1
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Ye R, Zhao H, Wang X, Xue Y. Technological advancements in deciphering RNA-RNA interactions. Mol Cell 2024:S1097-2765(24)00543-4. [PMID: 39047724 DOI: 10.1016/j.molcel.2024.06.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/11/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
RNA-RNA interactions (RRIs) can dictate RNA molecules to form intricate higher-order structures and bind their RNA substrates in diverse biological processes. To elucidate the function, binding specificity, and regulatory mechanisms of various RNA molecules, especially the vast repertoire of non-coding RNAs, advanced technologies and methods that globally map RRIs are extremely valuable. In the past decades, many state-of-the-art technologies have been developed for this purpose. This review focuses on those high-throughput technologies for the global mapping of RRIs. We summarize the key concepts and the pros and cons of different technologies. In addition, we highlight the novel biological insights uncovered by these RRI mapping methods and discuss the future challenges for appreciating the crucial roles of RRIs in gene regulation across bacteria, viruses, archaea, and mammals.
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Affiliation(s)
- Rong Ye
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailian Zhao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Wang
- State Key Laboratory of Female Fertility Promotion, Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yuanchao Xue
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Heimdörfer D, Vorleuter A, Eschlböck A, Spathopoulou A, Suarez-Cubero M, Farhan H, Reiterer V, Spanjaard M, Schaaf CP, Huber LA, Kremser L, Sarg B, Edenhofer F, Geley S, de Araujo MEG, Huettenhofer A. Truncated variants of MAGEL2 are involved in the etiologies of the Schaaf-Yang and Prader-Willi syndromes. Am J Hum Genet 2024; 111:1383-1404. [PMID: 38908375 PMCID: PMC11267527 DOI: 10.1016/j.ajhg.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/24/2024] Open
Abstract
The neurodevelopmental disorders Prader-Willi syndrome (PWS) and Schaaf-Yang syndrome (SYS) both arise from genomic alterations within human chromosome 15q11-q13. A deletion of the SNORD116 cluster, encoding small nucleolar RNAs, or frameshift mutations within MAGEL2 result in closely related phenotypes in individuals with PWS or SYS, respectively. By investigation of their subcellular localization, we observed that in contrast to a predominant cytoplasmic localization of wild-type (WT) MAGEL2, a truncated MAGEL2 mutant was evenly distributed between the cytoplasm and the nucleus. To elucidate regulatory pathways that may underlie both diseases, we identified protein interaction partners for WT or mutant MAGEL2, in particular the survival motor neuron protein (SMN), involved in spinal muscular atrophy, and the fragile-X-messenger ribonucleoprotein (FMRP), involved in autism spectrum disorders. The interactome of the non-coding RNA SNORD116 was also investigated by RNA-CoIP. We show that WT and truncated MAGEL2 were both involved in RNA metabolism, while regulation of transcription was mainly observed for WT MAGEL2. Hence, we investigated the influence of MAGEL2 mutations on the expression of genes from the PWS locus, including the SNORD116 cluster. Thereby, we provide evidence for MAGEL2 mutants decreasing the expression of SNORD116, SNORD115, and SNORD109A, as well as protein-coding genes MKRN3 and SNRPN, thus bridging the gap between PWS and SYS.
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Affiliation(s)
- David Heimdörfer
- Institute of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
| | - Alexander Vorleuter
- Institute of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Alexander Eschlböck
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Angeliki Spathopoulou
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Marta Suarez-Cubero
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Hesso Farhan
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Veronika Reiterer
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Melanie Spanjaard
- Institute of Human Genetics, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Leopold Kremser
- Institute of Medical Biochemistry, Protein Core Facility, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Bettina Sarg
- Institute of Medical Biochemistry, Protein Core Facility, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Frank Edenhofer
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Stephan Geley
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Alexander Huettenhofer
- Institute of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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3
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Jagielski NP, Rai AK, Rajan KS, Mangal V, Garikipati VNS. A contemporary review of snoRNAs in cardiovascular health: RNA modification and beyond. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102087. [PMID: 38178918 PMCID: PMC10765057 DOI: 10.1016/j.omtn.2023.102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
As cardiovascular diseases continue to be the leading cause of death worldwide, groundbreaking research is being conducted to mitigate their effects. This review looks into the potential of small nucleolar RNAs (snoRNAs) and the opportunity to use these molecular agents as therapeutic biomarkers for cardiovascular issues specific to the heart. Through an investigation of snoRNA biogenesis, functionality, and roles in cardiovascular diseases, this review relates our past and present knowledge of snoRNAs to the current scientific literature. Considering the initial discovery of snoRNAs and the studies thereafter analyzing the roles of snoRNAs in disease, we look forward to uncovering many other noncanonical functions that could lead researchers closer to finding preventive and curative solutions for cardiovascular diseases.
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Affiliation(s)
- Noah Peter Jagielski
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Amit Kumar Rai
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - K. Shanmugha Rajan
- Department of Chemical and Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel
| | - Vatsal Mangal
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Venkata Naga Srikanth Garikipati
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
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4
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Isaac R, Vinik Y, Mikl M, Nadav-Eliyahu S, Shatz-Azoulay H, Yaakobi A, DeForest N, Majithia AR, Webster NJ, Shav-Tal Y, Elhanany E, Zick Y. A seven-transmembrane protein-TM7SF3, resides in nuclear speckles and regulates alternative splicing. iScience 2022; 25:105270. [PMID: 36304109 PMCID: PMC9593240 DOI: 10.1016/j.isci.2022.105270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 06/08/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
The seven-transmembrane superfamily member 3 protein (TM7SF3) is a p53-regulated homeostatic factor that attenuates cellular stress and the unfolded protein response. Here we show that TM7SF3 localizes to nuclear speckles; eukaryotic nuclear bodies enriched in splicing factors. This unexpected location for a trans -membranal protein enables formation of stable complexes between TM7SF3 and pre-mRNA splicing factors including DHX15, LARP7, HNRNPU, RBM14, and HNRNPK. Indeed, TM7SF3 regulates alternative splicing of >330 genes, mainly at the 3'end of introns by directly modulating the activity of splicing factors such as HNRNPK. These effects are observed both in cell lines and primary human pancreatic islets. Accordingly, silencing of TM7SF3 results in differential expression of 1465 genes (about 7% of the human genome); with 844 and 621 genes being up- or down-regulated, respectively. Our findings implicate TM7SF3, as a resident protein of nuclear speckles and suggest a role for seven-transmembrane proteins as regulators of alternative splicing.
