1
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James JP, Riis LB, Søkilde R, Malham M, Høgdall E, Langholz E, Nielsen BS. Short noncoding RNAs as predictive biomarkers for the development from inflammatory bowel disease unclassified to Crohn's disease or ulcerative colitis. PLoS One 2024; 19:e0297353. [PMID: 38408066 PMCID: PMC10896517 DOI: 10.1371/journal.pone.0297353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/22/2023] [Indexed: 02/28/2024] Open
Abstract
Numerous pathogenic processes are mediated by short noncoding RNAs (sncRNA). Twenty percent of inflammatory bowel disease (IBD) patients are labelled as IBD unclassified (IBDU) at disease onset. Most IBDU patients are reclassified as Crohn's disease (CD) or ulcerative colitis (UC) within few years. Since the therapeutic methods for CD and UC differ, biomarkers that can forecast the categorization of IBDU into CD or UC are highly desired. Here, we investigated whether sncRNAs can predict CD or UC among IBDU patients. 35 IBDU patients who were initially diagnosed with IBDU were included in this retrospective investigation; of them, 12, 15, and 8 were reclassified into CD (IBDU-CD), UC (IBDU-UC), or remained as IBDU (IBDU-IBDU), respectively. Eight IBD patients, were included as references. SncRNA profiling on RNA from mucosal biopsies were performed using Affymetrix miRNA 4.0 array. Selected probe sets were validated using RT-qPCR. Among all patients and only adults, 306 and 499 probe sets respectively were differentially expressed between IBDU-CD and IBDU-UC. Six of the probe sets were evaluated by RT-qPCR, of which miR-182-5p, miR-451a and ENSG00000239080 (snoU13) together with age and sex resulted in an AUC of 78.6% (95% CI: 60-97) in discriminating IBDU-CD from IBDU-UC. Based on the three sncRNAs profile it is possible to predict if IBDU patients within 3 years will be reclassified as CD or UC. We showed that the expression profile of IBDU patients differ from that of definite CD or UC, suggesting that a subgroup of IBDU patients may compose a third unique IBD subtype.
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Affiliation(s)
- Jaslin P. James
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
| | - Lene Buhl Riis
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rolf Søkilde
- Bioneer A/S, Hørsholm, Kogle Allé 2, Hørsholm, Denmark
| | - Mikkel Malham
- The Pediatric Department, Copenhagen University Hospital—Amager and Hvidovre, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ebbe Langholz
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Gastroenheden, Herlev University Hospital, Herlev, Denmark
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2
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Adibi JJ, Zhao Y, Koistinen H, Mitchell RT, Barrett ES, Miller R, O'Connor TG, Xun X, Liang HW, Birru R, Smith M, Moog NK. Molecular pathways in placental-fetal development and disruption. Mol Cell Endocrinol 2024; 581:112075. [PMID: 37852527 PMCID: PMC10958409 DOI: 10.1016/j.mce.2023.112075] [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: 07/10/2023] [Revised: 09/11/2023] [Accepted: 09/24/2023] [Indexed: 10/20/2023]
Abstract
The first trimester of pregnancy ranks high in priority when minimizing harmful exposures, given the wide-ranging types of organogenesis occurring between 4- and 12-weeks' gestation. One way to quantify potential harm to the fetus in the first trimester is to measure a corollary effect on the placenta. Placental biomarkers are widely present in maternal circulation, cord blood, and placental tissue biopsied at birth or at the time of pregnancy termination. Here we evaluate ten diverse pathways involving molecules expressed in the first trimester human placenta based on their relevance to normal fetal development and to the hypothesis of placental-fetal endocrine disruption (perturbation in development that results in abnormal endocrine function in the offspring), namely: human chorionic gonadotropin (hCG), thyroid hormone regulation, peroxisome proliferator activated receptor protein gamma (PPARγ), leptin, transforming growth factor beta, epiregulin, growth differentiation factor 15, small nucleolar RNAs, serotonin, and vitamin D. Some of these are well-established as biomarkers of placental-fetal endocrine disruption, while others are not well studied and were selected based on discovery analyses of the placental transcriptome. A literature search on these biomarkers summarizes evidence of placenta-specific production and regulation of each biomarker, and their role in fetal reproductive tract, brain, and other specific domains of fetal development. In this review, we extend the theory of fetal programming to placental-fetal programming.
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Affiliation(s)
- Jennifer J Adibi
- Department of Epidemiology, University of Pittsburgh School of Public Health, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Yaqi Zhao
- St. Jude's Research Hospital, Memphis, TN, USA
| | - Hannu Koistinen
- Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | - Rod T Mitchell
- Department of Paediatric Endocrinology, Royal Hospital for Children and Young People, Edinburgh BioQuarter, Edinburgh, UK
| | - Emily S Barrett
- Environmental and Population Health Bio-Sciences, Rutgers University School of Public Health, Piscataway, NJ, USA
| | - Richard Miller
- Department of Obstetrics and Gynecology, University of Rochester Medical Center, Rochester, NY, USA
| | - Thomas G O'Connor
- Department of Psychiatry, University of Rochester Medical Center, Rochester, NY, USA
| | - Xiaoshuang Xun
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Hai-Wei Liang
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Rahel Birru
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Megan Smith
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nora K Moog
- Department of Medical Psychology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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3
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Chen AY, Owens MC, Liu KF. Coordination of RNA modifications in the brain and beyond. Mol Psychiatry 2023; 28:2737-2749. [PMID: 37138184 DOI: 10.1038/s41380-023-02083-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023]
Abstract
Gene expression regulation is a critical process throughout the body, especially in the nervous system. One mechanism by which biological systems regulate gene expression is via enzyme-mediated RNA modifications, also known as epitranscriptomic regulation. RNA modifications, which have been found on nearly all RNA species across all domains of life, are chemically diverse covalent modifications of RNA nucleotides and represent a robust and rapid mechanism for the regulation of gene expression. Although numerous studies have been conducted regarding the impact that single modifications in single RNA molecules have on gene expression, emerging evidence highlights potential crosstalk between and coordination of modifications across RNA species. These potential coordination axes of RNA modifications have emerged as a new direction in the field of epitranscriptomic research. In this review, we will highlight several examples of gene regulation via RNA modification in the nervous system, followed by a summary of the current state of the field of RNA modification coordination axes. In doing so, we aim to inspire the field to gain a deeper understanding of the roles of RNA modifications and coordination of these modifications in the nervous system.
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Affiliation(s)
- Anthony Yulin Chen
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, 19081, USA
| | - Michael C Owens
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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4
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Thalalla Gamage S, Bortolin-Cavaillé ML, Link C, Bryson K, Sas-Chen A, Schwartz S, Cavaillé J, Meier JL. Antisense pairing and SNORD13 structure guide RNA cytidine acetylation. RNA (NEW YORK, N.Y.) 2022; 28:1582-1596. [PMID: 36127124 PMCID: PMC9670809 DOI: 10.1261/rna.079254.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/02/2022] [Indexed: 05/21/2023]
Abstract
N4-acetylcytidine (ac4C) is an RNA nucleobase found in all domains of life. The establishment of ac4C in helix 45 (h45) of human 18S ribosomal RNA (rRNA) requires the combined activity of the acetyltransferase NAT10 and the box C/D snoRNA SNORD13. However, the molecular mechanisms governing RNA-guided nucleobase acetylation in humans remain unexplored. After applying comparative sequence analysis and site-directed mutagenesis to provide evidence that SNORD13 folds into three main RNA helices, we report two assays that enable the study of SNORD13-dependent RNA acetylation in human cells. First, we demonstrate that ectopic expression of SNORD13 rescues h45 in a SNORD13 knockout cell line. Next, we show that mutant snoRNAs can be used in combination with nucleotide resolution ac4C sequencing to define structure and sequence elements critical for SNORD13 function. Finally, we develop a second method that reports on the substrate specificity of endogenous NAT10-SNORD13 via mutational analysis of an ectopically expressed pre-rRNA substrate. By combining mutational analysis of these reconstituted systems with nucleotide resolution ac4C sequencing, our studies reveal plasticity in the molecular determinants underlying RNA-guided cytidine acetylation that is distinct from deposition of other well-studied rRNA modifications (e.g., pseudouridine). Overall, our studies provide a new approach to reconstitute RNA-guided cytidine acetylation in human cells as well as nucleotide resolution insights into the mechanisms governing this process.
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Affiliation(s)
| | - Marie-Line Bortolin-Cavaillé
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse III; UPS; CNRS; 31062 Cedex 9, Toulouse, France
| | - Courtney Link
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Keri Bryson
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Aldema Sas-Chen
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6195001 Tel Aviv, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jérôme Cavaillé
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse III; UPS; CNRS; 31062 Cedex 9, Toulouse, France
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
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5
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Liao H, Gaur A, McConie H, Shekar A, Wang K, Chang JT, Breton G, Denicourt C. Human NOP2/NSUN1 regulates ribosome biogenesis through non-catalytic complex formation with box C/D snoRNPs. Nucleic Acids Res 2022; 50:10695-10716. [PMID: 36161484 PMCID: PMC9561284 DOI: 10.1093/nar/gkac817] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022] Open
Abstract
5-Methylcytosine (m5C) is a base modification broadly found on various RNAs in the human transcriptome. In eukaryotes, m5C is catalyzed by enzymes of the NSUN family composed of seven human members (NSUN1-7). NOP2/NSUN1 has been primarily characterized in budding yeast as an essential ribosome biogenesis factor required for the deposition of m5C on the 25S ribosomal RNA (rRNA). Although human NOP2/NSUN1 has been known to be an oncogene overexpressed in several types of cancer, its functions and substrates remain poorly characterized. Here, we used a miCLIP-seq approach to identify human NOP2/NSUN1 RNA substrates. Our analysis revealed that NOP2/NSUN1 catalyzes the deposition of m5C at position 4447 on the 28S rRNA. We also find that NOP2/NSUN1 binds to the 5′ETS region of the pre-rRNA transcript and regulates pre-rRNA processing through non-catalytic complex formation with box C/D snoRNAs. We provide evidence that NOP2/NSUN1 facilitates the recruitment of U3 and U8 snoRNAs to pre-90S ribosomal particles and their stable assembly into snoRNP complexes. Remarkably, expression of both WT and catalytically inactive NOP2/NSUN1 in knockdown background rescues the rRNA processing defects and the stable assembly of box C/D snoRNP complexes, suggesting that NOP2/NSUN1-mediated deposition of m5C on rRNA is not required for ribosome synthesis.
