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NOP56 - a Hub for Box C/D snoRNP Autoregulation and Nucleolar Maintenance

Research output: Book/anthology/dissertation/reportPh.D. thesisResearch

Human gene expression is a highly coordinated multi-step process, reliant on a multitude of macromolecular complexes and several surveillance and quality control systems, to ensure the integrity of gene expression and avoid accumulation of flawed and potential detrimental gene products. Nonsense-mediated RNA decay (NMD), is a translation-dependent RNA quality control system, which target mRNAs harbouring premature stop codons. This thesis takes basis in an in-depth transcriptome-wide analysis of human cells, illuminating important molecular details of NMD, and supporting that several highly expressed snoRNA host-genes are subjected to an alternative splicing (AS)-coupled NMD gene regulation. snoRNAs play important roles in the guidance of essential post-transcriptional modifications of the ribosomal RNA, and their biogenesis is dependent on the functional splicing of their host gene. The discovery of AS-coupled NMD sensitive snoRNA host-genes, led us to a comprehensive analysis of the snoRNA host gene; NOP56, which acts as a hub for the coordination between box C/D snoRNP core proteins and global snoRNA levels, ultimately maintaining the nucleolar integrity. Our results demonstrate that AS of the NOP56 pre-mRNA, enable the exclusion or inclusion, respectively, of one of the embedded box C/D snoRNAs; snoRD86, causing the production of two major splice variants; a protein-coding mRNA encoding the NOP56 protein and a nonsense (ns)-mRNA subjected to cytoplasmic degradation by NMD. Intriguingly, our data support that snoRD86, through the adaptation of different RNP conformations in cis, dictates the usage of alternative splice donors within NOP56 pre-mRNA, ultimately controlling the levels of the limiting box C/D snoRNP core protein NOP56, in accordance with the availability of snoRNP assembly factors, the global box C/D snoRNA levels and NOP56 itself. Also, our data demonstrate that snoRD86 constitutes the 5’ end of a highly stable 3’ fragment (snoRD86 cSPA lncRNA), originating from the NMD specific SMG6-mediated endonucleolysis during degradation of the NOP56 ns-mRNA. Ongoing studies imply that cytoplasmic NOP56 ns-mRNA and snoRD86 cSPA lncRNA play important roles in the maintenance of the nucleolar structure and function. We propose that NOP56 ns-mRNA and its derivative snoRD86 cSPA lncRNA, functions as cytoplasmic sequestering-vehicles, relieving the nucleoplasm of excess nucleoplasmic box C/D snoRNPs. Furthermore, preliminary data suggest a possible connection between NOP56 ns-mRNA and/or snoRD86 cSPA lncRNA and the ubiquitin proteasome pathway, possibly by a snoRD86-mediated conveyance of snoRNP core proteins to decay machineries. In summary, through our studies of the interplay between the NMD pathway and snoRNA host genes, we have uncovered an autoregulatory feedback mechanism that ensures tight coordination between snoRNA levels and their protein partners.
Original languageDanish
Place of publicationAarhus
PublisherAarhus Universitet
Number of pages228
Publication statusPublished - Sep 2020

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