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Affiliation(s)
- Roi Isaac
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yaron Vinik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Martin Mikl
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Biology, University of Haifa, Haifa, Israel
| | - Shani Nadav-Eliyahu
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hadas Shatz-Azoulay
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adi Yaakobi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Natalie DeForest
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Amit R. Majithia
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas J.G. Webster
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eytan Elhanany
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yehiel Zick
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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5
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Singh S, Shyamal S, Panda AC. Detecting RNA-RNA interactome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1715. [PMID: 35132791 DOI: 10.1002/wrna.1715] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
The last decade has seen a robust increase in various types of novel RNA molecules and their complexity in gene regulation. RNA molecules play a critical role in cellular events by interacting with other biomolecules, including protein, DNA, and RNA. It has been established that RNA-RNA interactions play a critical role in several biological processes by regulating the biogenesis and function of RNA molecules. Interestingly, RNA-RNA interactions regulate the biogenesis of diverse RNA molecules, including mRNAs, microRNAs, tRNAs, and circRNAs, through splicing or backsplicing. Structured RNAs like rRNA, tRNA, and snRNAs achieve their functional conformation by intramolecular RNA-RNA interactions. In addition, functional consequences of many intermolecular RNA-RNA interactions have been extensively studied in the regulation of gene expression. Hence, it is essential to understand the mechanism and functions of RNA-RNA interactions in eukaryotes. Conventionally, RNA-RNA interactions have been identified through diverse biochemical methods for decades. The advent of high-throughput RNA-sequencing technologies has revolutionized the identification of global RNA-RNA interactome in cells and their importance in RNA structure and function in gene expression regulation. Although these technologies revealed tens of thousands of intramolecular and intermolecular RNA-RNA interactions, we further look forward to future unbiased and quantitative high-throughput technologies for detecting transcriptome-wide RNA-RNA interactions. With the ability to detect RNA-RNA interactome, we expect that future studies will reveal the higher-order structures of RNA molecules and multi-RNA hybrids impacting human health and diseases. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Suman Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Center for Biotechnology, Faridabad, India
| | | | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
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6
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Shefer K, Boulos A, Gotea V, Arafat M, Ben Chaim Y, Muharram A, Isaac S, Eden A, Sperling J, Elnitski L, Sperling R. A novel role for nucleolin in splice site selection. RNA Biol 2021; 19:333-352. [PMID: 35220879 PMCID: PMC8890436 DOI: 10.1080/15476286.2021.2020455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 12/10/2021] [Indexed: 01/12/2023] Open
Abstract
Latent 5' splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and specifically with initiator-tRNA in the nucleus, but not in the cytoplasm. Next, we show the association of ini-tRNA and NCL with pre-mRNA. We further show that recovery of suppression of latent splicing by initiator-tRNA complementation is NCL dependent. Finally, upon nucleolin knockdown we show activation of latent splicing in hundreds of coding transcripts having important cellular functions. We thus propose nucleolin, a component of the endogenous spliceosome, through its direct binding to initiator-tRNA and its effect on latent splicing, as the first protein of a nuclear quality control mechanism regulating splice site selection to protect cells from latent splicing that can generate defective mRNAs.
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Affiliation(s)
- Kinneret Shefer
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Ayub Boulos
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Maram Arafat
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Yair Ben Chaim
- Department of Natural Sciences, The Open University, RaananaIsrael
| | - Aya Muharram
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Sara Isaac
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Amir Eden
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, RehovotIsrael
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
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7
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Thibault PA, Ganesan A, Kalyaanamoorthy S, Clarke JPWE, Salapa HE, Levin MC. hnRNP A/B Proteins: An Encyclopedic Assessment of Their Roles in Homeostasis and Disease. BIOLOGY 2021; 10:biology10080712. [PMID: 34439945 PMCID: PMC8389229 DOI: 10.3390/biology10080712] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022]
Abstract
The hnRNP A/B family of proteins is canonically central to cellular RNA metabolism, but due to their highly conserved nature, the functional differences between hnRNP A1, A2/B1, A0, and A3 are often overlooked. In this review, we explore and identify the shared and disparate homeostatic and disease-related functions of the hnRNP A/B family proteins, highlighting areas where the proteins have not been clearly differentiated. Herein, we provide a comprehensive assembly of the literature on these proteins. We find that there are critical gaps in our grasp of A/B proteins' alternative splice isoforms, structures, regulation, and tissue and cell-type-specific functions, and propose that future mechanistic research integrating multiple A/B proteins will significantly improve our understanding of how this essential protein family contributes to cell homeostasis and disease.
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Affiliation(s)
- Patricia A. Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Aravindhan Ganesan
- ArGan’s Lab, School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Subha Kalyaanamoorthy
- Department of Chemistry, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Joseph-Patrick W. E. Clarke
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Hannah E. Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Michael C. Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Correspondence:
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8
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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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9
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Azevedo-Favory J, Gaspin C, Ayadi L, Montacié C, Marchand V, Jobet E, Rompais M, Carapito C, Motorin Y, Sáez-Vásquez J. Mapping rRNA 2'-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants. RNA Biol 2021; 18:1760-1777. [PMID: 33596769 PMCID: PMC8583080 DOI: 10.1080/15476286.2020.1869892] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In all eukaryotic cells, the most abundant modification of ribosomal RNA (rRNA) is methylation at the ribose moiety (2ʹ-O-methylation). Ribose methylation at specific rRNA sites is guided by small nucleolar RNAs (snoRNAs) of C/D-box type (C/D snoRNA) and achieved by the methyltransferase Fibrillarin (FIB). Here we used the Illumina-based RiboMethSeq approach for mapping rRNA 2ʹ-O-methylation sites in A. thaliana Col-0 (WT) plants. This analysis detected novel C/D snoRNA-guided rRNA 2ʹ-O-methylation positions and also some orphan sites without a matching C/D snoRNA. Furthermore, immunoprecipitation of Arabidopsis FIB2 identified and demonstrated expression of C/D snoRNAs corresponding to majority of mapped rRNA sites. On the other hand, we show that disruption of Arabidopsis Nucleolin 1 gene (NUC1), encoding a major nucleolar protein, decreases 2ʹ-O-methylation at specific rRNA sites suggesting functional/structural interconnections of 2ʹ-O-methylation with nucleolus organization and plant development. Finally, based on our findings and existent database sets, we introduce a new nomenclature system for C/D snoRNA in Arabidopsis plants.
