Increased urinary C-type natriuretic peptide excretion may be an early marker of renal tubulointerstitial fibrosis

The cDNAs encoding allatotropin (AT) and allatotropin-like peptides (ATLPs) were isolated from the silkworm, Bombyx mori. Similar to those of the tobacco hornworm, Manduca sexta, four peptides (AT, ATLP1, ATLP2, and ATLP3) are present in three different variants generated by alternative splicing. RT-PCR analyses showed that these splice variants are expressed in the central nervous system with differing expression patterns in each ganglion. Immunohistochemistry using an anti-AT antibody confirmed that AT-expressing cells were located in these central nervous ganglia as well as in two large anterior cells of the frontal ganglia. Injection of synthetic AT and ATLP-1 into B. mori larvae increased the latency to feed, indicating that AT and ATLP might function in the regulation of feeding behavior in B. mori.     

Identification of three new splice variants of the SNARE protein SNAP-23.

SNAP-23 has an important role in protein-trafficking processes in mammalian cells and until yet two isoforms of SNAP-23 (SNAP-23a and SNAP-23b) have been described. In the present report, we have identified the existence of three new SNAP-23 isoforms (named SNAP-23c, SNAP-23d, and SNAP-23e), which arise from alternative splicing. By RT-PCR all five splice variants were shown to be expressed in four different human inflammatory cells (eosinophils, basophils, neutrophils, and peripheral blood mononuclear cells). Transfection of the human basophilic KU-812 cell line with plasmid constructs containing the cDNAs of the five splice variants located SNAP-23a and SNAP-23b primarily in the plasma membrane. The other three splice variants were localized both intracellularly and in the plasma membrane.     

Evidence of the modulation of mRNA splicing fidelity in humans by oxidative stress and p53.

The majority of human genes generate mRNA splice variants and while there is little doubt that alternative splicing is an important biological phenomenon, it has also become apparent that some splice variants are associated with disease. To elucidate the molecular mechanisms responsible for generating aberrant splice variants, we have investigated alternative splicing of the human genes HPRT and POLB following oxidative stress in different genetic backgrounds. Our study revealed that splicing fidelity is sensitive to oxidative stress. Following treatment of cells with H2O2, the overall frequency of aberrant, unproductive splice variants increased in both loci. At least in POLB, splicing fidelity is p53 dependent. In the absence of p53, the frequency of POLB splice variants is elevated but oxidative stress does not further increase the frequency of splice variants. Our data indicate that mis-splicing following oxidative stress represents a novel and significant genotoxic outcome and that it is not simply DNA lesions induced by oxidative stress that lead to mis-splicing but changes in the alternative splicing machinery itself.     

Alternative splicing and gene structure of the transforming growth factor beta-activated kinase 1

We have identified a fourth splice variant of the TGF beta-activated kinase (TAK1), called TAK1-d, and identified an error in the previously published TAK1-c sequence. Our data shows that the c and d variants encode proteins whose carboxyl ends differ markedly from those of variants a and b. Analysis of the human TAK1 gene sequence, located at 6q16.1-q16.3, shows that the coding sequence is organised in 17 exons. The four splice variants result from alternative splicing of exons 12 and 16, the reading frame of exon 17 being determined by the presence or absence of exon 16. Study of the relative levels of expression of the four splice variants showed significant variations between tissues. Our evidence suggests that the alternative splicing of the TAK1 mRNA may have important functional implications.     

Increased large conductance calcium-activated potassium (BK) channel expression accompanied by STREX variant downregulation in the developing mouse CNS

Background  

Large conductance calcium- and voltage activated potassium (BK) channels are important determinants of neuronal excitability through effects on action potential duration, frequency and synaptic efficacy. The pore- forming subunits are encoded by a single gene, KCNMA1, which undergoes extensive alternative pre mRNA splicing. Different splice variants can confer distinct properties on BK channels. For example, insertion of the 58 amino acid stress-regulated exon (STREX) insert, that is conserved throughout vertebrate evolution, encodes channels with distinct calcium sensitivity and regulation by diverse signalling pathways compared to the insertless (ZERO) variant. Thus, expression of distinct splice variants may allow cells to differentially shape their electrical properties during development. However, whether differential splicing of BK channel variants occurs during development of the mammalian CNS has not been examined.     

