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Shen LP, Zhang WC, Deng JR, Qi ZH, Lin ZW, Wang ZD. Advances in the mechanism of small nucleolar RNA and its role in DNA damage response. Mil Med Res 2024; 11:53. [PMID: 39118131 PMCID: PMC11308251 DOI: 10.1186/s40779-024-00553-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) were previously regarded as a class of functionally conserved housekeeping genes, primarily involved in the regulation of ribosome biogenesis by ribosomal RNA (rRNA) modification. However, some of them are involved in several biological processes via complex molecular mechanisms. DNA damage response (DDR) is a conserved mechanism for maintaining genomic stability to prevent the occurrence of various human diseases. It has recently been revealed that snoRNAs are involved in DDR at multiple levels, indicating their relevant theoretical and clinical significance in this field. The present review systematically addresses four main points, including the biosynthesis and classification of snoRNAs, the mechanisms through which snoRNAs regulate target molecules, snoRNAs in the process of DDR, and the significance of snoRNA in disease diagnosis and treatment. It focuses on the potential functions of snoRNAs in DDR to help in the discovery of the roles of snoRNAs in maintaining genome stability and pathological processes.
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Affiliation(s)
- Li-Ping Shen
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Wen-Cheng Zhang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Jia-Rong Deng
- Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Zhen-Hua Qi
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Zhong-Wu Lin
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Zhi-Dong Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
- Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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2
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Zeng Y, Yuan Z, Li J, Yang L, Li C, Xiang Y, Wu L, Xia T, Zhong L, Li Y, Wu N. Small non-coding RNA signatures in atrial appendages of patients with atrial fibrillation. J Cell Mol Med 2024; 28:e18483. [PMID: 39051629 PMCID: PMC11193094 DOI: 10.1111/jcmm.18483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/28/2024] [Indexed: 07/27/2024] Open
Abstract
The development of high-throughput technologies has enhanced our understanding of small non-coding RNAs (sncRNAs) and their crucial roles in various diseases, including atrial fibrillation (AF). This study aimed to systematically delineate sncRNA profiles in AF patients. PANDORA-sequencing was used to examine the sncRNA profiles of atrial appendage tissues from AF and non-AF patients. Differentially expressed sncRNAs were identified using the R package DEGseq 2 with a fold change >2 and p < 0.05. The target genes of the differentially expressed sncRNAs were predicted using MiRanda and RNAhybrid. Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. In AF patients, the most abundant sncRNAs were ribosomal RNA-derived small RNAs (rsRNAs), followed by transfer RNA-derived small RNAs (tsRNAs), and microRNAs (miRNAs). Compared with non-AF patients, 656 rsRNAs, 45 miRNAs, 191 tsRNAs and 51 small nucleolar RNAs (snoRNAs) were differentially expressed in AF patients, whereas no significantly differentially expressed piwi-interacting RNAs were identified. Two out of three tsRNAs were confirmed to be upregulated in AF patients by quantitative reverse transcriptase polymerase chain reaction, and higher plasma levels of tsRNA 5006c-LysCTT were associated with a 2.55-fold increased risk of all-cause death in AF patients (hazard ratio: 2.55; 95% confidence interval, 1.56-4.17; p < 0.001). Combined with our previous transcriptome sequencing results, 32 miRNA, 31 snoRNA, 110 nucleus-encoded tsRNA, and 33 mitochondria-encoded tsRNA target genes were dysregulated in AF patients. GO and KEGG analyses revealed enrichment of differentially expressed sncRNA target genes in AF-related pathways, including the 'calcium signaling pathway' and 'adrenergic signaling in cardiomyocytes.' The dysregulated sncRNA profiles in AF patients suggest their potential regulatory roles in AF pathogenesis. Further research is needed to investigate the specific mechanisms of sncRNAs in the development of AF and to explore potential biomarkers for AF treatment and prognosis.
