Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites / 基因组蛋白质组与生物信息学报·英文版

Vertebrate genomes are characterized with CpG deficiency, particularly for GC-poor regions. The GC content-related CpG deficiency is probably caused by context-dependent deamination of methylated CpG sites. This hypothesis was examined in this study by comparing nucleotide frequencies at CpG flanking positions among invertebrate and vertebrate genomes. The finding is a transition of nucleotide preference of 5' T to 5' A at the invertebrate-vertebrate boundary, indicating that a large number of CpG sites with 5' Ts were depleted because of global DNA methylation developed in vertebrates. At genome level, we investigated CpG observed/expected (obs/exp) values in 500 bp fragments, and found that higher CpG obs/exp value is shown in GC-poor regions of invertebrate genomes (except sea urchin) but in GC-rich sequences of vertebrate genomes. We next compared GC content at CpG flanking positions with genomic average, showing that the GC content is lower than the average in invertebrate genomes, but higher than that in vertebrate genomes. These results indicate that although 5' T and 5' A are different in inducing deamination of methylated CpG sites, GC content is even more important in affecting the deamination rate. In all the tests, the results of sea urchin are similar to vertebrates perhaps due to its fractional DNA methylation. CpG deficiency is therefore suggested to be mainly a result of high mutation rates of methylated CpG sites in GC-poor regions.

Palindromic sequence-mediated de novo chromosome translocation in sperm samples derived from normal and oligospermic males / 中华男科学杂志

<p><b>OBJECTIVE</b>To systematically explore the occurrence of a novel type of chromosome translocation in human sperm samples.</p><p><b>METHODS</b>Specific translocation junction fragments were quantified using nested and/or multi-nested PCR in sperm DNA derived from 28 oligospermic patients and 32 normal controls.</p><p><b>RESULTS</b>t(11;22) was detected in 49 samples. At least 4 samples were found to have t(1;22) (p21.2;q11.2), t(17;22) (q11;q11) or t(X;22) (q27;q11). The mutation rate seemed to be associated not with age or semen volume, but with sperm concentration (r = -0.389, P < 0.05) and motility (r = -0.397, P < 0.05). Correlation was not found between homology of palindromic sequences and mutation rate.</p><p><b>CONCLUSION</b>Palindromic sequence mediated chromosome translocation is common in human sperm, and associated with sperm concentration and motility. Measurement of such mutations may provide a molecular-level reference for assessing sperm quality.</p>

Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

The energy of interaction between complementary nucleotides in promoter sequences of E. coli was calculated and visualized. The graphic method for presentation of energy properties of promoter sequences was elaborated on. Data obtained indicated that energy distribution through the length of promoter sequence results in picture with minima at -35, -8 and +7 regions corresponding to areas with elevated AT (adenine-thymine) content. The most important difference from the random sequences area is related to -8. Four promoter groups and their energy properties were revealed. The promoters with minimal and maximal energy of interaction between complementary nucleotides have low strengths, the strongest promoters correspond to promoter clusters characterized by intermediate energy values.