Diverse eukaryotic transcripts suggest short tandem repeats have cellular functions

Abstract

Previously thought “junk” DNA, short tandem repeats consisting of (GATA) n, or its compliment, were found in varied metazoan eukaryotic genomes but were rare in yeast and bacterial genomes. The (GATA) n sequence was found in cDNAs encoding mRNAs with known functions. At least 16 of 18 such transcripts encode membrane-associated proteins including: plasma membranes, synapses, mitochondrial membranes, nuclear envelopes, and brush border membranes. Flanking sequences were diverse but (GATA) n sequences clustered around 500 bases from stop codons. The (GATA) n sequences occurred in both orientations and showed constrained polymorphism. In sets of splice variants with and without (GAUA) n, the STR containing transcripts were the most abundant. These observations suggest that (GATA) n sequences probably function. In many cases, the function may be to encode post-transcriptional signals for mRNAs encoding membrane-associated proteins.