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The human photoreceptor rim protein gene (ABCR): genomic structure and primer set information for mutation analysis
S M Azarian1, C F Megarity, J Weng
1Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas 75235-9111, USA.
Abstract:
Rim protein (RmP) is an integral membrane glycoprotein localized to the rims of photoreceptor outer-segment discs. It belongs to the ABC transporter superfamily, but its function in the retina has not been determined. The gene for human RmP (ABCR) is affected in several recessively inherited human retinal degenerations, including Stargardt's macular dystrophy, retinitis pigmentosa, and cone-rod dystrophy. The complete structure of ABCR has not been determined. Here, we report the cloning of the human ABCR gene and present its complete intron-exon structure. The gene contains 50 exons that range in size from 33 to 406 bp. Almost all of the splice junctions follow the AG/GT rule. We have identified the site of transcription initiation by 5' RACE. The first several hundred bases upstream of the transcription unit are relatively conserved between mouse and human and contain several predicted cis-regulatory elements including a TATA-like box at -27 bp, and two Ret-4-like elements that reportedly confer photoreceptor-specific gene expression. We also present a complete set of tested oligonucleotide primers for the amplification and analysis of exons 1-50 by the polymerase chain reaction. These data should help with the identification of new disease-causing mutations in ABCR.
Insights
Researchers cloned the human Rim protein gene (ABCR), revealing its 50-exon structure and regulatory elements. This provides tools for identifying mutations linked to retinal degenerations like Stargardt disease.
Area of Science:
- Genetics
- Ophthalmology
- Molecular Biology
Background:
- Rim protein (RmP) is an ABC transporter in photoreceptor discs.
- ABCR gene mutations cause retinal degenerations (Stargardt, RP, CRD).
- The complete structure and regulatory elements of ABCR were previously unknown.
Purpose of the Study:
- To clone the human ABCR gene.
- To determine the complete intron-exon structure of ABCR.
- To identify regulatory elements and develop tools for mutation analysis.
Main Methods:
- Gene cloning and sequencing.
- 5' RACE for transcription start site identification.
- Bioinformatic analysis of promoter regions.
- Development of PCR primers for exon analysis.
Main Results:
- The human ABCR gene was cloned and its 50-exon structure elucidated.
- Splice junctions predominantly follow the AG/GT rule.
- Conserved regulatory elements, including a TATA-like box and Ret-4-like elements, were identified upstream.
- A comprehensive set of PCR primers for ABCR exons was generated.
Conclusions:
- The detailed ABCR gene structure and regulatory information are now available.
- These findings facilitate the identification of novel disease-causing mutations in ABCR.
- This research aids in understanding the genetic basis of inherited retinal diseases.