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Affiliation(s)
- J Azevedo-Favory
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR5096, 66860 Perpignan, France
| | - C Gaspin
- Université Fédérale de Toulouse, INRAE, MIAT, 31326, Castanet-Tolosan, France.,Université Fédérale de Toulouse, INRAE, BioinfOmics, Genotoul Bioinformatics facility, 31326
| | - L Ayadi
- Université de Lorraine, CNRS, INSERM, IBSLor, (UMS2008/US40), Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France.,Université de Lorraine, CNRS, IMoPA (UMR7365), F-54000 Nancy, France
| | - C Montacié
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR5096, 66860 Perpignan, France
| | - V Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor, (UMS2008/US40), Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France
| | - E Jobet
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR5096, 66860 Perpignan, France
| | - M Rompais
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS/Université de Strasbourg, Strasbourg, France
| | - C Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS/Université de Strasbourg, Strasbourg, France
| | - Y Motorin
- Université de Lorraine, CNRS, INSERM, IBSLor, (UMS2008/US40), Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France.,Université de Lorraine, CNRS, IMoPA (UMR7365), F-54000 Nancy, France
| | - J Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR5096, 66860 Perpignan, France
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10
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Bratkovič T, Božič J, Rogelj B. Functional diversity of small nucleolar RNAs. Nucleic Acids Res 2020; 48:1627-1651. [PMID: 31828325 PMCID: PMC7038934 DOI: 10.1093/nar/gkz1140] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/17/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are short non-protein-coding RNAs with a long-recognized role in tuning ribosomal and spliceosomal function by guiding ribose methylation and pseudouridylation at targeted nucleotide residues of ribosomal and small nuclear RNAs, respectively. SnoRNAs are increasingly being implicated in regulation of new types of post-transcriptional processes, for example rRNA acetylation, modulation of splicing patterns, control of mRNA abundance and translational efficiency, or they themselves are processed to shorter stable RNA species that seem to be the principal or alternative bioactive isoform. Intriguingly, some display unusual cellular localization under exogenous stimuli, or tissue-specific distribution. Here, we discuss the new and unforeseen roles attributed to snoRNAs, focusing on the presumed mechanisms of action. Furthermore, we review the experimental approaches to study snoRNA function, including high resolution RNA:protein and RNA:RNA interaction mapping, techniques for analyzing modifications on targeted RNAs, and cellular and animal models used in snoRNA biology research.
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Affiliation(s)
- Tomaž Bratkovič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI1000 Ljubljana, Slovenia
| | - Janja Božič
- Jozef Stefan Institute, Department of Biotechnology, Jamova cesta 39, SI1000 Ljubljana, Slovenia.,Biomedical Research Institute BRIS, Puhova ulica 10, SI1000 Ljubljana, Slovenia
| | - Boris Rogelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI1000 Ljubljana, Slovenia.,Jozef Stefan Institute, Department of Biotechnology, Jamova cesta 39, SI1000 Ljubljana, Slovenia.,Biomedical Research Institute BRIS, Puhova ulica 10, SI1000 Ljubljana, Slovenia.,University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI1000 Ljubljana, Slovenia
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11
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Filippova JA, Matveeva AM, Zhuravlev ES, Balakhonova EA, Prokhorova DV, Malanin SJ, Shah Mahmud R, Grigoryeva TV, Anufrieva KS, Semenov DV, Vlassov VV, Stepanov GA. Are Small Nucleolar RNAs "CRISPRable"? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells. Front Pharmacol 2019; 10:1246. [PMID: 31780925 PMCID: PMC6856654 DOI: 10.3389/fphar.2019.01246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/27/2019] [Indexed: 01/20/2023] Open
Abstract
CRISPR technologies are nowadays widely used for targeted knockout of numerous protein-coding genes and for the study of various processes and metabolic pathways in human cells. Most attention in the genome editing field is now focused on the cleavage of protein-coding genes or genes encoding long non-coding RNAs (lncRNAs), while the studies on targeted knockout of intron-encoded regulatory RNAs are sparse. Small nucleolar RNAs (snoRNAs) present a class of non-coding RNAs encoded within the introns of various host genes and involved in post-transcriptional maturation of ribosomal RNAs (rRNAs) in eukaryotic cells. Box C/D snoRNAs direct 2'-O-methylation of rRNA nucleotides. These short RNAs have specific elements in their structure, namely, boxes C and D, and a target-recognizing region. Here, we present the study devoted to CRISPR/Cas9-mediated editing of box C/D snoRNA genes in Gas5. We obtained monoclonal cell lines carrying mutations in snoRNA genes and analyzed the levels of the mutant box C/D snoRNA as well as the 2'-O-methylation status of the target rRNA nucleotide in the obtained cells. Mutations in SNORD75 in the obtained monoclonal cell line were shown to result in aberrant splicing of Gas5 with exclusion of exons 3 to 5, which was confirmed by RT-PCR and RNA-Seq. The obtained results suggest that SNORD75 contains an element for binding of some factors regulating maturation of Gas5 pre-lncRNA. We suggest that METTL3/METTL14 is among such factors, and m6A-methylation pathways are involved in regulation of Gas5 splicing. Our results shell light on the role of SNORDs in regulating splicing of the host gene.
