<scp>CLP1</scp> as a novel player in linking <scp>tRNA</scp> splicing to neurodegenerative disorders

Weitzer, Stefan; Hanada, Toshikatsu; Penninger, Josef; Martı́nez, Javier

doi:10.1002/wrna.1255

Cited by 50 publications

(42 citation statements)

References 110 publications

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“…Cross talk between an endonuclease and a polynucleotide kinase has also been observed between the mammalian tRNA splicing endonuclease complex (TSEN) and the Clp1 polynucleotide kinase. Clp1 is required for the integrity and nuclease activity of the TSEN complex; however, in contrast to Grc3, kinase activity of Clp1 is not dependent on the TSEN complex (13,14,33). Another example of molecular cross talk has been observed in mammalian polynucleotide kinase phosphatase, where mutations that ablate phosphatase activity also block kinase activity, ensuring that 5′-phosphorylation of damaged DNA does not occur before removal of 3′-adducts (34)(35)(36).…”

Section: Discussionmentioning

confidence: 99%

Grc3 programs the essential endoribonuclease Las1 for specific RNA cleavage

Pillon

Sobhany

Borgnia

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Las1 is a recently discovered endoribonuclease that collaborates with Grc3-Rat1-Rai1 to process precursor ribosomal RNA (rRNA), yet its mechanism of action remains unknown. Disruption of the mammalian Las1 gene has been linked to congenital lethal motor neuron disease and X-linked intellectual disability disorders, thus highlighting the necessity to understand Las1 regulation and function. Here, we report that the essential Las1 endoribonuclease requires its binding partner, the polynucleotide kinase Grc3, for specific C2 cleavage. Our results establish that Grc3 drives Las1 endoribonuclease cleavage to its targeted C2 site both in vitro and in Saccharomyces cerevisiae. Moreover, we observed Las1-dependent activation of the Grc3 kinase activity exclusively toward single-stranded RNA. Together, Las1 and Grc3 assemble into a tetrameric complex that is required for competent rRNA processing. The tetrameric Grc3/Las1 cross talk draws unexpected parallels to endoribonucleases RNaseL and Ire1, and establishes Grc3/ Las1 as a unique member of the RNaseL/Ire1 RNA splicing family. Together, our work provides mechanistic insight for the regulation of the Las1 endoribonuclease and identifies the tetrameric Grc3/ Las1 complex as a unique example of a protein-guided programmable endoribonuclease.pre-rRNA processing | endoribonuclease | polynucleotide kinase | HEPN domain | Las1 N ucleases are found throughout all walks of life and are involved in numerous biological processes, including DNA replication and repair, RNA processing and maturation, and cell defense and death (1). Despite their long history, new nucleases continue to be discovered. For example, the discovery of the ability to program CRISPR-associated nucleases at specific sites by guide RNAs has led to an explosion in gene editing (2, 3). Another recently identified nuclease is the endoribonuclease Las1 (Las1L in mammals), which plays a vital role in eukaryotic ribosome assembly (4). Mutations in the LAS1L gene have been linked to a congenital motor neuron disease (5) and X-linked intellectual disability disorders (6), highlighting the need to further understand the activity of this essential enzyme.Ribosome assembly begins within the nucleolus of the cell with the transcription of the pre-ribosomal RNA (rRNA) by RNA Pol I, which is transcribed as a long polycistronic precursor, known as the 35S pre-rRNA in Saccharomyces cerevisiae (Sc) (7,8). The 35S pre-rRNA includes the 18S, 5.8S, and 25S rRNA as well as two external sequences [5′-and 3′-external transcribed spacers (ETSs)] and two internal sequences [internal transcribed spacers (ITS1 and ITS2)]. Removal of these four spacer sequences is a complex process requiring numerous exonucleases and endonucleases (9). Cleavage within ITS1 separates the 40S and 60S maturation pathways, whereas the subsequent removal of the ITS2 is an important step in the 60S maturation pathway. The first step in the removal of ITS2 is the separation of the precursors of the 5.8S and 25S rRNA by cleavage at the C2 site, which lies alo...

