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regulation of molecular networks by the nucleolar detention pathway. (A) Under normal growth conditions cellular proteins are highly mobile and capable of executing essential cellular functions such as: ubiquitination (vHL), proteasomal degradation (sUG1), DNA replication (POLD1) and methylation (DNMt1). (B) Activation of the nucleolar detention pathway immobilizes proteins in the nucleolus away from their downstream effectors inhibiting basic cellular functions. (C) Capture and immobilization of NoDs-containing proteins in the nucleolus is mediated by inducible noncoding rNAs that originate from stimulus-specific loci within the ribosomal intergenic spacer.
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Molecular dynamics ensures that proteins and other factors reach their site of action in a timely and efficient manner. This is essential to the formation of molecular complexes, as they require an ever-changing framework of specific interactions to facilitate a model of self-assembly. Therefore, the absence or reduced availability of any key compo...
Contexts in source publication
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... ON Canada through the barrier of the cell membrane, with minimal invasiveness and map the dynamic properties of intracellular par- ticles. Historically, most have assumed that some level of mobility was necessary for molecules to carry out their cellular role, i.e., DNA polymerase must traverse along the genome to facilitate DNA rep- lication (Fig. 1A). However, the question of how proteins and RNA are present in the right place at the right time is not well ...
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... 20 The most dramatic display of altered protein dynamics was observed for the E3 ubiquitin ligases VHL and MDM2. 21 Under normal physiological conditions, these highly dynamic molecules are diffused through- out the cytoplasm or nucleus, allowing them to locate their downstream effec- tors and target them for proteasomal degradation 22,23 (Fig. 1A). However, in response to diverse stimuli, such as acido- sis, heat shock and transcriptional stress, a novel class of inducible long noncod- ing RNA expressed from distinct loci within the ribosomal intergenic spacer (IGS RNA) has been shown to capture and immobilize these molecules within the nucleolus, 21,24 away from their tar- ...
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... stimuli, such as acido- sis, heat shock and transcriptional stress, a novel class of inducible long noncod- ing RNA expressed from distinct loci within the ribosomal intergenic spacer (IGS RNA) has been shown to capture and immobilize these molecules within the nucleolus, 21,24 away from their tar- gets, rendering them functionally inert 14 ( Fig. 1B and C). the addition of chemical/peptide groups or alterations in conformation and stabil- ity. 17 Currently, hundreds of phosphatases, kinases, proteases and other modifying enzymes have been identified to fine-tune molecular networks by shifting the affin- ity of proteins toward one binding part- ner or another. However, many of these ...
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... localization 18 or the stage of the cell cycle. 19 Nucleostemin, In conclusion, the potentially stagger- ing array of NoDP targets hints at the systemic nature of RNA-mediated regula- tion of protein dynamics. These molecules have diverse functions in ubiquitination, proteasomal degradation, protein folding, DNA replication and methylation (Fig. 1), indicating that the NoDP may control all aspects of cellular life. 21,24,34,35 With the emergence of molecular dynamics, we rec- ommend that photobleaching experiments become standard practice when studying the relocalization of molecules, especially within the nucleolus. Further examination of the nucleolar detentiome should high- ...
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... trafficking. In many cases, molecules are targeted to a particular region in order to perform a specific cellular function. Conversely, nucleolar detention functions by removing important factors from their active sites, thereby disrupting molecular networks through the temporary impris- onment of key cellular factors within the nucleolus (Fig. ...
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Citations
... A series of studies from the Lee laboratory and colleagues have shown that proteins can be captured and immobilized in the nucleolus during a stress-induced process termed "nucleolar detention" (Abraham et al., 2020;Audas et al., 2012aAudas et al., , 2012bJacob et al., 2013;Wang et al., 2018). This was shown with acid exposure and with heat stress, and the protein association was shown to be dependent on stress-specific induction of noncoding RNAs from the intergenic spacer (IGS) region of rDNA loci. ...
... IGS ncRNAs are known to be induced in response to different forms of stress, including heat shock, acidosis, and transcriptional stress (Audas et al., 2012a;Jacob et al., 2013;Marijan et al., 2019). In response to these stimuli, IGS ncRNAs promote the sequestration of specific stress-induced proteins and misfolded proteins within the nucleolus, preventing their deleterious effects on other cellular processes (Audas et al., 2012b). However, prolonged or excessive stress can overwhelm this protective mechanism, leading to nucleolar dysfunction and the formation of stress-induced aggregates. ...
