Alternative splicing and nonsense-mediated mRNA decay regulate gene expression of serum response factor.

Serum response factor (SRF) is an important transcription factor that regulates a variety of genes in many tissues during development, maturation and aging. The SRF protein also controls the expression of SRF target genes, including the SRF gene itself. However, it is incompletely established how SRF isoforms contribute to the regulation of SRF gene expression. In the present study, we report the identification of three novel SRF isoforms in human tissue. We found that one novel isoform, SRF-triangle up3, contained a premature termination codon (PTC), which was a target of nonsense-mediated mRNA decay (NMD). By contrast, the SRF-triangle up345 isoform protein was able to specifically bind to the serum response element, and to repress the SRF gene promoter activity. Therefore, we propose that SRF isoforms regulate expression of the SRF gene via two different mechanisms. One mechanism is to reduce the abundance of SRF transcripts via coupled alternative splicing and NMD, the other one is to regulate the SRF gene expression via a feedback mechanism in which the SRF isoform proteins bind to the SRF gene promoter region. Analysis of hundreds of SRF cDNA clones derived from human hearts of fetuses, young adults, old and very old individuals revealed that SRF isoform transcripts were increased in the human heart with advancing age. Our data indicate that the SRF isoforms were differentially expressed in the human versus mouse cardiac muscle. Alternative splicing and NMD likely maintain a delicate balance of SRF transcripts and/or proteins among the full-length SRF form and various SRF isoforms that are critical to the regulation of many SRF target genes, including the SRF gene itself.

[1]  E. Rieber,et al.  Autoimmunity as a Result of Escape from RNA Surveillance1 , 2006, The Journal of Immunology.

[2]  Jiang Chang,et al.  Inhibitory Cardiac Transcription Factor, SRF-N, Is Generated by Caspase 3 Cleavage in Human Heart Failure and Attenuated by Ventricular Unloading , 2003, Circulation.

[3]  Maxwell C. Furr,et al.  Model of functional cardiac aging: young adult mice with mild overexpression of serum response factor. , 2003, American journal of physiology. Regulatory, integrative and comparative physiology.

[4]  J. Concordet,et al.  Targeted Inactivation of Serum Response Factor in the Developing Heart Results in Myocardial Defects and Embryonic Lethality , 2004, Molecular and Cellular Biology.

[5]  R. Prywes,et al.  Identification of transcriptional activation and inhibitory domains in serum response factor (SRF) by using GAL4-SRF constructs , 1993, Molecular and cellular biology.

[6]  D. Black.  Protein Diversity from Alternative Splicing A Challenge for Bioinformatics and Post-Genome Biology , 2000, Cell.

[7]  M. Lefranc,et al.  T cell receptor γ cDNA in human fetal liver and thymus: Variable regions of γ chains are restricted to VγI or V9, due to the absence of splicing of the V10 and V11 leader intron , 1994 .

[8]  J. Campisi.  Senescent Cells, Tumor Suppression, and Organismal Aging: Good Citizens, Bad Neighbors , 2005, Cell.

[9]  I. Ariel,et al.  Stretch-induced alternative splicing of serum response factor promotes bronchial myogenesis and is defective in lung hypoplasia. , 2000, The Journal of clinical investigation.

[10]  B. Friguet,et al.  Maintenance of proteins and aging: The role of oxidized protein repair , 2006, Free radical research.

[11]  Da-Zhi Wang,et al.  Activation of Cardiac Gene Expression by Myocardin, a Transcriptional Cofactor for Serum Response Factor , 2001, Cell.

[12]  C. Bertolotto,et al.  Cleavage of the Serum Response Factor during Death Receptor-induced Apoptosis Results in an Inhibition of the c-FOS Promoter Transcriptional Activity* , 2000, The Journal of Biological Chemistry.

[13]  J. Vijg,et al.  Genetics of longevity and aging. , 2005, Annual review of medicine.

[14]  Wei Zhou,et al.  Dominant Negative Murine Serum Response Factor: Alternative Splicing within the Activation Domain Inhibits Transactivation of Serum Response Factor Binding Targets , 1999, Molecular and Cellular Biology.

[15]  J. Metcalfe,et al.  Four isoforms of serum response factor that increase or inhibit smooth-muscle-specific promoter activity. , 2000, The Biochemical journal.

