Evidence that transient replication errors initiate nuclear genome mutations

DNA synthesis during genomic replication generates mismatches that lead to mutations. Point mutations may be caused by base-base mismatches that yields base substitutions or by primer- or template-strand slippage, which yield insertions and deletions (indels), respectively. Evidence obtained 40 years ago with DNA polymerases in vitro indicated that transient DNA intermediates also initiate substitutions and indels. Here, we provide evidence in vivo that the rates of specific single-base mutations at or adjacent to the 3'-terminus of the primer strand of mononucleotide runs increase change with run length. We propose that four such TIM (transient initiator mutagenesis) pathways are active during replication of the yeast nuclear genome in vivo and may be a universal feature of DNA replication.