Symmetrical And Evolutionary Analysis Of Palindromes On The X Chromosome

"The 21st century is the century of life science", with the accomplishment of Human Genome Project and many model organisms genome sequencing, a great amount of DNA data makes a great gulf fixed between the level of molecule and biological information system. Anatomizing the nature of biological phenomena by using information technology has become the focus for scientists. By processing the biological information, the detailed and systematic understanding can be obtained from the scattered sequence data. In particular, the symmetry of life system has aroused the attention for many biologosts, excavating these special structures and functions is currently an important topic in biological research area.Since it was reported that the human Y chromosome contains a large number of palindromes with rotational symmetry in 2003, these sequences with sepecial functions aroused great interest. At the same time, whether the another sex chromosome also contains long palindromes stimulated people's curiosity, if so, what's the difference between the X-palindromes and Y-palindromes? Fortunately, in 2004, scientists found that the human X chromosome contains a lot of highly homologous palindromes. However, these palindromes also have many male-specific genes rather than female-specific genes. In this work, we try to understand the structural features mainly by statistical analysis of some X-palindromes, and explore the origin and evolution of palindromes and related genes by comparing with other primates. The main content are as follows:1. Based on the analysis of primate palindromes, we find that mutations within species are prone to occure between bases with similar structures. The deletion are easily occure near the simple repeats. The number of asymmetrical mutations are the most in the human X-palindrome. In addition, bases are prone to become similar bases to the neighboring ones. The human palindrome has the largest number of asymmetrical mutations, which followed by the chimpanzee, orangutan, and finally the rhesus monkey.2. Results indicate that the frequency of conversion is higher than that of transversion by analysing the point mutation of the primate MAGE/CSAG-palindromes. The frequency of G/C→A/T is different from the A/T→G/C, which shows that the genome composition is not at equilibrium. Comparing with orangutan, mutations are the least in the human palindrome, however, the symmetry is not high. However, composition of the human NXF2-palindrome on both arms are at equilibrium during the evolution.3. We can observe the the reverse complementary structural characteristics in the human and chimpanzee X-palindromes using DNA walk representation. It is easy to observe that regions with biological functions have different patterns by using of wavelet analysis. Finally, evolutional relationship between the human and chimpanzee palindromes are discussed based on the special distribution of repeats.4. It is found that most mutations on the primate MAGEA/CSAG-palindromes of the X chromosomes are symmetrical by sequence alignment. Compared with human and chimpanzee, orangutan palindrome has the most mutations, which makes its highest symmetry between the arms. Although most mutations occurred on the arms are symmetrical, the composition of the arms are not at equilibrium during the evolution.At present, although there are some progress about the structure and evolution of the X-palindromes, it is still a challenge for biologists. In this work, results about statistical characters and evolutional relationship may provide some basis for understanding the structures and genes, as well as some new ideas and information for the orgin and evolution of these X-palindromes.