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Targeted Mutagenesis of Zebrafish Hair Cell TARGETED MUTAGENESIS OF ZEBRAFISH HAIR CELL MECHANOTRANSDUCTION-RELATED GENES USING CRISPR/CAS9 by Shengxuan Wang Submitted in partial fulfillment of the requirements for the degree of Master of Science Thesis Advisor: Brian M. McDermott Jr., Ph.D. Department of Biology CASE WESTERN RESERVE UNIVERSITY January, 2019 1 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We here approve the thesis/dissertation of Shengxuan Wang Candidate for the Master of Science degree*. Karen Abbott, Ph.D. Chair of Committee Brian M. McDermott, Ph.D. Ruben Stepanyan, Ph.D. Sarah Diamond, Ph.D. (date) 08/29/2018 *We also verify the written approval has been obtained for any proprietary material contained there. 2 TABLE OF CONTENTS LIST OF FIGURES ............................................................................................................. 4 ACKNOWLEDEGMENT .................................................................................................... 5 LIST OF ABREVIATIONS ................................................................................................... 6 ABSTRACT ....................................................................................................................... 8 CHAPTER 1: INTRODUCTION ........................................................................................... 9 Hearing ............................................................................................................. 10 Hair cell ............................................................................................................. 11 Tip link .............................................................................................................. 15 Zebrafish as a model organism.......................................................................... 16 CRISPR/Cas9 ..................................................................................................... 17 CHAPTER 2: MATERIALS AND METHODS ....................................................................... 20 CHAPTER 3: TARGETING MET CHANNEL RELATED GENE USING CRISPR/CAS9 ............... 28 MET channel apparatus candidate genes .......................................................... 29 TMC protein family ........................................................................................... 30 LHFPL5 .............................................................................................................. 33 MACF1 .............................................................................................................. 34 RESULTS ....................................................................................................................... 38 Using CRISPR/Cas9 to knock out tmc5 in zebrafish ............................................ 38 Using CRISPR/Cas9 to knock out lhfpl5b in zebrafish ......................................... 48 Using CRISPR/Cas9 to knock out macf1b in zebrafish ........................................ 54 DISCUSSION .................................................................................................................. 59 REFERENCE ................................................................................................................... 61 3 LIST OF FIGURES FIGURE 1………………………………………………………………………………………………………………………11 FIGURE 2………………………………………………………………………………………………………………………12 FIGURE 3………………………………………………………………………………………………………………………14 FIGURE 4………………………………………………………………………………………………………………………15 FIGURE 5………………………………………………………………………………………………………………………18 FIGURE 6………………………………………………………………………………………………………………………19 FIGURE 7………………………………………………………………………………………………………………………22 FIGURE 8………………………………………………………………………………………………………………………30 FIGURE 9………………………………………………………………………………………………………………………31 FIGURE 10…………………………………………………………………………………………………………………….34 FIGURE 11…………………………………………………………………………………………………………………….35 FIGURE 12……….……………………………………………………………………………………………………………36 FIGURE 13………………………………………………………………………………………………………………….…37 FIGURE 14………………………………………………………………………………………………………………….…39 FIGURE 15…………………………………………………………………………………………………………………….40 FIGURE 16…………………………………………………………………………………………………………….