loop extrusion explains many features of TADs (15, 16): (i) TADs have no”
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds (2016, methodology): “We calculated the contact probability I(s) using the method we employed in (4, 26), focusing on chromosome 1 as a representative chromosome.”
Activity-by-Contact model of enhancer-promoter regulation from thousands of CRISPR perturbations (2019, methodology): “Because contact frequencies in Hi-C data correlate well across cell types and are largely determined by 1D genomic distance 21,22 , we compared versions of the ABC model in which we estimated Contact for each DE-G pair using either K562 Hi-C data, the average of Hi-C data from 10 human cell types,…”