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Evidence that processing of ribonucleotides in DNA by topoisomerase 1 is leading-strand specific.

Journal article
Authors Jessica S Williams
Anders R Clausen
Scott A Lujan
Lisette Marjavaara
Alan B Clark
Peter M Burgers
Andrei Chabes
Thomas A Kunkel
Published in Nature structural & molecular biology
Volume 22
Issue 4
Pages 291-7
ISSN 1545-9985
Publication year 2015
Published at
Pages 291-7
Language en
Keywords DNA, metabolism, DNA Polymerase II, metabolism, physiology, DNA Repair, DNA Replication, DNA Topoisomerases, Type I, metabolism, physiology, Ribonucleotides, metabolism, Saccharomyces cerevisiae, genetics, Saccharomyces cerevisiae Proteins, metabolism, physiology
Subject categories Biochemistry, Genetics


Ribonucleotides incorporated during DNA replication are removed by RNase H2-dependent ribonucleotide excision repair (RER). In RER-defective yeast, topoisomerase 1 (Top1) incises DNA at unrepaired ribonucleotides, initiating their removal, but this is accompanied by RNA-DNA-damage phenotypes. Here we show that these phenotypes are incurred by a high level of ribonucleotides incorporated by a leading strand-replicase variant, DNA polymerase (Pol) ɛ, but not by orthologous variants of the lagging-strand replicases, Pols α or δ. Moreover, loss of both RNases H1 and H2 is lethal in combination with increased ribonucleotide incorporation by Pol ɛ but not by Pols α or δ. Several explanations for this asymmetry are considered, including the idea that Top1 incision at ribonucleotides relieves torsional stress in the nascent leading strand but not in the nascent lagging strand, in which preexisting nicks prevent the accumulation of superhelical tension.

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