DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci.

Autor:	Liu Y; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.; These authors contributed equally: Yuzhen Liu, Christopher D. McGann., McGann CD; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; These authors contributed equally: Yuzhen Liu, Christopher D. McGann., Krebs M; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA., Perkins TA Jr; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Fields R; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Camplisson CK; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA., Nwizugbo DZ; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA., Hsu C; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA., Avanessian SC; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA., Tsue AF; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Department of Pharmacology, University of Washington, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA., Kania EE; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Department of Pharmacology, University of Washington, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA., Shechner DM; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Department of Pharmacology, University of Washington, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA., Beliveau BJ; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA., Schweppe DK; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.; Institute of Stem Cell and Regenerative Medicine, University of Washington, USA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2024 Jul 29. Date of Electronic Publication: 2024 Jul 29.
DOI:	10.1101/2024.07.24.604987
Abstrakt:	The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition of chromatin and the regulatory proteins that reside there. Understanding these DNA-protein interactions at the level of specific genomic loci has remained challenging due to technical limitations. Here, we introduce a method termed "DNA O-MAP", which uses programmable peroxidase-conjugated oligonucleotide probes to biotinylate nearby proteins. We show that DNA O-MAP can be coupled with sample multiplexed quantitative proteomics and next-generation sequencing to quantify DNA-protein and DNA-DNA interactions at specific genomic loci. Competing Interests: Competing Interest Statement D.K.S. is a collaborator with Thermo Fisher Scientific, Genentech, Calico Labs, and AI Proteins. C.K.C., A.F.T., E.K., D.M.S., and B.J.B. have filed a patent application covering aspects of this work. B.J.B. is listed as an inventor on patent applications related to the SABER technology related to this work.
Databáze:	MEDLINE
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