The properties of CpG islands in the putative promoter regions of human immunoglobulin (Ig) genes.
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.
Liu
Guang B
GB
Vision, Touch and Hearing Research Centre, Faculty of Biomedical Sciences, The University of Queensland, Brisbane, Qld 4072, Australia. g.liu@uq.edu.au
Yan
Hong
H
Jiang
Ya F
YF
Chen
Rong
R
Pettigrew
John D
JD
Zhao
Kong-Nan
KN
D000818:Animals; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D020868:Gene Silencing; D015894:Genome, Human; D018392:Genomic Imprinting / Q000235:genetics; D006801:Humans; D007136:Immunoglobulins / Q000235:genetics*; D051379:Mice; D011401:Promoter Regions, Genetic / Q000235:genetics*; D013045:Species Specificity; D014158:Transcription, Genetic
D007136:Immunoglobulins