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Affiliation(s)
- Julia A Filippova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya M Matveeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii S Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgenia A Balakhonova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Daria V Prokhorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Sergey J Malanin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Raihan Shah Mahmud
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Tatiana V Grigoryeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ksenia S Anufrieva
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Moscow, Russia.,Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry V Semenov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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12
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Sperling R. Small non-coding RNA within the endogenous spliceosome and alternative splicing regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194406. [PMID: 31323432 DOI: 10.1016/j.bbagrm.2019.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Splicing and alternative splicing (AS), which occur in the endogenous spliceosome, play major roles in regulating gene expression, and defects in them are involved in numerous human diseases including cancer. Although the mechanism of the splicing reaction is well understood, the regulation of AS remains to be elucidated. A group of essential regulatory factors in gene expression are small non-coding RNAs (sncRNA): e.g. microRNA, mainly known for their inhibitory role in translation in the cytoplasm; and small nucleolar RNA, known for their role in methylating non-coding RNA in the nucleolus. Here I highlight a new aspect of sncRNAs found within the endogenous spliceosome. Assembled in non-canonical complexes and through different base pairing than their canonical ones, spliceosomal sncRNAs can potentially target different RNAs. Examples of spliceosomal sncRNAs regulating AS, regulating gene expression, and acting in a quality control of AS are reviewed, suggesting novel functions for spliceosomal sncRNAs. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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13
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Wu B, Huang L, Qiu W, Liu X, Shen Y, Lu Y, Yang Z, Li X, Cui B, Xu S, Qiao H, Qiu R, Yao L, Kan Y, Li D. Small nucleolar RNA Sf-15 regulates proliferation and apoptosis of Spodoptera frugiperda Sf9 cells. BMC Mol Biol 2019; 20:12. [PMID: 30971200 PMCID: PMC6458620 DOI: 10.1186/s12867-019-0128-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small nucleolar RNAs (snoRNAs) function in guiding 2'-O-methylation and pseudouridylation of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). In recent years, more and more snoRNAs have been found to play novel roles in mRNA regulation, such as pre-mRNA splicing or RNA editing. In our previous study, we found a silkworm C/D box snoRNA Bm-15 can interact with Notch receptor gene in vitro. To further study the function of Bm-15, we cloned its homolog Sf-15 from Spodoptera frugiperda and investigate the function of Sf-15 in Sf9 cells. RESULTS We showed that knocking down of Sf-15 can inhibit the proliferation, then induce apoptosis of insect S. frugiperda Sf9 cells, but the results were reversed when Sf-15 was overexpressed. De novo sequencing of transcriptome of Sf9 cells showed that the expression of 21 apoptosis-related genes were increased upon Sf-15 repression. Further analysis showed that a Ca2+-induced cell death pathway gene Cn (PPP3C, the serine/threonine-protein phosphatase 2B catalytic subunit), was significantly increased upon Sf-15 depression but decreased when Sf-15 was overexpressed, which indicated that Cn might be a potential target of Sf-15. CONCLUSIONS We conclude that C/D box snoRNA Sf-15 can participate in apoptosis through regulating the expression of Ca2+-induced cell death pathway gene Cn in Sf9 cells. This is the first time that we found snoRNAs exhibiting dual functions in insect, which reveals a novel layer of ncRNA modulation in cell growth and death.
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Affiliation(s)
- Bo Wu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Lei Huang
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Wujie Qiu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Xiao Liu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yawen Shen
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yiping Lu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Zonglin Yang
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Xinmei Li
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Bin Cui
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Shidong Xu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Huili Qiao
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Reng Qiu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
| | - Dandan Li
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
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14
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Ectopic expression of Snord115 in choroid plexus interferes with editing but not splicing of 5-Ht2c receptor pre-mRNA in mice. Sci Rep 2019; 9:4300. [PMID: 30862860 PMCID: PMC6414643 DOI: 10.1038/s41598-019-39940-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/01/2019] [Indexed: 01/01/2023] Open
Abstract
Serotonin 5-HT2C receptor is a G-protein coupled excitatory receptor that regulates several biochemical pathways and has been implicated in obesity, mental state, sleep cycles, autism, neuropsychiatric disorders and neurodegenerative diseases. The activity of 5-HT2CR is regulated via alternative splicing and A to I editing of exon Vb of its pre-mRNA. Snord115 is a small nucleolar RNA that is expressed in mouse neurons and displays an 18-nucleotide base complementary to exon Vb of 5-HT2CR pre-mRNA. For almost two decades this putative guide element of Snord115 has wandered like a ghost through the literature in attempts to elucidate the biological significance of this complementarity. In mice, Snord115 is expressed in neurons and absent in the choroid plexus where, in contrast, 5-Ht2cr mRNA is highly abundant. Here we report the analysis of 5-Ht2cr pre-mRNA posttranscriptional processing via RNA deep sequencing in a mouse model that ectopically expresses Snord115 in the choroid plexus. In contrast to previous reports, our analysis demonstrated that Snord115 does not control alternative splicing of 5-Ht2cr pre-mRNA in vivo. We identified a modest, yet statistically significant reduction of 5-Ht2cr pre-mRNA A to I editing at the major A, B, C and D sites. We suggest that Snord115 and exon Vb of 5Ht2cr pre-mRNA form a double-stranded structure that is subject to ADAR-mediated A to I editing. To the best of our knowledge, this is the first comprehensive Snord115 gain-of-function analysis based on in vivo mouse models.
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15
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Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. The cellular landscape of mid-size noncoding RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1530. [PMID: 30843375 PMCID: PMC6619189 DOI: 10.1002/wrna.1530] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/06/2023]
Abstract
Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA-binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Vincent Boivin
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Laurence Faucher-Giguère
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Michelle Scott
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sherif Abou-Elela
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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16
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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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17
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Dick ALW, Khermesh K, Paul E, Stamp F, Levanon EY, Chen A. Adenosine-to-Inosine RNA Editing Within Corticolimbic Brain Regions Is Regulated in Response to Chronic Social Defeat Stress in Mice. Front Psychiatry 2019; 10:277. [PMID: 31133890 PMCID: PMC6512728 DOI: 10.3389/fpsyt.2019.00277] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 04/10/2019] [Indexed: 11/13/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a co-/posttranscriptional modification of double-stranded RNA, catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes, which results in recognition of inosine as guanosine by translational and splicing machinery causing potential recoding events in amino acid sequences. A-to-I editing is prominent within brain-specific transcripts, and dysregulation of editing at several well-studied loci (e.g., Gria2, Htr2c) has been implicated in acute and chronic stress in rodents as well as neurological (e.g., Alzheimer's) and psychopathological disorders such as schizophrenia and major depressive disorder. However, only a small fraction of recoding sites has been investigated within the brain following stress, and our understanding of the role of RNA editing in transcriptome regulation following environmental stimuli remains poorly understood. Thus, we aimed to investigate A-to-I editing at hundreds of loci following chronic social defeat stress (CSDS) in mice within corticolimbic regions responsive to chronic stress regulation. Adult male mice were subjected to CSDS or control conditions for 21 days and dynamic regulation of A-to-I editing was investigated 2 and 8 days following the final defeat within both the medial prefrontal cortex (mPFC) and basolateral amygdala (BLA). Employing a targeted resequencing approach, which utilizes microfluidics-based multiplex polymerase chain reaction (PCR) coupled with next-generation sequencing, we analyzed A-to-I editing at ∼100 high-confidence editing sites within the mouse brain. CSDS resulted in acute regulation of transcripts encoding several ADAR enzymes, which normalized 8 days following the final defeat and was specific for susceptible mice. In contrast, sequencing analysis revealed modest and dynamic regulation of A-to-I editing within numerous transcripts in both the mPFC and BLA of resilient and susceptible mice at both 2 and 8 days following CSDS with minimal overlap between regions and time points. Editing within the Htr2c transcript and relative abundance of Htr2c messenger RNA (mRNA)variants were also observed within the BLA of susceptible mice 2 days following CSDS. These results indicate dynamic RNA editing within discrete brain regions following CSDS in mice, further implicating A-to-I editing as a stress-sensitive molecular mechanism within the brain of potential relevance to resiliency and susceptibility to CSDS.
