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Doctor of Philosophy, Phd Nicola Meola Functional Characterization of Non-Coding Rnas in the Mammalian Retina O] F Open Research Online The Open University’s repository of research publications and other research outputs Functional Characterization of Non-Coding RNAs in the Mammalian Retina Thesis How to cite: Meola, Nicola (2011). Functional Characterization of Non-Coding RNAs in the Mammalian Retina. PhD thesis The Open University. For guidance on citations see FAQs. c 2011 The Author https://creativecommons.org/licenses/by-nc-nd/4.0/ Version: Version of Record Link(s) to article on publisher’s website: http://dx.doi.org/doi:10.21954/ou.ro.0000f18b Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online’s data policy on reuse of materials please consult the policies page. oro.open.ac.uk UNRGSTRi CT6D Doctor of Philosophy, PhD Nicola Meola Functional Characterization of Non-Coding RNAs in The Mammalian Retina o] f i c (U Q. O 0) .c cavsAntiA mrmnt vusccxAtte J- ( l£ A l T M M U i m CCNlTtCHl Discipline: Life and Biomolecular Sciences Affiliated Research Center: Telethon Institute of Genetics and Medicine Thesis submitted in accordance with the requirements of the Open University for the degree of “Doctor of Philosophy” August 2011 Date oj S\^bmx66wv; |G 1 2_oM Date oJ M\rardL- 15 D %oi\ ProQuest Number: 13837557 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a com plete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest ProQuest 13837557 Published by ProQuest LLC(2019). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States C ode Microform Edition © ProQuest LLC. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106- 1346 to LINA i “ I have had my results for a long time: hut I do not yet know how I am to arrive at them ” Karl Friedrich Gauss Table of contents TABLE OF CONTENTS I. LIST OF FIGURES AND TABLES.......................................................................... IV II. ABBREVIATIONS................................................................................................. VIII III. ABSTRACT............................................................................................................... X 1 INTRODUCTION ................................................................................................................... 1 1.1. THE RETINA...........................................................................................................1 1.1.1 Anatomy of the retina .........................................................................................1 1.1.2 The photoreceptors ............................................................................................ 4 1.1.2.1 Formation of the photoreceptor outer segments ...................... 8 1.1.2.2 Phototransduction and the visual cycle ........................ 10 1.1.3 Retinal development .........................................................................................13 1.1.3.1 Programmed cell death in the developing retina ....................................... 17 1.1.3.2 Retinal cell determination ..........................................................................19 1.1.4 Stem cells and transdifferentiation in the retina ...............................................23 1.1.5 Immortalized retinal cell lines ..........................................................................26 1.1.6 Inherited photoreceptor degenerative diseases.............. 29 1.1.6.1 Gene therapy approaches: retinal AAV vectors ........................................32 1.2 LONG NON-CODING RNAS: NEW FUNCTIONAL PLAYERS.......................35 1.2.1 “RNA World” ...................................................................................................35 1.2.2 Long non-coding RNAs (IncRNAs) .................................................................37 1.2.3 Genomic organization of IncRNAs ..................................................................39 1.2.4 Functional examples of IncRNAs .....................................................................41 1.2.4.1 Transcriptional and post-transcriptional regulation ...................................41 I Table of contents 1.2.4.2 Chromatin modification ............................................................................ 47 1.2.4.3 Regulation of enhancer activity .................................................................51 1.2.5 Genomic reprogramming and organization of nuclear structures.....................54 1.2.6 Long non-coding RNAs in the retina ................................................................56 1.3 AIMS OF THE THESIS.........................................................................................58 2 MATERIALS AND METHODS........................................................................................61 2.1 Generation of the plasmids for Vax2osl overexpression ........................................ 61 2.2 Expression studies...................................................................................................62 2.3 Synthesis of RNA probes for in situ hybrydization ................................................ 65 2.4 Transformation of E.coli with plasmid DNA .........................................................65 2.5 Isolation of plasmid DNA from E.coli ...................................................................66 2.6 Linearization of the plasmids ..................................................................................66 2.7 In vitro RNA transcription ......................................................................................67 2.8 RNA in situ hybridization on cryostat sections ......................................................67 2.9 Cell culture ..............................................................................................................69 2.10 Immunofluorescence and FACS ............................................................................70 2.11 RNA interference ..................................................................................................71 2.12 Tunel Assay ..........................................................................................................72 2.13 AAV virus and BrdU administration ....................................................................73 2.14 Statistics................................................................................................................ 74 3 RESU LTS................................................................................................................................ 74 3.1 GENOMIC ORGANIZATION OF IncRNAS VAX20S, 0TX20S AND SIX30S..14 3.1.1 Expression pattern of IncRNAs Vax2os, Otx2os and Six3os in the mouse retina .............................................................................................................................77 3.2 FUNCTIONAL CHARACTERIZATION OF IncRNA VAX20SIN VITRO 86 II Table of contents 3.2.1 In vitro expression studies and identification of a putative VAX20S human homolog .................................................. 90 3.2.2 Vax2osl overexpression impairs the cell cycle progression of differentiating 661W cells................................................................................................................... 95 3.3 IN VIVO STUDIES................................................................................................103 3.3.1 Misexpression of Vax2osl affects retinal progenitor cell proliferation 103 3.3.2 Vax2osl plays a role in the cell cycle progression and differentiation of photoreceptor progenitor cells ....................................................................................110 4 DISCUSSION........................................................................................................................120 4.1 Expression analysis of IncRNAs Six3os, Otx2os and Vax2os in the mouse retina ....................................................................................................................120 4.2 Functional characterization of IncRNA Vax2os in the mouse retina ..................... 124 IV. REFERENCES........................................................................................................129 V. ACKNOWLEDGEMENTS............................................................................................ 151 III List of fisures and tables I. LIST OF FIGURES AND TABLES Figure 1. Schematic view of the human eye anatomy .......................................................................... 1 Figure 2. Organization of retina ......................................................................................................... 2 Figure 3. Enlarged diagram of the fovea and visualization of the macula lutea .............. 3 Figure 4. Schematic representation o f rod and cone photoreceptors and photoreceptor intraflagellar transport (IFT) at the connecting cilium ...............................................................5 Figure 5. Spectral sensitivity of human photoreceptors...................................................................... 6 Figure 6. Schematic surface-view representation of the cone distribution across the human and mouse retina................................................................................................................................6
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