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Affiliation(s)
- Han Liao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Anushri Gaur
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Hunter McConie
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Amirtha Shekar
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Karen Wang
- Wiess College, Rice University, Houston, TX 77251, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Ghislain Breton
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
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6
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Bortolin-Cavaillé ML, Quillien A, Thalalla Gamage S, Thomas J, Sas-Chen A, Sharma S, Plisson-Chastang C, Vandel L, Blader P, Lafontaine DLJ, Schwartz S, Meier J, Cavaillé J. Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution. Nucleic Acids Res 2022; 50:6284-6299. [PMID: 35648437 PMCID: PMC9226516 DOI: 10.1093/nar/gkac404] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/28/2022] [Accepted: 05/31/2022] [Indexed: 01/06/2023] Open
Abstract
NAT10 is an essential enzyme that catalyzes N4-acetylcytidine (ac4C) in eukaryotic transfer RNA and 18S ribosomal RNA. Recent studies suggested that rRNA acetylation is dependent on SNORD13, a box C/D small nucleolar RNA predicted to base-pair with 18S rRNA via two antisense elements. However, the selectivity of SNORD13-dependent cytidine acetylation and its relationship to NAT10's essential function remain to be defined. Here, we demonstrate that SNORD13 is required for acetylation of a single cytidine of human and zebrafish 18S rRNA. In-depth characterization revealed that SNORD13-dependent ac4C is dispensable for human cell growth, ribosome biogenesis, translation and development. This loss of function analysis inspired a cross-evolutionary survey of the eukaryotic rRNA acetylation 'machinery' that led to the characterization of many novel metazoan SNORD13 genes. This includes an atypical SNORD13-like RNA in Drosophila melanogaster which guides ac4C to 18S rRNA helix 45 despite lacking one of the two rRNA antisense elements. Finally, we discover that Caenorhabditis elegans 18S rRNA is not acetylated despite the presence of an essential NAT10 homolog. Our findings shed light on the molecular mechanisms underlying SNORD13-mediated rRNA acetylation across eukaryotic evolution and raise new questions regarding the biological and evolutionary relevance of this highly conserved rRNA modification.
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Affiliation(s)
- Marie-Line Bortolin-Cavaillé
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | | | | | - Justin M Thomas
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Aldema Sas-Chen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sunny Sharma
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041 Gosselies, Belgium
| | - Célia Plisson-Chastang
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Laurence Vandel
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Patrick Blader
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041 Gosselies, Belgium
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Jérôme Cavaillé
- To whom correspondence should be addressed. Tel: +33 561335927; Fax: +33 561335886;
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7
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Dysregulation of Small Nucleolar RNAs in B-Cell Malignancies. Biomedicines 2022; 10:biomedicines10061229. [PMID: 35740251 PMCID: PMC9219770 DOI: 10.3390/biomedicines10061229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/17/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) are responsible for post-transcriptional modification of ribosomal RNAs, transfer RNAs and small nuclear RNAs, and thereby have important regulatory functions in mRNA splicing and protein translation. Several studies have shown that snoRNAs are dysregulated in human cancer and may play a role in cancer initiation and progression. In this review, we focus on the role of snoRNAs in normal and malignant B-cell development. SnoRNA activity appears to be essential for normal B-cell differentiation and dysregulated expression of sno-RNAs is determined in B-cell acute lymphoblastic leukemia, chronic lymphocytic leukemia, B-cell non-Hodgkin’s lymphoma, and plasma cell neoplasms. SnoRNA expression is associated with cytogenetic/molecular subgroups and clinical outcome in patients with B-cell malignancies. Translocations involving snoRNAs have been described as well. Here, we discuss the different aspects of snoRNAs in B-cell malignancies and report on their role in oncogenic transformation, which may be useful for the development of novel diagnostic biomarkers or therapeutic targets.
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8
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snoRNAs: functions and mechanisms in biological processes, and roles in tumor pathophysiology. Cell Death Dis 2022; 8:259. [PMID: 35552378 PMCID: PMC9098889 DOI: 10.1038/s41420-022-01056-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Small nucleolar RNAs (snoRNAs), a type of non-coding RNA, are widely present in the nucleoli of eukaryotic cells and play an important role in rRNA modification. With the recent increase in research on snoRNAs, new evidence has emerged indicating that snoRNAs also participate in tRNA and mRNA modification. Studies suggest that numerous snoRNAs, including tumor-promoting and tumor-suppressing snoRNAs, are not only dysregulated in tumors but also show associations with clinical prognosis. In this review, we summarize the reported functions of snoRNAs and the possible mechanisms underlying their role in tumorigenesis and cancer development to guide the snoRNA-based clinical diagnosis and treatment of cancer in the future.
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9
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McFadden EJ, Baserga SJ. U8 variants on the brain: a small nucleolar RNA and human disease. RNA Biol 2022; 19:412-418. [PMID: 35389826 PMCID: PMC8993069 DOI: 10.1080/15476286.2022.2048563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs vital for ribosomal RNA (rRNA) maturation. The U8 snoRNA, encoded by the SNORD118 gene in humans, is an atypical C/D box snoRNA as it promotes rRNA cleavage rather than 2′–O–methylation and is unique to vertebrates. The U8 snoRNA is critical for cleavage events that produce the mature 5.8S and 28S rRNAs of the large ribosomal subunit. Unexpectedly, single nucleotide polymorphisms (SNPs) in the SNORD118 gene were recently found causal to the neurodegenerative disease leukoencephalopathy, brain calcifications, and cysts (LCC; aka Labrune syndrome), but its molecular pathogenesis is unclear. Here, we will review current knowledge on the function of the U8 snoRNA in ribosome biogenesis, and connect it to the preservation of brain function in humans as well as to its dysregulation in inherited white matter disease.
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Affiliation(s)
- Emily J McFadden
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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10
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Han C, Sun LY, Luo XQ, Pan Q, Sun YM, Zeng ZC, Chen TQ, Huang W, Fang K, Wang WT, Chen YQ. Chromatin-associated orphan snoRNA regulates DNA damage-mediated differentiation via a non-canonical complex. Cell Rep 2022; 38:110421. [PMID: 35354054 DOI: 10.1016/j.celrep.2022.110421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/04/2021] [Accepted: 01/31/2022] [Indexed: 12/21/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are commonly acknowledged as a class of homogeneous non-coding RNAs that guide ribosomal RNA modifications. However, snoRNAs referred to as orphans have largely unknown functions. Here, we systematically profile chromatin-associated snoRNAs (casnoRNAs) in mammalian cells and identify a subgroup of orphan casnoRNAs responding to DNA damage stress, among which SNORA73 shows the most marked reduction in chromatin enrichment. Downregulated SNORA73 maintains cancer genome stability and differentiation block in hematopoietic malignancy. Mechanistically, casnoRNA the 5' end non-canonical structure of SNORA73 is critical for its function and binding to poly (ADP-ribose) polymerase 1 (PARP1). SNORA73 inhibits PARP1 auto-PARylation to affect cancer genome stability by forming a small nucleolar ribonucleoprotein (snoRNP) with PARP1 and canonical H/ACA proteins DKC1/NHP2. Our findings reveal the role of an orphan snoRNA serving as casnoRNA and highlights a link between non-canonical structure of snoRNA and their functional diversity.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xue-Qun Luo
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Qi Pan
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Zhan-Cheng Zeng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Tian-Qi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wei Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Ke Fang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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11
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Green MR, Sambrook J. Preparation of Labeled DNA, RNA, and Oligonucleotide Probes. Cold Spring Harb Protoc 2022; 2022:2022/1/pdb.top100578. [PMID: 34983861 DOI: 10.1101/pdb.top100578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Labeled nucleic acids and oligonucleotides are typically generated by enzymatic methods such as end-labeling, random priming, nick translation, in vitro transcription, and variations of the polymerase chain reaction (PCR). Some of these methods place the label in specific locations within the nucleic acid (e.g., at the 5' or 3' terminus); others generate molecules that are labeled internally at multiple sites. Some methods yield labeled single-stranded products, whereas others generate double-stranded nucleic acids. Finally, some generate probes of defined length, whereas others yield a heterogeneous population of labeled molecules. Options available for generating and detecting labeled nucleic acids, as well as advice on designing oligonucleotides for use as probes, is included here.