Senataxin is an evolutionarily conserved RNA-DNA helicase involved in DNA repair and transcription termination that is associated with human neurodegenerative disorders. Here, we investigated whether Senataxin loss affects protein homeostasis based on previous work showing R-loop-driven accumulation of DNA damage and protein aggregates in human cells. We find that Senataxin loss results in the accumulation of insoluble proteins, including many factors known to be prone to aggregation in neurodegenerative disorders. These aggregates are located primarily in the nucleolus and are promoted by upregulation of non-coding RNAs expressed from the intergenic spacer region of ribosomal DNA. We also map sites of R-loop accumulation in human cells lacking Senataxin and find higher RNA-DNA hybrids within the ribosomal DNA, peri-centromeric regions, and other intergenic sites but not at annotated protein-coding genes. These findings indicate that Senataxin loss affects the solubility of the proteome through the regulation of transcription-dependent lesions in the nucleus and the nucleolus.
... In this process, the stress RNAs transcribed from certain IGS regions are detained within the nucleoli and temporarily inactivate proteins, e.g. components of replication machinery, equipped with a "detention signal" (Audas et al. 2012;Wang et al. 2019;Pirogov et al. 2019). It was supposed that tethering the detained proteins to the stress ncRNAs requires co-transcriptional formation of an R-loop (Vydzhak et al. 2020). ...
Non-canonical structures (NCS) refer to the various forms of DNA that differ from the B-conformation described by Watson and Crick. It has been found that these structures are usual components of the genome, actively participating in its essential functions. The present review is focused on the nine kinds of NCS appearing or likely to appear in human ribosomal DNA (rDNA): supercoiling structures, R-loops, G-quadruplexes, i-motifs, DNA triplexes, cruciform structures, DNA bubbles, and A and Z DNA conformations. We discuss the conditions of their generation, including their sequence specificity, distribution within the locus, dynamics, and beneficial and detrimental role in the cell.
... It would also be important to look at possible relocalisation of PARylation related proteins potentially induced by various viruses, as significantly altered distribution (including perhaps sequestration to defined cellular regions) may greatly affect PARylation efficiency. It is well known, for example, that the nucleolus can act as a sequestration centre which may capture and detain various cellular factors [49]. ...
ADP-ribosylation (ADPRylation) is a versatile posttranslational modification in eukaryotic cells which is involved in the regulation of a wide range of key biological processes, including DNA repair, cell signalling, programmed cell death, growth and development and responses to biotic and abiotic stresses. Members of the poly(ADP-ribosyl) polymerase (PARP) family play a central role in the process of ADPRylation. Protein targets can be modified by adding either a single ADP-ribose moiety (mono(ADP-ribosyl)ation; MARylation), which is catalysed by mono(ADP-ribosyl) transferases (MARTs or PARP “monoenzymes”), or targets may be decorated with chains of multiple ADP-ribose moieties (PARylation), via the activities of PARP “polyenzymes”. Studies have revealed crosstalk between PARylation (and to a lesser extent, MARylation) processes in plants and plant–virus interactions, suggesting that these tight links may represent a novel factor regulating plant antiviral immunity. From this perspective, we go through the literature linking PARylation-associated processes with other plant regulation pathways controlling virus resistance. Once unraveled, these links may serve as the basis of innovative strategies to improve crop resistance to viruses under challenging environmental conditions which could mitigate yield losses.
... One mechanism that has been proposed is detention of proteins in "nucleolar detention centres" by stress-inducible, long noncoding RNA derived from the ribosomal intergenic spacer region [48]. Proteins detained by this mechanism encode a specific nucleolar detention sequence (NoDS) and include VHL, HSP70, MDM2/PML, and POLD1 [49]. Nucleolar detention centres were recently found to have amyloidogeniclike characteristics, therefore NoDS were renamed "amyloid converting motifs" (ACM) and detention centres renamed "amyloid bodies" or A-bodies [35,37]. ...
... One mechanism that has been proposed is detention of proteins in "nucleolar detention centres" by stress-inducible, long noncoding RNA derived from the ribosomal intergenic spacer region [48]. Proteins detained by this mechanism encode a specific nucleolar detention sequence (NoDS) and include VHL, HSP70, MDM2/PML, and POLD1 [49]. Nucleolar detention centres were recently found to have amyloidogenic-like characteristics, therefore NoDS were renamed "amyloid converting motifs" (ACM) and detention centres renamed "amyloid bodies" or A-bodies [35,37]. ...
