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DNase Hi-C was designed to overcome the limitations associated with restriction enzyme-based Hi-C approaches. Advances in molecular techniques led to the development of an improved version of this technique known as in situ DNase Hi-C that is dramatically simplified and easy to use.\n\nThe in situ DNase Hi-C protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. Chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor, and proximity ligation is carried out in the intact nucleus to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. 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\n

\n Image source: Ramani et. al. Nature Protocols 2016, Figure 1 \n
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\n Image source: Ramani et. al. Nature Protocols 2016, Figure 1 \n
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DNase Hi-C

\n

DNase Hi-C is a method to detect and quantify pairwise interactions between chromosome regions across the entire genome. DNase Hi-C was designed to overcome the limitations associated with restriction enzyme-based Hi-C approaches. Advances in molecular techniques led to the development of an improved version of this technique known as in situ DNase Hi-C that is dramatically simplified and easy to use.

\n

The in situ DNase Hi-C protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. Chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor, and proximity ligation is carried out in the intact nucleus to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is constructed by shearing the DNA, selecting the biotin-containing fragments with streptavidin magnetic beads and PCR amplification. After high throughput sequencing, analysis of the resulting paired-end sequences produces a matrix that quantitatively characterizes the whole-genome chromatin contacts.

\n

See Ramani et al 2016 for more details on in situ DNase Hi-C.

\n
\n

\n Image source: Ramani et. al. Nature Protocols 2016, Figure 1 \n
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(2019)", "authors": ["Kim JS", "He X", "Liu J", "Duan Z", "Kim T", "Gerard J", "Kim B", "Pillai MM", "Lane WS", "Noble WS", "Budnik B", "Waldman T"], "@id": "/publications/d5f08680-be3a-462b-a11a-73991e5b0ef1/", "abstract": "The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins.", "display_title": "Kim JS et al. (2019) PMID:31010829", "status": "current", "url": "https://www.ncbi.nlm.nih.gov/pubmed/31010829", "title": "Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression.", "@type": ["Publication", "Item"], "journal": "The Journal of biological chemistry", "ID": "PMID:31010829", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"authors": ["Kim JS", "He X", "Liu J", "Duan Z", "Kim T", "Gerard J", "Kim B", "Pillai MM", "Lane WS", "Noble WS", "Budnik B", "Waldman T"], "@type": ["Publication", "Item"], "ID": "PMID:31010829", "abstract": "The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins.", "journal": "The Journal of biological chemistry", "@id": "/publications/d5f08680-be3a-462b-a11a-73991e5b0ef1/", "uuid": "d5f08680-be3a-462b-a11a-73991e5b0ef1", "date_published": "2019-05-31", "display_title": "Kim JS et al. (2019) PMID:31010829", "status": "current", "title": "Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}