{"pi": {"error": "no view permissions"}, "url": "https://www.4dnucleome.org/tcpa_trial.html", "name": "TCPA-2017-08", "title": "DEVELOPMENT OF TRAC-LOOP, A NOVEL TECHNIQUE TO DETECT GENOME-WIDE CHROMATIN INTERACTIONS", "status": "current", "project": "4DN", "description": "TCPA: Most current techniques for genome-wide analysis of chromatin interactions are based on the \nchromosome conformation capture (3C) technique. Because the traditional Hi-C technique uses a 6-bp restriction enzyme to cut chromatin, which usually finds one cleavage site every 5000bp in the genome, it does not have sufficient resolution for identification of enhancer-promoter interactions. Significant improvement has been achieved by the in situ Hi-C protocol, which uses a 4-bp cutter enzyme and reaches a resolution of about 1kb, thus enabling identification of specific enhancer-promoter interactions at high-resolution. However, this method requires a costly sequencing depth of 5 to 10 billions of paired-end tags (PETs) per library, which prohibits its application to a large number of samples. Other 3C-based techniques have been developed to focus on interactions at selected regions by capture Hi-C or tethered through specific proteins by ChIA-PET have helped to increase resolution by focusing on potential regulatory regions of the genome. However, a recent study compared \nchromatin interactions detected by fluorescence in situ hybridization (FISH) and 3C-based assays and found a high degree of discrepancy between the two techniques, suggesting that cross-validation of interaction data using different strategies is critical. \nWe propose to develop a novel technique, TrAC-loop, for Transposition-mediated Analysis of \nChromatin loops in the genome. The method does not require SDS-mediated partial decondensation of chromatin, restriction enzyme digestion, or proximity-based ligation of chromatin fragments. TrAC-loop directly captures interacting chromatin regions by Tn5-mediated transposition of a bivalent ME (mosaic end) linker without disrupting the nuclear structure. Thus, this novel strategy avoids potential artifacts derived from SDS-mediated partial decondensation of chromatin, restriction enzyme digestion and proximity-based re-ligation of chromatin fragments that are used in the 3C assays. Our strategy represents a shift in paradigm. All other genome-wide methods of mapping chromatin interactions use 3C-based techniques, whereas ours use transposition. Although transposition has been used to tag \nchromatin, this is the first time it is used to join chromatin segments.", "date_created": "2018-01-23T17:45:14.033118+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2018-12-17T17:38:31.194148+00:00"}, "viewing_group": "4DN", "schema_version": "1", "@id": "/awards/TCPA-2017-08/", "@type": ["Award", "Item"], "uuid": "0116e3c0-fb5a-491c-a9c2-8e17df70bfc1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "DEVELOPMENT OF TRAC-LOOP, A NOVEL TECHNIQUE TO DETECT GENOME-WIDE CHROMATIN INTERACTIONS", "external_references": [], "center_title": "TCPA - Zhao", "pi_name": "Keji Zhao", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}