Morton Brian R, Bi Irie V, McMullen Michael D, Gaut Brandon S
Department of Biological Sciences, Barnard College, Columbia University, New York, New York 10027, USA.
Genetics. 2006 Jan;172(1):569-77. doi: 10.1534/genetics.105.049916. Epub 2005 Oct 11.
We examine variation in mutation dynamics across a single genome (Zea mays ssp. mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generated by resequencing 1776 transcribed regions. We report several relationships between flanking base composition and mutation pattern. The A + T content of the two sites immediately flanking the mutation site is correlated with rate, transition bias, and GC --> AT pressure. We also observe a significant CpG effect, or increase in transition rate at CpG sites. At the regional level we find that the strength of the CpG effect is correlated with regional A + T content, ranging from a 1.7-fold increase in transition rate in relatively G + C-rich regions to a 2.6-fold increase in A + T-rich regions. We also observe a relationship between locus A + T content and GC --> AT pressure. This regional effect is in opposition to the influence of the two immediate neighbors in that GC --> AT pressure increases with increasing locus A + T content but decreases with increasing flanking base A + T content and may represent a relationship between genome location and mutation bias. The data indicate multiple context effects on mutations, resulting in significant variation in mutation dynamics across the genome.
我们使用通过对1776个转录区域进行重测序产生的10472个单核苷酸多态性（SNP）数据集，研究了单个基因组（玉米亚种玉米）中突变动态的变化与区域及侧翼碱基组成的关系。我们报告了侧翼碱基组成与突变模式之间的几种关系。紧邻突变位点的两个位点的A + T含量与突变率、转换偏向以及GC→AT压力相关。我们还观察到显著的CpG效应，即CpG位点的转换率增加。在区域水平上，我们发现CpG效应的强度与区域A + T含量相关，在相对富含G + C的区域转换率增加1.7倍，在富含A + T的区域增加2.6倍。我们还观察到基因座A + T含量与GC→AT压力之间的关系。这种区域效应与紧邻的两个邻居的影响相反，因为GC→AT压力随着基因座A + T含量的增加而增加，但随着侧翼碱基A + T含量的增加而降低，这可能代表了基因组位置与突变偏向之间的关系。数据表明对突变存在多种背景效应，导致全基因组突变动态存在显著差异。
