Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far

Mamontova, Victoria; Trifault, Barbara; Boten, Lea; Burger, Kaspar

doi:10.3390/ncrna7030042

Cited by 9 publications

(11 citation statements)

References 128 publications

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“…Below we discuss the plethora of non-rRNAs transcribed from the rDNA locus, highlighting both differences from yeast to mammals and the related but distinct functions of these transcripts. Several excellent reviews dealing with related issues have been published in the last few years ( Lindström et al 2018 ; Pirogov et al 2019 ; Yan et al 2019 ; Vydzhak et al 2020 ; Mamontova et al 2021 ).…”

Section: Nucleoli Express Multiple Ncrnasmentioning

confidence: 99%

Beyond rRNA: nucleolar transcription generates a complex network of RNAs with multiple roles in maintaining cellular homeostasis

Feng

Manley

2022

Genes Dev.

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Nucleoli are the major cellular compartments for the synthesis of rRNA and assembly of ribosomes, the macromolecular complexes responsible for protein synthesis. Given the abundance of ribosomes, there is a huge demand for rRNA, which indeed constitutes ∼80% of the mass of RNA in the cell. Thus, nucleoli are characterized by extensive transcription of multiple rDNA loci by the dedicated polymerase, RNA polymerase (Pol) I. However, in addition to producing rRNAs, there is considerable additional transcription in nucleoli by RNA Pol II as well as Pol I, producing multiple noncoding (nc) and, in one instance, coding RNAs. In this review, we discuss important features of these transcripts, which often appear species-specific and reflect transcription antisense to pre-rRNA by Pol II and within the intergenic spacer regions on both strands by both Pol I and Pol II. We discuss how expression of these RNAs is regulated, their propensity to form cotranscriptional R loops, and how they modulate rRNA transcription, nucleolar structure, and cellular homeostasis more generally.

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Section: Nucleoli Express Multiple Ncrnasmentioning

confidence: 99%

Beyond rRNA: nucleolar transcription generates a complex network of RNAs with multiple roles in maintaining cellular homeostasis

Feng

Manley

2022

Genes Dev.

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“…It is currently unclear, whether the nucleolar NONO localisation is linked to the DDR. The nucleolus tethers numerous non-nucleolar proteins in response to cellular stress ( Audas et al, 2012 ; Chen and Stark, 2019 ; Frottin et al, 2019 ; Mamontova et al, 2021 ). Upon heat shock, for example, >200 proteins associate with nucleolar NPM1, including NONO.…”

Section: Discussionmentioning

confidence: 99%

In vivo Proximity Labeling of Nuclear and Nucleolar Proteins by a Stably Expressed, DNA Damage-Responsive NONO-APEX2 Fusion Protein

Trifault

Mamontova

Burger

2022

Front. Mol. Biosci.

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Cellular stress can induce DNA lesions that threaten the stability of genes. The DNA damage response (DDR) recognises and repairs broken DNA to maintain genome stability. Intriguingly, components of nuclear paraspeckles like the non-POU domain containing octamer-binding protein (NONO) participate in the repair of DNA double-strand breaks (DSBs). NONO is a multifunctional RNA-binding protein (RBP) that facilitates the retention and editing of messenger (m)RNA as well as pre-mRNA processing. However, the role of NONO in the DDR is poorly understood. Here, we establish a novel human U2OS cell line that expresses NONO fused to the engineered ascorbate peroxidase 2 (U2OS:NONO-APEX2-HA). We show that NONO-APEX2-HA accumulates in the nucleolus in response to DNA damage. Combining viability assays, subcellular localisation studies, coimmunoprecipitation experiments and in vivo proximity labeling, we demonstrate that NONO-APEX2-HA is a stably expressed fusion protein that mimics endogenous NONO in terms of expression, localisation and bona fide interactors. We propose that in vivo proximity labeling in U2OS:NONO-APEX2-HA cells is capable for the assessment of NONO interactomes by downstream assays. U2OS:NONO-APEX2-HA cells will likely be a valuable resource for the investigation of NONO interactome dynamics in response to DNA damage and other stimuli.

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“…LncRNAs participate in forming partial nucleolus networks, regulating ribosome genesis, and modulating the function and structure of the nucleolus. LncRNA facilitates regulatory crosstalk of RNA Pol II transcription with the nucleolus, and some lncRNAs are encoded on the human ribosomal DNA locus ( Vydzhak et al, 2020 ; Mamontova et al, 2021 ).…”

Section: Biogenesis Degradation and Exosome Formation Of Lncrnasmentioning

confidence: 99%

Kidney diseases and long non-coding RNAs in the limelight

Liu

Zhang

et al. 2022

Front. Physiol.

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The most extensively and well-investigated sequences in the human genome are protein-coding genes, while large numbers of non-coding sequences exist in the human body and are even more diverse with more potential roles than coding sequences. With the unveiling of non-coding RNA research, long-stranded non-coding RNAs (lncRNAs), a class of transcripts >200 nucleotides in length primarily expressed in the nucleus and rarely in the cytoplasm, have drawn our attention. LncRNAs are involved in various levels of gene regulatory processes, including but not limited to promoter activity, epigenetics, translation and transcription efficiency, and intracellular transport. They are also dysregulated in various pathophysiological processes, especially in diseases and cancers involving genomic imprinting. In recent years, numerous studies have linked lncRNAs to the pathophysiology of various kidney diseases. This review summarizes the molecular mechanisms involved in lncRNAs, their impact on kidney diseases, and associated complications, as well as the value of lncRNAs as emerging biomarkers for the prevention and prognosis of kidney diseases, suggesting their potential as new therapeutic tools.

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Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far

Cited by 9 publications

References 128 publications

Beyond rRNA: nucleolar transcription generates a complex network of RNAs with multiple roles in maintaining cellular homeostasis

Beyond rRNA: nucleolar transcription generates a complex network of RNAs with multiple roles in maintaining cellular homeostasis

In vivo Proximity Labeling of Nuclear and Nucleolar Proteins by a Stably Expressed, DNA Damage-Responsive NONO-APEX2 Fusion Protein

Kidney diseases and long non-coding RNAs in the limelight

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