HETEROGENEITY OF GENOMES - MEASURES AND VALUES
HETEROGENEITY OF GENOMES - MEASURES AND VALUES
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DOI：
10.1073/pnas.91.26.12837
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发表时间：
1994-12-20
影响因子：
11.1
通讯作者：
BLAISDELL, BE
中科院分区：
文献类型：
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作者：
KARLIN, S;LADUNGA, I;BLAISDELL, BE
基因组的同质性进行了调查的广泛基础的DNA序列的二核苷酸相对丰度的距离（简称δ距离）和olgonucleotide组成的极端。它表明，在同一物种中的不同基因组序列之间的Δ距离是低的，只有约2或3倍的随机DNA中发现的距离，通常小于种间的Δ距离。短寡核苷酸的极端包括在大多数温和噬菌体序列中TpA的代表性不足和GpC的代表性过高;在大多数真细菌基因组中CTAG的代表性不足;在大多数噬菌体中GATC的代表性不足;在脊椎动物、所有动物线粒体基因组和许多嗜热细菌序列中CpG抑制;以及在所有动物线粒体组和叶绿体基因组中GpG/CpG的代表性过高。解释集中在DNA结构（二核苷酸堆积能，DNA曲率和超螺旋，核小体组织），上下文相关的突变事件，甲基化效应，复制和修复过程。
Genomic homogeneity is investigated for a broad base of DNA sequences in terms of dinucleotide relative abundance distances (abbreviated delta-distances) and of of olgonucleotide compositional extremes. It is shown that delta-distances between different genomic sequences in the same species are low, only about 2 or 3 times the distance found in random DNA, and are generally smaller than the between-species delta-distances. Extremes in short oligonucleotides include underrepresentation of TpA and overrepresentation of GpC in most temperate bacteriophage sequences; underrepresentation of CTAG in most eubacterial genomes; underrepresentation of GATC in most bacteriophage; CpG suppression in vertebrates, in all animal mitochondrial genomes, and in many thermophilic bacterial sequences; and overrepresentation of GpG/CpC in ail animal mitochondrial sets and chloroplast genomes. Interpretations center on DNA structures (dinucleotide stacking energies, DNA curvature and superhelicity, nucleosome organization), context-dependent mutational events, methylation effects, and processes of replication and repair.