Limits...
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.

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

Sequence alignment of conserved regions upstream of the coding sequence of CPNE1 and RBM12 among multiple species. A. conservation of exon 1; B. conservation of exon 2; C. conservation in both the splicing acceptor region of intron2 and the non-coding sequence of exon 3.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2568002&req=5

Figure 5: Sequence alignment of conserved regions upstream of the coding sequence of CPNE1 and RBM12 among multiple species. A. conservation of exon 1; B. conservation of exon 2; C. conservation in both the splicing acceptor region of intron2 and the non-coding sequence of exon 3.

Mentions: Sequence conservation among different species, especially species that are set apart by hundreds of million years of evolution, may indicate strong selection constraint and probably functional implications. Next we compared the promoter region and 5'UTR sequences from multiple species and tried to identify the motifs that remain conserved during evolutionary courses. Interestingly, sequences from the three non-coding exons for these two genes showed strong sequence conservation among different species. The only other region that showed high level conservation is the splicing acceptor of intron2 (Figure 5), with a conservation level probably higher than most splicing acceptor regions, indicating a possible role in alternative splicing regulation.


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)

Sequence alignment of conserved regions upstream of the coding sequence of CPNE1 and RBM12 among multiple species. A. conservation of exon 1; B. conservation of exon 2; C. conservation in both the splicing acceptor region of intron2 and the non-coding sequence of exon 3.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2568002&req=5

Figure 5: Sequence alignment of conserved regions upstream of the coding sequence of CPNE1 and RBM12 among multiple species. A. conservation of exon 1; B. conservation of exon 2; C. conservation in both the splicing acceptor region of intron2 and the non-coding sequence of exon 3.
Mentions: Sequence conservation among different species, especially species that are set apart by hundreds of million years of evolution, may indicate strong selection constraint and probably functional implications. Next we compared the promoter region and 5'UTR sequences from multiple species and tried to identify the motifs that remain conserved during evolutionary courses. Interestingly, sequences from the three non-coding exons for these two genes showed strong sequence conservation among different species. The only other region that showed high level conservation is the splicing acceptor of intron2 (Figure 5), with a conservation level probably higher than most splicing acceptor regions, indicating a possible role in alternative splicing regulation.

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