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

Is the Expression of Androgen Receptor Protein Associated With the Length of AC Repeats in the Type III 5-α Reductase Gene in Prostate Cancer Patients?

Purpose

Type III 5-α reductase (SRD5A3; steroid 5-α reductase 3) may be associated with the progression of prostate cancer (PCa). The aim of our study was to determine whether the length of AC repeats in the SRD5A3 gene is associated with the risk of PCa and the expression of androgen receptor (AR) protein in Korean men.

Materials and Methods

We compared the length of AC repeats in the short tandem repeat (STR) region of the SRD5A3 gene in 68 PCa patients and 81 control subjects by genotyping. A total of 55 patients in the PCa group underwent radical prostatectomy. We evaluated the expression of AR protein by using Western blotting and tested the association between the type of AC repeats in the SRD5A3 gene and AR protein expression and clinical and pathologic parameters.

Results

The short type of STR had less than 21 copies of AC repeats in the SRD5A3 gene. The SS type (short and short type) of STR of the SRD5A3 gene was 2.2 times as likely to occur in PCa patients as in controls (odds ratio, 2.21; 95% confidence interval, 1.14 to 4.31; p=0.019). However, AC repeats of the SRD5A3 gene were not associated with AR protein expression or clinical or pathologic parameters in PCa samples.

Conclusions

These results suggest that the short AC repeats of SRD5A3 polymorphism are associated with an increased risk of PCa. SRD5A3 polymorphism may contribute to a genetic predisposition for PCa.

Glycoprotein C Gene of Caprine Herpesvirus Type 1 Contains Short Sequence Repeats (SSR)

Caprine herpesvirus 1 (CpHV-1) is responsible for vaginal and respiratory disease in goats. Infection by vaginal route is usually restricted to the genital tract whereas by nasal route the virus can spread throughout the body. In order to evaluate genomic diversity, nucleotide sequences of glycoprotein C (gC) of 13 (n.8 vaginal, n.5 nasal) CpHV-1 strains were analyzed. Amino acid (aa) sequences showed a variable number of short sequence repeats (SSR). Nucleotide and amino acid sequences of amplified products showed to contain a variable number of short sequence repeats among the examined strains. These results indicated that CpHV-1 isolates had genetic diversity in the gC gene regarding the number of SSR: 4 SSR of 60 bp in one strain, 2 SSR of 30 bp in seven strains and 1 SSR of 15 bp in three strains. Two strains had no SSR.

Genome-wide analysis of tandem repeats in Daphnia pulex--a comparative approach

Background

DNA tandem repeats (TRs) are not just popular molecular markers, but are also important genomic elements from an evolutionary and functional perspective. For various genomes, the densities of short TR types were shown to differ strongly among different taxa and genomic regions. In this study we analysed the TR characteristics in the genomes of Daphnia pulex and 11 other eukaryotic species. Characteristics of TRs in different genomic regions and among different strands are compared in details for D. pulex and the two model insects Apis mellifera and Drosophila melanogaster.

Results

Profound differences in TR characteristics were found among all 12 genomes compared in this study. In D. pulex, the genomic density of TRs was low compared to the arthropod species D. melanogaster and A. mellifera. For these three species, very few common features in repeat type usage, density distribution, and length characteristics were observed in the genomes and in different genomic regions. In introns and coding regions an unexpectedly high strandedness was observed for several repeat motifs. In D. pulex, the density of TRs was highest in introns, a rare feature in animals. In coding regions, the density of TRs with unit sizes 7-50 bp were more than three times as high as for 1-6 bp repeats.

Conclusions

TRs in the genome of D. pulex show several notable features, which distinguish it from the other genomes. Altogether, the highly non-random distribution of TRs among genomes, genomic regions and even among different DNA-stands raises many questions concerning their functional and evolutionary importance. The high density of TRs with a unit size longer than 6 bp found in non-coding and coding regions underpins the importance to include longer TR units in comparative analyses.

