The properties of CpG islands in the putative promoter regions of human immunoglobulin (Ig) genes

Liu, Guang B. and Yan, Hong and Jiang, Ya F. and Chen, Rong and Pettigrew, John D. and Zhao, Kong-Nan (2005) The properties of CpG islands in the putative promoter regions of human immunoglobulin (Ig) genes. Gene, 358 (1). pp. 127-138. ISSN 0378-1119

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Abstract

[Abstract]; CpG island is a GC-rich motif occurred in gene promoter region, which can play important roles in gene silencing and imprinting. Here, we present a set of discriminant functions that can recognize the structural and compositional features of CpG islands in the putative promoter regions (PPRs) of human and mouse immunoglobulin (Ig) genes. We showed that the PPRs of both human and mouse Ig genes irrespective of gene chromosomal localization are apparently CpG island poor, with a low percentage of the CpG islands overlapped with the transcription start site (TSS). The human Ig genes that have CpG islands in the PPRs show a very narrow range of CpG densities. 47% of the Ig genes fall in the range of 3.5–4 CpGs/100 bp. In contrast, the non-Ig genes examined have a wide range of the density of CpG island, with 10.5% having the density of 8.1–15 CpGs/100 bp. Meantime, five patterns of the CpG distributions within the CpG islands have been classified: Pat A, B, C, D, and E. 21.6% and 10.8% of the Ig genes fall into the Pat B and Pat D groups, respectively, which were significantly higher than the non-Ig genes examined (8.2% and 3.8%). Moreover, the length of CpG islands is shorter in human Ig genes than in non-Ig genes but is much longer than in mouse orthologues. These findings provide a clear picture of non-neutral and nonrandom occurrence of the CpG islands in the PPRs of human and mouse Ig genes, which facilitate rational recommendations regarding their nomenclature. D 2005 Elsevier B.V. All rights reserved.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: Copyright 2005 Elsevier. Author's version reproduced in accordance with the copyright policy of the publisher. First published in Gene. This journal is available online: use hypertext links above.
Depositing User: Dr Guang Liu
Faculty / Department / School: Historic - Faculty of Sciences - Department of Biological and Physical Sciences
Date Deposited: 22 Apr 2010 12:07
Last Modified: 02 Jul 2013 23:48
Uncontrolled Keywords: human genome; mouse genome; CpG density; CpG distribution pattern
Fields of Research (FOR2008): 06 Biological Sciences > 0604 Genetics > 060407 Genome Structure and Regulation
Socio-Economic Objective (SEO2008): E Expanding Knowledge > 97 Expanding Knowledge > 970106 Expanding Knowledge in the Biological Sciences
Identification Number or DOI: doi: 10.1016/j.gene.2005.06.002
URI: http://eprints.usq.edu.au/id/eprint/7594

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