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Regulation of polyadenylation and splicing of mRNA. RNA-protein interactions. bioinformatics of gene expressionOur goal is to understand the basic machinery which processes pre-mRNA in the nucleus and apply that understanding towards analysis of how pre-mRNA processing is regulated. Unlike initiation of transcription. which is essentially an on-off type of switch. post-transcriptional control of gene expression allows mammalian cells to produce. from a single transcription event. an enormous variety of protein products. This is because a single pre-mRNA transcript can be alternatively spliced and/or polyadenylated resulting in different combinations of exons being assembled into a mature mRNA. Additional levels of control are also possible since alternative processing of pre-mRNAs can exclude or include RNA sequence elements which differentially regulate mRNA stability. localization and translational efficiency. Alterations and errors of pre-mRNA processing can lead to aberrant gene expression and disease. Both pre-mRNA and mRNA have been the primary targets for therapeutic methods based on antisense RNA and ribozyme technologies. By understanding the mechanisms underlying these processes we will contribute towards improving these therapies. Because lower. single-cell eukaryotes rarely regulate or alternatively process their pre-mRNAs we focus nearly exclusively on mammalian systems. Methodologies include both biochemical. bioinformatic and reconstitution analysis coupled with studies in tissue culture cells. The goal is to identify both cis-acting RNA sequence elements as well as trans-acting protein factors and understand how they combine to result in regulated pre-mRNA processing. Additionally. we perform extensive biochemical analysis of RNA-protein interactions. Selected PublicationsLi Y, Ho ES, Gunderson SI, Kiledjian M. (2009) Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5'-end stem-loop structures. Nucleic Acids Res. 37(7):2227-37. Goraczniak R, Behlke MA, Gunderson SI. (2009) Gene silencing by synthetic U1 adaptors. Nat Biotechnol. 27(3):257-63. Jankowska A, Gunderson SI, Andrusiewicz M, Burczynska B, Szczerba A, Jarmolowski A, Nowak-Markwitz E, Warchol JB. (2008) Reduction of human chorionic gonadotropin beta subunit expression by modified U1 snRNA caused apoptosis in cervical cancer cells. Mol Cancer. 7:26. Abad X, Vera M, Jung SP, Oswald E, Romero I, Amin V, Fortes P, Gunderson SI. (2008) Requirements for gene silencing mediated by U1 snRNA binding to a target sequence. Nucleic Acids Res. 36(7):2338-52. Goraczniak R, Gunderson SI. (2008) The regulatory element in the 3'-untranslated region of human papillomavirus 16 inhibits expression by binding CUG-binding protein 1. J Biol Chem. 283(4):2286-96. Guan F, Caratozzolo RM, Goraczniak R, Ho ES, Gunderson SI. (2007) A bipartite U1 site represses U1A expression by synergizing with PIE to inhibit nuclear polyadenylation. RNA. 13(12):2129-40. Ma J. Gunderson SI. Phillips C. (2006) Non-snRNP U1A levels decrease during mammalian B-cell differentiation and release the IgM secretory poly(A) site from repression. RNA. 12(1):122-32. Lee JH. Cook JR. Yang ZH. Mirochnitchenko O. Gunderson SI. Felix AM. Herth N. Hoffmann R. Pestka S. (2005) PRMT7. a new protein arginine methyltransferase that synthesizes symmetric dimethylarginine. J Biol Chem. 280(5):3656-64. Miranda TB. Khusial P. Cook JR. Lee JH. Gunderson SI. Pestka S. Zieve GW. Clarke S. (2004) Spliceosome Sm proteins D1. D3. and B/B' are asymmetrically dimethylated at arginine residues in the nucleus. Biochem Biophys Res Commun. 323(2):382-7. Phillips. C.. Pachikara. N. and Gunderson. S.I. (2004) U1A inhibits cleavage at the IgM heavy chain secretory poly(A) by binding between the two downstream GU-rich regions. Molecular and Cellular Biology 24:6162-6171. Guan. F.. Palacios. D.. Hussein. R.I.. and Gunderson. S.I. (2003) Determinants within an 18 amino acid U1A autoregulatory domain that uncouple cooperative RNA binding. inhibition of polyadenylation and homodimerization. Molecular and Cellular Biology 23: 3163-3172. Fortes,P.. Cuevas. Y.. Guan,F.. Liu. P.. Pentlicky. S.. Jung. S.. Martínez-Chantar . M.L.. Prieto. J.. Rowe. D.. and Gunderson. S.I. (2003) Inhibiting expression of specific genes in mammalian cells using modified U1 snRNPs targeted to terminal exons of pre-mRNA. Proc. Natl. Acad. Sci. USA 100: 8264-8269. Phillips. C. and Gunderson S.I. (2003) Sequences adjacent to the 5¹ splice site control U1A binding upstream of the IgM heavy chain secretory poly(A) site. J. Biol. Chem. 278: 22102-22111. |
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