可变剪接与疾病的生物信息学研究概况

可变剪接是真核基因转录后期的重要调控机制,它使得同一条蛋白质编码基因能够产生多种转录体,极大的扩展了遗传信息的应用.研究发现,可变剪接与人类疾病有着密切的联系.错误的剪接会导致疾病,增加疾病的易感性与病变程度,甚至直接导致癌变.现对可变剪接调控机制与疾病的生物信息学研究进展进行综述.     

Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis

Alternative splicing enhances proteome diversity and modulates cancer-associated proteins. To identify tissue- and tumor-specific alternative splicing, we used the GeneChip Human Exon 1.0 ST Array to measure whole-genome exon expression in 102 normal and cancer tissue samples of different stages from colon, urinary bladder, and prostate. We identified 2069 candidate alternative splicing events between normal tissue samples from colon, bladder, and prostate and selected 15 splicing events for RT-PCR validation, 10 of which were successfully validated by RT-PCR and sequencing. Furthermore 23, 19, and 18 candidate tumor-specific splicing alterations in colon, bladder, and prostate, respectively, were selected for RT-PCR validation on an independent set of 81 normal and tumor tissue samples. In total, seven genes with tumor-specific splice variants were identified (ACTN1, CALD1, COL6A3, LRRFIP2, PIK4CB, TPM1, and VCL). The validated tumor-specific splicing alterations were highly consistent, enabling clear separation of normal and cancer samples and in some cases even of different tumor stages. A subset of the tumor-specific splicing alterations (ACTN1, CALD1, and VCL) was found in all three organs and may represent general cancer-related splicing events. In silico protein predictions suggest that the identified cancer-specific splice variants encode proteins with potentially altered functions, indicating that they may be involved in pathogenesis and hence represent novel therapeutic targets. In conclusion, we identified and validated alternative splicing between normal tissue samples from colon, bladder, and prostate in addition to cancer-specific splicing events in colon, bladder, and prostate cancer that may have diagnostic and prognostic implications.     

Effect of silver nanoparticles on the expression of 6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase-2 mRNA and its alternative splice variants in different rat organs

Bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-2 (PFKFB-2) is represented by several alternative splice variants and plays a significant role in the glycolysis regulation in the brain, lung, testis and heart cells. The expression of PFKFB-2 mRNA and its alternative splice variants in these rat vital organs after single intratracheal injection of silver nanoparticles was studied. It was shown that the expression of PFKFB-2 mRNA is significantly changed in different rat tissues under silver nanoparticles action. The effect of silver nanoparticles on the expression of PFKFB-2 mRNA was observed one day after its injection to animals. In 3 and 14 days the effect of silver nanoparticles was increased (in testes) or kept on the approximately same level (in other investigated tissues). The expression of PFKFB-2 mRNA in most tissues is returned to its control levels one year after the injection of silver nanoparticles to the rats. It was also shown that the expression of alternative splice variants of PFKFB-2 mRNA without functional activity of 6-phosphofructo-2-kinase is significantly increased in different tissues 1, 3 and 14 days after single injection of silver nanoparticles. The results of this investigation demonstrate clearly that silver nanoparticles significantly affect the expression of PFKFB-2 mRNA on the alternative splicing level in different vital organs and show their effect on the important mechanisms of metabolism regulation in the cells on the level of key enzyme gene expression.     

Molecular characterization of the family of choline transporter-like proteins and their splice variants

We show here that the choline transporter-like (CTL) family is more extensive than initially described with five genes in humans and complex alternative splicing. In adult rat tissues, CTL2-4 mRNAs are mainly detected in peripheral tissues, while CTL1 is widely expressed throughout the nervous system. During rat post-natal development, CTL1 is expressed in several subpopulations of neurones and in the white matter, where its spatio-temporal distribution profile recalls that of myelin basic protein, an oligodendrocyte marker. We identified two major rat splice variants of CTL1 (CTL1a and CTL1b) differing in their carboxy-terminal tails with both able to increase choline transport after transfection in neuroblastoma cells. In the developing brain, CTL1a is expressed in both neurones and oligodendroglial cells, whereas CTL1b is restricted to oligodendroglial cells. These findings suggest specific roles for CTL1 splice variants in both neuronal and oligodendrocyte physiology.