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A phosphoglycerate mutase brain isoform (PGAM 1) pseudogene is localized within the human Menkes disease gene (ATP7
H A Dierick1, J F Mercer, T W Glover
1Department of Pediatrics, University of Michigan, Ann Arbor 48109-0618, USA. H-Dierick@nwu.edu
Abstract:
We have identified a phosphoglycerate mutase brain isoform (PGAM 1, PGAM B) cDNA that is localized between exons 1 and 2 of the Menkes disease gene (ATP7 A, MNK) at Xq13.3. The cDNA shows 98% identity to the previously identified PGAM 1 cDNA (Sakoda et al., J. Biol. Chem. 263 (1988) 16899-16905) and probably represents a recent retroposition of this parent PGAM 1 mRNA. Although the typical features of a processed pseudogene are present, the open reading frame (ORF) of this PGAM cDNA is potentially expressed. There are 11 bp changes in the 765 bp ORF, none of which are nonsense mutations or deletions. The region upstream from the ORF shows some features of a possible promoter region, although it lacks a CpG island often associated with functional promoters. We analyzed the expression of this PGAM 1 cDNA using RT-PCR followed by restriction enzyme digestion based on a 1 bp missmatch in this cDNA to distinguish it from normal PGAM 1 gene expression. With this sensitive method, we could not find expression in any of the tissues examined. Taken together, we conclude that the PGAM 1 cDNA upstream from exon 2 of the Menkes gene is likely to be a processed pseudogene originating from a very recent retroposition of a PGAM 1 transcript. To our knowledge this is the first report of a pseudogene located within a gene.
Insights
A novel phosphoglycerate mutase (PGAM 1) brain isoform cDNA, likely a processed pseudogene, was found within the Menkes disease gene. Despite potential expression features, RT-PCR analysis confirmed no detectable expression in examined tissues.
Area of Science:
- Genetics
- Molecular Biology
- Human Disease Genetics
Background:
- A novel phosphoglycerate mutase (PGAM 1) brain isoform cDNA was identified.
- This cDNA is located within the Menkes disease gene (ATP7A) at Xq13.3.
- It shows high identity to a known PGAM 1 cDNA and likely resulted from recent retroposition.
Purpose of the Study:
- To investigate the nature and expression of the identified PGAM 1 cDNA.
- To determine if this cDNA, located within the Menkes gene, is a functional gene or a pseudogene.
- To report the first instance of a pseudogene situated within another gene.
Main Methods:
- cDNA sequencing and comparison to identify sequence identity and mutations.
- Analysis of potential promoter regions.
- Reverse Transcription Polymerase Chain Reaction (RT-PCR) coupled with restriction enzyme digestion to detect gene expression.
Main Results:
- The identified cDNA shares 98% identity with PGAM 1 and exhibits characteristics of a processed pseudogene.
- The open reading frame (ORF) showed potential for expression, but lacked a CpG island promoter.
- RT-PCR analysis detected no expression of this PGAM 1 cDNA in any tested tissues.
Conclusions:
- The PGAM 1 cDNA located upstream of exon 2 of the Menkes gene is concluded to be a processed pseudogene.
- This pseudogene likely originated from a recent retroposition event of a PGAM 1 transcript.
- This represents the first reported case of a pseudogene integrated within the structure of another gene.