Disruption of Transcriptional Coactivator Sub1 Leads to Genome-Wide Re-distribution of Clustered Mutations Induced by APOBEC in Active Yeast Genes

PLoS Genet. 2015 May 5;11(5):e1005217. doi: 10.1371/journal.pgen.1005217. eCollection 2015 May.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • APOBEC-1 Deaminase
  • Alleles
  • Amino Acid Transport Systems, Basic / genetics
  • Amino Acid Transport Systems, Basic / metabolism
  • Aspartate Carbamoyltransferase / genetics
  • Aspartate Carbamoyltransferase / metabolism
  • Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing) / genetics
  • Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing) / metabolism
  • Cation Transport Proteins / genetics
  • Cation Transport Proteins / metabolism
  • Cytidine Deaminase / genetics
  • Cytidine Deaminase / metabolism
  • DNA, Single-Stranded
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism
  • Gene Expression Regulation, Fungal*
  • Genes, Reporter
  • Genetic Association Studies
  • High-Throughput Nucleotide Sequencing
  • Mutation
  • Mutation Rate
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Sequence Analysis, DNA
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Transcriptional Activation*

Substances

  • Amino Acid Transport Systems, Basic
  • CAN1 protein, S cerevisiae
  • Cation Transport Proteins
  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • SUB1 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • URA2 protein, S cerevisiae
  • TRK1 protein, S cerevisiae
  • Aspartate Carbamoyltransferase
  • APOBEC-1 Deaminase
  • Cytidine Deaminase
  • Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)

Grant support

This work was supported by Eppley Pilot Project Grants (2014, 2015), Russian Foundation for Basic Research #15-04-08625, and Research Grant of St. Petersburg State University #1.38.426.2015 to YIP. Whole-genome sequencing was partially supported by Research Resource Center for Molecular and Cell Technologies, St. Petersburg State University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.