Showing papers by "Liqing Zhang published in 2004"

Mammalian Housekeeping Genes Evolve More Slowly than Tissue-Specific Genes

Abstract: Do housekeeping genes, which are turned on most of the time in almost every tissue, evolve more slowly than genes that are turned on only at specific developmental times or tissues? Recent large-scale gene expression studies enable us to have a better definition of housekeeping genes and to address the above question in detail. In this study, we examined 1581 human-mouse orthologous gene pairs for their patterns of sequence evolution, contrasting housekeeping genes with tissue-specific genes. Our results show that, in comparison to tissue-specific genes, housekeeping genes on average evolve more slowly and are under stronger selective constraints as reflected by significantly smaller values of Ka/Ks. Besides stronger purifying selection, we explored several other factors that can possibly slow down nonsynonymous rates in housekeeping genes. Although mutational bias might slightly slow the nonsynonymous rates in housekeeping genes, it is unlikely to be the major cause of the rate difference between the two types of genes. The codon usage pattern of housekeeping genes does not seem to differ from that of tissue-specific genes. Moreover, contrary to the old textbook concept, we found that approximately 74% of the housekeeping genes in our study belong to multigene families, not significantly different from that of the tissue-specific genes ( approximately 70%). Therefore, the stronger selective constraints on housekeeping genes are not due to a lower degree of genetic redundancy.

Patterns of Segmental Duplication in the Human Genome

Abstract: We analyzed the completed human genome for recent segmental duplications (size > or = 1 kb and sequence similarity > or = 90%) We found that approximately 4% of the genome is covered by duplications and that the extent of segmental duplication varies from 1% to 14% among the 24 chromosomes Intrachromosomal duplication is more frequent than interchromosomal duplication in 15 chromosomes The duplication frequencies in pericentromeric and subtelomeric regions are greater than the genome average by approximately threefold and fourfold We examined factors that may affect the frequency of duplication in a region Within individual chromosomes, the duplication frequency shows little correlation with local gene density, repeat density, recombination rate, and GC content, except chromosomes 7 and Y For the entire genome, the duplication frequency is correlated with each of the above factors Based on known genes and Ensembl genes, the proportion of duplications containing complete genes is 34% and 107%, respectively The proportion of duplications containing genes is higher in intrachromosomal than in interchromosomal duplications, and duplications containing genes have a higher sequence similarity and tend to be longer than duplications containing no genes Our simulation suggests that many duplications containing genes have been selectively maintained in the genome