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Affiliation(s)
- Yuhong Zeng
- Department of Epidemiology, College of Preventive MedicineArmy Medical University (Third Military Medical University)ChongqingPeople's Republic of China
| | - Zhiquan Yuan
- Department of Epidemiology, College of Preventive MedicineArmy Medical University (Third Military Medical University)ChongqingPeople's Republic of China
| | - Jun Li
- Thoracic and Cardiac Surgery, Southwest HospitalThe First Affiliated Hospital of Army Medical University (Third Military Medical University)ChongqingPeople's Republic of China
| | - Lanqing Yang
- Department of Epidemiology, College of Preventive MedicineArmy Medical University (Third Military Medical University)ChongqingPeople's Republic of China
| | - Chengying Li
- Department of Epidemiology, College of Preventive MedicineArmy Medical University (Third Military Medical University)ChongqingPeople's Republic of China
| | - Ying Xiang
- Department of Epidemiology, College of Preventive MedicineArmy Medical University (Third Military Medical University)ChongqingPeople's Republic of China
| | - Long Wu
- Department of Epidemiology, College of Preventive MedicineArmy Medical University (Third Military Medical University)ChongqingPeople's Republic of China
| | - Tingting Xia
- Department of Epidemiology, College of Preventive MedicineArmy Medical University (Third Military Medical University)ChongqingPeople's Republic of China
| | - Li Zhong
- Cardiovascular Disease CenterThird Affiliated Hospital of Chongqing Medical UniversityChongqingPeople's Republic of China
| | - Yafei Li
- Department of Epidemiology, College of Preventive MedicineArmy Medical University (Third Military Medical University)ChongqingPeople's Republic of China
| | - Na Wu
- Department of Epidemiology, College of Preventive MedicineArmy Medical University (Third Military Medical University)ChongqingPeople's Republic of China
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3
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Zhang W, Zhang M, Ma L, Jariyasakulroj S, Chang Q, Lin Z, Lu Z, Chen JF. Recapitulating and reversing human brain ribosomopathy defects via the maladaptive integrated stress response. SCIENCE ADVANCES 2024; 10:eadk1034. [PMID: 38306425 PMCID: PMC10836730 DOI: 10.1126/sciadv.adk1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Animal or human models recapitulating brain ribosomopathies are incomplete, hampering development of urgently needed therapies. Here, we generated genetic mouse and human cerebral organoid models of brain ribosomopathies, caused by mutations in small nucleolar RNA (snoRNA) SNORD118. Both models exhibited protein synthesis loss, proteotoxic stress, and p53 activation and led to decreased proliferation and increased death of neural progenitor cells (NPCs), resulting in brain growth retardation, recapitulating features in human patients. Loss of SNORD118 function resulted in an aberrant upregulation of p-eIF2α, the mediator of integrated stress response (ISR). Using human iPSC cell-based screen, we identified small-molecule 2BAct, an ISR inhibitor, which potently reverses mutant NPC defects. Targeting ISR by 2BAct mitigated ribosomopathy defects in both cerebral organoid and mouse models. Thus, our SNORD118 mutant organoid and mice recapitulate human brain ribosomopathies and cross-validate maladaptive ISR as a key disease-driving mechanism, pointing to a therapeutic intervention strategy.
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Affiliation(s)
- Wei Zhang
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Minjie Zhang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Li Ma
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Supawadee Jariyasakulroj
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Qing Chang
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Ziying Lin
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
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4
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Scaffei E, Buchignani B, Pasquariello R, Cristofani P, Canapicchi R, Biagi L, Giordano F, De Marco E, Crow YJ, Battini R. Case report: Clinical and neuroradiological longitudinal follow-up in Leukoencephalopathy with Calcifications and Cysts during treatment with bevacizumab. Front Neurol 2023; 14:1245014. [PMID: 37799282 PMCID: PMC10548379 DOI: 10.3389/fneur.2023.1245014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023] Open
Abstract
Leukoencephalopathy with Calcifications and Cysts (LCC) is a rare genetic microangiopathy exclusively affecting the central nervous system caused by biallelic mutations in SNORD118. Brain magnetic resonance imaging (MRI) is often diagnostic due to the highly characteristic triad of leukoencephalopathy, intracranial calcifications, and brain cysts. Age at onset, presentation and disease evolution can all vary, ranging from pauci-symptomatic disease to rapid evolution of signs with loss of motor and cognitive abilities. No specific therapies for LCC are currently licensed. According to the literature, bevacizumab might represent an effective modality to improve the clinical and MRI features of the disease. However, uncertainty remains as to the true efficacy of this approach, when to begin therapy, appropriate dosing, and the consequences of drug withdrawal. According to CARE guidelines, we describe the long-term clinical and neuro-radiological follow-up of a 10-year-old child with LCC. We report disease evolution following repeated cycles of treatment with bevacizumab. Our case report suggests that repeated cycles of bevacizumab might effectively modify disease progression, possibly indicating a time-dependent effect.