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Affiliation(s)
- Alec L W Dick
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | | | - Evan Paul
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Fabian Stamp
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of LifeSciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany.,Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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18
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Yu G, Zhao Y, Li H. The multistructural forms of box C/D ribonucleoprotein particles. RNA (NEW YORK, N.Y.) 2018; 24:1625-1633. [PMID: 30254138 PMCID: PMC6239191 DOI: 10.1261/rna.068312.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Structural biology studies of archaeal and yeast box C/D ribonucleoprotein particles (RNPs) reveal a surprisingly wide range of forms. If form ever follows function, the different structures of box C/D small ribonucleoprotein particles (snoRNPs) may reflect their versatile functional roles beyond what has been recognized. A large majority of box C/D RNPs serve to site-specifically methylate the ribosomal RNA, typically as independent complexes. Select members of the box C/D snoRNPs also are essential components of the megadalton RNP enzyme, the small subunit processome that is responsible for processing ribosomal RNA. Other box C/D RNPs continue to be uncovered with either unexpected or unknown functions. We summarize currently known box C/D RNP structures in this review and identify the Nop56/58 and box C/D RNA subunits as the key elements underlying the observed structural diversity, and likely, the diverse functional roles of box C/D RNPs.
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Affiliation(s)
- Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
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19
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Welden JR, Zhang Z, Duncan MJ, Falaleeva M, Wells T, Stamm S. The posterior pituitary expresses the serotonin receptor 2C. Neurosci Lett 2018; 684:132-139. [PMID: 29969651 DOI: 10.1016/j.neulet.2018.06.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/19/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
The serotonin receptor 2C (5HT2C) is an important drug target to treat obesity and depression. Its pre-mRNA undergoes alternative splicing, encoding a short RNA1 isoform that is localized intracellularly and a full-length isoform (RNA2) that can reach the cell membrane. These splicing isoforms are deregulated in Prader-Willi syndrome (PWS), due to the loss of a trans-acting regulatory RNA, SNORD115. Here we show that the 5HT2C mRNA is expressed in the posterior pituitary, suggesting that 5HT2C mRNA is generated in the hypothalamus and subsequently conveyed by axonal transport. In the pituitary, the ratio of 5HT2C isoforms is regulated by feeding, and can be manipulated using a splice-site changing oligonucleotide injected into the blood. The pituitary expression of the 5HT2C mRNA may constitute a previously unknown mechanism whereby serotonin in the circulation or drugs targeting the 5HT2C might induce side-effects. Finally, the deregulation of 5HT2C splicing isoforms in PWS could contribute to the known hormonal imbalances.
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Affiliation(s)
- Justin R Welden
- Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40503, United States
| | - Zhaiyi Zhang
- Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40503, United States
| | - Marilyn J Duncan
- Dept. of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, United States
| | - Marina Falaleeva
- Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40503, United States
| | - Timothy Wells
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
| | - Stefan Stamm
- Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40503, United States.
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20
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Lykke-Andersen S, Ardal BK, Hollensen AK, Damgaard CK, Jensen TH. Box C/D snoRNP Autoregulation by a cis-Acting snoRNA in the NOP56 Pre-mRNA. Mol Cell 2018; 72:99-111.e5. [PMID: 30220559 DOI: 10.1016/j.molcel.2018.08.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/18/2018] [Accepted: 08/09/2018] [Indexed: 01/23/2023]
Abstract
Box C/D snoRNAs constitute a class of abundant noncoding RNAs that associate with common core proteins to form catalytic snoRNPs. Most of these operate in trans to assist the maturation of rRNAs by guiding and catalyzing the 2'-O-methylation of specific nucleotides. Here, we report that the human intron-hosted box C/D snoRNA snoRD86 acts in cis as a sensor and master switch controlling levels of the limiting snoRNP core protein NOP56, which is important for proper ribosome biogenesis. Our results support a model in which snoRD86 adopts different RNP conformations that dictate the usage of nearby alternative splice donors in the NOP56 pre-mRNA. Excess snoRNP core proteins prevent further production of NOP56 and instead trigger the generation of a cytoplasmic snoRD86-containing NOP56-derived lncRNA via the nonsense-mediated decay pathway. Our findings reveal a feedback mechanism based on RNA structure that controls the precise coordination between box C/D snoRNP core proteins and global snoRNA levels.
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Affiliation(s)
- Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark.
| | - Britt Kidmose Ardal
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark
| | - Anne Kruse Hollensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark
| | - Christian Kroun Damgaard
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark.
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21
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Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1465. [PMID: 29341429 PMCID: PMC5947564 DOI: 10.1002/wrna.1465] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms.
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Affiliation(s)
| | - Tom S. Smith
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | - Eneko Villenueva
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
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Molecular hypotheses to explain the shared pathways and underlying pathobiological causes in catatonia and in catatonic presentations in neuropsychiatric disorders. Med Hypotheses 2018. [DOI: 10.1016/j.mehy.2018.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Bratkovič T, Modic M, Camargo Ortega G, Drukker M, Rogelj B. Neuronal differentiation induces SNORD115 expression and is accompanied by post-transcriptional changes of serotonin receptor 2c mRNA. Sci Rep 2018; 8:5101. [PMID: 29572515 PMCID: PMC5865145 DOI: 10.1038/s41598-018-23293-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/09/2018] [Indexed: 12/13/2022] Open
Abstract
The serotonin neurotransmitter system is widespread in the brain and implicated in modulation of neuronal responses to other neurotransmitters. Among 14 serotonin receptor subtypes, 5-HT2cR plays a pivotal role in controlling neuronal network excitability. Serotonergic activity conveyed through receptor 5-HT2cR is regulated post-transcriptionally via two mechanisms, alternative splicing and A-to-I RNA editing. Brain-specific small nucleolar RNA SNORD115 harbours a phylogenetically conserved 18-nucleotide antisense element with perfect complementarity to the region of 5ht2c primary transcript that undergoes post-transcriptional changes. Previous 5ht2c minigene studies have implicated SNORD115 in fine-tuning of both post-transcriptional events. We monitored post-transcriptional changes of endogenous 5ht2c transcripts during neuronal differentiation. Both SNORD115 and 5ht2c were upregulated upon neuronal commitment. We detected increased 5ht2c alternative exon Vb inclusion already at the stage of neuronal progenitors, and more extensive A-to-I editing of non-targeted sites A and B compared to adjacent adenosines at sites E, C and D throughout differentiation. As the extent of editing is known to positively correlate with exon Vb usage while it reduces receptor functionality, our data support the model where SNORD115 directly promotes alternative exon inclusion without the requirement for conversion of key adenosines to inosines, thereby favouring production of full-length receptor isoforms with higher potency.