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12
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Deogharia M, Gurha P. The "guiding" principles of noncoding RNA function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 13:e1704. [PMID: 34856642 DOI: 10.1002/wrna.1704] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/09/2021] [Accepted: 11/11/2021] [Indexed: 12/25/2022]
Abstract
The human genome is pervasively transcribed and yet only a small fraction of these RNAs (less than 2%) are known to code for proteins. The vast majority of the RNAs are classified as noncoding RNAs (ncRNAs) and are further subgrouped as small (shorter than 200 bases) and long noncoding RNAs. The ncRNAs have been identified in all three domains of life and regulate diverse cellular processes through transcriptional and posttranscriptional gene regulation. Most of these RNAs work in conjunction with proteins forming a wide array of base pairing interactions. The determinants of these base pairing interactions are now becoming more evident and show striking similarities among the diverse group of ncRNAs. Here we present a mechanistic overview of pairing between RNA-RNA or RNA-DNA that dictates the function of ncRNAs; we provide examples to illustrate that ncRNAs work through shared evolutionary mechanisms that encompasses a guide-target interaction, involving not only classical Watson-Crick but also noncanonical Wobble and Hoogsteen base pairing. We also highlight the similarities in target selection, proofreading, and the ruler mechanism of ncRNA-protein complexes that confers target specificity and target site selection. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA-Based Catalysis > RNA-Mediated Cleavage RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Manisha Deogharia
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, Houston, Texas, USA.,University of Texas Health Sciences Center at Houston, Houston, Texas, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, Houston, Texas, USA.,University of Texas Health Sciences Center at Houston, Houston, Texas, USA
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13
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Roles and mechanisms of exosomal non-coding RNAs in human health and diseases. Signal Transduct Target Ther 2021; 6:383. [PMID: 34753929 PMCID: PMC8578673 DOI: 10.1038/s41392-021-00779-x] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 02/07/2023] Open
Abstract
Exosomes play a role as mediators of cell-to-cell communication, thus exhibiting pleiotropic activities to homeostasis regulation. Exosomal non-coding RNAs (ncRNAs), mainly microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are closely related to a variety of biological and functional aspects of human health. When the exosomal ncRNAs undergo tissue-specific changes due to diverse internal or external disorders, they can cause tissue dysfunction, aging, and diseases. In this review, we comprehensively discuss the underlying regulatory mechanisms of exosomes in human diseases. In addition, we explore the current knowledge on the roles of exosomal miRNAs, lncRNAs, and circRNAs in human health and diseases, including cancers, metabolic diseases, neurodegenerative diseases, cardiovascular diseases, autoimmune diseases, and infectious diseases, to determine their potential implication in biomarker identification and therapeutic exploration.
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14
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Floro J, Dai A, Metzger A, Mora-Martin A, Ganem N, Cifuentes D, Wu CS, Dalal J, Lyons S, Labadorf A, Flynn R. SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing. Nucleic Acids Res 2021; 49:9424-9443. [PMID: 34365507 PMCID: PMC8450105 DOI: 10.1093/nar/gkab647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 07/08/2021] [Accepted: 07/21/2021] [Indexed: 11/22/2022] Open
Abstract
RNA provides the framework for the assembly of some of the most intricate macromolecular complexes within the cell, including the spliceosome and the mature ribosome. The assembly of these complexes relies on the coordinated association of RNA with hundreds of trans-acting protein factors. While some of these trans-acting factors are RNA-binding proteins (RBPs), others are adaptor proteins, and others still, function as both. Defects in the assembly of these complexes results in a number of human pathologies including neurodegeneration and cancer. Here, we demonstrate that Silencing Defective 2 (SDE2) is both an RNA binding protein and also a trans-acting adaptor protein that functions to regulate RNA splicing and ribosome biogenesis. SDE2 depletion leads to widespread changes in alternative splicing, defects in ribosome biogenesis and ultimately complete loss of cell viability. Our data highlight SDE2 as a previously uncharacterized essential gene required for the assembly and maturation of the complexes that carry out two of the most fundamental processes in mammalian cells.
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Affiliation(s)
- Jess Floro
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anqi Dai
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
- Bioinformatics Program, Boston University, Boston, MA 02118 USA
| | - Abigail Metzger
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alexandra Mora-Martin
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Neil J Ganem
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ching-Shyi Wu
- Department and Graduate Institute of Pharmacology, National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Jasbir Dalal
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adam Labadorf
- Bioinformatics Program, Boston University, Boston, MA 02118 USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118 USA
| | - Rachel L Flynn
- Departments of Pharmacology and Experimental Therapeutics, and Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
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15
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Bergeron D, Laforest C, Carpentier S, Calvé A, Fafard-Couture É, Deschamps-Francoeur G, Scott MS. SnoRNA copy regulation affects family size, genomic location and family abundance levels. BMC Genomics 2021; 22:414. [PMID: 34090325 PMCID: PMC8178906 DOI: 10.1186/s12864-021-07757-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/26/2021] [Indexed: 12/03/2022] Open
Abstract
Background Small nucleolar RNAs (snoRNAs) are an abundant class of noncoding RNAs present in all eukaryotes and best known for their involvement in ribosome biogenesis. In mammalian genomes, many snoRNAs exist in multiple copies, resulting from recombination and retrotransposition from an ancestral snoRNA. To gain insight into snoRNA copy regulation, we used Rfam classification and normal human tissue expression datasets generated using low structure bias RNA-seq to characterize snoRNA families. Results We found that although box H/ACA families are on average larger than box C/D families, the number of expressed members is similar for both types. Family members can cover a wide range of average abundance values, but importantly, expression variability of individual members of a family is preferred over the total variability of the family, especially for box H/ACA snoRNAs, suggesting that while members are likely differentially regulated, mechanisms exist to ensure uniformity of the total family abundance across tissues. Box C/D snoRNA family members are mostly embedded in the same host gene while box H/ACA family members tend to be encoded in more than one different host, supporting a model in which box C/D snoRNA duplication occurred mostly by cis recombination while box H/ACA snoRNA families have gained copy members through retrotransposition. And unexpectedly, snoRNAs encoded in the same host gene can be regulated independently, as some snoRNAs within the same family vary in abundance in a divergent way between tissues. Conclusions SnoRNA copy regulation affects family sizes, genomic location of the members and controls simultaneously member and total family abundance to respond to the needs of individual tissues. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07757-1.
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Affiliation(s)
- Danny Bergeron
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Cédric Laforest
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Stacey Carpentier
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Annabelle Calvé
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Étienne Fafard-Couture
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
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16
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Baldini L, Charpentier B, Labialle S. Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs. Noncoding RNA 2021; 7:ncrna7020030. [PMID: 34066559 PMCID: PMC8162545 DOI: 10.3390/ncrna7020030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.
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Affiliation(s)
| | - Bruno Charpentier
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
| | - Stéphane Labialle
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
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17
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Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action. Biochem Soc Trans 2021; 48:645-656. [PMID: 32267490 PMCID: PMC7200641 DOI: 10.1042/bst20191046] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
Abstract
Identified five decades ago amongst the most abundant cellular RNAs, small nucleolar RNAs (snoRNAs) were initially described as serving as guides for the methylation and pseudouridylation of ribosomal RNA through direct base pairing. In recent years, however, increasingly powerful high-throughput genomic approaches and strategies have led to the discovery of many new members of the family and surprising diversity in snoRNA functionality and mechanisms of action. SnoRNAs are now known to target RNAs of many biotypes for a wider range of modifications, interact with diverse binding partners, compete with other binders for functional interactions, recruit diverse players to targets and affect protein function and accessibility through direct interaction. This mini-review presents the continuing characterization of the snoRNome through the identification of new snoRNA members and the discovery of their mechanisms of action, revealing a highly versatile noncoding family playing central regulatory roles and connecting the main cellular processes.
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18
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Cui C, Liu Y, Gerloff D, Rohde C, Pauli C, Köhn M, Misiak D, Oellerich T, Schwartz S, Schmidt LH, Wiewrodt R, Marra A, Hillejan L, Bartel F, Wickenhauser C, Hüttelmaier S, Göllner S, Zhou F, Edemir B, Müller-Tidow C. NOP10 predicts lung cancer prognosis and its associated small nucleolar RNAs drive proliferation and migration. Oncogene 2021; 40:909-921. [PMID: 33288886 PMCID: PMC7862062 DOI: 10.1038/s41388-020-01570-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer death worldwide underlining the urgent need for new biomarkers and therapeutic targets for this disease. Long noncoding RNAs are critical players in NSCLC but the role of small RNA species is not well understood. In the present study, we investigated the role of H/ACA box small nucleolar RNAs (snoRNAs) and snoRNA-bound ribonucleoproteins (snoRNPs) in the tumorigenesis of NSCLC. H/ACA box snoRNPs including the NOP10 core protein were highly expressed in NSCLC. High levels of either NOP10 mRNA or protein were associated with poor prognosis in NSCLC patients. Loss of NOP10 and subsequent reduction of H/ACA box snoRNAs and rRNA pseudouridylation inhibited lung cancer cell growth, colony formation, migration, and invasion. A focused CRISPR/Cas9 snoRNA knockout screen revealed that genomic deletion of SNORA65, SNORA7A, and SNORA7B reduced proliferation of lung cancer cells. In line, high levels of SNORA65, SNORA7A, and SNORA7B were observed in primary lung cancer specimens with associated changes in rRNA pseudouridylation. Knockdown of either SNORA65 or SNORA7A/B inhibited growth and colony formation of NSCLC cell lines. Our data indicate that specific H/ACA box snoRNAs and snoRNA-associated proteins such as NOP10 have an oncogenic role in NSCLC providing new potential biomarkers and therapeutic targets for the disease.
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Affiliation(s)
- Chunhong Cui
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, 69120, Heidelberg, Germany
- Shanghai University of Medicine and Health Sciences, Shanghai, 201318, PR China
| | - Yi Liu
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Dennis Gerloff
- Department of Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
- Department of Dermatology and Venereology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Christian Rohde
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Cornelius Pauli
- Department of Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Marcel Köhn
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Danny Misiak
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, 60590, Frankfurt, Germany
- German Cancer Consortium/German Cancer Research Center, 69120, Heidelberg, Germany
- Department of Molecular Diagnostics/Translational Proteomics, Frankfurt Cancer Institute, 60596, Frankfurt, Germany
| | | | - Lars-Henning Schmidt
- Department of Medicine A, University of Münster, 48149, Münster, Germany
- Klinik für Pneumologie, Beatmungsmedizin und Thorakale Onkologie, Klinikum Ingolstadt, 85049, Ingolstadt, Germany
| | - Rainer Wiewrodt
- Department of Medicine A, University of Münster, 48149, Münster, Germany
| | - Alessandro Marra
- Department of Surgery, Thoracic Surgery, Rems-Murr-Kliniken, 71364, Winnenden, Germany
| | - Ludger Hillejan
- Department of Thoracic Surgery, Niels-Stensen-Kliniken, 49179, Ostercappeln, Germany
| | - Frank Bartel
- Institute of Pathology, Martin-Luther-University Halle-Wittenberg, 06097, Halle (Saale), Germany
| | - Claudia Wickenhauser
- Institute of Pathology, Martin-Luther-University Halle-Wittenberg, 06097, Halle (Saale), Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Stefanie Göllner
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Fengbiao Zhou
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Bayram Edemir
- Department of Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, 69120, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany.