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Affiliation(s)
- Elena Scaffei
- Department of Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA, University of Florence, Florence, Italy
| | - Bianca Buchignani
- Department of Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Rosa Pasquariello
- Department of Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Paola Cristofani
- Department of Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | | | - Laura Biagi
- Department of Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Flavio Giordano
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA, University of Florence, Florence, Italy
- Department of Neurosurgery, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Emanuela De Marco
- Paediatric Oncology and Haematology Department, Santa Chiara Hospital, Azienda Ospedaliero Universitaria Pisana, Pisa, Italy
| | - Yanick J. Crow
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Paris Descartes University, Paris, France
| | - Roberta Battini
- Department of Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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5
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Politano D, Catalano G, Pezzotti E, Varesio C, Sirchia F, Casella A, Rognone E, Pichiecchio A, Borgatti R, Orcesi S. Expanding the Natural History of SNORD118-Related Ribosomopathy: Hints from an Early-Diagnosed Patient with Leukoencephalopathy with Calcifications and Cysts and Overview of the Literature. Genes (Basel) 2023; 14:1817. [PMID: 37761957 PMCID: PMC10531261 DOI: 10.3390/genes14091817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Leukoencephalopathy with calcifications and cysts (LCC) is a rare autosomal recessive disorder showing a pediatric or adult onset. First described in 1996 by Labrune and colleagues, it was only in 2016 that bi-allelic variants in a non-protein coding gene, SNORD118, were found as the cause for LCC, differentiating this syndrome from coats plus (CP). SNORD118 transcribes for a small nucleolar RNA, which is necessary for correct ribosome biogenesis, hence the classification of LCC among ribosomopathies. The syndrome is characterized by a combination of white matter hyperintensities, calcifications, and cysts on brain MRI with varying neurological signs. Corticosteroids, surgery, and recently bevacizumab, have been tried with unclear results since the natural history of the disease remains elusive. To date, 67 patients with a pediatric onset of disease have been described in the literature, with a clinical-radiological follow-up carried out in only eleven of them. We described the clinical-radiological follow-up from birth to almost five years of age of a late-preterm patient diagnosed with LCC and carried out a thorough overview of pediatric patients described in the literature. It is important to gather serial clinical-radiological data from other patients to depict the natural history of this disease, aiming to deeply depict genotype-phenotype correlations and make the role of new therapeutics clearer.
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Affiliation(s)
- Davide Politano
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Guido Catalano
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Elena Pezzotti
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- U.O. Neuropsichiatria Infanzia e Adolescenza, ASST Bergamo Est, 24068 Seriate, Italy
| | - Costanza Varesio
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Fabio Sirchia
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Medical Genetics Unit, IRCCS San Matteo Foundation, 27100 Pavia, Italy
| | - Antonella Casella
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Elisa Rognone
- Neuroradiology Department, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Anna Pichiecchio
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Neuroradiology Department, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Renato Borgatti
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Simona Orcesi
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
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6
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Good DJ. Non-Coding RNAs in Human Health and Diseases. Genes (Basel) 2023; 14:1429. [PMID: 37510332 PMCID: PMC10380012 DOI: 10.3390/genes14071429] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are, arguably, the enigma of the RNA transcriptome. Even though there are more annotated ncRNAs (25,967) compared to mRNAs (19,827), we know far less about each of the genes that produce ncRNA, especially in terms of their regulation, molecular functions, and interactions. Further, we are only beginning to understand the role of differential regulation or function of ncRNAs caused by genetic and epigenetic perturbations, such as single nucleotide variants (SNV), deletions, insertions, and histone/DNA modifications. The 22 papers in this Special Issue describe the emerging roles of ncRNAs in neurological, cardiovascular, immune, and hepatic systems, to name a few, as well as in diseases such as cancer, Prader-Willi Syndrome, cardiac arrhythmias, and diabetes. As we begin to understand the function and regulation of this class of RNAs, strategies targeting ncRNAs could lead to improved therapeutic interventions for some conditions.
