The information contained within the human genome is decoded in a highly regulated and controlled manner. While the basic rules of decoding have been known for many decades, recent research is revealing a level of hidden complexity in which RNA signals and trans-acting factors can alter conventional protein synthesis to control gene expression. These findings have significant implications for our understanding of normal gene expression, and importantly, are providing insight into the molecular consequences of genetic mutations which lead to human disease.
The genetic code as presented in text books assumes genes are decoded by a linear mechanism such that translation initiates at a start codon and progresses three nucleotides at a time until a stop codon is encountered. However, the genetic code is far from universal and a significant number of genes have recently been identified in which the rules of the “universal” genetic code are altered as a means to control gene expression at the level of translation.
A recent significant effort in our laboratory is to understand the mechanism by which UGA codons (normally decoded as stop codons) are redefined to encode the 21 st amino acid selenocysteine. The selenocysteine residue is a highly reactive amino acid at physiological pH which is often utilized for specific enzymatic reactions. Selenoproteins play a role in many essential biological functions including protection against oxidative damage, production/inter-conversion of thyroid hormones, and normal muscle development. We are actively investigation the mechanisms of selenocysteine insertion and its regulation using a combination of biochemical, genetic, and cell based methodologies.
The insight gained from studying these, and other examples, of altered translation are also proving useful in understanding the molecular consequences of disease causing mutations. Genomic approaches have allowed for the rapid acquisition of DNA sequence for a number of genetic diseases. Even in diseases caused by mutations in a single gene, the phenotypes observed often do not correlate with that predicted based on the genotype. We are utilizing the genotype and phenotype date from over 1000 Duchenne and Becker Muscular Dystrophy patients in order to identify patients with discordant genotype/phenotype correlations. By understanding the post-transcriptional molecular mechanisms at work in these cases, we are gaining crucial insight into the pathways of normal protein expression and their dysfunction in human disease.
References to Publications:
Flanigan KM, Dunn DM, von Niederhausern A, Sotanzadeh P, Howard MT, et al. Nonsense mutation-associated Becker muscular dystrophy: interplay between exon definition and splicing regulatory elements within the DMD gene. Hum Mutat. 2010; Epub ahead of print.
Soltanzadeh P, Friez MJ, Dunn D, von Niederhausern A, Gurvich OL, Swoboda KJ, Sampson JB, Pestronk A, Connolly AM, Florence JM, Finkel RS, Bönnemann CG, Medne L, Mendell JR, Mathews KD, Wong BL, Sussman MD, Zonana J, Kovak K, Gospe SM Jr, Gappmaier E, Taylor LE, Howard MT, Weiss RB, Flanigan KM.Clinical and genetic characterization of manifesting carriers of DMD mutations.Neuromuscul Disord. 2010 Aug;20(8):499-504. Epub 2010 Jul 13.
Fixsen SM, Howard MT. Processive selenocysteine incorporation during synthesis of eukaryotic selenoproteins. J. Mol. Biol. 2010; April 24 Epub ahead of print.
Flanigan KM, Dunn DM, von Neiderhausern A, Soltanzadeh P, Gappmaier E, Howard MT et al., Mutational spectrum of DMD mutations in dystrophinopathy patients: application of modern diagnostic techniques to a large cohort. Hum. Mutat. 2009; 1657-1666.
Flanigan KM, Dunn DM, von Neiderhausern A, Howard MT, et al. DMD Trp3X nonsense mutation associated with a founder effect in North American families with mild Becker muscular dystrophy. Neuromuscular Disord. 2009; 743-748.
Hyvönen MT, Howard MT, Anderson CB, Grigorenko N, Khomutov AR, Vepsäläinen J, Alhonen L, Jänne J, Keinänen TA. Divergent regulation of the key enzymes of polyamine metabolism by chiral alpha-methylated polyamine analogues. Biochem. J. 2009; 321-328.
Gurvich OL, Maiti B, Weiss RB, Aggarwal G, Howard MT, Flanigan KM. DMD exon 1 truncating point mutations: amelioration of phenotype by alternative translation initiation in exon 6. Human Mutation 2009; 30: 633.
Maiti B, Arbogast S, Allamand V, Moyle MW, Anderson CB, Richard P, Guicheney P, Ferreiro A, Flanigan KM, Howard MT. A mutation in the SEPN1 selenocysteine redefinition element (SRE) reduces selenocysteine incorporation and leads to SEPN1-related myopathy. Hum. Mutation 2008; 30; 411-416.
Jurynec MJ, Xia R, Mackrill JJ, Gunther D, Crawford T, Flanigan KM, Abramson JJ, Howard MT, Grunwald DJ. Selenoprotein N is required for ryanodine receptor calcium release channel activity in human and zebrafish muscle. Proc. Natl. Acad. Sci. USA 2008; 105; 12485-12490.
Gurvich OL, Tuohy TM, Howard MT, Finkel RS, Medne L, Anderson CB, Weiss RB, Wilton SD, Flanigan KM. DMD pseudoexon mutations: splicing efficiency, phenotype, and potential therapy. Ann. Neurol. 2008; 63; 81-89.
Howard MT, Moyle MW, Aggarwal G, Carlson BA, Anderson CB. A recoding element that stimulates decoding of UGA codons by Sec tRAN[Ser]Sec. RNA 2007; 13; 912-920.
