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Petromyzon Marinus) University of Kentucky UKnowledge Theses and Dissertations--Biology Biology 2016 Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus) Stephanie A. Bryant University of Kentucky, [email protected] Digital Object Identifier: http://dx.doi.org/10.13023/ETD.2016.265 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Bryant, Stephanie A., "Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus)" (2016). Theses and Dissertations--Biology. 37. https://uknowledge.uky.edu/biology_etds/37 This Master's Thesis is brought to you for free and open access by the Biology at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Biology 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. Stephanie A. Bryant, Student Dr. Jeramiah Smith, Major Professor Dr. Dave Westneat, Director of Graduate Studies CHARACTERIZATION OF SOMATICALLY-ELIMINATED GENES DURING DEVELOPMENT OF THE SEA LAMPREY (PETROMYZON MARINUS) THESIS A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in the College of Arts and Sciences at the University of Kentucky By Stephanie Bryant Lexington, KY Director: Jeramiah Smith, Professor of Biology Lexington, Kentucky 2016 Copyright© Stephanie Bryant 2016 ABSTRACT OF THESIS CHARACTERIZATION OF SOMATICALLY-ELIMINATED GENES DURING DEVELOPMENT OF THE SEA LAMPREY (PETROMYZON MARINUS) The sea lamprey (Petromyzon marinus) undergoes programmed genome rearrangements (PGRs) during early development that facilitate the elimination of ~20% of the genome from the somatic cell lineage, resulting in distinct somatic and germline genomes. To improve our understanding of the evolutionary/developmental logic of PGR, we generated computational predictions to identify candidate germline-specific genes within a transcriptomic dataset derived from adult germline and the embryonic stages encompassing PGR. Validation studies identified 44 germline-specific genes and characterized patterns of transcription and DNA loss during early embryogenesis. Expression analyses reveal that several of these genes are differentially expressed during early embryogenesis and presumably function in early development of the germline. Ontology analyses indicate that many of these genes play known roles in germline development, pluripotency, and oncogenesis (when misexpressed). These studies provide support for the theory that PGR serves to segregate molecular functions related to germline development/pluripotency in order to prevent their potential misexpression in somatic cells. This larger set of eliminated genes also allows us to extend the evolutionary/developmental breadth of this theory, as some deleted genes (or their gnathostome homologs) appear to be associated with the early development of somatic lineages, perhaps through the evolution of novel functions within gnathostome lineages. Keywords: Lamprey, Development, Genome, Rearrangement, Vertebrate Stephanie A. Bryant April 29th 2016 CHARACTERIZATION OF SOMATICALLY-ELIMINATED GENES DURING DEVELOPMENT OF THE SEA LAMPREY (PETROMYZON MARINUS) By Stephanie Bryant Dr. Jeramiah Smith Director of Thesis Dr. Dave Westneat Director of Graduate Studies April 29th 2016 ACKNOWLEDGEMENTS I would like to thank my advisor Dr. Jeramiah Smith for his guidance throughout my graduate school career. I am grateful for his patience as he taught me the laboratory techniques and data analysis methods that made this thesis possible and for his guidance during the writing process. I would also like to thank Dr. Ashley Seifert for his unwavering confidence in me, Dr. Ann Morris for her continual encouragement and excellent Halloween parties, and Dr. Randal Voss for his professional insight and for allowing me to foray into axolotl research. In addition, I would like to thank Melissa Keinath and Joseph Herdy for their support and friendship, and Dr. Lakshmi Pillai of the Morris Lab for her infinite wisdom and sage advice. I also thank Brett Spear and Shirley Qui for granting access to real-time PCR resources used in this project. This work was funded by grants awarded to Dr. Jeramiah Smith and Dr. Chris Amemeyia by the National Institute of Health. Finally, I thank Josh Rock for his support and encouragement throughout the duration of my graduate career. iii TABLE OF CONTENTS Acknowledgements……………………………………………………….……………...iii List of Figures………………………………………………………….…………........…iv Section 1: Introduction…………………………………………………………...…...…...1 Section 2: Background………………………………...…………………………………..4 Section 3: Materials and Methods…...………...………………………………………….7 Animals…………………………………………………………..………………..7 Lamprey Embryos……………...…………………………………………………7 RNA Sequencing…………………………………………………………..……...8 Screening for Somatically-Eliminated Fragments……………………………...…8 Sequencing PCR Products………………………………………………………...9 Nanostring Gene Expression Analysis……………………………...…………...10 Real-Time PCR……………………………...……………………………..……11 Differential Expression Analysis………...………………………………………12 Gene Ontology Analysis…………………………………………………………12 Section 4: Results and Discussion…………………………………..……………………14 RNA Sequencing………………………………………………..…………….… 14 Screening for Somatically-Eliminated Fragments……….……………………….15 Real-Time PCR………………………………..…………………………………18 Nanostring Gene Expression Analysis……….…………………………………..19 Gene Ontology………………………………….………………………………..23 Section 5: Conclusions….…...………………………………………………………...…27 Vita……...…………………………………………………………………………….….33 iv LIST OF FIGURES Figure 1, Subset of validated deletions with homology information……………….……16 Figure 2, Full set of validated eliminations (n=44) …………………………………..…17 Figure 3, Relative abundance of a subset (n=23) of somatically-depleted genes based on qPCR in genomic DNA …………………………………………………………………19 Figure 4, Transcriptional profile and differential expression of somatically-depleted genes based on RNAseq estimates.…………………………………………………………..…21 Figure 5, Transcription and differential expression of somatically-depleted genes based on Nanostring estimates. …………………………………………………………….…..22 v SECTION 1- INTRODUCTION The sea lamprey (Petromyzon marinus) is a basal vertebrate representative of a lineage that diverged from our own ~550 million years ago, and is one of few vertebrates that undergo broad-scale programmed genome rearrangement (PGR) events (Smith, et al. 2009; Smith, et al. 2012). These events occur at 2.5 days post-fertilization (dpf), coinciding approximately with the mid-blastula transition, and facilitate the deletion of approximately 20% of the germline genome from the somatic cell lineage (Smith, et al. 2009). Genome and transcriptome sequencing indicates that a large number of single- copy DNAs, gene-coding fragments, and transcribed genes are eliminated during PGR, and many of these genes appear to correspond to human homologs related to germline pluripotency (Smith, et al. 2009; Smith, et al. 2012; Smith, et al. 2013). Previously identified genes eliminated during PGR include those with roles in cell proliferation (cancer/testis antigen 68, WNT7A/B), tumor suppression (RNA Binding Motif 47), and tumor progression and metastasis (Lysophosphatidic Acid Receptor 1) (Maglott, et al. 2011; Smith, et al. 2012). Somatic misexpression of genes with pluripotency/germline- specific functions may contribute to cancers or other disease states. (Hanahan and Weinberg 2000). As such, it is theorized that PGR may act as a permanent gene silencing mechanism that serves to limit pluripotency functions to the germline to prevent their misexpresson in the soma. While many of the genes eliminated during PGR are related to germline biology, many others have yet to be characterized. Studies aimed at identifying and characterizing a larger catalog of eliminated genes may provide further insight into the biological role of 1 PGR. The deep vertebrate ancestry of the sea lamprey
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