Genome-wide Maps of Alkylation Damage, Repair, and Mutagenesis in Yeast Reveal Mechanisms of Mutational Heterogeneity

DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape is unknown. Here we describe genome-wide maps of DNA base damage, repair, and mutagenesis at single nucleotide resolution in yeast treated with the alkylating agent methyl methanesulfonate (MMS). Analysis of these maps revealed that base excision repair (BER) of alkylation damage is significantly modulated by chromatin, with faster repair in nucleosome free regions, and slower repair and higher mutation density within strongly positioned nucleosomes. Both the translational and rotational settings of lesions within nucleosomes significantly influence BER efficiency; moreover, this effect is asymmetric relative to the nucleosome dyad and is regulated by histone modifications. Our data also indicate that MMS-induced A mutations are significantly enriched on the non-transcribed strand (NTS) of yeast genes, particularly in BER-deficient strains, due to higher damage formation on the NTS and transcription-coupled repair of the transcribed strand (TS). These findings reveal the influence of chromatin on repair and mutagenesis of base lesions on a genome-wide scale, and suggest a novel mechanism for transcription-associated mutation asymmetry, which is frequently observed in human cancers.DNA碱基损伤是基因组不稳定的重要诱因，目前对于基因组格局如何影响这类损伤病灶的形成与修复仍知之甚少。本研究绘制了经烷化剂甲基磺酸甲酯（methyl methanesulfonate, MMS）处理的酵母中，单核苷酸分辨率下的DNA碱基损伤、修复及诱变的全基因组图谱。对这些图谱的分析显示，烷化损伤的碱基切除修复（base excision repair, BER）过程会显著受染色质调控：在核小体缺失区域修复速度更快，而在稳定定位的核小体内部则修复更慢且突变密度更高。损伤在核小体中的平移定位与旋转定位均会显著影响碱基切除修复效率；且该效应相对于核小体对称轴呈不对称分布，并受组蛋白修饰调控。本研究数据还表明，由于非转录链（non-transcribed strand, NTS）上的损伤形成水平更高，且转录链（transcribed strand, TS）存在转录偶联修复，MMS诱导的A碱基突变在酵母基因的非转录链上显著富集，在碱基切除修复缺陷菌株中这一现象尤为突出。上述发现从全基因组尺度揭示了染色质对碱基损伤修复与诱变过程的调控作用，并为人类癌症中频繁观测到的转录相关突变不对称性提供了全新的机制解释。