Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes.

BACKGROUND: K-mer spectra of DNA sequences contain important information about sequence composition and sequence evolution. We want to reveal the evolution rules of genome sequences by studying the k-mer spectra of genome sequences. RESULTS: The intrinsic laws of k-mer spectra of 920 genome sequences from primate to prokaryote were analyzed. We found that there are two types of evolution selection modes in genome sequences, named as CG Independent Selection and TA Independent Selection. There is a mutual inhibition relationship between CG and TA independent selections. We found that the intensity of CG and TA independent selections correlates closely with genome evolution and G + C content of genome sequences. The living habits of species are related closely to the independent selection modes adopted by species genomes. Consequently, we proposed an evolution mechanism of genomes in which the genome evolution is determined by the intensities of the CG and TA independent selections and the mutual inhibition relationship. Besides, by the evolution mechanism of genomes, we speculated the evolution modes of prokaryotes in mild and extreme environments in the anaerobic age and the evolving process of prokaryotes from anaerobic to aerobic environment on earth as well as the originations of different eukaryotes. CONCLUSION: We found that there are two independent selection modes in genome sequences. The evolution of genome sequence is determined by the two independent selection modes and the mutual inhibition relationship between them.

Potential relations between post-spliced introns and mature mRNAs in the Caenorhabditis elegans genome.

There are potential interactions between introns and their corresponding coding sequences (CDSs) in ribosomal protein genes that have been proposed by our group and the interactions are achieved by sequence matches between the two kinds of sequences. Here, the optimal matching relations between mature mRNAs and their corresponding introns in Caenorhabditis elegans (C.elegans) were investigated by improved Smith-Waterman local alignment software. Our results showed that the remarkably matched regions appear in the untranslated regions (UTRs) of mRNAs, especially in the 3' UTR. The optimal matched segments (OMSs) are highly organized segments. In addition, the optimal matching relations were analysed between mature mRNAs and other introns. The matching strengths in the UTRs are clearly lower than those in their corresponding introns. Our studies indicate that there are potential interactions between mature mRNAs and their corresponding introns and the post-spliced introns should have other novel functions in the gene expression process.

Analysis on the interaction between post-spliced introns and corresponding protein coding sequences in ribosomal protein genes.

Many experiments show that intron loss/gain can influence many stages of mRNA metabolism. However, in the current work, post-spliced introns are not considered directly. Here, the optimal matched regions between introns and their protein coding sequences in ribosomal protein genes are intensively investigated by using the improved Smith-Waterman local alignment software. In introns, it is found that optimal matched regions are located in the central non-conserved regions, and their distribution characteristics are different from each intron group. We find two optimal matched regions in long introns, and the former one is more conservative than the latter one. We also find only one optimal matched region in short introns. In protein coding sequences, there are some optimal matched regions and forbidden regions, especially two conserved forbidden regions located at about 10% and 80% in the length of protein coding sequences. The forbidden regions may be potential protein-binding regions. Match rates of most optimal matched segments range among 65% and 75% and they belonged to weak match. The interaction between post-spliced introns and corresponding protein coding sequences may play a key role in gene expression.

Predicting nucleosome binding motif set and analyzing their distributions around functional sites of human genes.

Nucleosome positioning and remodeling correlate closely with the DNA sequence bias. It is possible that DNA motifs, interacted preferentially with histone octamers, direct the nucleosome positioning. Exploring the complete set of nucleosome binding motifs is of crucial importance for our understanding of the roles of nucleosomes in gene regulation. Based on the 8-mer multimodal spectra of the human genome, a systematic nucleosome binding motif set is inferred. Its structural features and density distributions for different types of sequences are consistent with the published data. Distributions of these motifs around several functional sites could describe the ground state of nucleosome distribution of these regions. Our results strongly support that the predicted nucleosome binding motif set is reliable. Our findings indicate that the recognition of distinct functional sites or sequences could be greatly improved by the help of a nucleosome array.