Novel insights into the molecular roles of UBP5 in controlling chromatin dynamics and plant development
James, Godwin
James, Godwin
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Publication Date
2023-04-03
Type
Thesis
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Abstract
Polycomb group (PcG) proteins are conserved chromatin regulators essential for controlling key developmental programs in eukaryotes. PcG proteins assemble together to form multi-protein complexes known as Polycomb Repressive Complexes (PRCs). PRCs have been involved in gene silencing via catalysing covalent histone modifications. Two of the best known PRCs, PRC1 and PRC2, respectively catalyse the incorporation of H2A monoubiquitination (H2Aub) and trimethylation of Lysine 27 of histone H3 (H3K27me3) and control gene expression. However, there is limited knowledge about PRCs’ interacting proteins and their interplay with PRCs’ activities, which is fundamental to understand the context of PRC-mediated gene regulation in plants. Here, I confirmed UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a novel interactor of the PRC2- associated factor PWO1 and SWINGER, PRC2 catalytic subunit. My results demonstrate that UBP5 regulates plant development, as inferred from the transcriptomic and phenotypic analysis of ubp5 plants. Notably, I have identified that UBP5 as a H2A deubiquitinase which counteracts H2Aub. Preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 enrichment further suggest the existence of a functional interplay between UBP5 and PRC2 in regulating epigenome dynamics. Thus, my data indicate that UBP5 is a new actor in the PcG-based gene regulation that influences both H2Aub and H3K27me3 at target genes thereby promoting gene expression. In addition, I focused on understanding the role of UBP5 in dry seeds and during germination to dissect the late germination phenotype of ubp5. Transcriptomic analyses of ubp5 dry seeds (DS) and imbibed seeds (IS) revealed strong global changes in transcriptional levels of several thousand of genes including seed germination regulators, histone variants and chromatin related genes. Similar to seedlings, UBP5 targets genes tend to be downregulated in seeds, suggesting a UBP5 key role in de-repression of genes in DS and IS. In addition, changes in the nuclear size and morphology in ubp5 DS and IS were identified. Therefore, UBP5 is proposed to have a dominant role in gene regulation in dry seeds and during germination probably via changes in nuclear dynamics and morphology. Overall, this research establishes the foundations to understand the molecular activities of UBP5 providing pioneering results about UBP5 epigenetic role in chromatin reshaping at different developmental stages. Furthermore, this study has contributed to a better understanding of the complex PRC2 protein network. In the future, this knowledge may offer opportunities for epigenomic editing and fine-tuning of gene expression.
Publisher
NUI Galway