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19
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Kaliatsi EG, Giarimoglou N, Stathopoulos C, Stamatopoulou V. Non-Coding RNA-Driven Regulation of rRNA Biogenesis. Int J Mol Sci 2020; 21:E9738. [PMID: 33419375 PMCID: PMC7766524 DOI: 10.3390/ijms21249738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/30/2022] Open
Abstract
Ribosomal RNA (rRNA) biogenesis takes place in the nucleolus, the most prominent condensate of the eukaryotic nucleus. The proper assembly and integrity of the nucleolus reflects the accurate synthesis and processing of rRNAs which in turn, as major components of ribosomes, ensure the uninterrupted flow of the genetic information during translation. Therefore, the abundant production of rRNAs in a precisely functional nucleolus is of outmost importance for the cell viability and requires the concerted action of essential enzymes, associated factors and epigenetic marks. The coordination and regulation of such an elaborate process depends on not only protein factors, but also on numerous regulatory non-coding RNAs (ncRNAs). Herein, we focus on RNA-mediated mechanisms that control the synthesis, processing and modification of rRNAs in mammals. We highlight the significance of regulatory ncRNAs in rRNA biogenesis and the maintenance of the nucleolar morphology, as well as their role in human diseases and as novel druggable molecular targets.
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Affiliation(s)
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| | - Vassiliki Stamatopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
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20
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Ojha S, Malla S, Lyons SM. snoRNPs: Functions in Ribosome Biogenesis. Biomolecules 2020; 10:biom10050783. [PMID: 32443616 PMCID: PMC7277114 DOI: 10.3390/biom10050783] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023] Open
Abstract
Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.
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Affiliation(s)
- Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Shawn M. Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-358-4280
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21
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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22
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Iyer-Bierhoff A, Krogh N, Tessarz P, Ruppert T, Nielsen H, Grummt I. SIRT7-Dependent Deacetylation of Fibrillarin Controls Histone H2A Methylation and rRNA Synthesis during the Cell Cycle. Cell Rep 2019; 25:2946-2954.e5. [PMID: 30540930 DOI: 10.1016/j.celrep.2018.11.051] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/17/2018] [Accepted: 11/12/2018] [Indexed: 12/31/2022] Open
Abstract
Fibrillarin (FBL) is a dual-function nucleolar protein that catalyzes 2'-O methylation of pre-rRNA and methylation of histone H2A at glutamine 104 (H2AQ104me). The mechanisms that regulate FBL activity are unexplored. Here, we show that FBL is acetylated at several lysine residues by the acetyltransferase CBP and deacetylated by SIRT7. While reversible acetylation does not impact FBL-mediated pre-rRNA methylation, hyperacetylation impairs the interaction of FBL with histone H2A and chromatin, thereby compromising H2AQ104 methylation (H2AQ104me) and rDNA transcription. SIRT7-dependent deacetylation of FBL ensures H2AQ104me and high levels of rRNA synthesis during interphase. At the onset of mitosis, nucleolar disassembly is accompanied by hyperacetylation of FBL, loss of H2AQ104me, and repression of polymerase I (Pol I) transcription. Overexpression of an acetylation-deficient, but not an acetylation-mimicking, FBL mutant restores H2AQ104me and transcriptional activity. The results reveal that SIRT7-dependent deacetylation impacts nucleolar activity by an FBL-driven circuitry that mediates cell-cycle-dependent fluctuation of rDNA transcription.
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Affiliation(s)
- Aishwarya Iyer-Bierhoff
- Molecular Biology of the Cell II, German Cancer Research Centre (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, 69120 Heidelberg, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Peter Tessarz
- Department of Chromatin and Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Thomas Ruppert
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Centre (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, 69120 Heidelberg, Germany.
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Abstract
Abstract
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research.
Lay Summary
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
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Burke MF, McLaurin DM, Logan MK, Hebert MD. Alteration of 28S rRNA 2'- O-methylation by etoposide correlates with decreased SMN phosphorylation and reduced Drosha levels. Biol Open 2019; 8:bio041848. [PMID: 30858166 PMCID: PMC6451326 DOI: 10.1242/bio.041848] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 12/15/2022] Open
Abstract
The most common types of modification in human rRNA are pseudouridylation and 2'-O ribose methylation. These modifications are performed by small nucleolar ribonucleoproteins (snoRNPs) which contain a guide RNA (snoRNA) that base pairs at specific sites within the rRNA to direct the modification. rRNA modifications can vary, generating ribosome heterogeneity. One possible method that can be used to regulate rRNA modifications is by controlling snoRNP activity. RNA fragments derived from some small Cajal body-specific RNAs (scaRNA 2, 9 and 17) may influence snoRNP activity. Most scaRNAs accumulate in the Cajal body - a subnuclear domain - where they participate in the biogenesis of small nuclear RNPs, but scaRNA 2, 9 and 17 generate nucleolus-enriched fragments of unclear function, and we hypothesize that these fragments form regulatory RNPs that impact snoRNP activity and modulate rRNA modifications. Our previous work has shown that SMN, Drosha and various stresses, including etoposide treatment, may alter regulatory RNP formation. Here we demonstrate that etoposide treatment decreases the phosphorylation of SMN, reduces Drosha levels and increases the 2'-O-methylation of two sites within 28S rRNA. These findings further support a role for SMN and Drosha in regulating rRNA modification, possibly by affecting snoRNP or regulatory RNP activity.
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Affiliation(s)
- Marilyn F Burke
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Douglas M McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Madelyn K Logan
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Michael D Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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25
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Stamm S, Lodmell JS. C/D box snoRNAs in viral infections: RNA viruses use old dogs for new tricks. Noncoding RNA Res 2019; 4:46-53. [PMID: 31193534 PMCID: PMC6533054 DOI: 10.1016/j.ncrna.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/27/2019] [Accepted: 02/13/2019] [Indexed: 12/17/2022] Open
Abstract
C/D box snoRNAs (SNORDs) are a highly expressed class of non-coding RNAs. Besides their well-established role in rRNA modification, C/D box snoRNAs form protein complexes devoid of fibrillarin and regulate pre-mRNA splicing and polyadenylation of numerous genes. There is an emerging body of evidence for functional interactions between RNA viruses and C/D box snoRNAs. The infectivity of some RNA viruses depends on enzymatically active fibrillarin, and many RNA viral proteins associate with nucleolin or nucleophosmin, suggesting that viruses benefit from their cytosolic accumulation. These interactions are likely reflected by morphological changes in the nucleolus, often leading to relocalization of nucleolar proteins and ncRNAs to the cytosol that are a characteristic feature of viral infections. Knock-down studies have also shown that RNA viruses need specific C/D box snoRNAs for optimal replication, suggesting that RNA viruses benefit from gene expression programs regulated by SNORDs, or that viruses have evolved “new” uses for these humble ncRNAs to advance their prospects during infection.
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Affiliation(s)
- Stefan Stamm
- University of Kentucky, Molecular and Cellular Biochemistry, 741 South Limestone, Lexington, KY 40536, USA
| | - J Stephen Lodmell
- Division of Biological Sciences and Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, MT, USA
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26
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Li L, Liang J, Luo H, Tam KM, Tse ECM, Li Y. A new chemical approach for proximity labelling of chromatin-associated RNAs and proteins with visible light irradiation. Chem Commun (Camb) 2019; 55:12340-12343. [DOI: 10.1039/c9cc06251c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new nucleus-localized singlet oxygen generator was designed and synthesized.
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Affiliation(s)
- Lan Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Jiying Liang
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Hao Luo
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - K. Ming Tam
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Edmund C. M. Tse
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Ying Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
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27
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Logan MK, Burke MF, Hebert MD. Altered dynamics of scaRNA2 and scaRNA9 in response to stress correlates with disrupted nuclear organization. Biol Open 2018; 7:bio.037101. [PMID: 30177550 PMCID: PMC6176948 DOI: 10.1242/bio.037101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Small Cajal body-specific RNAs (scaRNAs) are part of small Cajal body-specific ribonucleoproteins (scaRNPs) that modify small nuclear RNA (snRNA) in Cajal bodies (CBs). Several scaRNAs (scaRNA 2, 9 and 17) have been found to generate smaller, nucleolus-enriched fragments. We hypothesize that the fragments derived from scaRNA 2, 9 and 17 form regulatory RNPs that influence the level of modifications within rRNA by altering small nucleolar RNP (snoRNP) activity. Here we show that external factors such as DNA damaging agents can alter the scaRNA9 full length to processed fragment ratio. We also show that full-length scaRNA2 levels are likewise impacted by DNA damage, which correlates with the disruption of SMN, coilin and WRAP53 co-localization in CBs. The dynamics of scaRNA9 were also shown to be affected by Drosha levels, which suggests that this protein may participate in the biogenesis and processing of this non-coding RNA. Identification of factors that contribute to scaRNA 2, 9 and 17 processing may facilitate an assessment of how external stress can lead to changes in rRNA modifications.
