Computational analysis of base composition pattern and promoter elements in the putative promoter regions in relation to expression profiles of 682 human genes on chromosome 22.
Abstract The base composition pattern (BCP) in the putative promoter region (PPRs) up to 5 Kb lengths of 682 human genes on Chromosome 22 (Chr22) was examined. Two-dimensional (2D) and three-dimensional (3D) functions were designed to delineate the DNA base composition, with four major patterns identified. It is found that 17.6% genes include TATA box, 28.0% GC box, 18.9% CAAT box and 38.4% CpG islands, and approximately 10% genes have one of four putative initiator (Inr) motifs. The occurrence of the promoter elements is tightly associated with the base composition features in the promoter regions, and the associations of the base composition features with occurrence of the promoter elements in the promoter regions mediate tissue-wide expression of the genes in human. The occurrence of two or more promoter elements in the promoter regions is required for the medium- and wide-range expression profiles of the human genes on Chr22. Thus, the reported data shed light on the characteristics of the PPRs of the human genes on Chr22, which may improve our understanding of regulatory roles of the PPRs with occurrence of the promoter elements in gene expression.
Liu
Guang Bin
GB
Department of Biological and Physical Sciences, Faculty of Science, Centre for Systems Biology, The University of Southern Queensland, Toowoomba, Qld 4350, Australia. liu@usq.edu.au
Jiang
Ya Fang
YF
Yan
Hong
H
Zhao
Kong-Nan
KN
D001482:Base Composition / Q000235:genetics*; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D018899:CpG Islands / Q000235:genetics; D020862:GC Rich Sequence / Q000235:genetics; D005796:Genes / Q000235:genetics*; D006801:Humans; D011401:Promoter Regions, Genetic / Q000235:genetics*; D016385:TATA Box / Q000235:genetics