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Diverse eukaryotic transcripts suggest short tandem repeats have cellular functions.
Donald E Riley1, John N Krieger
1Department of Urology, University of Washington, Seattle, WA 98195, USA. dri@u.washington.edu
Biochemical and Biophysical Research Communications
|November 1, 2002
Summary
Short tandem repeats (STRs) like (GATA)n, once dismissed as "junk" DNA, are functional. These sequences are prevalent in metazoan genomes and likely encode signals for membrane-associated protein mRNAs.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Short tandem repeats (STRs), specifically (GATA)n sequences, were historically considered non-functional DNA.
- These repeats are found in various eukaryotic genomes but are rare in prokaryotes.
Purpose of the Study:
- To investigate the potential function of (GATA)n STRs.
- To determine the association of (GATA)n sequences with specific gene products and their cellular localization.
Main Methods:
- Bioinformatic analysis of metazoan eukaryotic genomes and cDNAs.
- Identification and characterization of (GATA)n repeat locations relative to gene sequences.
- Analysis of transcript abundance in splice variants.
Main Results:
- The (GATA)n sequence was identified in cDNAs encoding functional mRNAs.
- At least 16 out of 18 identified transcripts encoded membrane-associated proteins (e.g., plasma membrane, mitochondrial, nuclear envelope proteins).
- (GATA)n sequences were located near stop codons and were found in both orientations with constrained polymorphism.
- Transcripts containing (GATA)n were more abundant than splice variants lacking these repeats.
Conclusions:
- The (GATA)n sequences are not "junk" DNA and likely possess functional roles.
- These STRs may function as post-transcriptional regulatory signals for mRNAs encoding membrane-associated proteins.