Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/113323
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Type: Theses
Title: Conservation and function of RNA 5-methylcytosine in plants
Author: Burgess, Alice Louise
Issue Date: 2016
School/Discipline: School of Biological Sciences
Abstract: Post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m⁵C) is an important modification that regulates RNA metabolism, translation and stress responses and occurs in both eukaryotes and prokaryotes. Yet, to date, no transcriptome-wide identification of m⁵C sites has been undertaken in plants. Here, we present over a thousand m⁵C sites transcriptome-wide in mRNAs and ncRNAs (non-coding RNAs) in three tissue types; siliques, shoots and roots of Arabidopsis thaliana at single nucleotide resolution using high-throughput Illumina sequencing of bisulfite treated RNA (RBS-seq). We show that m⁵C methylation sites can be tissue-specific, or shared among the tissue types investigated. Among the shared m⁵C sites, some are differentially regulated between tissue types, while others are constitutively methylated at the same level across all three tissue types. Within mRNAs, the majority of m⁵C sites are located within coding sequences. A small, significant enrichment of m⁵C sites in 3’UTRs of mRNAs was observed when normalizing for length and sequence coverage. We also investigated ncRNAs and demonstrate conservation of rRNA and tRNA m⁵C sites across six species in the kingdom Plantae, suggesting important and highly conserved roles of this post-transcriptional modification. We identified over 100 m⁵C sites in diverse RNA classes such as mRNAs, lncRNAs (long non-coding RNAs), snoRNAs (small nucleolar RNAs) and tRNAs mediated by Arabidopsis tRNA methyltransferase 4B (TRM4B) in siliques, shoots and roots. TRM4 plays broad roles in many organisms for mediating oxidative stress tolerance and balancing stem cell self-renewal and differentiation. We discovered that these roles are also conserved in plants, as Arabidopsis trm4b mutants have shorter primary roots, which is linked to a reduced capacity for cells to divide in the root meristem. Furthermore, trm4b mutants are also more sensitive to oxidative stress and have reduced stability of non-methylated tRNAs. Here, we extend the known m⁵C sites in tRNAs mediated by Transfer RNA aspartic acid methyltransferase 1 (TRDMT1) and find no evidence of m⁵C sites mediated by TRDMT1 in other RNA classes. Additionally we demonstrate that rRNA methylation requires the conserved RNA methyltransferase (RMTase) NSUN5. Our results also suggest functional redundancy of the three predicted RMTase NOP2 paralogs in Arabidopsis. This thesis provides the first maps of the Arabidopsis m⁵C epitranscriptome and characterization of Arabidopsis genetic mutants needed to further probe functions of this new layer of gene regulation in plants.
Advisor: Searle, Iain
David, Rakesh
Dissertation Note: Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Biological Sciences, 2016.
Keywords: RNA methylation
5-methylcytosine
RNA modifications
epitranscriptome
TRM4
NSUN2
DNMT2
TRDMT1
Arabidopsis
Research by Publication
Provenance: This electronic version is made publicly available by the University of Adelaide in accordance with its open access policy for student theses. Copyright in this thesis remains with the author. This thesis may incorporate third party material which has been used by the author pursuant to Fair Dealing exceptions. If you are the owner of any included third party copyright material you wish to be removed from this electronic version, please complete the take down form located at: http://www.adelaide.edu.au/legals
DOI: 10.25909/5b3dbd8dc9bae
Appears in Collections:Research Theses

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