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Affiliation(s)
- Madelyn K Logan
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Marilyn F Burke
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Michael D Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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28
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Jeong-Yu S, Davis AF, Clayton DA. Subtle determinants of the nucleocytoplasmic partitioning of in vivo-transcribed RNase MRP RNA in Xenopus laevis oocytes. Gene Expr 2018; 5:155-67. [PMID: 8882639 PMCID: PMC6138017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
RNase MRP is a ribonucleoprotein originally identified on the basis of its ability to cleave RNA endonucleolytically from origins of mitochondrial DNA replication, rendering it a likely candidate for a role in priming leading-strand synthesis of mtDNA. In addition, a nuclear role for RNase MRP has been identified in yeast (Saccharomyces cerevisiae) ribosomal RNA processing. Consistent with a duality of function, RNase MRP has been localized to both mitochondria and nucleoli by in situ techniques. The RNA component of this ribonucleoprotein has been characterized from several different species. We previously cloned the gene for Xenopus laevis MRP RNA and showed that RNase MRP RNA is differentially expressed during amphibian development; in addition, the microinjected X. laevis RNase MRP RNA gene is correctly and efficiently transcribed in vivo. This article presents an analysis of the intracellular movement of in vivo-transcribed RNase MRP RNA in microinjected mature X. laevis oocytes. Although X. laevis MRP RNA is assembled into a ribonucleoprotein form and transported in an expected manner, human and mouse MRP RNAs exhibit markedly different transport patterns even though they are highly conserved in primary sequence. Furthermore, the only currently assigned protein (Th autoantigen) binding site in MRP RNA can be deleted without loss of nuclear export capacity. These results indicate that subtle determinants must exist for nucleocytoplasmic partitioning of this RNP and that the conserved Th autoantigen binding region appears unnecessary for the transit of in vivo-transcribed MRP RNA to the cytoplasm of mature X. laevis oocytes.
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Affiliation(s)
- S Jeong-Yu
- Department of Developmental Biology, Stanford University School of Medicine, CA 94305-5427, USA
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29
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Terns MP, Terns RM. Small nucleolar RNAs: versatile trans-acting molecules of ancient evolutionary origin. Gene Expr 2018; 10:17-39. [PMID: 11868985 PMCID: PMC5977530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The small nucleolar RNAs (snoRNAs) are an abundant class of trans-acting RNAs that function in ribosome biogenesis in the eukaryotic nucleolus. Elegant work has revealed that most known snoRNAs guide modification of pre-ribosomal RNA (pre-rRNA) by base pairing near target sites. Other snoRNAs are involved in cleavage of pre-rRNA by mechanisms that have not yet been detailed. Moreover, our appreciation of the cellular roles of the snoRNAs is expanding with new evidence that snoRNAs also target modification of small nuclear RNAs and messenger RNAs. Many snoRNAs are produced by unorthodox modes of biogenesis including salvage from introns of pre-mRNAs. The recent discovery that homologs of snoRNAs as well as associated proteins exist in the domain Archaea indicates that the RNA-guided RNA modification system is of ancient evolutionary origin. In addition, it has become clear that the RNA component of vertebrate telomerase (an enzyme implicated in cancer and cellular senescence) is related to snoRNAs. During its evolution, vertebrate telomerase RNA appears to have co-opted a snoRNA domain that is essential for the function of telomerase RNA in vivo. The unique properties of snoRNAs are now being harnessed for basic research and therapeutic applications.
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MESH Headings
- Animals
- Base Pairing
- Biological Transport
- Cell Nucleolus/metabolism
- Cell Nucleus/metabolism
- Eukaryotic Cells/metabolism
- Evolution, Molecular
- Methylation
- Prokaryotic Cells/metabolism
- Pseudouridine/metabolism
- RNA/metabolism
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Archaeal/genetics
- RNA, Archaeal/physiology
- RNA, Catalytic/metabolism
- RNA, Messenger/metabolism
- RNA, Ribosomal/biosynthesis
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/classification
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Small Nucleolar/physiology
- Ribonucleoproteins, Small Nucleolar/metabolism
- Ribosomes/metabolism
- Species Specificity
- Structure-Activity Relationship
- Telomerase/metabolism
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Affiliation(s)
- Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens 30602, USA.
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30
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Li Y, Aggarwal MB, Ke K, Nguyen K, Spitale RC. Improved Analysis of RNA Localization by Spatially Restricted Oxidation of RNA-Protein Complexes. Biochemistry 2018; 57:1577-1581. [PMID: 29474061 PMCID: PMC6234203 DOI: 10.1021/acs.biochem.8b00053] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent analysis of transcriptomes has revealed that RNAs perform a myriad of functions beyond encoding proteins. Critical to RNA function is its transport to unique subcellular locations. Despite the importance of RNA localization, it is still very challenging to study in an unbiased manner. We recently described the ability to tag RNA molecules within subcellular locations through spatially restricted nucleobase oxidation. Herein, we describe a dramatic improvement of this protocol through the localized oxidation and tagging of proteins. Isolation of RNA-protein complexes enabled the enrichment of challenging RNA targets on chromatin and presented a considerably optimized protocol for the analysis of RNA subcellular localization within living cells.
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31
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Langhendries JL, Nicolas E, Doumont G, Goldman S, Lafontaine DLJ. The human box C/D snoRNAs U3 and U8 are required for pre-rRNA processing and tumorigenesis. Oncotarget 2018; 7:59519-59534. [PMID: 27517747 PMCID: PMC5312328 DOI: 10.18632/oncotarget.11148] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/30/2016] [Indexed: 01/05/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) are emerging as a novel class of proto-oncogenes and tumor suppressors; their involvement in tumorigenesis remains unclear. The box C/D snoRNAs U3 and U8 are upregulated in breast cancers. Here we characterize the function of human U3 and U8 in ribosome biogenesis, nucleolar structure, and tumorigenesis. We show in breast (MCF-7) and lung (H1944) cancer cells that U3 and U8 are required for pre-rRNA processing reactions leading, respectively, to synthesis of the small and large ribosomal subunits. U3 or U8 depletion triggers a remarkably potent p53-dependent anti-tumor stress response involving the ribosomal proteins uL5 (RPL11) and uL18 (RPL5). Interestingly, the nucleolar structure is more sensitive to perturbations in lung cancer than in breast cancer cells. We reveal in a mouse xenograft model that the tumorigenic potential of cancer cells is reduced in the case of U3 suppression and totally abolished upon U8 depletion. Tumors derived from U3-knockdown cells displayed markedly lower metabolic volume and activity than tumors derived from aggressive control cancer cells. Unexpectedly, metabolic tracer uptake by U3-suppressed tumors appeared more heterogeneous, indicating distinctive tumor growth properties that may reflect non-conventional regulatory functions of U3 (or fragments derived from it) in mRNA metabolism.
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Affiliation(s)
- Jean-Louis Langhendries
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), BioPark Campus, Gosselies, Belgium
| | - Emilien Nicolas
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), BioPark Campus, Gosselies, Belgium
| | - Gilles Doumont
- Center for Microscopy and Molecular Imaging (CMMI), BioPark campus, Université Libre de Bruxelles, Belgium
| | - Serge Goldman
- Nuclear Medecine, Erasme Hospital, Université Libre de Bruxelles, Belgium.,Center for Microscopy and Molecular Imaging (CMMI), BioPark campus, Université Libre de Bruxelles, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), BioPark Campus, Gosselies, Belgium.,Center for Microscopy and Molecular Imaging (CMMI), BioPark campus, Université Libre de Bruxelles, Belgium
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32
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Li Y, Aggarwal MB, Nguyen K, Ke K, Spitale RC. Assaying RNA Localization in Situ with Spatially Restricted Nucleobase Oxidation. ACS Chem Biol 2017; 12:2709-2714. [PMID: 28952711 DOI: 10.1021/acschembio.7b00519] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report herein a novel chemical-genetic method for assaying RNA localization within living cells. RNA localization is critical for normal physiology as well as the onset of cancer and neurodegenerative disorders. Despite its importance, there is a real lack of chemical methods to directly assay RNA localization with high resolution in living cells. Our novel approach relies on in situ nucleobase oxidation by singlet oxygen generated from spatially confined fluorophores. We demonstrate that our novel method can identify RNA molecules localized within specific cellular compartments. We anticipate that this platform will provide the community with a much-needed methodology for tracking RNA localization within living cells, and set the stage for systematic large scale analysis of RNA localization in living systems.
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Affiliation(s)
- Ying Li
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Mahima B. Aggarwal
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Kim Nguyen
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Ke Ke
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Robert C. Spitale
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
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33
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Poole AR, Vicino I, Adachi H, Yu YT, Hebert MD. Regulatory RNPs: a novel class of ribonucleoproteins that potentially contribute to ribosome heterogeneity. Biol Open 2017; 6:1342-1354. [PMID: 28808137 PMCID: PMC5612246 DOI: 10.1242/bio.028092] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many ribonucleoproteins (RNPs), which are comprised of noncoding RNA and associated proteins, are involved in essential cellular processes such as translation and pre-mRNA splicing. One class of RNP is the small Cajal body-specific RNP (scaRNP), which contributes to the biogenesis of small nuclear RNPs (snRNPs) that are central components of the spliceosome. Three scaRNAs are internally processed, generating stable nucleolus-enriched RNAs of unknown function. Here, we provide data that show that these RNAs become part of RNPs we term regulatory RNPs (regRNPs). Most modifications within rRNA (predominantly pseudouridylation and ribose 2′-O-methylation) are conducted by small nucleolar RNPs (snoRNPs), and we provide evidence that the activity of at least some of these snoRNPs is under the control of regRNPs. Because modifications within rRNA can vary in different physiological or pathological situations, rRNA modifications are thought to be the major source of ribosome heterogeneity. Our identification of regRNPs thus provides a potential mechanism for how ribosome heterogeneity may be accomplished. This work also provides additional functional connections between the Cajal body and the nucleolus. Summary: Processed scaRNAs give rise to a novel regulatory RNP, which regulates the modification of ribosomal RNA. These findings provide insight into the mechanisms governing ribosome heterogeneity.
