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Antisense Afp Transcripts in Mouse Liver and Their Potential Role in Afp Gene Regulation

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University of Kentucky UKnowledge Theses and Dissertations--Microbiology, Microbiology, Immunology, and Molecular Immunology, and Molecular Genetics Genetics 2017 ANTISENSE AFP TRANSCRIPTS IN MOUSE LIVER AND THEIR POTENTIAL ROLE IN AFP GENE REGULATION Maria S. Dixon University of Kentucky, [email protected] Digital Object Identifier: https://doi.org/10.13023/ETD.2017.356 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Dixon, Maria S., "ANTISENSE AFP TRANSCRIPTS IN MOUSE LIVER AND THEIR POTENTIAL ROLE IN AFP GENE REGULATION" (2017). Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics. 14. https://uknowledge.uky.edu/microbio_etds/14 This Doctoral Dissertation is brought to you for free and open access by the Microbiology, Immunology, and Molecular Genetics at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. I agree that the document mentioned above may be made available immediately for worldwide access unless an embargo applies. I retain all other ownership rights to the copyright of my work. I also retain the right to use in future works (such as articles or books) all or part of my work. I understand that I am free to register the copyright to my work. REVIEW, APPROVAL AND ACCEPTANCE The document mentioned above has been reviewed and accepted by the student’s advisor, on behalf of the advisory committee, and by the Director of Graduate Studies (DGS), on behalf of the program; we verify that this is the final, approved version of the student’s thesis including all changes required by the advisory committee. The undersigned agree to abide by the statements above. Maria S. Dixon, Student Dr. Martha L. Peterson, Major Professor Dr. Ken Fields, Director of Graduate Studies ANTISENSE AFP TRANSCRIPTS IN MOUSE LIVER AND THEIR POTENTIAL ROLE IN AFP GENE REGULATION DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Medicine at the University of Kentucky By Maria S. Dixon Lexington, Kentucky Director: Dr. Martha L. Peterson, Professor of Microbiology, Immunology & Molecular Genetics Lexington, Kentucky 2017 Copyright © Maria S. Dixon 2017 ABSTRACT OF DISSERTATION ANTISENSE AFP TRANSCRIPTS IN MOUSE LIVER AND THEIR POTENTIAL ROLE IN AFP GENE REGULATION Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer, ranking the sixth most common cancer and third most common cause of cancer mortality worldwide. Alpha-fetoprotein (AFP) is a plasma protein that is highly expressed in the fetal liver and shut off after birth. AFP expression is elevated in regenerating adult liver and HCC and has been used extensively as a diagnostic marker of liver cancer. We have been studying mouse liver gene regulation to better understand mechanisms by which changes in gene expression contribute to liver development, homeostasis and disease. Zinc Fingers and Homeoboxes 2 (Zhx2) has been identified as a repressor of AFP, but the mechanism of this regulation remains unknown. Interestingly, all targets of Zhx2 that have been identified to date, including H19, Glypican 3, Elovl3 and Cytochrome P450 (CYP) genes, are also known to be misregulated in HCC. Thus, a better understanding of the mechanism by which these genes are regulated by Zhx2 will likely lead to new insights into gene regulation during HCC progression. Antisense transcripts belong to a diverse class of long noncoding RNA molecules >200 nucleotides in length that often structurally resemble mRNAs, but do not encode proteins. While studying AFP mRNA regulation by Zhx2 in the mouse, our lab identified novel antisense AFP (asAFP) RNA transcripts that partially overlap the 3’ half of the mouse AFP gene. ENCODE tracks of ChIP-seq data for histone modifications in mouse liver show that the genomic region around the 5’ end of asAFP RNA has peaks for marks associated with promoters and enhancers. To better understand asAFP regulation, I identified the asAFP RNA 5’ end and the promoter elements that drive transcription. asAFP RNAs are ~5kb alternatively spliced, mainly cytoplasmic transcripts containing 2-4 exons. These transcripts were also detected in adult mouse liver RNA- seq data. asAFP is likely a noncoding RNA because it contains several small open reading frames that are 98 aa or smaller with no known functional domains or homology to known proteins. There is no evidence for similar transcripts in human liver. The abundance of asAFP RNA inversely correlates