... Despite the dynamic nature of the nucleolar proteome, proteins sequestered in Abodies and aggresomes are generally present in a solid, immobile state [35,49,[61][62][63][64]. RelA accumulates in specific foci within the nucleolus in response to stress inducers and proteasome inhibition, suggesting it may also be present in immobile bodies. ...
The nuclear organelle, the nucleolus, plays a critical role in stress response and the regulation of cellular homeostasis. P53 as a downstream effector of nucleolar stress is well defined. However, new data suggests that NF-κB also acts downstream of nucleolar stress to regulate cell growth and death. In this review, we will provide insight into the NF-κB nucleolar stress response pathway. We will discuss apoptosis mediated by nucleolar sequestration of RelA and new data demonstrating a role for p62 (sequestosome (SQSTM1)) in this process. We will also discuss activation of NF-κB signalling by degradation of the RNA polymerase I (PolI) complex component, transcription initiation factor-IA (TIF-IA (RRN3)), and contexts where TIF-IA-NF-κB signalling may be important. Finally, we will discuss how this pathway is targeted by aspirin to mediate apoptosis of colon cancer cells.
... Reduced 47S rRNA Gene Transcription pRNA and PAPAS are not found in human cells, but a number of ncRNAs that originate from the IGS have been identified. These are associated with different stress responses; heat shock induces the expression of transcripts, IGS16, and IGS22, originating from loci 16 kb and 22 kb from the transcription start site and acidosis induces a transcript, IGS28, from a locus 28 kb, all of which in the sense direction [156,157]. These ncRNAs bind stress proteins, such as the chaperon HSP70 and the acidosis responsive von Hippel-Lindau (VHL) protein and sequester them from their site of action. ...
... These ncRNAs bind stress proteins, such as the chaperon HSP70 and the acidosis responsive von Hippel-Lindau (VHL) protein and sequester them from their site of action. DNMT1, POLD1, and RNA biogenesis factors, such as the RNA pol I and III factors RPA16 and RPA40, are other proteins that bind to these ncRNAs, further emphasising the role of these transcripts in sequestering and immobilising factors important in different pathways during stress [156,157]. Another long ncRNA, the PNCTR (pyrimidine-rich noncoding transcript), originating from 28 kb, is proposed to sequester the RNA binding protein PTBP1 to the perinucleolar centre, to interfere with splicing and prevent apoptosis [158]. This stress related RNA is overexpressed in cancers and suggested to form a scaffold for the peri-nucleolar centre, a structure which is larger in cancer cells. ...
Ribosomal transcription constitutes the major energy consuming process in cells and is regulated in response to proliferation, differentiation and metabolic conditions by several signalling pathways. These act on the transcription machinery but also on chromatin factors and ncRNA. The many ribosomal gene repeats are organised in a number of different chromatin states; active, poised, pseudosilent and repressed gene repeats. Some of these chromatin states are unique to the 47rRNA gene repeat and do not occur at other locations in the genome, such as the active state organised with the HMG protein UBF whereas other chromatin state are nucleosomal, harbouring both active and inactive histone marks. The number of repeats in a certain state varies on developmental stage and cell type; embryonic cells have more rRNA gene repeats organised in an open chromatin state, which is replaced by heterochromatin during differentiation, establishing different states depending on cell type. The 47S rRNA gene transcription is regulated in different ways depending on stimulus and chromatin state of individual gene repeats. This review will discuss the present knowledge about factors involved, such as chromatin remodelling factors NuRD, NoRC, CSB, B-WICH, histone modifying enzymes and histone chaperones, in altering gene expression and switching chromatin states in proliferation, differentiation, metabolic changes and stress responses.
... This conclusion was based on nucleolar Cp's failure to bind Mab3102, which binds at a dimer-dimer contact (43). It is not known if assembly was prevented by components in the nucleolus, such as a noncoding RNA (ncRNA), which have been known to immobilize proteins in the nucleolus and render them functionally inert (44,45). Many proteins are believed to be retained in the nucleolus via interactions with the resident proteins and/or RNAs (40). ...
