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

Liu, Guang Bin and Jiang, Ya Fang and Yan, Hong and Zhao, Kong-Nan (2006) 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. Mitochondrial DNA, 17 (4). pp. 270-281. ISSN 1042-5179

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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: Deposited in accordance with the copyright policy of the publisher.
Depositing User: Ms Debbie White
Faculty / Department / School: Historic - Faculty of Sciences - Department of Biological and Physical Sciences
Date Deposited: 11 Oct 2007 00:47
Last Modified: 02 Jul 2013 22:38
Uncontrolled Keywords: base composition pattern; promoter region; CpG island; putative initiator; downstream promoter elements; gene expression profiles
Fields of Research (FOR2008): 06 Biological Sciences > 0604 Genetics > 060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
10 Technology > 1004 Medical Biotechnology > 100499 Medical Biotechnology not elsewhere classified
10 Technology > 1004 Medical Biotechnology > 100403 Medical Molecular Engineering of Nucleic Acids and Proteins
Socio-Economic Objective (SEO2008): E Expanding Knowledge > 97 Expanding Knowledge > 970106 Expanding Knowledge in the Biological Sciences
Identification Number or DOI: doi: 10.1080/10425170600886136
URI: http://eprints.usq.edu.au/id/eprint/1553

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