Regulation of alternative pre-mRNA processing by small nucleolar RNAs

Summary

Principal Investigator: Stefan Stamm
Abstract: DESCRIPTION (provided by applicant): There is a fundamental gap in understanding the function of small RNAs that constitute a large part of human gene expression. For example, we do not know how the loss of small nucleolar RNA (snoRNA) expression contributes to the Prader-Willi syndrome, the most frequent genetic cause for life-threatening obesity. Our long-term goal is to elucidate the regulation of alternative splicing by small RNAs that are estimated to comprise more than 40% of human gene expression. The objective of this application is to determine which alternative splicing patterns are influenced by the snoRNAs missing in individuals with Prader-Willi syndrome and to understand the molecular basis by which one of these snoRNAs, HBII-52, influences alternative splicing patterns. The central hypothesis is that snoRNAs missing in individuals with Prader- Willi syndrome regulate alternative splicing by masking splicing regulatory elements on pre- mRNAs. Thus these snoRNAs regulate expression of numerous genes by changing their alternative splicing patterns. The rationale for the proposed research is that the genes regulated by these snoRNAs represent drug targets for treatment of the Prader-Willi syndrome. This proposal is therefore relevant to the NIH's mission that pertains to developing fundamental knowledge that will potentially help to reduce the burdens of human disease. Guided by our first published report that the snoRNA HBII-52 influences alternative splicing and additional strong preliminary data, this hypothesis will be tested by pursuing two specific aims: 1) Identify the pre-mRNAs that are regulated by the snoRNAs missing in people with Prader-Willi syndrome;and 2) Determine how HBII-52 regulates alternative splice site usage and test alternatives for its expression. Under the first aim, changes in pre-mRNA processing will be determined after ectopically expressing individual snoRNAs using bioinformatic predictions and splice-site sensitive DNA arrays. Under the second aim, we will identify the repressor activity that competes with the snoRNA HBII-52 and determine its mode of action, using an established in vitro system. The proposed work is innovative, because it shows a complete new role for snoRNAs in the regulation of alternative pre-mRNA splicing. It may well change the current `textbook knowledge'that snoRNAs only regulate non-mRNAs. The proposed research is significant because it would show a novel role of snoRNAs, identify the molecular defects in Prader-Willi syndrome and help to predict the influence of small RNAs on splice site selection. PUBLIC HEALTH RELEVANCE: The proposed studies delve into an under-investigated area of gene expression and have the potential applicability to understand the molecular cause of the Prader-Willi Syndrome and potentially other forms of inherited obesity. The proposed research is relevant for public health, because it investigates a new mechanism of human gene expression. Understanding this mechanism is the basis to improve diagnostics and therapeutic options for human diseases caused by defects in pre-mRNA processing.
Funding Period: 2009-08-01 - 2013-07-31
more information: NIH RePORT

Top Publications

  1. pmc Sudemycin E influences alternative splicing and changes chromatin modifications
    Paolo Convertini
    Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Department of Chemical Biology and Therapeutics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA and GenoSplice Technology, Hopital Saint Louis, Av Claude Vellefaux, 75010 Paris, France
    Nucleic Acids Res 42:4947-61. 2014
  2. pmc Ligand-induced activation of a formin-NPF pair leads to collaborative actin nucleation
    Brian R Graziano
    Department of Biology, Brandeis University, Waltham, MA 02454, USA
    J Cell Biol 201:595-611. 2013
  3. pmc Genome wide array analysis indicates that an amyotrophic lateral sclerosis mutation of FUS causes an early increase of CAMK2N2 in vitro
    Paolo Convertini
    Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, 741 South Limestone, Lexington, KY 40536 0509, USA
    Biochim Biophys Acta 1832:1129-35. 2013
  4. ncbi The 5' untranslated region of the serotonin receptor 2C pre-mRNA generates miRNAs and is expressed in non-neuronal cells
    Zhaiyi Zhang
    Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA
    Exp Brain Res 230:387-94. 2013
  5. pmc Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure
    Manli Shen
    Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA
    Nucleic Acids Res 41:3819-32. 2013
  6. pmc Processing of snoRNAs as a new source of regulatory non-coding RNAs: snoRNA fragments form a new class of functional RNAs
    Marina Falaleeva
    Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, KY, USA
    Bioessays 35:46-54. 2013
  7. doi Function of alternative splicing
    Olga Kelemen
    Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
    Gene 514:1-30. 2013
  8. pmc A retroelement modifies pre-mRNA splicing: the murine Glrb(spa) allele is a splicing signal polymorphism amplified by long interspersed nuclear element insertion
    Kristina Becker
    Institut fur Biochemie, Emil Fischer Zentrum, Universitat Erlangen Nurnberg, 91054 Erlangen, Germany
    J Biol Chem 287:31185-94. 2012
  9. pmc Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis
    Jussi Pihlajamaki
    Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
    Cell Metab 14:208-18. 2011
  10. pmc C6 pyridinium ceramide influences alternative pre-mRNA splicing by inhibiting protein phosphatase-1
    Chiranthani Sumanasekera
    Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
    Nucleic Acids Res 40:4025-39. 2012

