Alternative titles; symbols
HGNC Approved Gene Symbol: SRRM4
Cytogenetic location: 12q24.23 Genomic coordinates (GRCh38): 12:118,981,541-119,163,051 (from NCBI)
SRRM4 promotes alternative splicing and inclusion of neural-specific exons in target mRNAs (Calarco et al., 2009).
By sequencing clones obtained from a size-fractionated adult brain cDNA library, Nagase et al. (2001) cloned SRRM4, which they called KIAA1853. The deduced protein contains 708 amino acids. RT-PCR detected highest expression in adult brain, followed by fetal brain. Expression was detected in all specific adult brain regions examined and in spinal cord, with highest expression in cerebellum. Very weak expression was detected in adult kidney and testis and fetal liver, and little to no expression was detected in other tissues examined.
By searching databases for genes encoding proteins with ser/arg (SR) repeats, Calarco et al. (2009) identified mouse Srrm4, which they called Nsr100. They identified Srrm4 orthologs in several vertebrate species, including human. The deduced mouse and human proteins contain 608 and 611 amino acids, respectively, and both contain prominent runs of SR and RS repeats. Microarray analysis revealed increased Nsr100 expression in developing mouse embryo and highly restricted expression in adult mouse nervous system and sensory organs. Immunohistochemical analysis showed that Nsr100 was enriched in nuclei of cultured mouse neuronal cells, but not glial cells. Western blot analysis detected mouse and human NSR100 at an apparent molecular mass of 100 kD in neuronal and retinoblastoma cell lines, but not in any nonneuronal cell lines tested. Use of a monoclonal antibody directed against phosphoepitopes showed that Nsr100 was highly phosphorylated.
Using in situ hybridization, Nakano et al. (2012) found that Srrm4 was expressed in sensory hair cells and spiral ganglion of mouse inner ear. RT-PCR showed that Srrm4 mRNA was present in mouse brain, but not in kidney, liver, or spleen.
By radiation hybrid analysis, Nagase et al. (2001) mapped the SRRM4 gene to chromosome 12.
Gross (2019) mapped the SRRM4 gene to chromosome 12q24.23 based on an alignment of the SRRM4 sequence (GenBank BC152471) with the genomic sequence (GRCh38).
Calarco et al. (2009) showed that Nsr100 was expressed prior to induced differentiation in the mouse neuronal cell line Neuro2a. Short hairpin RNA-mediated knockdown of Nsr100 in Neuro2a cells had no effect on cell viability, but it reduced neurite extension. Knockdown of Nsr100 in mouse embryonic stem cells or adult neural stem cells had no effect on morphology or proliferation, but it reduced neurosphere formation. Microarray and RT-PCR analyses revealed that knockdown of Nsr100 significantly reduced neuron-specific alternative splicing of over 100 genes. Neuro2a cell lines expressing several test minigenes showed that both Nsr100 and Ptbp2 (608449) were required for inclusion of neuron-specific exons. Nsr100 appeared to bind a C/U-rich motif located within intronic regions upstream or downstream of the regulated exons. Mutation analysis of a Daam1 (606626) reporter minigene identified a repressor element that resulted in skipping of Daam1 exon 16 in the absence of Nsr100. In situ hybridization showed that Nsr100 was specifically expressed in developing central nervous system of zebrafish, and knockdown of Nsr100 resulted in neural degeneration of the brain and spinal cord. Calarco et al. (2009) concluded that NSR100 functions with PTBP2, and possibly other binding partners, and is required for expression of neural-specific genes and normal neural development.
Nakano et al. (2012) found that a 2,710-bp deletion in the Srrm4 gene was responsible for hair-cell loss, deafness, and balance defects in the spontaneous mutant Bronx waltzer (bv) mouse. The deletion removed a portion of the last intron and the entire coding region of the last exon of Srrm4, truncated the Srrm4 protein, and interfered with the stability or synthesis of the truncated protein. Transcriptomewide analysis of pre-mRNA splicing in sensory patches of bv/bv mouse embryonic inner ear revealed that Srrm4 modified gene expression through alternative splicing of transcriptional regulators specifically in hair cells, but not in other Srrm4-expressing tissues. RT-PCR analysis demonstrated that Srrm4-dependent alternative splicing required the C-terminal region of Srrm4. Computer analysis and mutagenesis experiments revealed that conserved GC motifs upstream of splice acceptor sites of Srrm4-regulated targets were necessary for interaction with Srrm4. Knockdown of srrm4 in zebrafish resulted in body axis deformity and hair-cell loss, which could be restored by expression of wildtype srrm4 but not by expression of the zebrafish srrm4 equivalent of the bv mutant.
Calarco, J. A., Superina, S., O'Hanlon, D., Gabut, M., Raj, B., Pan, Q., Skalska, U., Clarke, L., Gelinas, D., van der Kooy, D., Zhen, M., Ciruna, B., Blencowe, B. J. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell 138: 898-910, 2009. [PubMed: 19737518] [Full Text: https://doi.org/10.1016/j.cell.2009.06.012]
Gross, M. B. Personal Communication. Baltimore, Md. 5/8/2019.
Nagase, T., Nakayama, M., Nakajima, D., Kikuno, R., Ohara, O. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res. 8: 85-95, 2001. [PubMed: 11347906] [Full Text: https://doi.org/10.1093/dnares/8.2.85]
Nakano, Y., Jahan, I., Bonde, G., Sun, X., Hildebrand, M. S., Engelhardt, J. F., Smith, R. J. H., Cornell, R. A., Fritzsch, B., Banfi, B. A mutation in the Srrm4 gene causes alternative splicing defects and deafness in the Bronx waltzer mouse. PLoS Genet. 8: e1002966, 2012. [PubMed: 23055939] [Full Text: https://doi.org/10.1371/journal.pgen.1002966]