with AFP mRNA levels during postnatal liver development. Normally, asAFP RNA levels are high and AFP mRNA levels are low in the adult mouse liver. However, in the absence of Zhx2, AFP mRNA levels are higher and asAFP RNA levels are reduced, suggesting asAFP may be involved in the developmental regulation of AFP. Antisense transcripts function through a variety of mechanisms to positively or negatively regulate the expression of target genes. To explore the role of asAFP RNA in AFP gene regulation, I expressed segments of asAFP RNA in a mouse liver cell line and measured endogenous AFP mRNA levels. My data revealed that all segments of asAFP repressed endogenous AFP mRNA in trans. To determine the mechanism by which asAFP RNA regulates AFP, I expressed asAFP segments that overlapped only with exons or introns of AFP. The asAFP segments that overlap with the exons showed greater repression of endogenous AFP mRNA levels than those overlapping with intronic sequences. Additionally, I considered whether asAFP RNA repression of AFP mRNA may involve RNA editing by Adenosine deaminase acting on RNA (ADAR). ADARs convert adenosine to inosine in double-stranded RNAs that results in RNA degradation. My data indicate that AFP and asAFP dsRNA is not extensively edited, suggesting ADAR mediated decay is not involved in the regulation of AFP mRNA expression. However, further studies are required to determine the mechanism of cytoplasmic AFP mRNA degradation. Together, my data characterizes the transcriptional regulation of novel mouse asAFP transcripts and provides a model system to investigate how these transcripts regulate AFP mRNA through RNA-RNA interaction. KEYWORDS: Long Noncoding RNA, asAFP, AFP, RNA-RNA interaction, gene regulation Maria S. Dixon Student’s Signature Date ANTISENSE AFP TRANSCRIPTS IN MOUSE LIVER AND THEIR POTENTIAL ROLE IN AFP GENE REGULATION By Maria S. Dixon Martha L. Peterson Director of Dissertation Ken Fields Director of Graduate Studies Date I dedicate this dissertation to my loving husband. ACKNOWLEDGEMENTS “For I know the plans I have for you, declares the Lord,” Jeremiah 29:11. I give all thanks and praises to my Lord and Savior, Jesus Christ for guiding me throughout this journey. I would like to thank my mentor, Dr. Martha Peterson for your support and guidance through the most challenging years of my life. I am grateful to my committee members: Dr. Brett Spear, Dr. Brian Rymond and Dr. Subbarao Bondada for their guidance and feedback throughout my doctoral studies. Special thanks to Dr. John D’Orazio for not only serving as my external examiner, but for graciously allowing me to use his laboratory equipment for the completion of many of my experiments. I am truly grateful to Drs. Shirley Qiu, Jieyun Jiang and Lilia Turcios for their guidance, patience and expertise, which has molded me into the scientist that I am today. Special thanks to all the members of the Spear lab for your feedback during lab meetings and support. I would also like to thank the Microbiology, Immunology and Molecular Genetics department, Ms. Kate Fresca, and Dr. Beth Garvy for providing an amazing and supportive academic environment. My friends have been my “rams in the bush” and have given me unwavering support and love during the last five years. I am truly blessed to have such an amazing group of people in my life. Thank you, Cheavar Blair, LaQueta Shelton, Isabel Derera, Will Arnold, Katie Mckenna, Drs. Karine Oben, Sara Alhakeem, and Grant Jones. I am so proud of each of you and I am going to miss you dearly! To my mentees, Maya James and Brittany Rice, thank you for encouraging talks and motivating me to finish the course. I don’t know where I would be without my family. To my parents, Major and Bonnie Smith, thank you for your unconditional love, support, and guidance. To my grandmother, Viola Hughes, you have been a true inspiration in my life. Special thanks to my sister and cousin, Monique Smith and Deedra Hughes for being my best friends and angels on earth. To my Kentucky mother, Ms. Susan Jones, thank you for your love, prayers, and encouraging words. Lastly, I am extremely grateful to my loving husband, William L. Dixon III. You are truly my Miracle on earth! Thank you for being my biggest cheerleader and loving me through thick and thin; you have shown me the true meaning of unconditional love. I love you! iii TABLE OF CONTENTS ACKNOWLEDGEMENTS ....................................................................................
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