Hepatitis B virus (HBV) core protein (Cp) can be found in the nucleus and cytoplasm of infected hepatocytes; however, it preferentially segregates to a specific compartment correlating with disease status. Regulation of this intracellular partitioning of Cp remains obscure. In this paper, we report that cellular compartments are filled and vacated by Cp in a time- and concentration-dependent manner in both transfections and infections. At early times after transfection, Cp, in a dimeric state, preferentially localizes to the nucleolus. Later, the nucleolar compartment is emptied and Cp progresses to being predominantly nuclear, with a large fraction of the protein in an assembled state. Nuclear localization is followed by cell-wide distribution, and then Cp becomes exclusively cytoplasmic. The same trend in Cp movement is seen during an infection. Putative nucleolar retention signals have been identified and appear to be structure dependent. Export of Cp from the nucleus involves the CRM1 exportin. Time-dependent flux can be recapitulated by modifying Cp concentration, suggesting transitions are regulated by reaching a threshold concentration.
IMPORTANCE
HBV is an endemic virus. More than 250 million people suffer from chronic HBV infection and about 800,000 die from HBV-associated disease each year. HBV is a pararetrovirus; in an infected cell, viral DNA in the nucleus is the template for viral RNA that is packaged in nascent viral capsids in the cytoplasm. Inside those capsids, while resident in cytoplasm, the linear viral RNA is reverse transcribed to form the circular double-stranded DNA (dsDNA) of the mature virus. The HBV core (or capsid) protein plays a role in almost every step of the viral life cycle. Here, we show the core protein appears to follow a programmed, sequential localization from cytoplasmic translation then into the nucleolus, to the nucleus, and back to the cytoplasm. Localization is primarily a function of time, core protein concentration, and assembly. This has important implications for our understanding of the mechanisms of antivirals that target HBV capsid assembly.
... Four lncRNAs classes known to date can be also classified as arcRNAs in addition to NEAT1 (Mannen et al., 2016). Ribosomal DNA (rDNA) intergenic spacer (rIGSRNA) in the nucleolar detention center primes the assembly of A-bodies that are rapidly assembled in response to stress and disassembled after stress stimuli removal (Audas et al., 2016;Audas, Jacob, & Lee, 2012). Human satellite 3 and 2 lncRNA is a scaffolding RNA in the nuclear stress body, nuclear Cancer-Associated Satellite Transcript (CAST) bodies and in ooplasmic RNP granules assembled in maturing oocytes (Biamonti & Vourc'h, 2010;Dobrynin, Korchagina, Prjibelski, & Shafranskaya, 2020;Hall et al., 2017;Jolly et al., 2004;Valgardsdottir et al., 2008). ...
... pre-rRNA transcripts (47S pre-rRNA in mammals) consist of 18S, 5.8S, and 28S rRNA sequences and external and internal transcribed spacers (ETS, ITS), which are eliminated during processing. However, in stressed cells, different lncRNA are transcribed from rIGS (Audas et al., 2016(Audas et al., , 2012Ninomiya & Hirose, 2020;Wang, Tao, et al., 2018. These transcripts are capable of binding and sequestrating a wide diversity of proteins via discrete nucleolar detention sequence (NoDS). ...
... Nucleolus is not only a site for ribosome biosynthesis, but also a regulator of such processes as mitosis, cell cycle progression and stress response (Lam & Trinkle-Mulcahy, 2015;Latonen, 2019). Audas et al. (2012) described a phenomenon of "nucleolar detention" that occurred in the nucleolus of stressed cells as a result of the phase separation driven by lncRNA. The process of nuclear detention results in immobilization of non-nucleolar proteins within the nucleolus that, in turn, blocks rapidly and reversibly numerous cellular processes in response to stress ( Jacob, Audas, Uniacke, Trinkle-Mulcahy, & Lee, 2013;Lam & Trinkle-Mulcahy, 2015). ...
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Membraneless organelles (bodies, granules, etc.) are spatially distinct sub-nuclear and cytoplasmic foci involved in all the processes in a living cell, such as development, cell death, carcinogenesis, proliferation, and differentiation. Today the list of the membraneless organelles includes a wide spectrum of intranuclear and cytoplasmic bodies. Proteins with intrinsically disordered regions are the key players in the membraneless body assembly. However, recent data assume an important role of RNA molecules in the process of the liquid–liquid phase separation. High-level expression of RNA above a critical concentration threshold is mandatory to nucleate interactions with specific proteins and for seeding membraneless organelles. RNA components are considered by many authors as the principal determinants of organelle identity.
Tandemly repeated (TR) DNA of big satellites (a TR family that includes centromeric and pericentromeric DNA sequences) was believed to be transcriptionally silent for a long period. Now we know about the TR transcription upregulation during gameto- and embryogenesis, carcinogenesis, stress response. In the review, we summarize the recent data about the involvement of TR RNA in the formation of nuclear membraneless granules, bodies, etc., with different functions being in some cases an initiator of the structures assembly. These RNP structures sequestrate and inactivate different proteins and transcripts. The TR induced sequestration is one of the key principles of nuclear architecture and genome functioning. Studying the role of the TR-based membraneless organelles in stress and disease will bring some new ideas for translational medicine.
