Characterization of DNA-PK-bound end fragments using GLASS-ChIP

Rajashree A Deshpande; Tanya T Paull

doi:10.1016/bs.mie.2021.08.014

Characterization of DNA-PK-bound end fragments using GLASS-ChIP

Methods Enzymol. 2021:661:205-217. doi: 10.1016/bs.mie.2021.08.014. Epub 2021 Sep 21.

Authors

Rajashree A Deshpande¹, Tanya T Paull²

Affiliations

¹ The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.
² The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States. Electronic address: tpaull@utexas.edu.

PMID: 34776213
DOI: 10.1016/bs.mie.2021.08.014

Abstract

Endonucleolytic cleavage of DNA ends by the human Mre11-Rad50-Nbs1 (MRN) complex occurs in a manner that is promoted by DNA-dependent Protein Kinase (DNA-PK). A method is described to isolate DNA-PK-bound fragments released from chromatin in human cells using a modified Gentle Lysis and Size Selection chromatin immunoprecipitation (GLASS-ChIP) protocol. This method, combined with real-time PCR or next-generation sequencing, can identify sites of MRN endonucleolytic cutting adjacent to DNA-PK binding sites in human cells.

Keywords: DNA repair; DNA-PK; Double-strand break; MRN.

MeSH terms

Acid Anhydride Hydrolases / genetics
Acid Anhydride Hydrolases / metabolism
Cell Cycle Proteins* / genetics
Cell Cycle Proteins* / metabolism
Chromatin Immunoprecipitation
DNA / metabolism
DNA Repair
DNA-Binding Proteins* / genetics
DNA-Binding Proteins* / metabolism
Humans
MRE11 Homologue Protein / metabolism
Protein Kinases / genetics

Substances

Cell Cycle Proteins
DNA-Binding Proteins
DNA
Protein Kinases
MRE11 Homologue Protein
Acid Anhydride Hydrolases