Embryonic nervous system genes predominate in searches for dinucleotide simple sequence repeats flanked by conserved sequences

To study evolution of dinucleotide simple sequence repeats (diSSRs) we searched recently available mammalian genomes for UTR-localized diSSRs with conserved upstream flanking sequences (CFS). There were 252 reported Homo sapiens genes containing the repeats (AC)n, (GT)n, (AG)n or (CT)n in their UTRs including 22 (8.7%) with diSSR-upstream flanking sequences conserved comparing divergent mammalian lineages represented by Homo sapiens and the marsupial, Monodelphis domestica. Of these 22 genes, 19 had known functions including 18 (95%) that proved critical for mammalian nervous systems (Fishers exact test, P<0.0001). The remaining gene, Cd2ap, proved critical for development of kidney podocytes, cells that have multiple similarities to neurons. Gene functions included voltage and chloride channels, synapse-associated proteins, neurotransmitter receptors, axon and dendrite pathfinders, a NeuroD potentiator and other neuronal activities. Repeat length polymorphism was confirmed for 68% of CFS diSSRs even though these repeats were nestled among highly conserved sequences. This finding supports a hypothesis that SSR polymorphism has functional implications. A parallel study was performed on the self-complementary diSSRs (AT)n and (GC)n. When flanked by conserved sequences, the self-complementary diSSR (AT)n was also associated with genes expressed in the developing nervous system. Our findings implicate functional roles for diSSRs in nervous system development.

Simple repeat evolution includes dramatic primary sequence changes that conserve folding potential

We previously demonstrated that many "weak-folding" simple repeats were replaced during evolution by alternative weak-folding repeats. This suggested repeat selection at the level of higher order structure potential. Here, we demonstrate similar phenomena for "strong-folding" simple repeats in non-coding DNA. The Rabgap1 gene's 3' UTR contained the self-complementary repeat (AT)n in Homo sapiens but, in Mus musculus, this site was occupied by the complementary repeats (GT)n and (AC)n. Similarly, primate Plag1 UTRs contained various (GT)n-(AC)n palindromes but in rodents, this site was occupied by (AT)n, preserving folding potential more than primary sequence. The Znf516, Senp1, Rock2, and other UTRs exhibited similar replacements. In the Bnc2 UTR, (AT)n was replaced by sequences that evolved with approximate symmetry about a central axis, a pattern difficult to explain without invoking selection to preserve secondary structure. These observations reflect a predictable evolutionary pattern for some common non-coding genomic sequences.

Coronin 3 and its role in murine brain morphogenesis

Coronins belong to the fundamental WD40-repeat proteins. They are mainly found at the submembraneous area, they bind F-actin in vitro, and most of the seven mammalian coronins have unclear roles. Coronin 3 is abundantly expressed in the adult CNS. All murine brain areas express coronin 3 during embryogenesis and the first postnatal stages. Expression in grey matter decreases postnatally, except for hippocampal pyramidal and dentate gyrus neurons, and cerebellar Purkinje cells, while levels in white matter increase in the course of myelination. Consistently, coronin 3 is abundant in differentiating neuro-2a and PC-12 cells and in primary oligodendrocytes. Treatment with PKC activator PMA reduced coronin 3 protein levels. To address its functions, neuro-2a and PC-12 cells were transfected with GFP-tagged coronin 3 versions. Full-length coronin 3 among other areas localized to outgrowing neurites, whereas truncated proteins efficiently suppressed neurite formation. Our results favour a role for coronin 3 in neuron morphogenesis and possibly migration.