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Section: Discussionmentioning

confidence: 99%

Grc3 programs the essential endoribonuclease Las1 for specific RNA cleavage

Pillon

Sobhany

Borgnia

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Future efforts in this area will be required in order to test this idea. However, given that defects in tRNA processing factors are known to cause neurodegenerative diseases (Budde et al 2008;Weitzer et al 2015), tricRNAs might also serve as important biomarkers of therapeutic agents aimed at restoring tRNA processing defects. Vectors for two circular Spinach2 constructs, pTRIC-Y:Sp2 (blue) and pTRIC-L:Sp2 (red), were transfected into HeLa cells and expression was determined using qRT-PCR.…”

Section: Discussionmentioning

confidence: 99%

Metazoan tRNA introns generate stable circular RNAs in vivo

Filonov

Noto

et al. 2015

RNA

170

144

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We report the discovery of a class of abundant circular noncoding RNAs that are produced during metazoan tRNA splicing. These transcripts, termed tRNA intronic circular (tric)RNAs, are conserved features of animal transcriptomes. Biogenesis of tricRNAs requires anciently conserved tRNA sequence motifs and processing enzymes, and their expression is regulated in an agedependent and tissue-specific manner. Furthermore, we exploited this biogenesis pathway to develop an in vivo expression system for generating "designer" circular RNAs in human cells. Reporter constructs expressing RNA aptamers such as Spinach and Broccoli can be used to follow the transcription and subcellular localization of tricRNAs in living cells. Owing to the superior stability of circular vs. linear RNA isoforms, this expression system has a wide range of potential applications, from basic research to pharmaceutical science.

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“…ASOs targeting the C9orf72 transcript downstream of the repeats reduce RNA foci levels (Donnelly et al, 2013; Jiang et al, 2016), attenuate sequestration of specific RBPs and normalize gene expression changes (Donnelly et al, 2013), suggesting that transcriptome alterations represent a direct downstream consequence of G 4 C 2 RNA toxicity. Upregulation of C9orf72 mRNA expression is associated with concomitant downregulation of genes enriched for functions in RNA metabolism, such as genes encoding tRNA synthetases (Nataf and Pays, 2015) emphasizing the role of tRNA metabolism in motor neuron degeneration (Weitzer et al, 2015). Such downregulation of genes involved in the regulation of RNA metabolism is consistent with RBP sequestration by the C9orf72 hexanucleotide repeat expansion, as the reduced pool of RBPs is less able to promote the expression of such transcripts.…”

Section: Rna Toxicity: the Role Of Rna-binding Protein Sequestration mentioning

confidence: 99%

RNA Misprocessing in C9orf72-Linked Neurodegeneration

Barker

Niblock

Lee

et al. 2017

Front. Cell. Neurosci.

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A large GGGGCC hexanucleotide repeat expansion in the first intron or promoter region of the C9orf72 gene is the most common genetic cause of familial and sporadic Amyotrophic lateral sclerosis (ALS), a devastating degenerative disease of motor neurons, and of Frontotemporal Dementia (FTD), the second most common form of presenile dementia after Alzheimer’s disease. C9orf72-associated ALS/FTD is a multifaceted disease both in terms of its clinical presentation and the misregulated cellular pathways contributing to disease progression. Among the numerous pathways misregulated in C9orf72-associated ALS/FTD, altered RNA processing has consistently appeared at the forefront of C9orf72 research. This includes bidirectional transcription of the repeat sequence, accumulation of repeat RNA into nuclear foci sequestering specific RNA-binding proteins (RBPs) and translation of RNA repeats into dipeptide repeat proteins (DPRs) by repeat-associated non-AUG (RAN)-initiated translation. Over the past few years the true extent of RNA misprocessing in C9orf72-associated ALS/FTD has begun to emerge and disruptions have been identified in almost all aspects of the life of an RNA molecule, including release from RNA polymerase II, translation in the cytoplasm and degradation. Furthermore, several alterations have been identified in the processing of the C9orf72 RNA itself, in terms of its transcription, splicing and localization. This review article aims to consolidate our current knowledge on the consequence of the C9orf72 repeat expansion on RNA processing and draws attention to the mechanisms by which several aspects of C9orf72 molecular pathology converge to perturb every stage of RNA metabolism.

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CLP1 as a novel player in linking tRNA splicing to neurodegenerative disorders

Cited by 50 publications

References 110 publications

Grc3 programs the essential endoribonuclease Las1 for specific RNA cleavage

Grc3 programs the essential endoribonuclease Las1 for specific RNA cleavage

Metazoan tRNA introns generate stable circular RNAs in vivo

RNA Misprocessing in C9orf72-Linked Neurodegeneration

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