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Affiliation(s)
- Aaron R Poole
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Ian Vicino
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Hironori Adachi
- Department of Biochemistry and Biophysics, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Michael D Hebert
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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34
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Warren AJ. Molecular basis of the human ribosomopathy Shwachman-Diamond syndrome. Adv Biol Regul 2017; 67:109-127. [PMID: 28942353 PMCID: PMC6710477 DOI: 10.1016/j.jbior.2017.09.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 01/05/2023]
Abstract
Mutations that target the ubiquitous process of ribosome assembly paradoxically cause diverse tissue-specific disorders (ribosomopathies) that are often associated with an increased risk of cancer. Ribosomes are the essential macromolecular machines that read the genetic code in all cells in all kingdoms of life. Following pre-assembly in the nucleus, precursors of the large 60S and small 40S ribosomal subunits are exported to the cytoplasm where the final steps in maturation are completed. Here, I review the recent insights into the conserved mechanisms of ribosome assembly that have come from functional characterisation of the genes mutated in human ribosomopathies. In particular, recent advances in cryo-electron microscopy, coupled with genetic, biochemical and prior structural data, have revealed that the SBDS protein that is deficient in the inherited leukaemia predisposition disorder Shwachman-Diamond syndrome couples the final step in cytoplasmic 60S ribosomal subunit maturation to a quality control assessment of the structural and functional integrity of the nascent particle. Thus, study of this fascinating disorder is providing remarkable insights into how the large ribosomal subunit is functionally activated in the cytoplasm to enter the actively translating pool of ribosomes.
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MESH Headings
- Bone Marrow Diseases/metabolism
- Bone Marrow Diseases/pathology
- Cryoelectron Microscopy
- Exocrine Pancreatic Insufficiency/metabolism
- Exocrine Pancreatic Insufficiency/pathology
- Humans
- Lipomatosis/metabolism
- Lipomatosis/pathology
- Mutation
- Proteins/genetics
- Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/ultrastructure
- Shwachman-Diamond Syndrome
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Affiliation(s)
- Alan J Warren
- Cambridge Institute for Medical Research, Cambridge, UK; The Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
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35
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Falaleeva M, Welden JR, Duncan MJ, Stamm S. C/D-box snoRNAs form methylating and non-methylating ribonucleoprotein complexes: Old dogs show new tricks. Bioessays 2017; 39:10.1002/bies.201600264. [PMID: 28505386 PMCID: PMC5586538 DOI: 10.1002/bies.201600264] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
C/D box snoRNAs (SNORDs) are an abundantly expressed class of short, non-coding RNAs that have been long known to perform 2'-O-methylation of rRNAs. However, approximately half of human SNORDs have no predictable rRNA targets, and numerous SNORDs have been associated with diseases that show no defects in rRNAs, among them Prader-Willi syndrome, Duplication 15q syndrome and cancer. This apparent discrepancy has been addressed by recent studies showing that SNORDs can act to regulate pre-mRNA alternative splicing, mRNA abundance, activate enzymes, and be processed into shorter ncRNAs resembling miRNAs and piRNAs. Furthermore, recent biochemical studies have shown that a given SNORD can form both methylating and non-methylating ribonucleoprotein complexes, providing an indication of the likely physical basis for such diverse new functions. Thus, SNORDs are more structurally and functionally diverse than previously thought, and their role in gene expression is under-appreciated. The action of SNORDs in non-methylating complexes can be substituted with oligonucleotides, allowing devising therapies for diseases like Prader-Willi syndrome.
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Affiliation(s)
- Marina Falaleeva
- University Kentucky, Institute for Biochemistry, Lexington, KY, USA
| | - Justin R. Welden
- University Kentucky, Institute for Biochemistry, Lexington, KY, USA
| | | | - Stefan Stamm
- University Kentucky, Institute for Biochemistry, Lexington, KY, USA
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36
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Sharma S, Yang J, van Nues R, Watzinger P, Kötter P, Lafontaine DLJ, Granneman S, Entian KD. Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation. PLoS Genet 2017; 13:e1006804. [PMID: 28542199 PMCID: PMC5464676 DOI: 10.1371/journal.pgen.1006804] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 06/08/2017] [Accepted: 05/05/2017] [Indexed: 12/19/2022] Open
Abstract
Box C/D snoRNAs are known to guide site-specific ribose methylation of ribosomal RNA. Here, we demonstrate a novel and unexpected role for box C/D snoRNAs in guiding 18S rRNA acetylation in yeast. Our results demonstrate, for the first time, that the acetylation of two cytosine residues in 18S rRNA catalyzed by Kre33 is guided by two orphan box C/D snoRNAs-snR4 and snR45 -not known to be involved in methylation in yeast. We identified Kre33 binding sites on these snoRNAs as well as on the 18S rRNA, and demonstrate that both snR4 and snR45 establish extended bipartite complementarity around the cytosines targeted for acetylation, similar to pseudouridylation pocket formation by the H/ACA snoRNPs. We show that base pairing between these snoRNAs and 18S rRNA requires the putative helicase activity of Kre33, which is also needed to aid early pre-rRNA processing. Compared to yeast, the number of orphan box C/D snoRNAs in higher eukaryotes is much larger and we hypothesize that several of these may be involved in base-modifications.
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Affiliation(s)
- Sunny Sharma
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
- RNA Molecular Biology and CMMI, F.R.S./FNRS and Université Libre de Bruxelles Rue Profs Jeener & Brachet, Charleroi–Gosselies, Belgium
| | - Jun Yang
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Rob van Nues
- Institute of Structural and Molecular Biology, Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, United Kingdom
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Watzinger
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Peter Kötter
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Denis L. J. Lafontaine
- RNA Molecular Biology and CMMI, F.R.S./FNRS and Université Libre de Bruxelles Rue Profs Jeener & Brachet, Charleroi–Gosselies, Belgium
| | - Sander Granneman
- Institute of Structural and Molecular Biology, Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, United Kingdom
| | - Karl-Dieter Entian
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
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37
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Henras AK, Plisson-Chastang C, Humbert O, Romeo Y, Henry Y. Synthesis, Function, and Heterogeneity of snoRNA-Guided Posttranscriptional Nucleoside Modifications in Eukaryotic Ribosomal RNAs. Enzymes 2017; 41:169-213. [PMID: 28601222 DOI: 10.1016/bs.enz.2017.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribosomal RNAs contain numerous 2'-O-methylated nucleosides and pseudouridines. Methylation of the 2' oxygen of ribose moieties and isomerization of uridines into pseudouridines are catalyzed by C/D and H/ACA small nucleolar ribonucleoprotein particles, respectively. We review the composition, structure, and mode of action of archaeal and eukaryotic C/D and H/ACA particles. Most rRNA modifications cluster in functionally crucial regions of the rRNAs, suggesting they play important roles in translation. Some of these modifications promote global translation efficiency or modulate translation fidelity. Strikingly, recent quantitative nucleoside modification profiling methods have revealed that a subset of modification sites is not always fully modified. The finding of such ribosome heterogeneity is in line with the concept of specialized ribosomes that could preferentially translate specific mRNAs. This emerging concept is supported by findings that some human diseases are caused by defects in the rRNA modification machinery correlated with a significant alteration of IRES-dependent translation.
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Affiliation(s)
- Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Humbert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Romeo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.
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Abstract
Aside from nucleoli, Cajal bodies (CBs) are the best-characterized organelles of mammalian cell nuclei. Like nucleoli, CBs concentrate ribonucleoproteins (RNPs), in particular, spliceosomal small nuclear RNPs (snRNPs) and small nucleolar RNPs (snoRNPs). In one of the best-defined functions of CBs, most of the snoRNPs are involved in site-specific modification of snRNAs. The two major modifications are pseudouridylation and 2'-O-methylation that are guided by the box H/ACA and C/D snoRNPs, respectively. This review details the modifications, their function, the mechanism of modification, and the machineries involved. We dissect the different classes of noncoding RNAs that meet in CBs, guides and substrates. Open questions and conundrums, often raised and appearing due to experimental limitations, are pointed out and discussed. The emphasis of the review is on mammalian CBs and their function in modification of noncoding RNAs.
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Affiliation(s)
- U Thomas Meier
- a Albert Einstein College of Medicine , Department of Anatomy and Structural Biology , Bronx , NY , USA
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Jenkinson EM, Rodero MP, Kasher PR, Uggenti C, Oojageer A, Goosey LC, Rose Y, Kershaw CJ, Urquhart JE, Williams SG, Bhaskar SS, O’Sullivan J, Baerlocher GM, Haubitz M, Aubert G, Barañano KW, Barnicoat AJ, Battini R, Berger A, Blair EM, Brunstrom-Hernandez JE, Buckard JA, Cassiman DM, Caumes R, Cordelli DM, De Waele LM, Fay AJ, Ferreira P, Fletcher NA, Fryer AE, Goel H, Hemingway CA, Henneke M, Hughes I, Jefferson RJ, Kumar R, Lagae L, Landrieu PG, Lourenço CM, Malpas TJ, Mehta SG, Metz I, Naidu S, Õunap K, Panzer A, Prabhakar P, Quaghebeur G, Schiffmann R, Sherr EH, Sinnathuray KR, Soh C, Stewart HS, Stone J, Van Esch H, Van Mol CE, Vanderver A, Wakeling EL, Whitney A, Pavitt GD, Griffiths-Jones S, Rice GI, Revy P, van der Knaap MS, Livingston JH, O’Keefe RT, Crow YJ. Mutations in SNORD118 cause the cerebral microangiopathy leukoencephalopathy with calcifications and cysts. Nat Genet 2016; 48:1185-92. [PMID: 27571260 PMCID: PMC5045717 DOI: 10.1038/ng.3661] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 08/05/2016] [Indexed: 12/15/2022]
Abstract
Although ribosomes are ubiquitous and essential for life, recent data indicate that monogenic causes of ribosomal dysfunction can confer a remarkable degree of specificity in terms of human disease phenotype. Box C/D small nucleolar RNAs (snoRNAs) are evolutionarily conserved non-protein-coding RNAs involved in ribosome biogenesis. Here we show that biallelic mutations in the gene SNORD118, encoding the box C/D snoRNA U8, cause the cerebral microangiopathy leukoencephalopathy with calcifications and cysts (LCC), presenting at any age from early childhood to late adulthood. These mutations affect U8 expression, processing and protein binding and thus implicate U8 as essential in cerebral vascular homeostasis.