………43 FIGURE 17…………………………………………………………………………………………………………………….45 FIGURE 18…………………………………………………………………………………………………………………….46 FIGURE 19…………………………………………………………………………………………………………………….47 FIGURE 20…………………………………………………………………………………………………………………….48 FIGURE 21…………………………………………………………………………………………………………………….49 FIGURE 22…………………………………………………………………………………………………………………….51 FIGURE 23…………………………………………………………………………………………………………………….54 FIGURE 24…………………………………………………………………………………………………………………….56 FIGURE 25…………………………………………………………………………………………………………………….57 TABLE 1………………………………………………………………………………………………………………………..23 TABLE 2………………………………………………………………………………………………………………………..24 TABLE 3………………………………………………………………………………………………………………………..25 4 ACKNOWLEDGEMENT First of all, I want to express my deepest and sincerest appreciation to my advisor Dr. Brian M. McDermott. He encouraged me to chase my dream with his patience and caring, he lead my direction to science with his excellent guidance. Most importantly, he is a thoughtful friend that cares me and willing to support me as always. I would also like to express gratitude to the rest of my committee members, Dr. Ruben Stepanyan and DR. Sarah Diamond for their patience and encouragement. I greatly appreciate their time talking to me and answering my questions. Also I would like to express my thanks to the Department of Biology for the opportunity to let me study in a great university. My special thanks to Shaoyuan Zhu and Zongwei Chen, they are good friends and always willing to instruct me to overcome difficulties in science. I would also like to thank other lab members, Ahlam Salameh, Hoa Nguyen, Kayla Kindig, Michael Dercoli, Shenyu Sun. They give me many helps not only in research, but also in my life. Finally, I would like to thank my parents and my boyfriend Yi Cai, they give me continuous love that are important more than everything in the world. They give me courage to face all the problems and difficulties in my life. Thank you for your support and I will always love you. 5 List of Abbreviations OHCs outer hair cells IHCs inner hair cells MET mechanotransduction channel CDH23 cadherin 23 PCDH15 protocadherin 15 dpf days post fertilization PCR polymerase chain reaction ZFNs zinc-finger nuclease TALENs transcription activator–like effector nucleases CRISPR clustered regularly interspaced short palindromic repeats Cas9 CRISPR associated protein 9 DSBs DNA double strand breaks sgRNA single-guide RNA (sgRNA) nt nucleotide NEHJ nonhomologous end-joining HDR homology-directed repair bp base pair PAM protospacer adjacent motifs BLAST basic local Alignment search tool NCBI National Center for Biotechnology Information PCR polymerase chain reaction 6 TMIE transmembrane inner ear TMC transmembrane channel-like LHFPL5 lipoma HMGIC fusion partner – like 5 TMHS tetraspan membrane protein of hair cell stereocilia MACF1 microtubule actin cross-linking factor 1 ACF7 actin crosslinking family protein 7 ABD actin binding domain GAR Gas2-related AM anterior macula PC posterior crista UTR untranslated region 4-Di-2-ASP 4-(4-diethylaminostyryl)-1-methylpyridinium iodide PFA paraformaldehyde PBS phosphate buffered saline GS goat serum crRNA CRISPR RNA tracrRNA trans-activating crRNA 7 Targeted mutagenesis of zebrafish hair ceLL mechanotransduction-reLated genes using CRISPR/Cas9 Abstract The senses of hearing and balance depend on sensory receptors called hair cells that exist in the ear. Hair cells convert mechanical stimuli into electrical signals and transmit them to the brain. These cells have a unique structure on their apical surface called the hair bundle that allows for mechanotransduction. This ensemble is composed of stereocilia that insert into the hair cell’s cuticular plate. Mechanotransduction is essential for normal hearing function, but the molecular identity of the mechanotransduction channel is still unknown. In this study, several genes that are potentially related to mechanotransduction channels have been successfully mutagenized using CRISPR/Cas9. The resulting knock out fish can be studied to determine the role of each gene. 8 Chapter 1: Introduction 9 Hearing Hearing is one of the most important senses in the human body. However, according to the estimates on the magnitude of disabling hearing loss by the World Health Organization in 2012, 5.3% of the world’s population is suffering hearing loss. In 2018, around 466 million people worldwide have disabling hearing loss and 34 million of these are children. It is estimated that by 2050, over 900 million people will have disabling hearing loss. Therefore, it is extremely important to study the molecular mechanisms of hearing. Hearing in humans relies on the structure of the ear, which collects the sound waves from vibrations in the air and translates them to neural impulses that are interpreted by the brain. The mammalian ear has three components: the outer ear, the middle ear and the inner ear (Figure 1). Of the outer ear, the most apparent part is the auricle. The auricle captures sound waves and transfer them to the middle ear through the external auditory canal. The middle ear is an air-filled pouch in which airborne sound stimulates the tympanum and leads to the vibration of three tiny bones: the malleus, incus, and stapes. The stapes is partially inserted into the oval window, which is a membrane-covered opening to the cochlea. Vibrations of the stapes stimulates the cochlea,
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