Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity

Abstract

The gradual accumulation of mutations by any of a number of mutational processes is a major driving force of divergence and evolution. Here, we investigate a potentially novel mutational process that is based on the activity of members of the AID/ APOBEC family of deaminases. This gene family has been recently shown to introduce-in multiple types of cancer-enzyme-induced clusters of co-occurring somatic mutations caused by cytosine deamination. Going beyond somatic mutations, we hypothesized that APOBEC3-following its rapid expansion in primates-can introduce unique germline mutation clusters that can play a role in primate evolution. In this study, we tested this hypothesis by performing a comprehensive comparative genomic screen for APOBEC3-induced mutagenesis patterns across different hominids. We detected thousands of mutation clusters introduced along primate evolution which exhibit features that strongly fit the known patterns of APOBEC3G mutagenesis. These results suggest that APOBEC3G-induced mutations have contributed to the evolution of all genomes we studied. This is the first indication of site-directed, enzyme-induced genome evolution, which played a role in the evolution of both modern and archaic humans. This novel mutational mechanism exhibits several unique features, such as its higher tendency to mutate transcribed regions and regulatory elements and its ability to generate clusters of concurrent point mutations that all occur in a single generation. Our discovery demonstrates the exaptation of an anti-viral mechanism as a new source of genomic variation in hominids with a strong potential for functional consequences.

Rapid evolution of the human mutation spectrum

“…A recent study reported that two common germline variants affect both cancer risk and the somatic mutational spectrum by altering regulation of APOBEC DNA-editing enzymes 24 . Given that APOBEC activity appears to cause germline mutations as well 25 , we hypothesized that these two variants might also be germline mutators. Based on previous descriptions of the APOBEC signature 3, 26 , we classified TC→TT and TC→TG as potentially APOBEC-associated, all other mutations as non-APOBEC-associated, and tested for enrichment of APOBEC-associated variants on the candidate mutator haplotypes.…”

Multinucleotide mutations cause false inferences of lineage-specific positive selection

“…Codons with multiple differences between them can be interconverted only by serial single-nucleotide substitutions, the probability of which is the product of the probabilities of each independent event. Recent molecular studies have shown, however, that mutations affecting adjacent nucleotide sites often occur during replication, apparently because certain DNA microstructures recruit error-prone polymerases that lack proofreading activity and therefore make multiple errors close together [24][25][26][27][28][29][30][31][32][33] ; cytosine deaminases can also introduce clusters of co-occurring mutations 34,35 . Consistent with these mechanisms, genetic studies of human trios and mutationaccumulation experiments in laboratory organisms indicate that de novo clustered mutations occur more frequently than expected if each occurred independently 24, 30-32, 36,37 , and these MNMs are enriched in transversions.…”

APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context

“…In contrast, only a minority of heritable mutations are attributable to known mechanisms. Analyses of clustered mutations and L1 transposons have revealed a major role of low fidelity polymerase ζ and APOBEC3G in the generation of heritable mutations (Harris and Nielsen 2014;Seplyarskiy et al 2015;Zhu et al 2015;Knisbacher and Levanon 2016;Pinto et al 2016). Direct experiments have also uncovered the role of recombination in mutagenesis (Arbeithuber et al 2015;Yang et al 2015).…”

“…As APOBEC3A/B-induced mutagenesis affects singlestranded DNA, we suggest that, alongside the lagging strand during replication, it may also produce mutations on the nontemplate strand in transcribed regions, due to single strangeness of this strand during R loop formation (Skourti-Stathaki and Proudfoot 2014). The asymmetry observed in the CpCpW context may be related to the APOBEC3G transcription-associated activity that has been shown recently (Pinto et al 2016). …”

“…Only a few of the mutation types can be attributed to specific molecular processes. Most prominently, the CpG→TpG substitutions are known to result from spontaneous cytosine deamination of methyl-cytosine in the CpG context together with poor efficiency of subsequent base excision repair (Pfeifer 2006;Chen et al 2014); some mutations in the CpCpC motif arise due to activity of the APOBEC3G protein, which is normally involved in protection against viruses and retroelements (Knisbacher and Levanon 2016;Pinto et al 2016), and small insertions and deletions result from polymerase slippage on homonucleotide tracts and tandem repeats (Montgomery et al 2013).…”