Small tandem DNA duplications result from CST-guided Pol α-primase action at DNA break termini

Joost Schimmel; Núria Muñoz-Subirana; Hanneke Kool; Robin van Schendel; Marcel Tijsterman

doi:10.1038/s41467-021-25154-w

Small tandem DNA duplications result from CST-guided Pol α-primase action at DNA break termini

Nat Commun. 2021 Aug 10;12(1):4843. doi: 10.1038/s41467-021-25154-w.

Authors

Joost Schimmel¹, Núria Muñoz-Subirana¹, Hanneke Kool¹, Robin van Schendel¹, Marcel Tijsterman^{2

3}

Affiliations

¹ Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
² Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. m.tijsterman@lumc.nl.
³ Institute of Biology Leiden, Leiden University, Leiden, The Netherlands. m.tijsterman@lumc.nl.

Abstract

Small tandem duplications of DNA occur frequently in the human genome and are implicated in the aetiology of certain human cancers. Recent studies have suggested that DNA double-strand breaks are causal to this mutational class, but the underlying mechanism remains elusive. Here, we identify a crucial role for DNA polymerase α (Pol α)-primase in tandem duplication formation at breaks having complementary 3' ssDNA protrusions. By including so-called primase deserts in CRISPR/Cas9-induced DNA break configurations, we reveal that fill-in synthesis preferentially starts at the 3' tip, and find this activity to be dependent on 53BP1, and the CTC1-STN1-TEN1 (CST) and Shieldin complexes. This axis generates near-blunt ends specifically at DNA breaks with 3' overhangs, which are subsequently repaired by non-homologous end-joining. Our study provides a mechanistic explanation for a mutational signature abundantly observed in the genomes of species and cancer cells.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Sequence
Cell Cycle Proteins / genetics
Cell Cycle Proteins / metabolism
Cell Line
Cells, Cultured
DNA Breaks, Double-Stranded*
DNA End-Joining Repair
DNA Polymerase I / genetics
DNA Polymerase I / metabolism*
DNA Primase / genetics
DNA Primase / metabolism*
DNA, Single-Stranded
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism
Humans
Mice
Microsatellite Repeats / genetics*
Multiprotein Complexes / genetics
Multiprotein Complexes / metabolism
Mutation
Telomere / genetics
Telomere / metabolism
Telomere-Binding Proteins / genetics
Telomere-Binding Proteins / metabolism*
Tumor Suppressor p53-Binding Protein 1 / genetics
Tumor Suppressor p53-Binding Protein 1 / metabolism

Substances

Cell Cycle Proteins
Ctc1 protein, human
DNA, Single-Stranded
DNA-Binding Proteins
Multiprotein Complexes
SHLD1 protein, human
Stn1 protein, human
TP53BP1 protein, human
Telomere-Binding Proteins
Ten1 protein, human
Tumor Suppressor p53-Binding Protein 1
DNA Primase
DNA polymerase alpha-primase
DNA Polymerase I