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1. (WO2018107093) GENOME-WIDE MAPPING OF DNA-DNA PROXIMITIES IN THE NUCLEUS

Pub. No.:    WO/2018/107093    International Application No.:    PCT/US2017/065418
Publication Date: Fri Jun 15 01:59:59 CEST 2018 International Filing Date: Sat Dec 09 00:59:59 CET 2017
IPC: C12Q 1/68
C07K 14/47
C40B 50/14
Applicants: UNIVERSITY OF SOUTHERN CALIFORNIA
Inventors: CHEN, Lin
Title: GENOME-WIDE MAPPING OF DNA-DNA PROXIMITIES IN THE NUCLEUS
Abstract:
Disclosed are methods and systems for determining the three-dimensional structure of chromatin in eukaryotic cells. More specifically, disclosed are methods and systems for obtaining chromatin structural information by surface immobilization that includes tethering crosslinked protein:DNA complexes and/or ligated DNA complexes to media such as beads, gels, and or matrices during the conformation capture assay. In general, the method includes flash freezing a cell such that the structural organization of the chromatin or other protein:DNA complexes is preserved, cryomilling the cell, producing cross-linked protein:DNA complexes by cutting the chromatin using a chemical, physical or enzymatic method, substantially immobilizing the cross-linked protein:DNA complexes, ligating the cross-linked protein:DNA complexes intramolecularly such that the ligated protein:DNA complexes represent structural organization of the chromatin; characterizing the ligated DNA by sequencing or other methods; and identifying any structural organization of the chromatin. The structural organization preferably includes information relating to interacting loci of the chromatin.