Scientific Experts

  • Stefan Stamm
  • Manli Shen
  • Paolo Convertini
  • Zhaiyi Zhang
  • Marina Falaleeva
  • Amit Khanna
  • Pierre de la Grange
  • Olga Kelemen
  • Ruth Sperling
  • Brian R Graziano
  • Eduardo Eyras
  • Kristina Becker
  • Chiranthani Sumanasekera
  • Jussi Pihlajamaki
  • Fitzroy J Byfield
  • Shivendra Kishore
  • Chandraiah Lagisetti
  • Thomas R Webb
  • Craig Horbinski
  • Gustavo Palacios
  • Philip M Potter
  • Yvonne N Fondufe-Mittendorf
  • Bruce L Goode
  • Stanislav Bellaousov
  • Jiayu Zhang
  • Haining Zhu
  • Michael Hiller
  • Peter Stoilov
  • Amadis Pages
  • David H Mathews
  • Orit Malina
  • Lawrence J Hayward
  • Trevor P Creamer
  • Jessica G Pullen
  • Erin M Jonasson
  • Yuan Wen
  • Joseph Sperling
  • Christopher J Gould
  • Lily Agranat-Tamir
  • Volker Eulenburg
  • Monique Beullens
  • Natalya Benderska
  • Cord Michael Becker
  • Mathieu Bollen
  • Joseph A Adams
  • Manjula Sunkara
  • Brandon E Aubol
  • Emanuele Buratti
  • Carmen Villmann
  • Andrew Morris
  • Athena Andreadis
  • Marlen Braune
  • Francisco Baralle
  • Farrell Dearie
  • Paul B Savage
  • Pekka Miettinen
  • Josep C Jimenez-Chillaron
  • Paul A Janmey
  • Allison B Goldfine
  • Tanner Boes
  • Zhenwen Zhao
  • Imad Nasser
  • Andrew J Morris
  • Andrzej Namiot
  • Markku Laakso
  • Michael Q Zhang
  • Joshua Schroeder
  • Tiina Kuulasmaa
  • Marek Kowalski
  • Katarzyna Leszczynska
  • Carles Lerin
  • Robert Bucki
  • Jie Wu
  • Paula Itkonen
  • Hongmei Ren
  • Mary Elizabeth Patti
  • Serene Josiah
  • Furkan Burak
  • Peter J Park
  • Thomas Floss
  • Sarah Crunkhorn
  • Mathieu Rederstorff
  • Katrina Cruz
  • Wolfgang Wurst
  • Yan Xu
  • Piotr J Balwierz
  • Robert D Nicholls
  • Mihaela Stefan
  • Mihaela Zavolan
  • Jingyi Hui