... It is transcribed by pol II in the anti-sense direction, and its 10 kb product called "promoter and pre-rRNA anti-sense" (PAPAS) causes the repression of rRNA synthesis through different pathways [33][34][35][36][37][38]. A number of IGS sequences, some of which have already been identified, participate in the "nucleolar detention" [39], which takes place under stress conditions: the non-coding RNAs (ncRNAs) produced by these sequences recognize, detain within the nucleoli, and temporarily inactivate certain proteins equipped with a "detention signal" [18,[39][40][41][42]. Alu sequences scattered over the spacer also produce transcripts, which may be involved in the maintenance of the nucleolar structure [43,44]. Other regions of IGS have been recently described as potentially functional [20,45]. ...
... It is transcribed by pol II in the anti-sense direction, and its 10 kb product called "promoter and pre-rRNA anti-sense" (PAPAS) causes the repression of rRNA synthesis through different pathways [33][34][35][36][37][38]. A number of IGS sequences, some of which have already been identified, participate in the "nucleolar detention" [39], which takes place under stress conditions: the non-coding RNAs (ncRNAs) produced by these sequences recognize, detain within the nucleoli, and temporarily inactivate certain proteins equipped with a "detention signal" [18,[39][40][41][42]. Alu sequences scattered over the spacer also produce transcripts, which may be involved in the maintenance of the nucleolar structure [43,44]. ...
In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.
... Nucleoli undergo reorganization during cellular stress conditions including DNA damage, temperature change, reactive oxygen species, osmotic stress, nutrient stress, or viral infection (39,47). They also act as a "detention center" to sequester and inhibit specific enzymes during stress (48). For example, the nucleolus regulates p53 export and degradation and can suppress p53 activation in response to oncogenic stress (40,49,50). ...
Significance
Due to the difficulty in their biochemical characterization, until recently intrinsically disordered proteins have gone largely unannotated. However, an appreciation for their biological significance is emerging, as they are now known to facilitate liquid–liquid phase separation (LLPS), which can produce membrane-lacking organelles that enable the spatial regulation of important cellular processes. This report characterizes the Ligand of Ate1 (Liat1) as an intrinsically disordered protein that participates in LLPS in the nucleolus, a prominent membrane-lacking organelle specialized in ribosome biogenesis. Furthermore, it shows that the lysyl-hydroxylase activity of Jumonji Domain Containing 6 modifies Liat1 and inhibits its nucleolar targeting and potential functions.
... See also Figures S3 and S4. 8 Cell Reports 33, 108377, November 10, 2020 Report ll OPEN ACCESS proteins involved in mRNA metabolism and cell-cycle regulation aggregate into NuRs upon acute HS ( Figure S5), providing a mechanism for the inhibition of global mRNA metabolism observed in these conditions. In S. cerevisiae, HS results in the formation of an intranuclear protein deposit named intranuclear quality-control compartment (INQ), adjacent to the nucleolus (Kaganovich et al., 2008;Miller et al., 2015), and in human cells to the segregation of nucleolar components and the formation of nucleolar aggregates named ''detention centers'' (Audas et al., 2012a(Audas et al., , 2012bJacob et al., 2013), or amyloid bodies (ABs) (Audas et al., 2016). In both cases, HS-induced protein aggregation is re-wired to sequester and immobilize misfolded proteins in an inactive form during HS. ...
Upon acute heat stress (HS), overall mRNA transcription, processing, and export are inhibited, leading to cell growth arrest. However, how cells turn off mRNA metabolism is not fully understood. Here, we show that acute HS results in the segregation and aggregation of multiple nuclear and nucleolar proteins into ring-like structures located at the nucleolar periphery (nucleolar rings [NuRs]). NuRs sequester essential factors required for nuclear mRNA metabolism and nuclear pore complex function, as well as cell-cycle regulators. When cells are switched back to growing temperatures, NuRs disaggregate, and their components relocate to their functional environments in an Hsf1- and Hsp104-dependent manner, and concomitantly with the reinitiation of cell growth. These findings highlight the contribution of reversible protein aggregation to the inhibition of overall RNA-related activities in the nucleus and its functional relevance in the maintenance of cellular homeostasis during acute HS.
