Alternative splicing

Characterization of a novel CAPN3 transcript generated by alternative splicing in cattle

S. Y. Liu, Jiang, H., Yuan, B., Gao, Y., Dai, L. S., and Zhang, J. B., “Characterization of a novel CAPN3 transcript generated by alternative splicing in cattle”, vol. 14, pp. 457-463, 2015.

Calpain-3 (CAPN3) is a member of the calpain family of Ca2+-regulated cysteine proteases, which play an important role in sarcomere remodeling and mitochondrial protein turnover, and thus, regulating beef tenderness in cattle. Currently, multiple CAPN3 transcripts have been detected in human, monkey, rat, and rabbit. However, whether this transcript is present in cattle remains unknown. In this study, we identified 2 CAPN3 transcripts in the skeletal muscle individuals of local black cattle from Jilin, China.

Dephosphorylation of NSSR1 regulates alternative splicing of the GluR-B minigene

W. Zhang, Li, L. L., Chen, X. H., and Peng, Z. Y., “Dephosphorylation of NSSR1 regulates alternative splicing of the GluR-B minigene”, vol. 13, pp. 1753-1763, 2014.

Neural salient serine/arginine-rich protein 1 (NSSR1, alternatively SRp38) is an important splicing factor that can repress pre-mRNA alternative splicing in cells during heat shock and mitosis. We show here that NSSR1 protein is dephosphorylated when cells are heat shocked or incubated with kinase inhibitor K252a. Both heat shock and K252a treatment increase the truncated splicing isoform of the GluR-B minigene pre-mRNA. We also investigated the roles of the RRM motif and three RS domains of NSSR1 in in vivo pre-mRNA splicing.

Increased expression of a novel splice variant of the complement component 4 (C4A) gene in mastitis-infected dairy cattle

Y. Yang, Huang, J. M., Ju, Z. H., Li, Q. L., Zhou, L., Li, R. L., Li, J. B., Shi, F. X., Zhong, J. F., and Wang, C. F., “Increased expression of a novel splice variant of the complement component 4 (C4A) gene in mastitis-infected dairy cattle”, vol. 11, pp. 2909-2916, 2012.

The complement system helps in the direct lysis of invading pathogens and modulates phagocytic, humoral and cellular immune responses. Complement 4 is a critical component in complement activity and protection against many bacterial pathogens because it is essential to classical and lectin activation pathways. We used reverse transcription and PCR to investigate alternative splicing and expression of the complement component 4 (C4A) gene in Chinese Holstein cattle. The PCR products were cloned and sequenced.

Expression of splice variants of cancer-testis genes ODF3 and ODF4 in the testis of a prostate cancer patient

S. Ghafouri-Fard, Ghafouri-Fard, S., and Modarressi, M. H., “Expression of splice variants of cancer-testis genes ODF3 and ODF4 in the testis of a prostate cancer patient”, vol. 11. pp. 3642-3648, 2012.

The outer dense fiber (ODF) genes encode proteins that co-assemble along the axoneme of the sperm tail. Recently, it was demonstrated that some ODF genes are aberrantly expressed in tumors, including prostate adenocarcinoma, basal cell carcinoma, and chronic myeloid lymphoma. We cloned ODF3 and ODF4 cDNA from the testis of a patient suffering from prostate adenocarcinoma and found two alternative splice variants of these genes.

Novel splice variants of the bovine PCK1 gene

Z. B. Zhang, Zhang, W., Li, R. L., Li, J. B., Zhong, J. F., Zhao, Z. S., and Huang, J. M., “Novel splice variants of the bovine PCK1 gene”, vol. 12, pp. 4028-4035, 2013.

Phosphoenolpyruvate carboxykinase 1 (PCK1), also named PEPCK-C, is a multiple-function gene that is involved in gluconeogenesis, glyceroneogenesis, reproduction, female fertility, and development of obesity and diabetes. How its many functions are regulated was largely unknown. Therefore, we investigated mRNA expression and possible splice variants of PCK1 by screening cDNA in nine tissues from Holstein bulls and cows.

Two splice variants of the bovine lactoferrin gene identified in Staphylococcus aureus isolated from mastitis in dairy cattle

J. M. Huang, Wang, Z. Y., Ju, Z. H., Wang, C. F., Li, Q. L., Sun, T., Hou, Q. L., Hang, S. Q., Hou, M. H., and Zhong, J. F., “Two splice variants of the bovine lactoferrin gene identified in Staphylococcus aureus isolated from mastitis in dairy cattle”, vol. 10, pp. 3199-3203, 2011.

Bovine lactoferrin (bLF) is a member of the transferrin family; it plays an important role in the innate immune response. We identified novel splice variants of the bLF gene in mastitis-infected and healthy cows. Reverse transcription-polymerase chain reaction (RT-PCR) and clone sequencing analysis were used to screen the splice variants of the bLF gene in the mammary gland, spleen and liver tissues. One main transcript corresponding to the bLF reference sequence was found in three tissues in both healthy and mastitis-infected cows.

Heteroduplex formation and S1 digestion for mapping alternative splicing sites

E. N. Ferreira, Rangel, M. C. R., Pineda, P. B., Vidal, D. O., Camargo, A. A., Souza, S. J., and Carraro, D. M., “Heteroduplex formation and S1 digestion for mapping alternative splicing sites”, vol. 7, pp. 958-969, 2008.

The identification of alternatively spliced transcripts has contributed to a better comprehension of developmental mechanisms, tissue-specific physiological processes and human diseases. Polymerase chain reaction amplification of alternatively spliced variants commonly leads to the formation of heteroduplexes as a result of base pairing involving exons common between the two variants. S1 nuclease cleaves single-stranded loops of heteroduplexes and also nicks the opposite DNA strand.

A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins

N. Jo Sakabe, Vibranovski, M. Dulcetti, and de Souza, S. José, “A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins”, vol. 3, pp. 532-544, 2004.

Alternative splicing increases protein diversity through the generation of different mRNA molecules from the same gene. Although alternative splicing seems to be a widespread phenomenon in the human transcriptome, it is possible that different subgroups of genes present different patterns, related to their biological roles. Analysis of a subgroup may enhance common features of its members that would otherwise disappear amidst a heterogeneous population. Extracellular matrix (ECM) proteins are a good set for such analyses since they are structurally and functionally related.

Splicing factors are differentially expressed in tumors

N. Kirschbaum-Slager, Lopes, G. M. P., Galante, P. A. F., Riggins, G. J., and de Souza, S. J., “Splicing factors are differentially expressed in tumors”, vol. 3, pp. 512-520, 2004.

Although alternative splicing of many genes has been found associated with different stages of tumorigenesis and splicing variants have been characterized as tumor markers, it is still not known whether these examples are sporadic or whether there is a broader association between the two phenomena. In this report we evaluated, through a bioinformatics approach, the expression of splicing factors in both normal and tumor tissues. This was possible by integrating data produced by proteomics, serial analysis of gene expression (SAGE) and microarray experiments.

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