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Affiliation(s)
- Emma M. Jenkinson
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Mathieu P. Rodero
- INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Paris Descartes – Sorbonne Paris Cité University, Institut Imagine, Hôpital Necker, Paris, France
| | - Paul R. Kasher
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Carolina Uggenti
- INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Paris Descartes – Sorbonne Paris Cité University, Institut Imagine, Hôpital Necker, Paris, France
| | - Anthony Oojageer
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Laurence C. Goosey
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Yohann Rose
- INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Paris Descartes – Sorbonne Paris Cité University, Institut Imagine, Hôpital Necker, Paris, France
| | - Christopher J. Kershaw
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Molecular and Cellular Function, University of Manchester, UK
| | - Jill E. Urquhart
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Simon G. Williams
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Sanjeev S. Bhaskar
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - James O’Sullivan
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Gabriela M. Baerlocher
- Department of Hematology, Inselspital, Bern University Hospital, University of Bern, Bern Switzerland
- Experimental Hematology, Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Monika Haubitz
- Department of Hematology, Inselspital, Bern University Hospital, University of Bern, Bern Switzerland
- Experimental Hematology, Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Geraldine Aubert
- Repeat Diagnostics Inc, North Vancouver, British Columbia, Canada
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Kristin W. Barañano
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Angela J. Barnicoat
- Department of Clinical Genetics, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris, Pisa, Italy
| | - Andrea Berger
- Department of Neuropediatrics, Klinikum Weiden, Weiden, Germany
- Department of Neuropediatrics, Klinikum Harlaching, Munich, Germany
| | - Edward M. Blair
- Department Of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Janice E. Brunstrom-Hernandez
- Director, 1 CP Place, PLLC, Plano Texas USA
- Department of Neurology, Washington University School of Medicine, St. Louis Children’s Hospital, St. Louis, USA
| | - Johannes A. Buckard
- Department of Neuropediatrics, Sozialpädiatrisches Zentrum am EVK Düsseldorf, Düsseldorf, Germany
| | - David M. Cassiman
- Metabolic Center, Leuven University Hospitals and KU Leuven, Leuven, Belgium
| | - Rosaline Caumes
- Department of Neuropediatrics, Hopital Roger Salengro, Lille, France
| | | | - Liesbeth M. De Waele
- Department of Paediatric Neurology, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, Paediatric Neurology, University of Leuven, Leuven, Belgium
| | - Alexander J. Fay
- Department of Neurology, Washington University School of Medicine, St. Louis Children’s Hospital, St. Louis, USA
| | - Patrick Ferreira
- Division of Medical Genetics, Alberta Children's Hospital, Calgary, Canada
| | | | - Alan E. Fryer
- Department of Clinical Genetics, Liverpool Women’s NHS Foundation Trust, Liverpool, UK
| | - Himanshu Goel
- Hunter Genetics, Hunter New England Local Health District, Waratah, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia
| | - Cheryl A. Hemingway
- Department of Paediatric Neurology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Marco Henneke
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Georg August University, Göttingen, Germany
| | - Imelda Hughes
- Pediatric Neurology, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | | | - Ram Kumar
- Department of Paediatric Neurology, Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Lieven Lagae
- Department of Development and Regeneration, Paediatric Neurology, University of Leuven, Leuven, Belgium
| | - Pierre G. Landrieu
- Department of Paediatric Neurology, CHU Paris-Sud Bicetre, Le Kremlin Bicetre, France, 94270
| | - Charles M. Lourenço
- Neurogenetics Division, Clinics Hospital of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Timothy J. Malpas
- Department of Paediatrics, Jersey General Hospital, St Helier, Jersey
| | - Sarju G. Mehta
- East Anglian Regional Genetics Service, Addenbrookes Hospital, Cambridge, UK
| | - Imke Metz
- Department of Neuropathology, University Medical Center, Georg August University, Göttingen, Germany
| | - Sakkubai Naidu
- Hugo Moser Research Institute, Kennedy Krieger Institute, Johns Hopkins Medical Institutions, Neurology & Pediatrics, Baltimore, USA
| | - Katrin Õunap
- Department of Genetics, Tartu University Hospital, Tartu, Estonia
- Department of Pediatrics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Axel Panzer
- Epilepsy Center/ Paediatric Neurology, DRK Kliniken Berlin-Westend, Berlin, Germany
| | - Prab Prabhakar
- Department of Paediatric Neurology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Geraldine Quaghebeur
- Department of Neuroradiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Research Institute, Dallas, Texas, USA
| | | | | | - Calvin Soh
- Neuroradiology Department, Salford Royal NHS Foundation Trust, Salford, UK
| | - Helen S. Stewart
- Department Of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - John Stone
- Department of Clinical Neurosciences, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Christine E.G. Van Mol
- Department of pediatrics-neonatology, St. Augustinusziekenhuis, Oosterveldlaan 24, Wilrijk, Belgium
| | - Adeline Vanderver
- Department of Neurology, George Washington University School of Medicine, Children’s National Health System, Washington DC, USA
- Center for Genetic Medicine Research, George Washington University School of Medicine, Children’s National Health System, Washington DC, USA
| | - Emma L. Wakeling
- North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, Harrow, UK
| | - Andrea Whitney
- Department of Child Neurology, University Hospital Southampton NHS Trust, Southampton, UK
| | - Graham D. Pavitt
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Molecular and Cellular Function, University of Manchester, UK
| | - Sam Griffiths-Jones
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Molecular and Cellular Function, University of Manchester, UK
| | - Gillian I. Rice
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Paris; Paris Descartes–Sorbonne Paris Cite University, Imagine Institute, Paris
| | - Marjo S. van der Knaap
- Child Neurology and Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
- Functional Genomics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | | | - Raymond T. O’Keefe
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Molecular and Cellular Function, University of Manchester, UK
| | - Yanick J. Crow
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, UK
- INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Paris Descartes – Sorbonne Paris Cité University, Institut Imagine, Hôpital Necker, Paris, France
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40
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Ismael H, Altmeyer S, Stahl H. Regulation of the U3-, U8-, and U13snoRNA Expression by the DEAD Box Proteins Ddx5/Ddx17 with Consequences for Cell Proliferation and Survival. Noncoding RNA 2016; 2:ncrna2040011. [PMID: 29657268 PMCID: PMC5831926 DOI: 10.3390/ncrna2040011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/22/2016] [Accepted: 08/09/2016] [Indexed: 12/17/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) in cooperation with their associated proteins (snoRNPs) contribute to the maturation of ribosomal RNA, transfer RNA, and other transcripts. Most snoRNPs mediate chemical base modifications of their RNA substrates, and a few others, like those formed by the C/D snoRNAs U3, U8, and U13, are needed for the structural organization and maturation of primary transcripts. The U3-, U8-, and U13snoRNAs are encoded by autonomous genes, and our knowledge about their expression regulation is limited. In this study, a significant increase in the concentrations of U3-, U8-, and U13snoRNA after a knockdown of DEAD box proteins Ddx5/Ddx17 in HeLa cells is observed. These alterations are shown to be caused by transcriptional suppression mediated by Ddx5/Ddx17 via histone deacetylase 1 in a promoter-dependent way. The biological function of this expression control may be related to the role of Ddx5/Ddx17 in cell proliferation. The U3snoRNA is shown here to be essential for the proliferation and viability of human cells. Moreover, it was found that U3snoRNA interacts with Argonaute 2 in the RNA-induced silencing complexes (RISC), pointing to a microRNA-like function. For this reason, the 3′ untranslated region of the A-kinase anchor protein 9 (AKAP9)-mRNA could be identified as a potential target.
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Affiliation(s)
- Hala Ismael
- Department of Medical Biochemistry and Molecular Biology, University of Saarland, Medical Center, Building 45, 66421 Homburg, Germany.
| | - Simone Altmeyer
- Department of Medical Biochemistry and Molecular Biology, University of Saarland, Medical Center, Building 45, 66421 Homburg, Germany.
| | - Hans Stahl
- Department of Medical Biochemistry and Molecular Biology, University of Saarland, Medical Center, Building 45, 66421 Homburg, Germany.
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Sondalle SB, Baserga SJ, Yelick PC. The Contributions of the Ribosome Biogenesis Protein Utp5/WDR43 to Craniofacial Development. J Dent Res 2016; 95:1214-20. [PMID: 27221611 DOI: 10.1177/0022034516651077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Fairly recently, it was recognized that human ribosomopathies-developmental defects caused by mutations in ribosome biogenesis proteins-can exhibit tissue-specific defects rather than the expected global defects. This apparent anomaly-that seemingly ubiquitously expressed and required ribosomal proteins can have distinct functions in cell and tissue differentiation-has spurred new areas of research focused on better understanding translational mechanisms, biogenesis, and function in diverse cell types. This renewed appreciation for, and need to better understand, roles for ribosomal proteins in human development and disease has identified surprising similarities and differences in a variety of human ribosomopathies. Here, we discuss ribosomal protein functions in health and disease, focusing on the ribosome biogenesis protein Utp5/WDR43. New and exciting research in this field is anticipated to provide insight into a variety of previously understudied craniofacial dysostoses and result in significantly improved knowledge and understanding of roles for translational machinery in human craniofacial development and disease.
