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Large amounts of ultra-high molecular weight hyaluronan (HA) have been described as the main cause of cancer resistance in naked mole-rats (Heterocephalus glaber, NMR). Our work examined HA metabolism in these rodents more closely. HA was localized and quantified using HA binding proteins. Its molecular weight was determined using size exclusion chromatography and gel electrophoresis, HA family gene expression using RNAseq analysis, and hyaluronidase activity using zymography. Guinea pigs (Cavia porcellus) and mice (Mus musculus) were used as controls for some experiments. We found that HA localization was similar in NMR, guinea pig, and mouse tissues but NMR had larger amounts and higher molecular weight (maximum, around 2.5 MDa) of HA in serum and almost all tissues tested. We could not find ultra-high molecular weight HA (≥ 4 MDa) in NMR samples, in contrast to previous descriptions. Hyaluronidase-1 had lower expression and activity in NMR than mouse lymph nodes. RNAseq results showed that, among HA family genes, Tnfaip6 and hyaluronidase-3 (Hyal3) were systematically overexpressed in NMR tissues. In conclusion, NMR samples, contrary to expectations, do not harbor ultra-high molecular weight HA, although its amount and average molecular weight are higher in NMR than in guinea pig tissues and serum. Although hyaluronidase expression and activity are lower in NMR than mouse lymph nodes, this not sufficient to explain the presence of high molecular weight HA. A different activity of the NMR HA synthases remains possible. These characteristics, together with extremely high Hyal3 and Tnfaip6 expression, may provide the NMR with a bespoke, and perhaps protective, HA metabolism. [ABSTRACT FROM AUTHOR]

With the advent of next-generation sequencing technologies transcriptome sequencing (RNA-seq) became widely used to study the genetic background of ageing processes and related diseases. We describe the power of this method in the study of two novel age research model organisms, the short-lived killifish Nothobranchius furzeri and the long-lived naked mole rat Heterocephalus glaber. A third example illustrates the utility of RNA-seq in a multispecies approach elucidating the role of mild stress in healthy ageing. [ABSTRACT FROM AUTHOR]

The voltage-gated sodium channel subtype NaV1.8 ( SCN10A) is exclusively expressed in dorsal root ganglia (DRG) and plays a critical role in pain perception. We isolated mRNA from human, rat, and mouse DRGs and screened for alternatively spliced isoforms of the SCN10A mRNA using 454 sequencing. In all three species, we found an event of subtle alternative splicing at a NAGNAG tandem acceptor that results in isoforms including or lacking glutamine 1030 (NaV1.8+Q and NaV1.8-Q, respectively) within the cytoplasmic loop between domains II and III. The relative amount of NaV1.8-Q mRNA in adult DRG was measured with 14.1 ± 0.1% in humans and 11.2 ± 0.2% in rats. This is in contrast to an abundance of 64.3 ± 0.3% in mouse DRG. Thus, the NAGNAG tandem acceptor in SCN10A is conserved among rodents and humans but its alternative usage apparently occurs with species-specific abundance. Analysis of human NaV1.8+Q and -Q isoforms in whole-cell patch-clamp experiments after heterologous expression in the neuroblastoma cell line Neuro-2A revealed no obvious impact of the splicing event on channel function. [ABSTRACT FROM AUTHOR]

Background/Aims: Prostate cancer represents the cancer with the highest worldwide prevalence in men. Chromosome 8p23 has shown suggestive genetic linkage to early-onset familial prostate cancer and is frequently deleted in cancer cells of the urogenital tract. Within this locus some β-defensin genes (among them DEFB4, DEFB103, DEFB104) are localized, which are arranged in a gene cluster shown to exhibit an extensive copy number variation in the population. This structural variation considerably hampers genetic studies. In a new approach considering both sequence as well as copy number variations we aimed to compare the defensin locus at 8p23 in prostate cancer patients and controls. Methods: We apply PCR/cloning-based haplotyping and high-throughput copy number determination methods which allow assessment of both individual haplotypes and gene copy numbers not accessible to conventional SNP-based genotyping. Results: We demonstrate association of four common DEFB104 haplotypes with the risk of prostate cancer in two independent patient cohorts. Moreover, we show that high copy numbers (>9) of the defensin gene cluster are significantly underrepresented in both patient samples. Conclusions: Our findings imply a role of the antibacterial defensins in prostate cancerogenesis qualifying distinct gene variants and copy numbers as potential tumor markers. Copyright © 2008 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Several species have genomes in which the four nucleotides are not equally represented (Glöckner 2000). Interestingly, shifts to very high A/T or G/C levels can occur in several distinct branches of the tree of life. The underlying reasons for these shifts therefore may be of different origin. Now entire chromosome sequences from two different A/T-rich genomes,Dictyostelium discoideumandPlasmodium falciparum, are available (Bowman et al. 1999; Gardner et al. 2002; Glöckner et al. 2002). This gives us the opportunity to investigate how a high A/T content may influence the signals that are the landmarks for gene specification. We found that, in contrast with most known metazoan and plant genomes, splice signals contain, little information other than the canonical GT-AG dinucleotides. Intron lengths in A/T rich organisms, on the other hand, are comparable to those of other lower eukaryotes. Intergenic regions show, dependent on the orientation of adjacent genes, a size pattern with a ratio of 1 (3'-3') to 2 (3'-5') to 3 (5'-5'). Overall, gene organization patterns seem not to be influenced by the A/T bias. Surprisingly, the slightly higher A/T content of theP. falciparumgenome compared to that ofD. discoideum(80.1 versus 77.4%) is not achieved by increased A/T richness in intergenic regions. Instead both the shift of the nucleotide usage in coding regions to A/T-rich codons and the longer intergenic regions make an equal contribution to the higher A/T content in this organism. [ABSTRACT FROM AUTHOR]

Presents a study that reported the sequence of chromosome 2 of the genome of the lower eukaryote Dictyostelium discoideum. Features of chromosome 2; Functional classification of Dictyostelium discoideum chromosome 2-coded proteins; List of Dictyostelium discoideum chromosome 2 genes with similarity to human disease genes.

A letter to the editor is presented in response to the article "Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?" in September 2006 issue.

Splice acceptors with the genomic NAGNAG motif may cause NAG insertion-deletions in transcripts, occur in 30% of human genes and are functional in at least 5% of human genes. We found five significant biases indicating that their distribution is nonrandom and that they are evolutionarily conserved and tissue-specific. Because of their subtle effects on mRNA and protein structures, these splice acceptors are often overlooked or underestimated, but they may have a great impact on biology and disease. [ABSTRACT FROM AUTHOR]