Characterization of DNA-PK-Bound End Fragments Using GLASS-ChIP

Rajashree A Deshpande; Tanya T Paull

doi:10.1007/978-1-0716-2063-2_11

Characterization of DNA-PK-Bound End Fragments Using GLASS-ChIP

Methods Mol Biol. 2022:2444:171-182. doi: 10.1007/978-1-0716-2063-2_11.

Authors

Rajashree A Deshpande¹, Tanya T Paull²

Affiliations

¹ The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
² The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. tpaull@utexas.edu.

PMID: 35290638
DOI: 10.1007/978-1-0716-2063-2_11

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 breaks; MRN complex.

MeSH terms

Chromatin Immunoprecipitation
DNA / genetics
DNA / metabolism
DNA Breaks, Double-Stranded
DNA-Binding Proteins* / genetics
DNA-Binding Proteins* / metabolism
Humans
Protein Kinases* / genetics

Substances

DNA-Binding Proteins
DNA
Protein Kinases