A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome

Gittens, William H, Johnson, Dominic J, Allison, Rachal M, Cooper, Tim J, Thomas, Holly and Neale, Matthew J (2019) A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome. Nature Communications, 10. a4846. ISSN 2041-1723

[img] PDF - Published Version
Available under License Creative Commons Attribution.

Download (8MB)

Abstract

DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes—and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage—distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.

Item Type: Article
Keywords: Top2, Spo11, CC-seq, topoisomerase, topological stress, nucleotide-resolution
Schools and Departments: School of Life Sciences > Sussex Centre for Genome Damage and Stability
Research Centres and Groups: Genome Damage and Stability Centre
Subjects: Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0447 Genes. Alleles. Genome
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0460 Mutations > QH0467 Genetic repair mechanisms
Depositing User: William Gittens
Date Deposited: 07 Jan 2020 09:04
Last Modified: 07 Jan 2020 09:15
URI: http://sro.sussex.ac.uk/id/eprint/88899

View download statistics for this item

📧 Request an update
Project NameSussex Project NumberFunderFunder Ref
Biochemical reconstitution of DNA repair reactions on intact chromatinG0986EUROPEAN UNION311336
Spatial regulation of meiotic recombinationG2004WELLCOME TRUST200843/Z/16/Z
Control and impact of meiotic DNA resection on recombination and genome stabilityG1538BBSRC-BIOTECHNOLOGY & BIOLOGICAL SCIENCES RESEARCH COUNCILBB/M010279/1