Detail Information

Publications14

  1. pmc Sudemycin E influences alternative splicing and changes chromatin modifications
    Paolo Convertini
    Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Department of Chemical Biology and Therapeutics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA and GenoSplice Technology, Hopital Saint Louis, Av Claude Vellefaux, 75010 Paris, France
    Nucleic Acids Res 42:4947-61. 2014
    ..Thus, in addition to the reversible changes in alternative splicing, sudemycin E causes changes in chromatin modifications that result in chromatin condensation, which is a likely contributing factor to cancer cell death. ..
  2. pmc Ligand-induced activation of a formin-NPF pair leads to collaborative actin nucleation
    Brian R Graziano
    Department of Biology, Brandeis University, Waltham, MA 02454, USA
    J Cell Biol 201:595-611. 2013
    ..These observations define a new mode of formin regulation, which has important implications for understanding NPF-nucleator pairs in diverse systems...
  3. pmc Genome wide array analysis indicates that an amyotrophic lateral sclerosis mutation of FUS causes an early increase of CAMK2N2 in vitro
    Paolo Convertini
    Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, 741 South Limestone, Lexington, KY 40536 0509, USA
    Biochim Biophys Acta 1832:1129-35. 2013
    ..It indicates that, despite the obvious cytoplasmic accumulation, FUS-ΔNLS can act through a nuclear gain of function mechanism...
  4. ncbi The 5' untranslated region of the serotonin receptor 2C pre-mRNA generates miRNAs and is expressed in non-neuronal cells
    Zhaiyi Zhang
    Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA
    Exp Brain Res 230:387-94. 2013
    ..The data indicate that the transcriptional unit expressing HTR2C is more complex than previously recognized and likely deregulated in Prader-Willi syndrome. ..
  5. pmc Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure
    Manli Shen
    Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA
    Nucleic Acids Res 41:3819-32. 2013
    ..Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch...
  6. pmc Processing of snoRNAs as a new source of regulatory non-coding RNAs: snoRNA fragments form a new class of functional RNAs
    Marina Falaleeva
    Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, KY, USA
    Bioessays 35:46-54. 2013
    ..We propose that processed snoRNAs acquire new roles in gene expression and represent a new class of regulatory RNAs distinct from canonical snoRNAs...
  7. doi Function of alternative splicing
    Olga Kelemen
    Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
    Gene 514:1-30. 2013
    ..Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed...
  8. pmc A retroelement modifies pre-mRNA splicing: the murine Glrb(spa) allele is a splicing signal polymorphism amplified by long interspersed nuclear element insertion
    Kristina Becker
    Institut fur Biochemie, Emil Fischer Zentrum, Universitat Erlangen Nurnberg, 91054 Erlangen, Germany
    J Biol Chem 287:31185-94. 2012
    ..Conversely, the LINE1 effect on splicing may be modulated by individual polymorphisms, depending on the insertional environment within the host genome...
  9. pmc Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis
    Jussi Pihlajamaki
    Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
    Cell Metab 14:208-18. 2011
    ..Together, our results indicate that reduced expression of SFRS10, as observed in tissues from obese humans, alters LPIN1 splicing, induces lipogenesis, and therefore contributes to metabolic phenotypes associated with obesity...
  10. pmc C6 pyridinium ceramide influences alternative pre-mRNA splicing by inhibiting protein phosphatase-1
    Chiranthani Sumanasekera
    Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
    Nucleic Acids Res 40:4025-39. 2012
    ..Our results indicate that lipids can influence pre-mRNA processing by regulating the phosphorylation status of specific regulatory factors, which is mediated by protein phosphatase activity...
  11. doi Cathelicidin LL-37 increases lung epithelial cell stiffness, decreases transepithelial permeability, and prevents epithelial invasion by Pseudomonas aeruginosa
    Fitzroy J Byfield
    Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Immunol 187:6402-9. 2011
    ..These results suggested that the antibacterial effect of LL-37 involves an LL-37-dependent increase in cell stiffness that prevents epithelial invasion by bacteria...
  12. pmc Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression
    Manli Shen
    Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
    Nucleic Acids Res 39:9720-30. 2011
    ..The data suggest a conserved processing pattern for some C/D box snoRNAs and abundant expression of longer, non-coding RNAs in the cell that can potentially form dsRNAs...
  13. pmc Regulation of alternative splicing by short non-coding nuclear RNAs
    Amit Khanna
    University of Kentucky, Molecular and Cellular Biochemistry, South Limestone, Lexington, KY, USA
    RNA Biol 7:480-5. 2010
    ..We review the current knowledge of this emerging class of RNAs and discuss evidence that some of these short RNAs could function in alternative splice site selection...
  14. pmc The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing
    Shivendra Kishore
    Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
    Hum Mol Genet 19:1153-64. 2010
    ..This processed snoRNA functions in alternative splice-site selection. Its substitution could be a therapeutic principle for PWS...