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Promoter-sharing by different genes in human genome--CPNE1 and RBM12 gene pair as an example.

Yang W, Ng P, Zhao M, Wong TK, Yiu SM, Lau YL - BMC Genomics (2008)

Bottom Line: In a whole genome analysis of alternative splicing events, we found that two distinct genes, copine I (CPNE1) and RNA binding motif protein 12 (RBM12), share the most 5' exons and therefore the promoter region in human.Conservation of this genomic structure in evolutionary courses indicates potential functional interaction between the two genes.More than 20 other gene pairs in human genome were found to have the similar genomic structure in a genome-wide analysis, and it may represent a unique pattern of genomic arrangement that may affect expression regulation of the corresponding genes.

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Affiliation: Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, PR China. yangwl@hkucc.hku.hk

ABSTRACT

Background: Regulation of gene expression plays important role in cellular functions. Co-regulation of different genes may indicate functional connection or even physical interaction between gene products. Thus analysis on genomic structures that may affect gene expression regulation could shed light on the functions of genes.

Results: In a whole genome analysis of alternative splicing events, we found that two distinct genes, copine I (CPNE1) and RNA binding motif protein 12 (RBM12), share the most 5' exons and therefore the promoter region in human. Further analysis identified many gene pairs in human genome that share the same promoters and 5' exons but have totally different coding sequences. Analysis of genomic and expressed sequences, either cDNAs or expressed sequence tags (ESTs) for CPNE1 and RBM12, confirmed the conservation of this phenomenon during evolutionary courses. The co-expression of the two genes initiated from the same promoter is confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) in different tissues in both human and mouse. High degrees of sequence conservation among multiple species in the 5'UTR region common to CPNE1 and RBM12 were also identified.

Conclusion: Promoter and 5'UTR sharing between CPNE1 and RBM12 is observed in human, mouse and zebrafish. Conservation of this genomic structure in evolutionary courses indicates potential functional interaction between the two genes. More than 20 other gene pairs in human genome were found to have the similar genomic structure in a genome-wide analysis, and it may represent a unique pattern of genomic arrangement that may affect expression regulation of the corresponding genes.

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Alternative splicing forms of CPNE1 and RBM12 in human, mouse and zebrafish in the 5'UTR. GenBank accession nos. for representative cDNA or EST sequences for Human CPNE1: 1. [GenBank:NM_152930], 2. [GenBank:NM_152931], 3. [GenBank:NM_152927], 4. [GenBank:NM_152928], 5. [GenBank:NM_152925]; Human RBM12: 1. [GenBank:NM_006047], 2. [GenBank:NM_152838], 3. [GenBank:AB018308]; mouse CPNE1: 1. [GenBank:CF742269], 2. [GenBank:CN693202], 3. [GenBank:NM_170588], 4. [GenBank:NM_170590]; mouse RBM12: 1. [GenBank:BC052473], 2. [GenBank:AF393216]; zebrafish CPNE1: 1. [GenBank:XM_001338967], 2. [GenBank:EB992764], 3. [GenBank:XM_696989]; zebrafish RBM12: 1. [GenBank:DT275702], 2. [GenBank:EB783076].
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Figure 4: Alternative splicing forms of CPNE1 and RBM12 in human, mouse and zebrafish in the 5'UTR. GenBank accession nos. for representative cDNA or EST sequences for Human CPNE1: 1. [GenBank:NM_152930], 2. [GenBank:NM_152931], 3. [GenBank:NM_152927], 4. [GenBank:NM_152928], 5. [GenBank:NM_152925]; Human RBM12: 1. [GenBank:NM_006047], 2. [GenBank:NM_152838], 3. [GenBank:AB018308]; mouse CPNE1: 1. [GenBank:CF742269], 2. [GenBank:CN693202], 3. [GenBank:NM_170588], 4. [GenBank:NM_170590]; mouse RBM12: 1. [GenBank:BC052473], 2. [GenBank:AF393216]; zebrafish CPNE1: 1. [GenBank:XM_001338967], 2. [GenBank:EB992764], 3. [GenBank:XM_696989]; zebrafish RBM12: 1. [GenBank:DT275702], 2. [GenBank:EB783076].

Mentions: In addition to the co-regulation of the expression of these two genes through shared promoter region, the two genes also share non-coding exons, which are also conserved during evolutionary courses. We have examined the alternative splicing patterns of the two genes in different species, especially focusing on the 5'UTR where most alternative splicing forms are derived. As shown in Figure 4, most of the alternative splicing forms and the gene structure in the 5' UTR are well conserved between human, mouse and zebrafish, indicating that the sequences in the 5' UTR may have a functional role.


