|Research and Education
|1)Decipherment of splicing code|
Recent whole genome sequence analyses revealed that a high degree of proteomic complexity is achieved with a limited number of genes. This surprising finding underscores the importance of alternative splicing, through which a single gene can generate structurally and functionally distinct protein isoforms. Alternative splicing events are dynamically regulated in developmental stage-dependent and tissue specific manners. Pre-mRNAs contain a ‘splicing code’ made up of loosely defined consensus sequences that define the splice junctions and a bewildering number and diversity of relatively short cis-acting elements within exons as well as introns. To decipher the splicing code, we have developed transgenic alternative splicing reporter systems that enable us to visualize alternative splicing events in living nematode. With this reporter system, we have identified trans-acting factors and cis-elements involved in the splicing regulation and found some evolutionally conserved regulation mechanisms of alternative splicing.We recently developed transgenic reporter mice that enable us to visualize dynamic alternative splicing events in single cell resolution.
2) Development of new drugs to cure RNA diseases
There is a growing awareness that misregulations of mRNA processing are causative of many human diseases including hereditary, inflammatory and tumorigenic diseases. Thus new therapeutic approaches that target RNA processing mechanisms are highly anticipated. We focused on the mRNA splicing process, and have developed compounds that alter the alternative splicing events or even reverse some misregulated splicing events. Using splicing reporter systems, we screen and select chemical modifiers of splicing, examine their biological function during developmental stages, and consider their applications to crure hitherto intractable diseases.
3) Mathematical modeling of spontaneous pattern formation process during mammalian development.
During vertebrate development, spontaneous pattern formation (formation of pattern out of seemingly homogeneous initial state) is frequently observed, such as lung branching, limb skeletogenesis and skull suture interdigitation. These processes are quite complex and we cannot understand them by simply analyzing each gene involved. We formulated mathematical models which represents essential feature of these pattern formation process, and are now trying to verify the models by developing novel experimental methods.
||Ninomiya K, Kataoka N, and Hagiwara M. (2011) Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor. J Cell Biol (in press).|
||Nishida A, Kataoka N, Takeshima Y, Yagi M, Awano, H, Ota, M, Itoh K, Hagiwara M, and Matsuo M (2011) Chemical treatment enhances skipping of a mutated exon in the dystrophin gene. Nature Commun 2, 308.|
||Ogawa Y, Nonaka Y, Goto T, Ohnishi E, Hiramatsu T, Kii I, Yoshida M , Ikura T , Onogi H , Shibuya H , Hosoya T, Ito N, and Hagiwara M (2010) Development of a novel selective inhibitor of the Down syndrome-related kinase Dyrk1A. Nature Commun.1, 86.|
||Kuroyanagi H, Ohno G, Sakane, H, Maruoka, H, and Hagiwara M (2010) Visualization and genetic analysis of alternative splicing regulation in vivo using fluorescence reporters in transgenic Caenorhabditis elegans. Nature Protoc. 5, 1495-1517.|
||Ohno, G., Hagiwara, M. and Kuroyanagi, H. (2008) STAR family RNA-binding protein ASD-2 regulates developmental switching of mutually exclusive alternative splicing in vivo. Genes & Dev., 22,360-374.|
||Kuroyanagi, H, Ohno, G., Mitani, S., and Hagiwara, M. (2007) Fox-1 family and SUP-12 coordinately regulate tissue-specific alternative splicing in vivo. Mol. Cell. Biol. 27, 8612-8621.|
||Ideue T, Sasaki Y, Hagiwara M and Hirose T. (2007) Introns play an essential role in splicing-dependent formation of the exon junction complex. Genes & Dev., 21, 1993-1998.|
||Kaida D, Motoyoshi H, Tashiro E, Nojima T, Hagiwara M, Ishigami K, Watanabe H, Kitahara T, Yoshida T, Nakajima H, Tani T, Horinouchi S and Yoshida M (2007) A novel cell cycle inhibitor spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nature Chem. Biol., 3, 576-583.|