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Affiliation(s)
- Tomaž Bratkovič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Biology, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Miha Modic
- Institute of Stem Cell Research and the Induced Pluripotent Stem Cell Core Facility, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Germán Camargo Ortega
- Institute of Stem Cell Research and the Induced Pluripotent Stem Cell Core Facility, Helmholtz Center Munich, 85764, Neuherberg, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilian University Munich, Munich, Germany
| | - Micha Drukker
- Institute of Stem Cell Research and the Induced Pluripotent Stem Cell Core Facility, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Boris Rogelj
- Jozef Stefan Institute, Department of Biotechnology, Jamova 39, 1000, Ljubljana, Slovenia. .,Biomedical Research Institute BRIS, Puhova 10, 1000, Ljubljana, Slovenia. .,University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000, Ljubljana, Slovenia.
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Stamm S, Gruber SB, Rabchevsky AG, Emeson RB. The activity of the serotonin receptor 2C is regulated by alternative splicing. Hum Genet 2017; 136:1079-1091. [PMID: 28664341 PMCID: PMC5873585 DOI: 10.1007/s00439-017-1826-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/17/2017] [Indexed: 01/28/2023]
Abstract
The central nervous system-specific serotonin receptor 2C (5HT2C) controls key physiological functions, such as food intake, anxiety, and motoneuron activity. Its deregulation is involved in depression, suicidal behavior, and spasticity, making it the target for antipsychotic drugs, appetite controlling substances, and possibly anti-spasm agents. Through alternative pre-mRNA splicing and RNA editing, the 5HT2C gene generates at least 33 mRNA isoforms encoding 25 proteins. The 5HT2C is a G-protein coupled receptor that signals through phospholipase C, influencing the expression of immediate/early genes like c-fos. Most 5HT2C isoforms show constitutive activity, i.e., signal without ligand binding. The constitutive activity of 5HT2C is decreased by pre-mRNA editing as well as alternative pre-mRNA splicing, which generates a truncated isoform that switches off 5HT2C receptor activity through heterodimerization; showing that RNA processing regulates the constitutive activity of the 5HT2C system. RNA processing events influencing the constitutive activity target exon Vb that forms a stable double stranded RNA structure with its downstream intron. This structure can be targeted by small molecules and oligonucleotides that change exon Vb alternative splicing and influence 5HT2C signaling in mouse models, leading to a reduction in food intake. Thus, the 5HT2C system is a candidate for RNA therapy in multiple models of CNS disorders.
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Affiliation(s)
- Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.
| | - Samuel B Gruber
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Alexander G Rabchevsky
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA
| | - Ronald B Emeson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
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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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26
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Cavaillé J. Box C/D small nucleolar RNA genes and the Prader-Willi syndrome: a complex interplay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28296064 DOI: 10.1002/wrna.1417] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 12/22/2022]
Abstract
The nucleolus of mammalian cells contains hundreds of box C/D small nucleolar RNAs (SNORDs). Through their ability to base pair with ribosomal RNA precursors, most play important roles in the synthesis and/or activity of ribosomes, either by guiding sequence-specific 2'-O-methylations or by facilitating RNA folding and cleavages. A growing number of SNORD genes with elusive functions have been discovered recently. Intriguingly, the vast majority of them are located in two large, imprinted gene clusters at human chromosome region 15q11q13 (the SNURF-SNRPN domain) and at 14q32 (the DLK1-DIO3 domain) where they are expressed, respectively, only from the paternally and maternally inherited alleles. These placental mammal-specific SNORD genes have many features of the canonical SNORDs that guide 2'-O-methylations, yet they lack obvious complementarity with ribosomal RNAs and, surprisingly, they are processed from large, tandemly repeated genes expressed preferentially in the brain. This review summarizes our understanding of the biology of these peculiar SNORD genes, focusing particularly on SNORD115 and SNORD116 in the SNURF-SNRPN domain. It examines the growing evidence that altered levels of these SNORDs and/or their host-gene transcripts may be a primary cause of Prader-Willi syndrome (PWS; a rare disorder characterized by overeating and obesity) as well as abnormalities in signaling through the 5-HT2C serotonin receptor. Finally, the hypothesis that PWS may be a ribosomopathy (ribosomal disease) is also discussed. WIREs RNA 2017, 8:e1417. doi: 10.1002/wrna.1417 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jérôme Cavaillé
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse; UPS and CNRS, LMBE, Toulouse, France
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Jazurek M, Ciesiolka A, Starega-Roslan J, Bilinska K, Krzyzosiak WJ. Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases. Nucleic Acids Res 2016; 44:9050-9070. [PMID: 27625393 PMCID: PMC5100574 DOI: 10.1093/nar/gkw803] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/01/2016] [Indexed: 12/11/2022] Open
Abstract
RNA–protein complexes play a central role in the regulation of fundamental cellular processes, such as mRNA splicing, localization, translation and degradation. The misregulation of these interactions can cause a variety of human diseases, including cancer and neurodegenerative disorders. Recently, many strategies have been developed to comprehensively analyze these complex and highly dynamic RNA–protein networks. Extensive efforts have been made to purify in vivo-assembled RNA–protein complexes. In this review, we focused on commonly used RNA-centric approaches that involve mass spectrometry, which are powerful tools for identifying proteins bound to a given RNA. We present various RNA capture strategies that primarily depend on whether the RNA of interest is modified. Moreover, we briefly discuss the advantages and limitations of in vitro and in vivo approaches. Furthermore, we describe recent advances in quantitative proteomics as well as the methods that are most commonly used to validate robust mass spectrometry data. Finally, we present approaches that have successfully identified expanded repeat-binding proteins, which present abnormal RNA–protein interactions that result in the development of many neurological diseases.