Promoter-sharing by different genes in human genome--CPNE1 and RBM12 gene pair as an example.

Yang W, Ng P, Zhao M, Wong TK, Yiu SM, Lau YL - BMC Genomics (2008)

Alternative splicing forms of CPNE1 and RBM12 in human, mouse and zebrafish in the 5'UTR. GenBank accession nos. for representative cDNA or EST sequences for Human CPNE1: 1. [GenBank:NM_152930], 2. [GenBank:NM_152931], 3. [GenBank:NM_152927], 4. [GenBank:NM_152928], 5. [GenBank:NM_152925]; Human RBM12: 1. [GenBank:NM_006047], 2. [GenBank:NM_152838], 3. [GenBank:AB018308]; mouse CPNE1: 1. [GenBank:CF742269], 2. [GenBank:CN693202], 3. [GenBank:NM_170588], 4. [GenBank:NM_170590]; mouse RBM12: 1. [GenBank:BC052473], 2. [GenBank:AF393216]; zebrafish CPNE1: 1. [GenBank:XM_001338967], 2. [GenBank:EB992764], 3. [GenBank:XM_696989]; zebrafish RBM12: 1. [GenBank:DT275702], 2. [GenBank:EB783076].
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 4: Alternative splicing forms of CPNE1 and RBM12 in human, mouse and zebrafish in the 5'UTR. GenBank accession nos. for representative cDNA or EST sequences for Human CPNE1: 1. [GenBank:NM_152930], 2. [GenBank:NM_152931], 3. [GenBank:NM_152927], 4. [GenBank:NM_152928], 5. [GenBank:NM_152925]; Human RBM12: 1. [GenBank:NM_006047], 2. [GenBank:NM_152838], 3. [GenBank:AB018308]; mouse CPNE1: 1. [GenBank:CF742269], 2. [GenBank:CN693202], 3. [GenBank:NM_170588], 4. [GenBank:NM_170590]; mouse RBM12: 1. [GenBank:BC052473], 2. [GenBank:AF393216]; zebrafish CPNE1: 1. [GenBank:XM_001338967], 2. [GenBank:EB992764], 3. [GenBank:XM_696989]; zebrafish RBM12: 1. [GenBank:DT275702], 2. [GenBank:EB783076].
Mentions: In addition to the co-regulation of the expression of these two genes through shared promoter region, the two genes also share non-coding exons, which are also conserved during evolutionary courses. We have examined the alternative splicing patterns of the two genes in different species, especially focusing on the 5'UTR where most alternative splicing forms are derived. As shown in Figure 4, most of the alternative splicing forms and the gene structure in the 5' UTR are well conserved between human, mouse and zebrafish, indicating that the sequences in the 5' UTR may have a functional role.

Bottom Line: In a whole genome analysis of alternative splicing events, we found that two distinct genes, copine I (CPNE1) and RNA binding motif protein 12 (RBM12), share the most 5' exons and therefore the promoter region in human.Conservation of this genomic structure in evolutionary courses indicates potential functional interaction between the two genes.More than 20 other gene pairs in human genome were found to have the similar genomic structure in a genome-wide analysis, and it may represent a unique pattern of genomic arrangement that may affect expression regulation of the corresponding genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, PR China. yangwl@hkucc.hku.hk

ABSTRACT

Background: Regulation of gene expression plays important role in cellular functions. Co-regulation of different genes may indicate functional connection or even physical interaction between gene products. Thus analysis on genomic structures that may affect gene expression regulation could shed light on the functions of genes.

Results: In a whole genome analysis of alternative splicing events, we found that two distinct genes, copine I (CPNE1) and RNA binding motif protein 12 (RBM12), share the most 5' exons and therefore the promoter region in human. Further analysis identified many gene pairs in human genome that share the same promoters and 5' exons but have totally different coding sequences. Analysis of genomic and expressed sequences, either cDNAs or expressed sequence tags (ESTs) for CPNE1 and RBM12, confirmed the conservation of this phenomenon during evolutionary courses. The co-expression of the two genes initiated from the same promoter is confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) in different tissues in both human and mouse. High degrees of sequence conservation among multiple species in the 5'UTR region common to CPNE1 and RBM12 were also identified.

Conclusion: Promoter and 5'UTR sharing between CPNE1 and RBM12 is observed in human, mouse and zebrafish. Conservation of this genomic structure in evolutionary courses indicates potential functional interaction between the two genes. More than 20 other gene pairs in human genome were found to have the similar genomic structure in a genome-wide analysis, and it may represent a unique pattern of genomic arrangement that may affect expression regulation of the corresponding genes.

Show MeSH
Related in: MedlinePlus