The Application Of Wavelet Transform In Detection Of Isochore Boundaries

The mosaic organization of mammalian genomes (including human being) composed of many regions of rather homogeneous GC content was revealed by the ultracentrifugation experiments of bulk DNA in the mid-1970s. The long DNA segments (>>300 Kb, on average) of fairly homogenous GC contents lately were given name 'isochore'. Acccording to Bernardi's analysis, the gene distribution are related to isochores. Nowadays the availability of the human genome draft sequences offers an unprecedented opportunity to explore and understand the genomic organization at the sequence level. Incorporated with the Z curve method, the technique of wavelet multiresolution (also known as multiscale) analysis has been proposed to identify the boundaries of isochores in the human genome. The human MHC sequence and the longest contigs of human chromosomes 21 and 22 are used as examples. The boundary between the isochores of Class III and Class II in the MHC sequence has been detected and found to be situated at the position 2,490,368 bp. This result is in good agreement with the experimental evidence. An isochore with a length of about 7 Mb in chromosome 21 has been identified, and found to be gene- and Alu- poor. We have also found that the GC content of chromosome 21 is more homogenous than that of chromosome 22. Compared with the window-based methods, the present method has the highest resolution for identifying the boundaries of isochores, even at a scale of single base. Compared with the entropic segmentation method, the present method has the merits of more intuitiveness and less calculations. The important conclusion drawn in this study is that the segmentation points, at which the GC content undergoes relatively dramatic changes, do exit in the human genome. These 'singularity' points may be considered to be candidates of isochore boundaries in the human genome. The method presented is a general one, and can be used to analyze any other genomes.Additionally, the author also did some works on short genes (>90 bp and <300 bp) of the completely sequenced bacterial genomes. I collected all the short genes of them and did some fundamental analysis.