1: Genomics Proteomics Bioinformatics. 2005 Aug;3(3):158-68.

Neighboring-nucleotide effects on the mutation patterns of the rice genome.

Zhao H, Li QZ, Zeng CQ, Yang HM, Yu J.

Beijing Genomics Institute, Chinese Academy of Sciences (CAS), Beijing 101300,
China.

DNA composition dynamics across genomes of diverse taxonomy is a major subject of
genome analyses. DNA composition changes are characteristics of both replication 
and repair machineries. We investigated 3,611,007 single nucleotide polymorphisms
(SNPs) generated by comparing two sequenced rice genomes from distant inbred
lines (subspecies), including those from 242,811 introns and 45,462
protein-coding sequences (CDSs). Neighboring-nucleotide effects (NNEs) of these
SNPs are diverse, depending on structural content-based classifications
(genome-wide, intronic, and CDS) and sequence context-based categories (A/C, A/G,
A/T, C/G, C/T, and G/T substitutions) of the analyzed SNPs. Strong and evident
NNEs and nucleotide proportion biases surrounding the analyzed SNPs were observed
in 1-3 bp sequences on both sides of an SNP. Strong biases were observed around
neighboring nucleotides of protein-coding SNPs, which exhibit a periodicity of
three in nucleotide content, constrained by a combined effect of codon-related
rules and DNA repair mechanisms. Unlike a previous finding in the human genome,
we found negative correlation between GC contents of chromosomes and the
magnitude of corresponding bias of nucleotide C at -1 site and G at +1 site.
These results will further our understanding of the mutation mechanism in rice as
well as its evolutionary implications.