Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1994 Telomeric nucleic acids: C-strand structure and a telomerase RNA mutant Shawn Cameron Ahmed Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Biophysics Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Ahmed, Shawn Cameron, "Telomeric nucleic acids: C-strand structure and a telomerase RNA mutant " (1994). Retrospective Theses and Dissertations. 10529. https://lib.dr.iastate.edu/rtd/10529 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. 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Ann Arbor, MI 48106 Telomeric nucleic acids: C-strand structure and a telomerase RNA mutant by Shawn Cameron Ahmed A Dissertation Submitted to the Graduate Faculty in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Department: Zoology and Genetics Interdepartmental Major: Molecular, Cellular and Developmental Biology Approved: Signature was redacted for privacy. In Charge of Mai.or Work Signature was redacted for privacy. For the Infta'departmental Signature was redacted for privacy. For the Major Department Signature was redacted for privacy. For the Graduate College Iowa State University Ames, Iowa 1994 ii Dedicated to my parents, l\/lohammed and Shirley iii TABLE OF CONTENTS ABSTRACT iv INTRODUCTION 1 CHAPTER 1: FORMATION OF NOVEL HAIRPIN STRUCTURES BY TELOMERIC C-STRAND OLIGONUCLEOTIDES 8 CHAPTER 2: HUMAN TELOMERIC C-STRAND TETRAPLEXES 18 CHAPTER 3: tgifl, A TELOMERASE RNA MUTANT WITH SHORT TELOMERES 30 GENERAL CONCLUSIONS 48 ACKNOWLEDGEMENTS 54 iv ABSTRACT Telomeres, the ends of linear chromosomes, are composed of simple tandem repeats which are usually G-C rich. Telomeres are essential for chromosome stability, organizing the nuclear architecture and ensuring complete replication of the chromosomal terminus. To understand how telomeres carry out these fundamental cellular roles, one must understand the structural and dynamic properties of telomeric repeat sequences. Structural and genetic approaches were taken to learn more about telomeric nucleic acids. The structural portion of my research concerned an unusual DNA structure formed by the C- rich strand of telomeric DNA. Telomeric C-strand sequences form non-Watson-Crick structures in supercoiled plasmids at low pH. Absorbance thermal denaturation, chemical modification and non- denaturing gel electrophoresis showed that telomeric C-strand oligonucleotides form stable structures at low pH. nuclear Overhauser effects indicated that these structures were four-stranded. In addition, these four-stranded C-structures were shown to mediate recognition and binding of identical nucleic acid sequences. Thus, a novel nucleic acid dimerization motif was discovered. The genetic portion of my research concerned analysis of a Tetrahymena mutant with short telomeres. This mutant was heterozygous for a telomerase RNA mutation. Telomerase is a ribonucleoprotein that uses its RNA component as a template for addition of telomeric repeats to chromosome termini. Therefore, telomerase is involved in telomere length regulation, a process that has been implicated in both aging and cancer. The mutant telomerase RNA gene caused telomere shortening when introduced into wildtype cells, and thus identifies a functionally important domain of the telomerase RNA. Although mutant telomerase activity was indistinguishable from wildtype activity in vitro, cells expressing high levels of the mutant telomerase RNA exhibited lethal phenotypes that were due to the presence of very short telomeres. 1 INTRODUCTION Thesis Organization. This introduction is meant to provide a broad general perspective of current l<nowledge in the field of telomeres as it relates to my research. The main body of this thesis is composed of three papers, and a conclusion at the end of this thesis touches on the fruits of my efforts and discusses research topics that may be worthy of further investigation. References for the introduction and conclusion are cited after the conclusion. The first two papers have been published in peer-reviewed journals. These two papers are the result of my investigations into telomeric C-strand structure. The third paper is a 'manuscript in preparation' and discusses my efforts to understand a telomerase RNA mutation that I discovered. All three papers have different formats because they either have been or will be published in different journals. References are given at the end of each paper. 1 am the primary author on each paper and personally completed most or all of the research described. My research was conducted with the guidance of Eric Henderson, the principal investigator. Agustin Kintanar provided invaluable assistance with NMR spectroscopy in paper 2. Mohammed Al-Anazi and Hong Sheng produced several of the mutants described in paper 3. Telomeres. Telomeres, chromatin domains at the ends of eukaryotic chromosomes, protect chromosomes from degradation and end-to-end fusion, presumably by burying the 'end' in a specialized nucleoprotein complex (Blackburn, 1991; Greider, 1990). Telomeres also help organize a chromosome's architecture within the nucleus and often cluster together at the nuclear periphery (Blackburn and Szostack, 1984). Chromosome ends without telomeres are unstable, and telomere loss often results in chromosome loss (Sandell and Zakian, 1993). Thus, telomeres are essential for genome viability and integrity. Conserved molecular mechanisms by which telomeres accomplish this task probably developed very early in eukaryotic evolution. Telomeric DNA. In most eukaryotes, telomeric DNA is composed of simple tandem repeats, though the sequence of these repeats can vary from organism to organism (Zakian, 1989). Most telomeric repeats have an asymmetric distribution of guanine and cytosine resulting in one strand being G-rich and the other C-rich. The G-strand always run 5' to 3' towards the end of the chromosome and extends as a single strand by about two repeats (Figure 1) (Henderson and Blackburn, 1989; Wellinger, et al., 1993). Evolutionary conservation of this strand composition bias suggests that it is important to telomere structure and function. Curiously, both strands of telomeric DNA can form their own unusual structures. •••^•AACCCC^ •••TTGGGGTTGGGGTTGGGG I simple, repetitive G-C rich sequences Figure 1. The Tetrahymena telomeric terminus has a 2 repeat 3' overhang. 2 Unusual DNA structures. DNA has the ability to adopt a variety of structures. Most DNA in a cell is double-stranded B-form DNA. However, double-stranded DNA can adopt alternative conformations such as A- and Z-DNA. In addition, three- and four-stranded DNA structures have been shown to exist. These less abundant DNA structures probably have specific biological functions (Rich, 1993). Methods for determining the biological function of an unusual DNA structure vary, but, in general, studies investigate sequences which form unusual structures and proteins that interact with these structures. Ultimately, mutational analysis of sequences which form such structures and of proteins that interact with them will enable us to understand their biological role. Telomeric DNA has been a useful 'model system' for studying unusual DNA structures. G-strand structures. In the presence of monovalent cations, the G-strand of telomeric DNA was shown to form unusual DNA structures (Henderson, et al., 1987) that were four- stranded (Williamson, et al., 1989; Sen and Gilbert, 1990). Since then, several groups have clearly demonstrated that the ends