[16]  Richard Treisman,et al.  Isolation and properties of cDNA clones encoding SRF, a transcription factor that binds to the c-fos serum response element , 1988, Cell.

[17]  R. Passier,et al.  Regulation of cardiac growth and development by SRF and its cofactors. , 2002, Cold Spring Harbor symposia on quantitative biology.

[18]  Timothy J. Nelson,et al.  SRF-dependent gene expression in isolated cardiomyocytes: regulation of genes involved in cardiac hypertrophy. , 2005, Journal of molecular and cellular cardiology.

[19]  R. Misra,et al.  Expression of the Serum Response Factor Gene Is Regulated by Serum Response Factor Binding Sites* , 1996, The Journal of Biological Chemistry.

[20]  E. Bacha,et al.  Increased expression of alternatively spliced dominant-negative isoform of SRF in human failing hearts. , 2002, American journal of physiology. Heart and circulatory physiology.

[21]  Juha Muilu,et al.  Conservation of human alternative splice events in mouse. , 2003, Nucleic acids research.

[22]  S. Brenner,et al.  Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[23]  A. Sharrocks,et al.  The MADS-box family of transcription factors. , 1995, European journal of biochemistry.

[24]  Tyson A. Clark,et al.  Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. , 2007, Genes & development.

[25]  D. Ginty,et al.  Restricted inactivation of serum response factor to the cardiovascular system. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Y. Zhong,et al.  Identification of a Novel Serum Response Factor Cofactor in Cardiac Gene Regulation* , 2004, Journal of Biological Chemistry.

[27]  W. Gish,et al.  Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. , 2001, Genome research.

[28]  A. Nordheim,et al.  Serum response factor is essential for mesoderm formation during mouse embryogenesis , 1998, The EMBO journal.

[29]  L. Kedes,et al.  The sarcomeric actin CArG-binding factor is indistinguishable from the c-fos serum response factor , 1989, Molecular and cellular biology.

[30]  L. Maquat.  Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics , 2004, Nature Reviews Molecular Cell Biology.

[31]  D. Garigan,et al.  Mutations That Increase the Life Span of C. elegans Inhibit Tumor Growth , 2006, Science.

[32]  N. Cheong,et al.  Serum Response Factor Cleavage by Caspases 3 and 7 Linked to Apoptosis in Human BJAB Cells* , 2001, The Journal of Biological Chemistry.

[33]  R. Treisman,et al.  Muscle-specific (CArG) and serum-responsive (SRE) promoter elements are functionally interchangeable in Xenopus embryos and mouse fibroblasts. , 1989, Development.

[34]  Christopher J. Lee,et al.  A genomic view of alternative splicing , 2002, Nature Genetics.

[35]  S. Ellard,et al.  The position of premature termination codons in the hepatocyte nuclear factor −1 beta gene determines susceptibility to nonsense-mediated decay , 2005, Human Genetics.

[36]  L. Maquat.  When cells stop making sense: effects of nonsense codons on RNA metabolism in vertebrate cells. , 1995, RNA.

[37]  T. Misteli,et al.  Lamin A-Dependent Nuclear Defects in Human Aging , 2006, Science.

[38]  L. Maquat,et al.  Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. , 2005, Current opinion in cell biology.

[39]  Christopher J. Lee,et al.  Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss , 2003, Nature Genetics.

[40]  J. Epstein,et al.  Cardiac hypertrophy and histone deacetylase-dependent transcriptional repression mediated by the atypical homeodomain protein Hop. , 2003, The Journal of clinical investigation.

[41]  H. Soreq,et al.  Pre‐mRNA splicing modulations in senescence , 2002, Aging cell.

[42]  D. Cane,et al.  The nonsense-mediated decay RNA surveillance pathway. , 2007, Annual review of biochemistry.

[43]  L. Maquat,et al.  A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. , 1998, Trends in biochemical sciences.

[44]  J. Miano,et al.  Serum response factor: toggling between disparate programs of gene expression. , 2003, Journal of molecular and cellular cardiology.

[45]  Maxwell C. Furr,et al.  Early Postnatal Cardiac Changes and Premature Death in Transgenic Mice Overexpressing a Mutant Form of Serum Response Factor* , 2001, The Journal of Biological Chemistry.