University of Pittsburgh, Department of Biological Sciences, Pittsburgh, United States of America.
PLoS Genet. 2020 Oct 6;16(10):e1009042. doi: 10.1371/journal.pgen.1009042. eCollection 2020 Oct.
A ~10-11 bp periodicity in dinucleotides imparting DNA bending, with shorter periods found in organisms with positively-supercoiled DNA and longer periods found in organisms with negatively-supercoiled DNA, was previously suggested to assist in DNA compaction. However, when measured with more robust methods, variation in the observed periods between organisms with different growth temperatures is not consistent with that hypothesis. We demonstrate that dinucleotide periodicity does not arise solely by mutational biases but is under selection. We found variation between genomes in both the period and the suite of dinucleotides that are periodic. Whereas organisms with similar growth temperatures have highly variable periods, differences in periods increase with phylogenetic distance between organisms. In addition, while the suites of dinucleotides under selection for periodicity become more dissimilar among more distantly-related organisms, there is a core set of dinucleotides that are strongly periodic among genomes in all domains of life. Notably, this core set of periodic motifs are not involved in DNA bending. These data indicate that dinucleotide periodicity is an ancient genomic architecture which may play a role in shaping the evolution of genes and genomes.
以前曾有人提出，二核苷酸的 10-11bp 周期性结构赋予 DNA 弯曲性，而在具有正超螺旋 DNA 的生物中，这种周期性较短，在具有负超螺旋 DNA 的生物中则较长，这有助于 DNA 的紧缩。然而，当使用更可靠的方法进行测量时，不同生长温度的生物之间观察到的周期变化与该假说并不一致。我们证明，二核苷酸周期性并非仅仅由突变偏倚产生，而是受到选择的影响。我们发现，在周期和周期性二核苷酸的组合方面，基因组之间存在差异。尽管具有相似生长温度的生物具有高度可变的周期，但周期差异随着生物之间的系统发育距离的增加而增加。此外，尽管周期性选择的二核苷酸组合在亲缘关系较远的生物中变得更加不同，但在所有生命领域的基因组中，都有一组核心的二核苷酸具有很强的周期性。值得注意的是，这组核心的周期性基序不参与 DNA 弯曲。这些数据表明，二核苷酸周期性是一种古老的基因组结构，可能在塑造基因和基因组的进化中发挥作用。
