Regulation of Gene Expression by Non-coding RNAs in Arabidopsis and Brachypodium

Abstract

Expansion of high-throughput sequencing technology has increased our understanding in the importance of pervasive transcription and the resulting indispensable molecules, noncoding RNAs (ncRNAs). A significant effort has been made in determining the biological relevance of ncRNAs, including the small RNAs (smRNAs) and long ncRNAs (lncRNAs). Studies have shown that ncRNAs can have very important regulatory functions such as the establishment and maintenance of the epigenetic architecture of eukaryotic genomes. However, these studies have only revealed the surface of ncRNAs’ functions in cells. Motivated by the previously “hidden” transcriptome regulated by the Arabidopsis exosome, we examined the role of ncRNAs in regulation of gene expression in two plant model systems, Arabidopsis and Brachypodium. We set out to investigate whether the Arabidopsis exosome complex modulates gene expression through regulating ncRNAs, including both smRNAs and lncRNAs. Thus, the role of Arabidopsis exosome complex in regulating smRNA metabolism was extensively investigated and we revealed the differences between Arabidopsis core exosome, yeast and human exosomes in modulating smRNAs. Although we have only begun to categorize the lncRNAs regulated by the Arabidopsis exosome, our data so far has led to intriguing speculations, including the possible role of exosome in transcriptional regulation via controlling lncRNAs. The challenges still remain, including establishing the regulatory role of specific lncRNAs regulated by the exosome and other factors at transcriptional or post-transcriptional levels in different cellular contexts, and most importantly, how the interaction between these lncRNAs and the chromatin is mediated. We also investigated the role of smRNAs in biotic and abiotic stress responses in Brachypodium. We identified a group of endogenous, stress-induced small interfering RNAs, sutr-siRNAs, and its novel mechanism in targeting cis elements involved in splice site selection. This finding will stimulate research of smRNA mediated stress responses in agricultural important crops. It also provides a framework for more suitable experimental systems, such as the Drosophila and mammalian cell cultures, to further investigate the associated mechanistic details of sutr-siRNAs. In this dissertation, we revealed new insights and detailed molecular mechanisms of the Arabidopsis exosome complex in regulation of gene expression, as well as provided a novel regulatory mechanism of endogenous siRNAs by being involved in splicing. Although many challenges still remain to fully determine the mechanistic details and biological significance of plant ncRNAs, the work presented in this dissertation has added to our understanding in regulation of gene expression through ncRNAs in plants.