Fugu intron oversize reveals the presence of U15 snoRNA coding sequences in some introns of the ribosomal protein S3 gene

Association of TSC gene variants and hypertension in Mongolian and Han populations

We investigated a possible association between genetic variations in the thiazide-sensitive Na-Cl cotransporter (TSC) gene and essential hypertension (EH) in the Mongolian and Han ethnic groups in Inner Mongolia. Our study included 385 unrelated Mongolian herdsmen and 523 Han farmers. Nine tagSNPs of TSC were identified from the Chinese HapMap database based on pairwise r(2) ≥ 0.5 and minor allele frequency ≥0.05. Genotyping was performed using the PCR/ligase detection reaction assay. Association between tagSNPs and hypertension was investigated under the additive model. There were significant differences between the genotype and allele frequencies of rs13306673 between the EH group and the control group in the Han population. Significant associations were found between the rs7204044 variant and EH in both the Mongolian and Han ethnic groups. The frequency of haplotype GCA in the EH group was significantly higher than in the control group in the Mongolian population. In the Han population, the frequency of haplotype TGG was significantly higher in the EH group than in controls, whereas haplotype TGA occurred significantly less often in EH than in controls. We suggest that rs7204044 of TSC is a genetic factor for EH in these two ethnicities and that rs13306673 is a genetic factor for EH in the Han population.

Associations between genetic variations in the FURIN gene and hypertension

Background

Hypertension is a complex disease influenced by multiple genetic and environmental factors. The Kazakh ethnic group is characterized by a relatively high prevalence of hypertension. Previous research indicates that the FURIN gene may play a pivotal role in the renin-angiotensin system and maintaining the sodium-electrolyte balance. Because these systems influence blood pressure regulation, we considered FURIN as a candidate gene for hypertension. The purpose of this study was to systematically investigate the association between genetic variations in the FURIN gene and essential hypertension in a Xinjiang Kazakh population.

Methods

We sequenced all exons and the promoter regions of the FURIN gene in 94 hypertensive individuals to identify genetic variations associated with the disorder. Genotyping was performed using the TaqMan polymerase chain reaction method for four representative common single nucleotide polymorphisms (SNPs, -7315C > T, 1970C > G, 5604C > G, 6262C > T) in 934 Kazakh Chinese people. One SNP (1970C > G) was replicated in 1,219 Uygur Chinese people.

Results

Nine novel and seven known single nucleotide polymorphisms were identified in the FURIN gene. The results suggest that 1970C > G was associated with a hypertension phenotype in Kazakh Chinese (additive model, P = 0.091; dominant model, P = 0.031, allele model, P = 0.030), and after adjustment with logistic regression analysis, ORs were 1.451 (95%CI 1.106-1.905, P = 0.008) and 1.496 (95% 1.103-2.028, P = 0.01) in additive and dominant models, respectively. In addition, the association between 1970C > G and hypertension was replicated in Uygur subjects (additive model, P = 0.042; dominant model, P = 0.102; allele model, P = 0.027) after adjustment in additive and dominant models, ORs were 1.327 (95% 1.07-1.646), P = 0.01 and 1.307 (95%CI 1.015-1.681, P = 0.038), respectively. G allele carriers exhibited significant lower urinary Na⁺ excretion rate than non-carriers in the Kazakh Chinese population (152.45 ± 76.04 uM/min vs 173.33 ± 90.02 uM/min, P = 0.007).

Conclusion

Our results suggest that the FURIN gene may be a candidate gene involved in human hypertension, and that the G allele of 1970C > G may be a modest risk factor for hypertension in Xinjiang Kazakh and Uygur populations.

Immunohistochemical Studies of Human Ribosomal Protein S3 (rpS3)

The human ribosomal protein S3 (rpS3) was expressed in E. coli using the pET-15b vector and the monoclonal antibodies (mAbs) were produced and characterized. A total of five hybridoma cell lines were established and the antibodies recognized a single band of molecular weight of 33 kDa on immunoblot with purified rpS3. When the purified rpS3 was incubated with the mAbs, the UV endonuclease activity of rpS3 was inhibited up to a maximum of 49%. The binding affinity of mAbs to rpS3 determined by using a biosensor technology showed that they have similar binding affinities. Using the anti-rpS3 antibodies as probes, we investigated the cross-reactivities of various other mammalian brain tissues and cell lines, including human. The immunoreactive bands on Western blots appeared to be the same molecular mass of 33 kDa in all animal species tested. They also appear to be extensively cross-reactive among different organs in rat. These results demonstrated that only one type of immunologically similar rpS3 protein is present in all of the mammalian brain tissues including human. Furthermore, these antibodies were successfully applied in immunohistochemistry in order to detect rpS3 in the gerbil brain tissues. Among the various regions in the brain tissues, the rpS3 positive neurons were predominantly observed in the ependymal cells, hippocampus and stantia nigra pars compacta. The different distributions of rpS3 in brain tissues reply that rpS3 protein may play an important second function in the neuronal cells.

