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

Article

Liu, Guang Bin, Jiang, Ya Fang, 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 Part A: DNA Mapping, Sequencing, and Analysis. 17 (4), pp. 270-281. https://doi.org/10.1080/10425170600886136
Article Title

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

ERA Journal ID2330
Article CategoryArticle
AuthorsLiu, Guang Bin (Author), Jiang, Ya Fang (Author), Yan, Hong (Author) and Zhao, Kong-Nan (Author)
Journal TitleMitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis
Mitochondrial DNA
Journal Citation17 (4), pp. 270-281
Number of Pages12
Year2006
PublisherTaylor & Francis
Place of PublicationAbingdon, United Kingdom
ISSN 2470-1394
2470-1408
1940-1736
1940-1744
Digital Object Identifier (DOI)https://doi.org/10.1080/10425170600886136
Web Address (URL)http://www.informaworld.com/smpp/content~content=a770190098~db=all~order=page
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.

Keywordsbase composition pattern; promoter region; CpG island; putative initiator; downstream promoter elements;gene expression profiles
ANZSRC Field of Research 2020310506. Gene mapping
320699. Medical biotechnology not elsewhere classified
320603. Medical molecular engineering of nucleic acids and proteins
Public Notes

File reproduced in accordance with the copyright policy of the publisher/author.

Byline AffiliationsCentre for Systems Biology
Peking Union Medical College, China
Xi'an Jiaotong University, China
University of Queensland
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