Structure and function of PTB and Fox, two regulators of alternative splicing
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1 Research Collection Doctoral Thesis Structure and function of PTB and Fox, two regulators of alternative splicing Author(s): Auweter, Sigrid D. Publication Date: 2007 Permanent Link: Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library
2 DISS. ETH Nr STRUCTURE AND FUNCTION OF PTS AND FOX, TWO REGULATORS OF ALTERNATIVE SPLICING A dissertation submitted to the SWISS FEDERAL INSTITUTE OF TECHNOLOGY ZURICH for the degree of Doctor of Sciences presented by SIGRID 0 AUWETER Dip!. Natw. ETH born 01. May 1979 citizen of Germany accepted on the recommendation of Prof. Dr. Frederic Allain, examiner Prof. Dr. Nenad Ban, co-examiner Dr. David Neuhaus. co-examiner 2007
3 Summary When the human genome was initially sequenced and analyzed, the alignment of exprcssed sequence tags with the genomic DNA sequence revealed that about 60% of all human genes are alternativcly spliced (Lander ct al., 2001). Hence, alternative splicing is a major mechanism to increase proteome diversity and to achieve genetic regulation in man. Misregulation ofalternative splicing is implicated in many human diseases like certain types of cancer, cystie fibrosis, or neurological disorders. Frequently, mutations that affect alternative splicing cause more severe defects than mutations that merely change the identity of individual amino acids, as they can disrupt inc1usion of entire exons or activate cryptic splice sites (Blencowe, 2006; Licatalosi and DamelI, 2006). Alternative splicing is regulated by numerous protein factors that recognize specific sequences within immature messenger RNAs (pre-mkblas). The aim ofthis thesis was to gain a more detailed understanding of splicing regulation by studying the structurc and function oftwo splicing factors, the polypyrimidine tract binding protein (PTB) and the protein Fox. These proteins are key factors in controlling splicing regulation ofthe c-src pre-mrna, which encodes a receptor tyrosine kinase in which a short exon is selectively inciuded in neurons but exciuded in all other cell types. The structures of the RNA recognition motif domains (RRMs) of PTB and Fox were solved in complex with their target RNA sequences using NMR spectroscopy. The structure of the Fox RRM/RNA eomplcx reveals a nove1 mode of RNA recognition by an RRM and the structure ofptb in complex with polypyrimidine tracts suggests a new model for splicing repression. Furthennore, the RNA binding properties of PTB and Fox were analyzed and evidence that argues for a model that explains c-src splicing regulation by competition of PTB and Fox for overlapping binding sites was collected.
4 Zusammenfassung Im Zuge der Sequenzierung des menschlichen Genoms ergab eine vergleichende Sequenzanalyse von zytoplasmatischen RNAs mit der genomischen DNA Sequenz, dass etwa 60% aller menschlichen Gene alternativ gespleisst werden (Lander et al., 2001). Dies bedeutet, dass alternatives Spleissen einen der wichtigsten Mechanismen zur Erweiterung der Diversität des Proteoms und zur Erreichung genetischer Regulation im Menschen darstellt. Die Misregulierung von alternativem Spleissen steht in Zusammenhang mit verschiedenen menschlichen Krankheiten, wie bestimmten Krebsarten, zystischer Fibrose, oder neurologischen Störungen. Oft verursachen Mutationen, die alternatives Spleissen beeinflussen, schwerere Defekte als Mutationen, die lediglich die die Identität einzelner Aminosäuren verändern, weil sre das Einschliessen ganzer Exons verhindern oder kryptische Spleiss-Stellen akitvieren können (Bleneowe, 2006; Licatalosi and Damcll, 2006). Alternatives Spleissen wird von unzähligen Proteinfaktoren reguliert, die spezifische Sequenzen innerhalb der unreifen messenger RNA (prämrna) erkennen. Das Ziel dieser Arbeit war es, durch die Untersuchung von Struktur und Funktion zweier Spleissfaktoren, dem Polypyrimidin-Trakt bindenden Protein (PTB) und dem Protein Fox, ein detaillierteres Verständnis der Regulation des RNA Spleissens zu erlangen. Diese Proteine sind Schlüsselfaktoren für die Kontrolle des Spleissens der c-src prä-mrna, die für eine Rezeptor-Tyrosinkinase kodiert und in die ein kurzes Exon selektiv in Neuronen eingeschlossen wird, während es in allen anderen Zelltypen ausgeschlossen wird. Die Strukturen der RNA-bindenden Domänen ("RNA recognition motif domains", RRMs) von PTB und Fox wurden im Komplex mit ihren RNA Zielsequenzen und mit Hilfe von NMR Spektroskopie gelöst. Die Struktur des Fox RRM/RNA Komplexes offenbart eine neuartige Form der RNA Erkennung durch eine RRM Domäne und die Struktur von PTB im Komplex mit Polypyrimidin Sequenzen impliziert ein neues Modell der Spleiss-Unterdrückung. Ausserdem wurden die RNA Bindungseigenschaften von PTB und Fox analysiert und Hinweise, die für ein Modell
5 argumentieren, das die Regulation des c-src NI Exons durch Kompetition von PTB und Fox um überlappende Bindestellen erklärt, wurden gesammelt.
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