Petros LM, Graminski GF, Robinson S, Burns MR, Kisiel N, Gesteland RF, Atkins JF, Kramer DL, Howard MT, Weeks RS. Polyamine analogs with xylene rings induce antizyme frameshifting, reduce ODC activity, and deplete cellular polyamines. J. Biochem. 2006; 140; 657-666.
Henderson CM, Anderson CB, and Howard MT. Antisense induced ribosomal frameshifting. Nucleic Acids Research 2006; 34; 4302-4310.
Zook MB, Howard MT, Gomathinayagam S, Atkins JF, and Eisenlohr LC. Epitopes derived by incidental translational frameshifting give rise to a protective CTL response. Journal of Immunology. 2006; 176:6928-6934.
Wooding S, Bufe B, Grassi G, Howard MT, Stone AC, Vazquez M, Dunn DM, Meyerhof W, Weiss RB, Bamshad MJ. Independent evolution of bitter taste sensitivity in humans and chimpanzees. Nature 2006; 440:930-934.
Petros LM, Howard MT, Gesteland RF, Atkins JF. Polyamine sensing during antizyme mRNA programmed frameshifting. Biochem. Biophys. Res. Commun. 2005; 338:1478-1489.
Howard MT, Aggarwal, G, Anderson CB, Khatri S, Flanigan KM, and Atkins JF. Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons. EMBO J. 2005; 24:1596-1607.
Baranov PV, Henderson CM, Anderson CB, Gesteland RF, Atkins JF, and Howard MT. Programmed Ribosomal Frameshifting in Decoding the SARS-CoV Genome. Virology 2005; 332: 498-510.
Howard MT, Gesteland RF, Atkins JF. Efficient stimulation of site-specific ribosomal frameshifting by antisense oligonucleotides. RNA 2004; 10:1053-1061.
Howard MT, Malik N, Anderson CB, Voskuil JLA, Atkins JF, Gibbons RJ. Attenuation of an amino-terminal premature stop codon mutation in the ATRX gene by an alternative mode of translational initiation. Journal of Medical Genetics 2004;41:951-956.
Howard MT, Anderson CB, Fass U, Khatri S, Gesteland RF, Atkins JF, Flanigan KM. Readthrough of Dystrophin Stop Codon Mutations Induced by Aminoglycosides. Annals of Neurology 2004;55:422-426.
Adey NB, Lei M, Howard MT, Jensen JD, Mayo DA, Butel DL, Coffin SC, et al. Gains in sensitivity with a device that mixes microarray hybridization solution in a 25-um-thick chamber. Analy Chem 2002;74: 6413-6417.
Howard MT,Shirts BH, Zhou J, Carlson CL, Matsufuji S, Gesteland RF, Weeks RS, Atkins JF. Cell culture analysis of the regulatory frameshift event required for the expression of mammalian antizymes. Genes to Cells 2000;6:931-941.
Howard MT, Shirts BH, Petros LM, Flanigan KM, Gesteland RF, Atkins JF. Sequence specificity of aminoglycoside induced stop codon readthrough: Potential implications for treatment of Duchenne Muscular Dystrophy. Annals of Neurology 2000;48:164-169.
Nelson WC, Howard MT, Matson SW. The traY gene product and integration host factor stimulate Escherichia coli helicase I-catalyzed nicking at the F plasmid oriT. J Biol Chem 1995;270:28374-28380.
Howard MT, Nelson WC, Matson SW. Stepwise assembly of a relaxosome at the F plasmid origin of transfer. J Biol Chem 1995;270:28381-28386.
Howard MT, Neece SH, Matson SW, Kreuzer KN. Disruption of a topoisomerase-DNA cleavage complex by a DNA helicase. Proc Natl Acad Sci 1994;91:1203-1207.
Howard MT, Griffith JD. A cluster of strong topoisomerase II sites are located near an integrated Human Immunodificiency Virus. J of Mol Biol 1993;232:1060-1068.
Howard MT, Sandman K, Reeve J, Griffith JD. HMf, a histone-related protein from the hyperthermophilic archeon Methanothermus fervidus, binds preferentially to DNA containing phased tracts of adenines. J of Bact 1992;174:7864-7867.
Howard MT, Lee MP, Hsieh TS, Griffith JD. Drosophila Topoisomerase II-DNA interactions are affected by DNA structure. J Mol Biol 1991;217:53-62.
Wang YH, Howard MT, Griffith JD. Phased adenine tracts do not induce sequence directed bending. Biochem 1991;30:5443-5449.
Berry, MJ, Howard, MT. Reprogramming the Ribosome for Selenoprotein Expression: RNA Elements and Protein Factors. In Recoding: Expansion of decoding rules enriches gene expression. Springer, New York, NY. 2009
Atkins JF, Baranov PV, Fayet O, Herr AJ, Howard MT, Ivanov IP, Matsufuji S, Miller WA, Moore BM, Prére MF, Wills NM, Jhou J, Gesteland RF. Overriding standard decoding: Implications of recoding for ribosome function and enrichment of gene expression. Cold Spring Harbor Symposia on Quantitative Biology.Volume LXVI:217-232. 2001
Howard MT, Griffith JD. Possible roles of DNA topology in DNA-topoisomerase II interactions, in DNA Topoisomerases in Cancer. Oxford University Press, New York, NY. 1991
Michael Howard, Ph.D.
Department of Human Genetics
University of Utah
15 N 2030 E RM 7410
Salt Lake City, Utah 84112-5330