Genomic structure and transcriptional studies on the mouse ribosomal protein S3 gene: Expression of U15 small nucleolar RNA

Ribosomal protein S3 (rpS3) is a multifunctional ribosomal protein (RP) which is known to function as a DNA repair endonuclease as well as an RP. Recently, it was reported that rpS3 is involved in apoptosis. We identified the complete 4760 base pair genomic structure of the mouse rpS3 gene, which is composed of 7 exons and 6 introns. Promoter study revealed that transcription of the mouse rpS3 gene started at two C residues embedded in the 5'-terminal oligopyrimidine tract (5'-TOP); this was then compared with the human counterpart. Functional U15 small nucleolar RNAs (snoRNAs) were expressed from the first and the fifth introns. About 300 base pairs (bps) upstream of the 5'-untranslated region (5'-UTR) of the mouse rpS3 gene was sufficient to show maximum transcription activity. This report shows the conservation of the genomic structure of the rpS3 gene in vertebrates and characteristics of its promoter similar to those of promoters of other mammalian RPs.

Identification and comparative analysis of the RpL14 gene from Takifugu rubripes

The ribosomal protein RpL14 gene has been characterized in several species, including, human, rat and fruit fly. Haploinsufficiency for the gene causes the Minute phenotype in Drosophila, and it has been proposed as a regulator in the tumorigenic pathway in human. Several features concerning the gene structure have been studied, and some of these differ between human/rat and Drosophila. To address functional and evolutionary questions about these differences we have isolated and sequenced a cDNA and a genomic clone covering the RpL14 gene from the pufferfish Takifugu rubripes (Fugu). The Fugu RpL14 gene is approximately 2 Kb, with 5 introns, and encodes a protein of 137 amino acids. The protein contains a KOW-motif and a nuclear localization signal, which are conserved among a wide range of RPL14 proteins. On the other hand, a variable amino acid (alanine) repeat observed in human is missing in Takifugu rubripes, and the protein is shorter than its mammalian counterparts. Compared with human, the RpL14 gene in Fugu contains introns localized at identical positions in the gene, and most of them are shorter. A comparison of the RpL14 gene structure from a broad range of organisms indicates that both loss and gain of introns have occurred during the evolution of the gene.

Evolutionary profiling of the U49 snoRNA gene

Small nucleolar RNAs (snoRNAs) are involved in precursor ribosomal RNA (pre-rRNA) processing and rRNA base modifications (2'-O-ribose methylation and pseudouridylation). Their genomic organization show great flexibility: some are individually or polycistronically transcribed, while others are encoded within introns of other genes. Here, we present an evolutionary analysis of the U49 gene in seven species. In all species analyzed, U49 contains the typical hallmarks of C and D box motifs, and a conserved 12-15 nt sequence complementary to rRNA that define them as homologs. In mouse, human, and Drosophila U49 is found encoded within introns of different genes, and in plants it is transcribed polycistronically from four different locations. In addition, U49 has two copies in two different introns of the RpL14 gene in Drosophila. The results indicate a substantial degree of duplication and translocation of the U49 gene in evolution. In light of its variable organization we discuss which of the two proposed mechanisms of rearrangement has acted upon the U49 snoRNA gene: chromosomal duplication or transposition through an RNA intermediate.

Organization, sequence, and phylogenetic analysis of the ribosomal protein S3 gene from Drosophila virilis

Ribosomal protein S3 (RPS3) is a multifunctional ribosomal protein: it is a structural and functional component of the ribosome, and also a DNA repair enzyme involved in the DNA base excision repair pathway. Here we cloned and characterized the genomic organization of the ribosomal protein S3 gene (RpS3) homolog in Drosophila virilis. We then compared gene structure and protein sequences of RpS3 from vertebrates, invertebrates, and plants. These comparisons revealed that RpS3 genes from plants to mammals have highly conserved coding and amino acid sequences, and also protein size. Further comparisons of the protein sequences show that important domains are well conserved in both localization and sequence. In contrast, comparison of gene size and organization reveals differing patterns and levels of conservation. Whereas invertebrate RpS3 genes are small in size and gene organization is variable (from zero to four introns), vertebrates have a considerably larger (but variable) gene size and a uniform gene organization. The larger gene size in vertebrates is due to increased number and expansion of introns. Although the plant RpS3 genes are relatively small ( approximately 1.8 kb), their organization resembles that seen in vertebrates. The high conservation through different phyla may suggest that RPS3 might be under great functional constraints, both in its capacity as a component of the ribosome and as a component of a DNA repair system. Finally, electrophoretic mobility shift assays indicate that an upstream element binds a nuclear protein(s).

