Short tandem repeats are associated with diverse mRNAs encoding membrane‐targeted proteins

Abstract

Within the genomes of multicellular organisms, short tandem repeating sequences (STRs) are ubiquitous, yet usage patterns remain obscure. The repeats (AC)n and (GU)n appear frequently in the untranslated regions (UTRs) of messenger RNAs (mRNAs). To investigate STR usage patterns, we used three approaches: (1) comparisons of individual mRNA database sequences including annotations and linked references, (2) statistical analysis of complete, UTR databases and (3) study of a large gene family, the aquaporins. Among 500 (AC)n- or (GU)n-containing mRNAs, 58 (12%) had known functions. Of these, 50 (86%) encoded proteins whose activities involved membranes or lipids, including integral membrane proteins, peripheral membrane proteins, ion channels, lipid enzymes, receptors and secreted proteins. A control sequence (AU)n also occurred in mRNAs, but only 5% encoded membrane-related functions. Investigation of all reported 3' UTR sequences, demonstrated that the STR (AC)n was 9 times more common in mRNAs encoding membrane functions than in the total UTR database (P < 0.001). Similarly, (GU)n was 8 times more common in membrane-function mRNAs than in the total database (P < 0.001). These observations suggest that (AC)n and (GU)n may be UTR signals for some mRNAs encoding membrane-targeted proteins.

Simple repeat replacements support similar functions of distinct repeats in inter-species mRNA homologs

“…Although the current database had limited reports of STR-containing, AQP mRNA homologs in multiple species, such information was available for AQP3 mRNAs. Comparison of R. norvegicus AQP3 mRNA with H. sapiens AQP3 mRNA (Altschul et al, 1997;Nejsum et al, 2002), demonstrated a striking replacement involving (AG)n and an interrupted (GU)n sequence, as previously reported (Riley and Krieger, 2004). The current report provides a consensus-strength map showing 88% coding sequence identity, UTR divergence, and short blocks of identical sequence adjacent to the replacement (Fig.…”

“…We first estimated how many orthologous mRNA pairs had been reported. A previous search of a non-redundant, untranslated sequence database (UTRdb version, 2.2.1, 4 -13 -01, 368,154 sequences; available from, http://bighost.area.ba.cnr.it/BIG/UTRHome/) revealed that, of 368,154 total UTRs, only 499 UTRs (0.136%) contained the STRs, (AC)n>14 or (GU)n>14 (Riley and Krieger, 2004). The Homologene database (available from http://www.ncbi.nlm.nih.gov/HomoloGene/) currently contains 23,103, rodent -H. sapiens mRNA orthologs, but most lacked STRs (Zhang et al, 2000).…”

“…For example, within the 13-member, AQP mRNA family (Nejsum et al, 2002) the STRs, (AC)n, (AG)n or (GU)n were variously found in the 3V UTRs (Riley and Krieger, 2004). Comparing intra-species AQP mRNAs, divergence of coding sequences prevented clear alignments of the STRs and their flanking sequences.…”

“…For example, the STR, (GATA)n was associated with mRNAs encoding membrane-targeted functions (Riley and Krieger, 2002). The STRs, (AC)n, (GU)n, and, to some extent, (AG)n were also associated with mRNAs encoding either membranetargeted functions or transcription factors with transmembrane-like domains (Riley and Krieger, 2004). In contrast, STRs capable of extensive, internal, Watson -Crick base pairing, such as (AU)n, showed much less association with membrane-targeted mRNAs unless a weak-folding STR occurred in the same transcript.…”

Unigene derived SSR analysis for the Fugu rubripes and insights into the characteristics of EST-SSR distribution in tissues/organs

“…This finding of CA/GT motif rich is in accordance with recent report about common carp . Riley and Krieger (2004) reported that AC/GT was eight times more common in membrane-function mRNAs. This indicated that AC/GT repeats preferentially express in membrane proteins.…”