Evolution Analysis Of Palindromes In Human Y Chromosome

With the accomplishment of human genome project and the large-scale performing and the gradually completion of DNA sequencing of other species, large amount of DNA sequence informations in genomes are excavated and accumulated in various kinds of databases. At the same time, the fast evolution of bioinformatics and the exploitation of lots of softwares provide effective tools for DNA sequence analysis. The arrival of Internet is convenient for the search and obtaining of DNA data, so that one of the important tasks of current biological research is to grasp the prominent features of genomes holistically and systemically, and to analysis the species evolution process.In 2003, the DNA sequencing of human Y chromosome was accomplished, and the most pronounced structural features of the euchromatin of male-specific region in Y chromosome were eight massive palindromes (P1-P8). Almost all the testes-special-genes and transcription units occur in palindromes, thus these palindromes are of great significance for the male features' evolution. In vivo, long palindroms are instable and can lead to the break, deletion and death of genome, while the eight palindromes in Y chromosome have existed for at least millions of years. Because of the biological significance and the special evolution stability, this work deeply examines and discusses the sequence evolution features of these large palindromes in human Y chromosome. The main research content can be summarized into four aspects as follow:1. The work studies the substitution pattern and rate in repeat units of the tandem repeat regions contained in P2 and P3 palindromes. The results reveal the significantly different substitution processes between the tandem repeats in P2 and P3. As a consequence, the repeat region experiences a change by increasing its GC content in P2 while it sharply decreases its GC content toward a significant lower equilibrium value in P3. Based on the analysis, various different factors and models, as well as some impact coming from the special palindrome structures and the regional GC content influence, together control the repeats' mutation pattern.2. The work accurately examines the structural feature and the sequence composition of P2, P3. Subsequently, the common and diverse features of palindrome sequences are discussed, and an origin model of P3 is proposed.3. The work focus on the tandem repeats contained in the large P2 palindrome. A new attempt is proposed that: to represent a repeat array as the mosaic of several sub-repeat arrays. Through using the divergences among repeat units, and employing the cluster and correlation analysis methods, the relations among different elements contained in repeat sequences are determined. Many different evolutionary features among sub-repeats are revealed.4. The aim of work is to establish a method, through which some DNA sequence features can be revealed, so that the DNA segment tending to form genes can be distinguished. The initial-stage-result reveals that: the distribution of triplets containing "CG" seems to be of a quality that the various distances of intervals between two neighboring triplets occur in the same frequency.So far, there has been little knowledge about the sequence evolution and features of the eight palindromes in human Y chromosome male-specific region. The published research papers mainly focus on the diseases (male azoospermia) and the chromosome variability which are caused by the homologous sequences in palindromes. Only through looking up the papers about human Y chromosome and about the male azoospermia, people can receive some sequence and gene content informations of these eight massive palindromes. This paper analyses the evolution features of the palindromes in human Y chromosome, and deeply studies the origination and biological functions of palindromes, hoping to provide some knowledge foundations and research clues for the final understanding of sexual origin and stability evolution. The new analysis methods in our works can offer new thinkings and experiences for DNA sequence researches.