Berglund:Publications

http://openwetware.org/wiki/Berglund_Lab 2011 Cass DM, Hotchko R, Barber P, Jones K, Gates DP, Berglund JA. The four Zn fingers of MBNL1 provide a flexible platform for recognition of its RNA binding elements. BMC Mol Biol. 2011 May 6;12(1):20. http://www.biomedcentral.com/1471-2199/12/20

2010 Culler SJ, Hoff KG, Voelker RB, Berglund JA, Smolke CD.Functional selection and systematic analysis of intronic splicing elements identify active sequence motifs and associated splicing factors. Nucleic Acids Res. 2010 Aug;38(15):5152-65. Epub 2010 Apr 12.

Warf MB, Berglund JA.Role of RNA structure in regulating pre-mRNA splicing.Trends Biochem Sci. 2010 Mar;35(3):169-78. Epub 2009 Dec 1.

Goers ES, Purcell J, Voelker RB, Gates DP, Berglund JA.MBNL1 binds GC motifs embedded in pyrimidines to regulate alternative splicing.Nucleic Acids Res. 2010 Apr 1;38(7):2467-84. Epub 2010 Jan 13.

Culler SJ, Hoff KG, Voelker RB, Berglund JA, Smolke CD.Functional selection and systematic analysis of intronic splicing elements identifies active sequence motifs and associated splicing factors.Nucleic Acids Res. 2010 Apr 12. [Epub ahead of print]

Voelker RB, Berglund JA. Two ways to misregulate mRNAs in myotonic dystrophy. Nat Struct Mol Biol. 2010 Feb;17(2):141-2. No abstract available.

Warf MB and Berglund JA. Role of RNA structure in regulating pre-mRNA splicing.Trends Biochem Sci. 2010 Mar;35(3):169-178. Epub 2009 Dec 1. (http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCV-4XV2JFP-1&_user=2148430&_coverDate=03%2F31%2F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000056308&_version=1&_urlVersion=0&_userid=2148430&md5=4fb3486d1849c0541375617d1a620b55)

Goers ES, Purcell J, Voelker RB, Gates DP, Berglund JA. MBNL1 binds GC motifs embedded in pyrimidines to regulate alternative splicing. Nucleic Acids Res. 2010.(http://nar.oxfordjournals.org/cgi/content/full/gkp1209v1)

2009 Berglund, John Andrew; Warf, M. Bryan; Matthys, Catherine; Haley, Michael M.; Hilton, Cameron L. Uses of pentamidine and related compounds. PCT Int. Appl. (2009),    66 pp. Warf MB, Berglund JA. Role of RNA structure in regulating pre-mRNA splicing.Trends Biochem Sci. 2009. (http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCV-4XV2JFP-1&_user=2148430&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000056308&_version=1&_urlVersion=0&_userid=2148430&md5=9f1a3528228450b3fefe06c1dcb15dba)

Warf MB, Nakamori M, Matthys CM, Thornton CA, Berglund JA. Pentamidine reverses the splicing defects associated with myotonic dystrophy. Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18551-6. (http://www.pnas.org/content/106/44/18551.long) Warf MB, Diegel JV, von Hippel PH, Berglund JA. The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing. PNAS May 26th, 2009.(http://www.pnas.org/content/early/2009/05/25/0900342106.long)

2008 Goers ES, Voelker RB, Gates DP, Berglund JA. RNA binding specificity of Drosophila muscleblind. Biochemistry. 2008 Jul 8;47(27):7284-94. Murray JI, Voelker RB, Henscheid KL, Warf MB, Berglund JA. Identification of motifs that function in the splicing of non-canonical introns.Genome Biol. 2008 Jun 12;9(6):R97. Henscheid KL, Voelker RB, Berglund JA. Alternative Modes of Binding by U2AF65 at the Polypyrimidine Tract. Biochemistry. 2008 Jan 8;47(1):449-59. 2007 Garrey SM, Cass DM, Wandler AM, Scanlan MS, Berglund JA. Transposition of two amino acids changes a promiscuous RNA binding protein into a sequence-specific RNA binding protein. RNA. 2007 Nov 13(14) 1-11. Warf MB, Berglund JA. MBNL binds similar RNA structures in the CUG repeats of myotonic dystrophy and its pre-mRNA substrate cardiac troponin T. RNA. 2007 Dec;13(12):2238-51. Voelker RB, Berglund JA. A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. Genome Res. 2007 Jul;17(7):1023-33.

2006 Garrey SM, Voelker R, Berglund JA. An extended RNA binding site for the yeast branchpoint binding protein and the role of its Zn knuckle domains in RNA binding. J. Biological Chemistry. 2006. Sep 15;281(37):27443-53. Cass DM, Berglund JA. SF3b155 N-terminal Domain, a scaffold important for splicing. Biochemistry. 2006. Aug 22;45(33):10092-101.

2005 Mooers BH, Logue JS, Berglund JA. The structural basis of myotonic dystrophy from the crystal structure of CUG repeats. Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16626-31.

Henscheid KL, Shin DS, Cary SC, Berglund JA. The splicing factor U2AF65 is functionally conserved in the thermotolerant deep-sea worm Alvinella pompejana. Biochim Biophys Acta. 2005 Mar 10;1727(3):197-207.

2003 Berglund JA. Expanding the structural repertoire of g-quadruplexes. Structure. 2003 Nov;11(11):1315-6.

Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 2003 Apr 24;422(6934):859-68.

2001 Peled-Zehavi H, Berglund JA, Rosbash M, Frankel AD. 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. 2001 Aug;21(15):5232-41.

Berglund JA, Rosbash M, Schultz SC. Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines. RNA. 2001 May;7(5):682-91.

1998 Berglund JA, Fleming ML, Rosbash M. The KH domain of the branchpoint sequence binding protein determines specificity for the pre-mRNA branchpoint sequence. RNA. 1998 Aug;4(8):998-1006.

Berglund JA, Abovich N, Rosbash M. A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition. Genes Dev. 1998 Mar 15;12(6):858-67.

1997 Berglund JA, Chua K, Abovich N, Reed R, Rosbash M. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Cell. 1997 May 30;89(5):781-7.

Berglund JA, Charpentier B, Rosbash M. A high affinity binding site for the HIV-1 nucleocapsid protein. Nucleic Acids Res. 1997 Mar 1;25(5):1042-9.

1996 Lietzke SE, Barnes CL, Berglund JA, Kundrot CE. The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites. Structure. 1996 Aug 15;4(8):917-30.