Complete genomic structure of human rpS3: identification of functional U15b snoRNA in the fifth intron

Analysis of the complete genomic structure of the human ribosomal protein S3 (rpS3) gene revealed the presence of a functional U15b snoRNA gene in its intron. Human ribosomal protein S3 (rpS3) gene of 6115 bp long has been identified to contain six introns and seven exons in this study. The first and fifth introns of human S3 gene contain functional U15 snoRNA genes. Although Xenopus and Fugu counterparts also have six introns and seven exons, S3 gene of Fugu contains two functional U15 snoRNAs in the fourth and sixth introns and two pseudo genes for U15 snoRNAs in the first and fifth introns. In Xenopus S1 gene encoding ribosomal protein S3, however, three of its six introns contain U15 snoRNA gene sequence. Sequence comparison of the U15 genes from Xenopus, Fugu and human revealed that the regions involved in binding to 28S rRNA and the consensus sequence (C, D and D' boxes) for snoRNAs are highly conserved among those genes from these three species. Human U15a and U15b RNAs which are derived from the first and the fifth introns, respectively, have been identified to be functional by microinjection of human U15a and U15b snoRNAs into Xenopus oocyte. Northern blot and primer extension analyses confirm that human U15b snoRNA is expressed in vivo.

Intron loss in the SART1 genes of Fugu rubripes and Tetraodon nigroviridis

The human SART1 gene was initially identified in a screen for proteins recognised by IgE, which may be implicated in atopic disease. We have examined the genomic structure and cDNA sequence of the SART1 gene in the compact genomes of the pufferfish Fugu rubripes and Tetraodon nigroviridis. The entire coding regions of both the Fugu and Tetraodon SART1 genes are contained within single exons. The Fugu gene contains only one intron located in the 5' untranslated region. Southern blot hybridisation of Fugu genomic DNA confirmed the SART1 gene to be single copy. Partial genomic structures were also determined for the human, mouse, Drosophila and C. elegans SART1 homologues. The human and mouse genes both contain many introns in the coding region, the human gene possessing at least 20 exons. The Drosophila and C. elegans homologues contain 6 and 12 exons, respectively. This is only the second time such a difference in the organization of homologous Fugu and human genes has been reported. The Fugu and Tetraodon SART1 genes encode putative proteins of 772 and 774 aa, respectively, each having 65% amino acid identity to human SART1. Leucine zipper and basic motifs are conserved in the predicted Fugu and Tetraodon proteins.

Small RNA database

The small RNA database is a compilation of all the small size RNA sequences available to date, including nuclear, nucleolar, cytoplasmic and mitochondria small RNAs from eukaryotic organisms and small RNAs from prokaryotic cells as well as viruses. Currently, approximately 600 small RNA sequences are in our database. It also gives the sources of individual RNAs and their GenBank accession numbers. The small RNA database can be accessed through the WWW (World Wide Web). Our WWW URL address is: http://mbcr.bcm.tmc. edu/smallRNA/smallrna.html . The new small RNA sequences published since our last compilation are listed in this paper (Table 1).

The comparative genomic structure and sequence of the surfeit gene homologs in the puffer fish Fugu rubripes and their association with CpG-rich islands

The puffer fish Fugu rubripes (Fugu) has a compact genome approximately one-seventh the size of man, mainly owing to small intron size and the presence of few dispersed repetitive DNA elements, which greatly facilitates the study of its genes at the genomic level. It has been shown previously that, whereas the Surfeit genes are tightly clustered at a single locus in mammals and birds, the genes are found at three separate loci in the Fugu genome. Here, Fugu gene homologs of all six Surfeit genes (Surf-1 to Surf-6) have been cloned and sequenced, and their gene structure has been compared with that of their mammalian and avian homologs. The predicted protein products of each gene are well conserved between vertebrate species, and in most cases their gene structures are identical to their mammalian and avian homologs except for the Fugu Surf-6 gene, which was found to lack an intron present in the mouse gene. In addition, we have identified conserved regulatory elements at the 5' and 3' ends of the Surf-3/rpL7a gene by comparison with the mammalian and chicken Surf-3/rpL7a gene homologs, including the presence of a polypyrimidine tract at the extreme 5' end of this ribosomal protein gene. The Fugu Surfeit gene homologs appear to be associated with CpG-rich islands, like the Surfeit genes in higher vertebrates, but these Fugu CpG islands are similar to the nonclassical islands characteristic of other fish species. Our observations support the use of the Fugu genome to study vertebrate gene structure, to predict the structure of mammalian genes, and to identify vertebrate regulatory elements. [The sequence data described in this paper have been submitted to the data library under accession nos. Y15170 (Surf-2, Surf-4), Y15171 (Surf-3, Surf-1, Surf-6), and Y15172 (Surf-5.)]