Exact tandem repeats analyzer (E-TRA): a new program for DNA sequence mining

Exact Tandem Repeats Analyzer 1.0 (E-TRA) combines sequence motif searches with keywords such as 'organs', 'tissues', 'cell lines' and 'development stages' for finding simple exact tandem repeats as well as non-simple repeats. E-TRA has several advanced repeat search parameters/options compared to other repeat finder programs as it not only accepts GenBank, FASTA and expressed sequence tags (EST) sequence files, but also does analysis of multiple files with multiple sequences. The minimum and maximum tandem repeat motif lengths that E-TRA finds vary from one to one thousand. Advanced user defined parameters/options let the researchers use different minimum motif repeats search criteria for varying motif lengths simultaneously. One of the most interesting features of genomes is the presence of relatively short tandem repeats (TRs). These repeated DNA sequences are found in both prokaryotes and eukaryotes, distributed almost at random throughout the genome. Some of the tandem repeats play important roles in the regulation of gene expression whereas others do not have any known biological function as yet. Nevertheless, they have proven to be very beneficial in DNA profiling and genetic linkage analysis studies. To demonstrate the use of E-TRA, we used 5,465,605 human EST sequences derived from 18,814,550 GenBank EST sequences. Our results indicated that 12.44% (679,800) of the human EST sequences contained simple and non-simple repeat string patterns varying from one to 126 nucleotides in length. The results also revealed that human organs, tissues, cell lines and different developmental stages differed in number of repeats as well as repeat composition, indicating that the distribution of expressed tandem repeats among tissues or organs are not random, thus differing from the un-transcribed repeats found in genomes.

Short tandem repeat (STR) replacements in UTRs and introns suggest an important role for certain STRs in gene expression and disease

Some untranslated sequence (UTR)-localized, short tandem repeats (STRs) exhibit evidence of selection pressure, including STR-coupling preferences, STR conservation, interspecies STR-STR replacements, and STR variants implicated in certain diseases. We wished to determine if STR replacements occurred near disease-related genes, including previously unstudied STRs as well as some STRs already implicated in disease. Among nine strong-candidate prostate cancer (CaP)-predisposing genes, three [steroid 5-alpha-reductase 2 (Srd5A-2), macrophage scavenger receptor-1 (MSR-1), and tumor necrosis factor receptor-21 (Tnfr-21)] exhibited striking STR replacements (P<0.001). The glomerular disease-related gene, CD2AP, exhibited an STR replacement flanked by well-conserved sequences, suggesting an STR-focused process. Another glomerular disease-related gene, rabphilin 3A, exhibited at least two STR replacements at the same UTR position comparing Drosophila melanogaster, Mus musculus, and Homo sapiens. Two genes implicated in blood-clotting disorders, von Willebrand factor (vWA) and fibrinogen alpha (FGA), exhibited multiple-intron STR replacements among mammals, extending STR replacement phenomena to introns. Among primates, a tyrosine hydroxylase (THO1) intron STR, previously implicated in both schizophrenia and drug withdrawal delirium, exhibited frequent replacements. Some STR replacements were early events in gene divergence. When STR sequences of closely related species were available, STR replacement was observed to be nearly as rapid as speciation. STR replacements expand the list of STR sequences that may contribute to genetic activity and to disease processes.

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

Simple repeats are ubiquitous in metazoan genomes, but function has been elusive. We reported that distinct, short tandem repeats (STRs) were coupled with rigorous polarity and register, suggesting order in simple repeat usage. Several STRs that lacked internal, canonical base pairs were associated with mRNAs encoding membrane functions and transcription factors. We hypothesized that diverse, simple repeats, such as (AC)n, (GU)n, (AG)n, (CU)n and (CUUU)n, had similar functions. The hypothesis predicts that closely related mRNAs would sometimes exhibit STR replacements. Comparing aquaporin 3 mRNAs, in rodents and humans, (GU)20 replaced (AG)29. Comparing biglycan mRNAs, (GU)25 replaced (CA)12. Comparing immunoglobulin superfamily member 9 mRNAs, the STR-couple, (CU)17(GU)9 replaced the STR-couple, (GU)19(GC)4. Comparing tumor necrosis factor receptor-21 mRNAs, (GU)24 replaced (CUUU)16. In a collection of 52 rodent-H. sapiens homologous mRNAs that had STRs, six (11.5%) STR-STR replacements occurred, significantly more than expected based on an STR frequency of 0.13% in all reported UTRs (p<0.001). Database studies and the observation of STR replacements among transcript homologs independently support the hypothesis that diverse repeat sequences, such as (AG)n, (AC)n, (GU)n, (CU)n and (CUUU)n, have similar usage that is consistent with analogous functions.