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Affiliation(s)
- S B Sondalle
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - S J Baserga
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - P C Yelick
- Department of Orthodontics, Division of Craniofacial and Molecular Genetics, Tufts University, Boston, MA, USA
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42
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Dupuis-Sandoval F, Poirier M, Scott MS. The emerging landscape of small nucleolar RNAs in cell biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:381-97. [PMID: 25879954 PMCID: PMC4696412 DOI: 10.1002/wrna.1284] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/18/2015] [Accepted: 03/20/2015] [Indexed: 01/07/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are a large class of small noncoding RNAs present in all eukaryotes sequenced thus far. As a family, they have been well characterized as playing a central role in ribosome biogenesis, guiding either the sequence-specific chemical modification of pre-rRNA (ribosomal RNA) or its processing. However, in higher eukaryotes, numerous orphan snoRNAs were described over a decade ago, with no known target or ascribed function, suggesting the possibility of alternative cellular functionality. In recent years, thanks in great part to advances in sequencing methodologies, we have seen many examples of the diversity that exists in the snoRNA family on multiple levels. In this review, we discuss the identification of novel snoRNA members, of unexpected binding partners, as well as the clarification and extension of the snoRNA target space and the characterization of diverse new noncanonical functions, painting a new and extended picture of the snoRNA landscape. Under the deluge of novel features and functions that have recently come to light, snoRNAs emerge as a central, dynamic, and highly versatile group of small regulatory RNAs. WIREs RNA 2015, 6:381–397. doi: 10.1002/wrna.1284
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Affiliation(s)
- Fabien Dupuis-Sandoval
- Biochemistry Department, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
| | - Mikaël Poirier
- Biochemistry Department, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
| | - Michelle S Scott
- Biochemistry Department and RNA Group, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
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43
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Holley CL, Li MW, Scruggs BS, Matkovich SJ, Ory DS, Schaffer JE. Cytosolic accumulation of small nucleolar RNAs (snoRNAs) is dynamically regulated by NADPH oxidase. J Biol Chem 2015; 290:11741-8. [PMID: 25792744 DOI: 10.1074/jbc.m115.637413] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 01/22/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) guide nucleotide modifications of cellular RNAs in the nucleus. We previously showed that box C/D snoRNAs from the Rpl13a locus are unexpected mediators of physiologic oxidative stress, independent of their predicted ribosomal RNA modifications. Here we demonstrate that oxidative stress induced by doxorubicin causes rapid cytoplasmic accumulation of the Rpl13a snoRNAs through a mechanism that requires superoxide and a nuclear splice variant of NADPH oxidase. RNA-sequencing analysis reveals that box C/D snoRNAs as a class are present in the cytoplasm, where their levels are dynamically regulated by NADPH oxidase. These findings suggest that snoRNAs may orchestrate the response to environmental stress through molecular interactions outside of the nucleus.
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Affiliation(s)
| | - Melissa W Li
- From the Diabetic Cardiovascular Disease Center and
| | | | - Scot J Matkovich
- Center for Pharmacogenomics, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missiouri 63110
| | - Daniel S Ory
- From the Diabetic Cardiovascular Disease Center and
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44
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Sharma S, Langhendries JL, Watzinger P, Kötter P, Entian KD, Lafontaine DLJ. Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. Nucleic Acids Res 2015; 43:2242-58. [PMID: 25653167 PMCID: PMC4344512 DOI: 10.1093/nar/gkv075] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 01/05/2023] Open
Abstract
The function of RNA is subtly modulated by post-transcriptional modifications. Here, we report an important crosstalk in the covalent modification of two classes of RNAs. We demonstrate that yeast Kre33 and human NAT10 are RNA cytosine acetyltransferases with, surprisingly, specificity toward both 18S rRNA and tRNAs. tRNA acetylation requires the intervention of a specific and conserved adaptor: yeast Tan1/human THUMPD1. In budding and fission yeasts, and in human cells, we found two acetylated cytosines on 18S rRNA, one in helix 34 important for translation accuracy and another in helix 45 near the decoding site. Efficient 18S rRNA acetylation in helix 45 involves, in human cells, the vertebrate-specific box C/D snoRNA U13, which, we suggest, exposes the substrate cytosine to modification through Watson-Crick base pairing with 18S rRNA precursors during small subunit biogenesis. Finally, while Kre33 and NAT10 are essential for pre-rRNA processing reactions leading to 18S rRNA synthesis, we demonstrate that rRNA acetylation is dispensable to yeast cells growth. The inactivation of NAT10 was suggested to suppress nuclear morphological defects observed in laminopathic patient cells through loss of microtubules modification and cytoskeleton reorganization. We rather propose the effects of NAT10 on laminopathic cells are due to reduced ribosome biogenesis or function.
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MESH Headings
- Acetylation
- Acetyltransferases/chemistry
- Acetyltransferases/metabolism
- Amino Acid Sequence
- Cell Line
- Conserved Sequence
- Cytosine/metabolism
- Humans
- N-Terminal Acetyltransferase E/chemistry
- N-Terminal Acetyltransferase E/metabolism
- N-Terminal Acetyltransferases
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Plant/chemistry
- RNA, Plant/metabolism
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/metabolism
- RNA, Small Nucleolar/metabolism
- RNA, Transfer/metabolism
- RNA-Binding Proteins/metabolism
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Sunny Sharma
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Jean-Louis Langhendries
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Peter Watzinger
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Peter Kötter
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Karl-Dieter Entian
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Denis L J Lafontaine
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium Center for Microscopy and Molecular Imaging, B-6041 Charleroi-Gosselies, Belgium
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45
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McMahon M, Contreras A, Ruggero D. Small RNAs with big implications: new insights into H/ACA snoRNA function and their role in human disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:173-89. [PMID: 25363811 DOI: 10.1002/wrna.1266] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/25/2014] [Accepted: 08/07/2014] [Indexed: 12/26/2022]
Abstract
A myriad of structurally and functionally diverse noncoding RNAs (ncRNAs) have recently been implicated in numerous human diseases including cancer. Small nucleolar RNAs (snoRNAs), the most abundant group of intron-encoded ncRNAs, are classified into two families (box C/D snoRNAs and box H/ACA snoRNAs) and are required for post-transcriptional modifications on ribosomal RNA (rRNA). There is now a growing appreciation that nucleotide modifications on rRNA may impart regulatory potential to the ribosome; however, the functional consequence of site-specific snoRNA-guided modifications remains poorly defined. Discovered almost 20 years ago, H/ACA snoRNAs are required for the conversion of specific uridine residues to pseudouridine on rRNA. Interestingly, recent reports indicate that the levels of subsets of H/ACA snoRNAs required for pseudouridine modifications at specific sites on rRNA are altered in several diseases, particularly cancer. In this review, we describe recent advances in understanding the downstream consequences of H/ACA snoRNA-guided modifications on ribosome function, discuss the possible mechanism by which H/ACA snoRNAs may be regulated, and explore prospective expanding functions of H/ACA snoRNAs. Furthermore, we discuss the potential biological implications of alterations in H/ACA snoRNA expression in several human diseases.
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Affiliation(s)
- Mary McMahon
- School of Medicine and Department of Urology, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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46
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Gupta Y, Witte M, Möller S, Ludwig RJ, Restle T, Zillikens D, Ibrahim SM. ptRNApred: computational identification and classification of post-transcriptional RNA. Nucleic Acids Res 2014; 42:e167. [PMID: 25303994 PMCID: PMC4267668 DOI: 10.1093/nar/gku918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED Non-coding RNAs (ncRNAs) are known to play important functional roles in the cell. However, their identification and recognition in genomic sequences remains challenging. In silico methods, such as classification tools, offer a fast and reliable way for such screening and multiple classifiers have already been developed to predict well-defined subfamilies of RNA. So far, however, out of all the ncRNAs, only tRNA, miRNA and snoRNA can be predicted with a satisfying sensitivity and specificity. We here present ptRNApred, a tool to detect and classify subclasses of non-coding RNA that are involved in the regulation of post-transcriptional modifications or DNA replication, which we here call post-transcriptional RNA (ptRNA). It (i) detects RNA sequences coding for post-transcriptional RNA from the genomic sequence with an overall sensitivity of 91% and a specificity of 94% and (ii) predicts ptRNA-subclasses that exist in eukaryotes: snRNA, snoRNA, RNase P, RNase MRP, Y RNA or telomerase RNA. AVAILABILITY The ptRNApred software is open for public use on http://www.ptrnapred.org/.
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Affiliation(s)
- Yask Gupta
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Mareike Witte
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Steffen Möller
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Ralf J Ludwig
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Tobias Restle
- Institute for Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Saleh M Ibrahim
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
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47
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Abstract
This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease.
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Affiliation(s)
| | - Cornelius F. Boerkoel
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-604-875-2157; Fax: +1-604-875-2376
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Nallar SC, Kalvakolanu DV. Regulation of snoRNAs in cancer: close encounters with interferon. J Interferon Cytokine Res 2013; 33:189-98. [PMID: 23570385 DOI: 10.1089/jir.2012.0106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The interferon (IFN) family of cytokines regulates many cellular processes, such as transcription, translation, post-translational modifications, and protein degradation. IFNs induce growth inhibition and/or cell death, depending on the cell type, by employing different proteins. This review describes a novel growth-suppressive pathway employed by IFNs that affects rRNA levels. Maturation of rRNA involves numerous noncoding small regulatory RNA-guided processes. These regulatory RNAs, called small nucleolar RNA (snoRNAs), function as a ribonucleoprotein particle (RNP) in the nucleolus. The biogenesis of snoRNPs is dependent on core protein and assembly factors. Our laboratory recently isolated a growth-suppressive protein gene associated with retinoid-IFN-induced mortality (GRIM)-1 using a genetic screen. IFN-inducible GRIM-1 (SHQ1) is an assembly factor that controls one arm of the snoRNP machinery. GRIM-1 inhibits sno/scaRNP formation to induce growth suppression via reduction in mature rRNA levels. Loss of GRIM-1 observed in certain cancers implicates it to be a novel tumor suppressor. Certain snoRNAs have been reported to act as either oncogenes or tumor suppressors in vitro. Recent studies have shown that certain sno/scaRNAs are further processed into micro RNA-like molecules to control translation of protein-coding RNAs. We present a model as to how these small regulatory RNAs influence cell growth and a potential role for GRIM-1 in this process.
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Affiliation(s)
- Shreeram C Nallar
- Department of Microbiology & Immunology, Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, MD 21201, USA
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Asami S, Rakwalska-Bange M, Carlomagno T, Reif B. Untersuchung von Protein-RNA-Interaktionsstellen mithilfe 1H-detektierter MAS-Festkörper-NMR-Spektroskopie. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Asami S, Rakwalska-Bange M, Carlomagno T, Reif B. Protein-RNA Interfaces Probed by1H-Detected MAS Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2013; 52:2345-9. [DOI: 10.1002/anie.201208024] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Indexed: 11/08/2022]
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