Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact

Abstract

Deciphering the multitude of epigenomic and genomic factors that influence the mutation rate is an area of great interest in modern biology. Recently, chromatin has been shown to play a part in this process. To elucidate this relationship further, we integrated our own ultra-deep sequenced human nucleosomal DNA data set with a host of published human genomic and cancer genomic data sets. Our results revealed, that differences in nucleosome occupancy are associated with changes in base-specific mutation rates. Increasing nucleosome occupancy is associated with an increasing transition to transversion ratio and an increased germline mutation rate within the human genome. Additionally, cancer single nucleotide variants and microindels are enriched within nucleosomes and both the coding and non-coding cancer mutation rate increases with increasing nucleosome occupancy. There is an enrichment of cancer indels at the theoretical start (74 bp) and end (115 bp) of linker DNA between two nucleosomes. We then hypothesized that increasing nucleosome occupancy decreases access to DNA by DNA repair machinery and could account for the increasing mutation rate. Such a relationship should not exist in DNA repair knockouts, and we thus repeated our analysis in DNA repair machinery knockouts to test our hypothesis. Indeed, our results revealed no correlation between increasing nucleosome occupancy and increasing mutation rate in DNA repair knockouts. Our findings emphasize the linkage of the genome and epigenome through the nucleosome whose properties can affect genome evolution and genetic aberrations such as cancer.

Fig 1. Nucleosomes and human genetic variation, and mutations.

A, Nucleosome occupancy scores (NOS) around flagged SNPs and common SNPs. B, The average transition to transversion ratio in 1,000 bp bins as a function of NOS, calculated from 1,092 individuals. C, The ancestral transition to transversion ratio calculated for 10 groups corresponding to increasing nucleosome occupancy. D, Normalized base-specific mutation rates (MR) of 10 groups corresponding to increasing nucleosome occupancy. E, Ancestral AA→AG MR in relation to nearest dyad. F, Fast Fourier transform (FFT) of the AA→AG MR. G, Effect of increasing nucleosome occupancy on germline mutations, asterisk denotes statistical significance (p-value < 0.01 by Z-test with Bonferroni correction) between first and last group.

Fig 2. Nucleosome occupancy and cancer mutations.

A, Cancer non-coding mutation rate (MR) in relation to nucleosome occupancy scores (NOS) with a Pearson’s correlation coefficient (PCC) of 0.833. Bottom x-axis corresponds to the bar graph depicting the NOS for 10 equally sized groups of increasing nucleosome occupancy. Top x-axis corresponds to the scatter plot depiction of the same data for each individual NOS. B, Raw counts of Cancer SNVs in relation to dyads. C, Cancer indel and microindel counts in relation to absolute distance to nearest dyad. Two small enrichments of indels are at 74 and 115 bp which correspond to the theoretical start and end locations of linker DNA between two nucleosomes. D, The total cancer (coding and non-coding) mutation rate as a function of NOS, Pearson’s correlation coefficient (PCC) of 0.989. Bottom x-axis corresponds to the bar graph depicting the NOS for 10 equally sized groups of increasing nucleosome occupancy. Top x-axis corresponds to the scatter plot depiction of the same data for each individual NOS.

Fig 3. Effect of nucleosome occupancy on mutation rate in DNA repair deficient yeast.

The non-coding mutation rate in yeast that lack DNA repair machinery in relation to nucleosome occupancy scores (NOS) with a Pearson’s correlation coefficient (PCC) of 0.048. Bottom x-axis corresponds to the bar graph depicting the NOS for 10 equally sized groups of increasing nucleosome occupancy. Top x-axis corresponds to the scatter plot depiction of the same data for each individual NOS.