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Affiliation(s)
- Deborah J Good
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA 24060, USA
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7
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He S, Chen S, Li S, Zhang J, Liang X. Complex cerebrovascular diseases in Roberts syndrome caused by novel biallelic
ESCO2
variations. Mol Genet Genomic Med 2023:e2177. [DOI: 10.1002/mgg3.2177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Affiliation(s)
- Shuang He
- Department of Neurology Zhengzhou University People's Hospital (Henan Provincial People's Hospital) Zhengzhou Henan 450003 China
| | - Shuai Chen
- Department of Neurology Zhengzhou University People's Hospital (Henan Provincial People's Hospital) Zhengzhou Henan 450003 China
| | - Shu‐Jian Li
- Department of Neurology Zhengzhou University People's Hospital (Henan Provincial People's Hospital) Zhengzhou Henan 450003 China
| | - Jie‐Wen Zhang
- Department of Neurology Zhengzhou University People's Hospital (Henan Provincial People's Hospital) Zhengzhou Henan 450003 China
| | - Xin‐Liang Liang
- Department of Neurology Zhengzhou University People's Hospital (Henan Provincial People's Hospital) Zhengzhou Henan 450003 China
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8
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Lu S, Chen Z, Liu Z, Liu Z. Unmasking the biological function and regulatory mechanism of NOC2L: a novel inhibitor of histone acetyltransferase. J Transl Med 2023; 21:31. [PMID: 36650543 PMCID: PMC9844006 DOI: 10.1186/s12967-023-03877-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
NOC2 like nucleolar associated transcriptional repressor (NOC2L) was recently identified as a novel inhibitor of histone acetyltransferase (INHAT). NOC2L is found to have two INHAT function domains and regulates histone acetylation in a histone deacetylases (HDAC) independent manner, which is distinct from other INHATs. In this review, we summarize the biological function of NOC2L in histone acetylation regulation, P53-mediated transcription, ribosome RNA processing, certain development events and carcinogenesis. We propose that NOC2L may be explored as a potential biomarker and a therapeutic target in clinical practice.
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Affiliation(s)
- Siyi Lu
- grid.411642.40000 0004 0605 3760Department of General Surgery, Peking University Third Hospital, Beijing, 100191 China
| | - Zhaoyu Chen
- grid.11135.370000 0001 2256 9319Department of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
| | - Zhenzhen Liu
- grid.414360.40000 0004 0605 7104Department of Thoracic Surgery, Beijing Jishuitan Hospital, Beijing, 100035 China
| | - Zhentao Liu
- grid.411642.40000 0004 0605 3760Department of Medical Oncology and Radiation Sickness, Peking University Third Hospital, Beijing, 100191 China
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9
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Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023; 20:715-736. [PMID: 37796118 PMCID: PMC10557570 DOI: 10.1080/15476286.2023.2254540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in ribosome biogenesis, snoRNAs are also implicated in several other cellular activities including regulation of splicing, transcription, RNA editing, cellular trafficking, and miRNA-like functions. Mature snoRNAs must undergo a series of processing steps tightly regulated by transiently associating factors and coordinated with other cellular processes including transcription and splicing. In addition to their mature forms, snoRNAs can contribute to gene expression regulation through their derivatives and degradation products. Here, we review the current knowledge on mechanisms of snoRNA maturation, including the different pathways of processing, and the regulatory mechanisms that control snoRNA levels and complex assembly. We also discuss the significance of studying snoRNA maturation, highlight the gaps in the current knowledge and suggest directions for future research in this area.
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Affiliation(s)
- Sarah F. Webster
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
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