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Affiliation(s)
- Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julia Starega-Roslan
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Bilinska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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28
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C/D-box snoRNA-derived RNA production is associated with malignant transformation and metastatic progression in prostate cancer. Oncotarget 2016; 6:17430-44. [PMID: 26041889 PMCID: PMC4627319 DOI: 10.18632/oncotarget.4172] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/02/2015] [Indexed: 12/14/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are dynamically regulated in different tissues and affected in disease. SnoRNAs are processed further to stable smaller RNAs. We sequenced the small RNA transcriptome of prostate cancer (PCa) at different PCa stages and generated a quantified catalogue of 3927 small non-coding RNAs (sncRNAs) detected in normal and malignant prostate tissue. From these, only 1524 are microRNAs. The remaining 2401 sncRNAs represent stable sncRNAs species that originate from snoRNA, tRNA and other sncRNAs. We show that snoRNA-derived RNAs (sdRNAs) display stronger differential expression than microRNAs and are massively upregulated in PCa. SdRNAs account for at least one third of all small RNAs with expression changes in tumor compared to normal adjacent tissue. Multiple sdRNAs can be produced from one snoRNA in a manner related to the conservation of structural snoRNA motifs. Q-PCR analysis in an independent patient cohort (n=106) confirmed the processing patterns of selected snoRNAs (SNORD44, SNORD78, SNORD74 and SNORD81) and the cancer-associated up-regulation of their sdRNAs observed in sequencing data. Importantly, expression of SNORD78 and its sdRNA is significantly higher in a subset of patients that developed metastatic disease demonstrating that snoRNA and sdRNAs may present as novel diagnostic and/or prognostic biomarkers for PCa.
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29
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Zurla C, Jung J, Santangelo PJ. Can we observe changes in mRNA "state"? Overview of methods to study mRNA interactions with regulatory proteins relevant in cancer related processes. Analyst 2016; 141:548-62. [PMID: 26605378 PMCID: PMC4701657 DOI: 10.1039/c5an01959a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA binding proteins (RBP) regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNA) through their interactions with specific cis-acting elements within target RNAs. Post-transcriptional regulatory mechanisms are directly involved in the control of the immune response and stress response and their alterations play a crucial role in cancer related processes. In this review, we discuss mRNAs and RNA binding proteins relevant to tumorigenesis, current methodologies for detecting RNA interactions, and last, we describe a novel method to detect such interactions, which combines peptide modified, RNA imaging probes (FMTRIPs) with proximity ligation (PLA) and rolling circle amplification (RCA). This assay detects native RNA in a sequence specific and single RNA sensitive manner, and PLA allows for the quantification and localization of protein-mRNA interactions with single-interaction sensitivity in situ.
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Affiliation(s)
- C Zurla
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - J Jung
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - P J Santangelo
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
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30
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Stamova B, Ander BP, Barger N, Sharp FR, Schumann CM. Specific Regional and Age-Related Small Noncoding RNA Expression Patterns Within Superior Temporal Gyrus of Typical Human Brains Are Less Distinct in Autism Brains. J Child Neurol 2015; 30:1930-46. [PMID: 26350727 PMCID: PMC4647182 DOI: 10.1177/0883073815602067] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 07/28/2015] [Indexed: 12/16/2022]
Abstract
Small noncoding RNAs play a critical role in regulating messenger RNA throughout brain development and when altered could have profound effects leading to disorders such as autism spectrum disorders (ASD). We assessed small noncoding RNAs, including microRNA and small nucleolar RNA, in superior temporal sulcus association cortex and primary auditory cortex in typical and ASD brains from early childhood to adulthood. Typical small noncoding RNA expression profiles were less distinct in ASD, both between regions and changes with age. Typical micro-RNA coexpression associations were absent in ASD brains. miR-132, miR-103, and miR-320 micro-RNAs were dysregulated in ASD and have previously been associated with autism spectrum disorders. These diminished region- and age-related micro-RNA expression profiles are in line with previously reported findings of attenuated messenger RNA and long noncoding RNA in ASD brain. This study demonstrates alterations in superior temporal sulcus in ASD, a region implicated in social impairment, and is the first to demonstrate molecular alterations in the primary auditory cortex.
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Affiliation(s)
- Boryana Stamova
- Department of Neurology, University of California at Davis, MIND Institute, Sacramento, CA, USA
| | - Bradley P. Ander
- Department of Neurology, University of California at Davis, MIND Institute, Sacramento, CA, USA
| | - Nicole Barger
- Department of Psychiatry & Behavioral Sciences, University of California at Davis, MIND Institute, Sacramento, CA, USA
| | - Frank R. Sharp
- Department of Neurology, University of California at Davis, MIND Institute, Sacramento, CA, USA
| | - Cynthia M. Schumann
- Department of Psychiatry & Behavioral Sciences, University of California at Davis, MIND Institute, Sacramento, CA, USA,Cynthia M. Schumann, PhD, Departments of Psychiatry & Behavioral Sciences, University of California at Davis, MIND Institute, 2805 50th Street, Sacramento, CA 95817, USA.
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31
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Abstract
The loss of two gene clusters encoding small nucleolar RNAs, SNORD115 and SNORD116 contribute to Prader-Willi syndrome (PWS), the most common syndromic form of obesity in humans. SNORD115 and SNORD116 are considered to be orphan C/D box snoRNAs (SNORDs) as they do not target rRNAs or snRNAs. SNORD115 exhibits sequence complementarity towards the serotonin receptor 2C, but SNORD116 shows no extended complementarities to known RNAs. To identify molecular targets, we performed genome-wide array analysis after overexpressing SNORD115 and SNORD116 in HEK 293T cells, either alone or together. We found that SNORD116 changes the expression of over 200 genes. SNORD116 mainly changed mRNA expression levels. Surprisingly, we found that SNORD115 changes SNORD116's influence on gene expression. In similar experiments, we compared gene expression in post-mortem hypothalamus between individuals with PWS and aged-matched controls. The synopsis of these experiments resulted in 23 genes whose expression levels were influenced by SNORD116. Together our results indicate that SNORD115 and SNORD116 influence expression levels of multiple genes and modify each other activity.
