Associate Professor of Chemistry
B.A., University of Colorado
Ph.D., Brandeis University
Member of: Institute of Molecular Biology
Office: Willamette Hall Room 334
Telephone: 541-346-5097
Lab: Willamette Hall Rooms 309 & 310
Telephone: 541-346-1576 or 541-346-1594
Website
Research Interests
The primary goal of the Berglund lab is to understand how introns are recognized in the process of pre-mRNA splicing. Pre-mRNA splicing is conserved from yeast to humans and a complex molecular machine, the spliceosome, is responsible for removing introns from pre-mRNAs. The factors (U1 snRNP - an RNA-protein particle, U2AF65, U2AF35 and BBP/SF1) shown in the figure are the primary factors responsible for initial intron recognition. We are using both biochemical and biophysical techniques to study these RNA-RNA, RNA-protein and protein-protein interactions. These interactions are critical because without the correct choice of splice sites, truncated proteins or proteins with the wrong sequence would be produced. Incorrect splice site selection is thought to be responsible for 15% or more of human diseases.
We are characterizing these RNA-RNA and RNA-protein interactions from multiple organisms. These include the yeast Saccharomyces cerevisiae which is an excellent model system because the introns are small and apparently there is very little or no regulation of splicing. However, in humans, the regulation of pre-mRNA splicing is very important. Almost all genes in humans contain introns and many of these genes are regulated at the level of pre-mRNA splicing. This regulation frequently results in alternative splicing which suggests that although there are only approximately 25,000 genes in the human genome the number of proteins produced is much higher than this. The control of this regulation occurs through RNA sequences found in either the intron or exon acting as either repressor or enhancer elements to influence the percentage of intron removal, splice site selection, or exon skipping. The interplay of the factors that bind these enhancer/repressor elements and their interactions with the general splicing factors (U2AF65/35, BBP/SF1 and U1 snRNP, see figure) is another focus within the lab.
Myotonic Dystrophy
The splicing factor, muscleblind (MBNL), regulates alternative splicing by affecting splice site selection (figure). Myotonic dystrophy (a form of muscular dystrophy) occurs when MBNL does not properly function. The dysfunction of MBNL occurs in a novel manner in the disease state MBNL is mis-localized and cannot act on its target pre-mRNAs. MBNL is mis-localized by binding to CUG triplet expansion repeats in the 3' UTR of the dystrophia myotonia protein kinase (DMPK) gene. Hundreds of CUG repeats are common in patients with myotonic dystrophy while unaffected individuals have 5-30 CUG repeats. Longer CUG repeats (1,000 or more) results in more MBNL protein being mis-localized and leads to a more serious form of myotonic dystrophy because the regulation of alternative splicing of various pre-mRNAs is more severely compromised due to the increasing amounts of mis-localized MBNL. Using biochemical and biophysical methods we are studying the interaction between MBNL and the triplet expansion CUG repeats as well as MBNL's interactions with its normal pre-mRNA targets to gain insight into the molecular mechanisms of myotonic dystrophy and alternative splicing.
Selected Publications
Goers, E.S., Voelker, R.B., Gates, D.P., Berglund, J.A. (2008) RNA binding specificity of Drosophila Muscleblind. Biochemistry 47(27):7284–7294.
Murray JI, Voelker RB, Henscheid KL, Warf MB, Berglund JA. (2008) Identification of motifs that function in the splicing of non-canonical introns.
Genome Biol. 9(6):R97. Epub 2008 Jun 12.
Henscheid KL, Voelker RB, Berglund JA (2008) Alternative modes of binding by U2AF65 at the polypyrimidine tract. Biochemistry 47(1):449-59.
Garrey SM, Cass DM, Wandler AM, Scanlan MS, Berglund JA. (2008)Transposition of two amino acids changes a promiscuous RNA binding protein into a sequence-specific RNA binding protein. RNA. 14(1):78-88.
Warf MB, Berglund JA. (2007) MBNL binds similar RNA structures in the CUG repeats of myotonic dystrophy and its pre-mRNA substrate cardiac troponin T. RNA 13(12):2238-51.
Voelker RB, Berglund JA (2007) A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. Genome Res. 17(7):1023-33.
Cass, D. M., Berglund, J. A. (2006) The SF3b155 N-Terminal Domain Is a Scaffold Important for Splicing. Biochemistry 45(33):10092-10101.
Garrey S.M., Voelker R, Berglund J.A. (2006) An extended RNA binding site for the yeast branchpoint binding protein and the role of its Zn knuckle domains in RNA binding. J Biol Chem. 2006 Jul 21; [Epub ahead of print]
Mooers B.H., Logue J.S., Berglund J.A. (2005) The structural basis of myotonic dystrophy from the crystal structure of CUG repeats. Proc Natl Acad Sci U S A. 102(46):16626-31. Epub 2005 Nov 3.
Henscheid, K.L., Shin, D.S., Cary, C.S., Berglund, J.A. (2005) The splicing factor U2AF65 is functionally conserved in the thermotolerant deep-sea worm Alvinella pompejana. Biochim Biophys Acta. 1727: 197-207.
Galagan, J.E., et al. (2003) The Genome Sequence of the Filamentous Fungus Neurospora crassa Nature 422 859-868.
Berglund J.A. (2003) Expanding the structural repertoire of g-quadruplexes. Structure (Camb) 11:1315-6.
Galagan, J.E., et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-68.
Peled-Zehavi, H., J.A. Berglund, M. Rosbash, A.D. Frankel. (2001) Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex. Mol Cell Biol 21:5232-41.
Berglund, JA, M. Rosbash, S.C. Schultz. (2001) Crystal structure of a model branchpoint -- U2 snRNA duplex containing bulged adenosines. RNA 7:682-91.
Berglund, JA, M.L. Fleming, M. Rosbash. (1998) The KH doman of the branchpoint sequence binding protein determines specificity for the pre-mRNA branchpoint sequence. RNA 4:998-1006.
Berglund, JA, N. Abovich, M. Rosbash. (1998) A cooperative interaction between U2AF65 and mBBP/SFI facilitates branchpoint region recognition. Genes Dev 12:858-67.
Berglund, JA, K. Chua, N. Abovich, R. Reed, and M. Rosbash. (1997) The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Cell 89:781-7.
297 Klamath Hall Hall