Disruption of Transcriptional Coactivator Sub1 Leads to Genome-Wide Re-distribution of Clustered Mutations Induced by APOBEC in Active Yeast Genes.
Mutations in genomes of species are frequently distributed non-randomly, resulting in mutation clusters, including recently discovered kataegis in tumors. DNA editing deaminases play the prominent role in the etiology of these mutations. To gain insight into the enigmatic mechanisms of localized hypermutagenesis that lead to cluster formation, we analyzed the mutational single nucleotide variations (SNV) data obtained by whole-genome sequencing of drug-resistant mutants induced in yeast diploids by AID/APOBEC deaminase and base analog 6-HAP. Deaminase from sea lamprey, PmCDA1, induced robust clusters, while 6-HAP induced a few weak ones. We found that PmCDA1, AID, and APOBEC1 deaminases preferentially mutate the beginning of the actively transcribed genes. Inactivation of transcription initiation factor Sub1 strongly reduced deaminase-induced can1 mutation frequency, but, surprisingly, did not decrease the total SNV load in genomes. However, the SNVs in the genomes of the sub1 clones were re-distributed, and the effect of mutation clustering in the regions of transcription initiation was even more pronounced. At the same time, the mutation density in the protein-coding regions was reduced, resulting in the decrease of phenotypically detected mutants. We propose that the induction of clustered mutations by deaminases involves: a) the exposure of ssDNA strands during transcription and loss of protection of ssDNA due to the depletion of ssDNA-binding proteins, such as Sub1, and b) attainment of conditions favorable for APOBEC action in subpopulation of cells, leading to enzymatic deamination within the currently expressed genes. This model is applicable to both the initial and the later stages of oncogenic transformation and explains variations in the distribution of mutations and kataegis events in different tumor cells.
Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.
Artem G
AG
Lada
Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia.
Sergei F
SF
Kliver
Department of Genetics, Cell Biology and Anatomy, and Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.
Alok
A
Dhar
Research Resource Center for Molecular and Cell Technologies, Research Park, St. Petersburg State University, St. Petersburg, Russia.
Dmitrii E
DE
Polev
Research Resource Center for Molecular and Cell Technologies, Research Park, St. Petersburg State University, St. Petersburg, Russia.
Alexey E
AE
Masharsky
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America; Institute of Cytology and Genetics, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
Igor B
IB
Rogozin
Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.
Youri I
YI
Pavlov
D000071479:APOBEC-1 Deaminase; D000483:Alleles; D026923:Amino Acid Transport Systems, Basic / Q000235:genetics / Q000378:metabolism; D001221:Aspartate Carbamoyltransferase / Q000235:genetics / Q000378:metabolism; D002223:Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing) / Q000235:genetics / Q000378:metabolism; D027682:Cation Transport Proteins / Q000235:genetics / Q000378:metabolism; D003564:Cytidine Deaminase / Q000235:genetics / Q000378:metabolism; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D017930:Genes, Reporter; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation; D059645:Mutation Rate; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D015533:Transcriptional Activation
D026923:Amino Acid Transport Systems, Basic; C502212:CAN1 protein, S cerevisiae; D027682:Cation Transport Proteins; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; C101206:SUB1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; C110837:URA2 protein, S cerevisiae; C068664:TRK1 protein, S cerevisiae; D001221:Aspartate Carbamoyltransferase; D000071479:APOBEC-1 Deaminase; D003564:Cytidine Deaminase; D002223:Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)