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32
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Berger CM, Gaume X, Bouvet P. The roles of nucleolin subcellular localization in cancer. Biochimie 2015; 113:78-85. [PMID: 25866190 DOI: 10.1016/j.biochi.2015.03.023] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/29/2015] [Indexed: 01/10/2023]
Abstract
Nucleolin (NCL) is one of the most abundant non ribosomal protein of the nucleolus where it plays a central role in polymerase I transcription. NCL is also found outside of the nucleolus, in the nucleoplasm, cytoplasm as well as on the cell membrane. It acts in all cell compartments to control cellular homeostasis and therefore each cellular pool of NCL can play a different role in cancer development. NCL overexpression and its increased localization at the cell membrane is a common feature of several tumor cells. In cancer cells, NCL overexpression influences cell survival, proliferation and invasion through its action on different cellular pathways. In this review, we describe how the multiple functions of NCL that are associated to its multiple cellular localization can participate to the development of cancer.
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Affiliation(s)
- Caroline Madeleine Berger
- Département de Biologie, Master Biosciences, ENS de Lyon, Lyon, France; Ecole Normale Supérieure de Lyon, Laboratoire Joliot-Curie, CNRS USR 3010, 46 allée d'Italie, 69364 Lyon Cedex 7, France
| | - Xavier Gaume
- Ecole Normale Supérieure de Lyon, Laboratoire Joliot-Curie, CNRS USR 3010, 46 allée d'Italie, 69364 Lyon Cedex 7, France
| | - Philippe Bouvet
- Ecole Normale Supérieure de Lyon, Laboratoire Joliot-Curie, CNRS USR 3010, 46 allée d'Italie, 69364 Lyon Cedex 7, France.
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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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Abstract
RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. Genomes typically encode dozens to hundreds of proteins containing RNA-binding domains, which collectively recognize diverse RNA sequences and structures. Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as determination of RNA–protein interactions in living cells. In parallel, many computational methods have been developed to analyze and interpret these data. The interplay between RNA secondary structure and RBP binding has also been a growing theme. Integrating RNA–protein interaction data with observations of post-transcriptional regulation will enhance our understanding of the roles of these important proteins.
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35
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Faoro C, Ataide SF. Ribonomic approaches to study the RNA-binding proteome. FEBS Lett 2014; 588:3649-64. [PMID: 25150170 DOI: 10.1016/j.febslet.2014.07.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/04/2014] [Accepted: 07/04/2014] [Indexed: 01/23/2023]
Abstract
Gene expression is controlled through a complex interplay among mRNAs, non-coding RNAs and RNA-binding proteins (RBPs), which all assemble along with other RNA-associated factors in dynamic and functional ribonucleoprotein complexes (RNPs). To date, our understanding of RBPs is largely limited to proteins with known or predicted RNA-binding domains. However, various methods have been recently developed to capture an RNA of interest and comprehensively identify its associated RBPs. In this review, we discuss the RNA-affinity purification methods followed by mass spectrometry analysis (AP-MS); RBP screening within protein libraries and computational methods that can be used to study the RNA-binding proteome (RBPome).
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Affiliation(s)
- Camilla Faoro
- School of Molecular Biosciences, University of Sydney, NSW, Australia
| | - Sandro F Ataide
- School of Molecular Biosciences, University of Sydney, NSW, Australia.
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36
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Bratkovič T, Rogelj B. The many faces of small nucleolar RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:438-43. [PMID: 24735946 DOI: 10.1016/j.bbagrm.2014.04.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 12/15/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are a class of evolutionally conserved non-coding RNAs traditionally associated with nucleotide modifications in other RNA species. Acting as guides pairing with ribosomal (rRNA) and small nuclear RNAs (snRNAs), snoRNAs direct partner enzymes to specific sites for uridine isomerization or ribose methylation, thereby influencing stability, folding and protein-interacting properties of target RNAs. In recent years, however, numerous non-canonical functions have also been ascribed to certain members of the snoRNA group, ranging from regulation of mRNA editing and/or alternative splicing to posttranscriptional gene silencing by a yet poorly understood pathway that may involve microRNA-like mechanisms. While some of these intriguing snoRNAs (the so-called orphan snoRNAs) have no sequence complementarity to rRNA or snRNA, others apparently display dual functionality, performing both traditional and newly elucidated functions. Here, we review the effects elicited by non-canonical snoRNA activities.
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Affiliation(s)
- Tomaž Bratkovič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Biology, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
| | - Boris Rogelj
- Jozef Stefan Institute, Department of Biotechnology, Jamova 39, SI-1000 Ljubljana, Slovenia.
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37
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Kehr S, Bartschat S, Tafer H, Stadler PF, Hertel J. Matching of Soulmates: coevolution of snoRNAs and their targets. Mol Biol Evol 2013; 31:455-67. [PMID: 24162733 DOI: 10.1093/molbev/mst209] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ribosomal and small nuclear RNAs (snRNAs) comprise numerous modified nucleotides. The modification patterns are retained during evolution, making it even possible to project them from yeast onto human. The stringent conservation of modification sites and the slow evolution of rRNAs and snRNAs contradicts the rapid evolution of small nucleolar RNA (snoRNA) sequences. To explain this discrepancy, we investigated the coevolution of snoRNAs and their targeted sites throughout vertebrates. To measure and evaluate the conservation of RNA-RNA interactions, we defined the interaction conservation index (ICI). It combines the quality of individual interaction with the scope of its conservation in a set of species and serves as an efficient measure to evaluate the conservation of the interaction of snoRNA and target. We show that functions of homologous snoRNAs are evolutionarily stable, thus, members of the same snoRNA family guide equivalent modifications. The conservation of snoRNA sequences is high at target binding regions while the remaining sequence varies significantly. In addition to elucidating principles of correlated evolution, we were able, with the help of the ICI measure, to assign functions to previously orphan snoRNAs and to associate snoRNAs as partners to known chemical modifications unassigned to a given snoRNA. Furthermore, we used predictions of snoRNA functions in conjunction with sequence conservation to identify distant homologies. Because of the high overall entropy of snoRNA sequences, such relationships are hard to detect by means of sequence homology search methods alone.
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Affiliation(s)
- Stephanie Kehr
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
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Tacheny A, Dieu M, Arnould T, Renard P. Mass spectrometry-based identification of proteins interacting with nucleic acids. J Proteomics 2013; 94:89-109. [PMID: 24060998 DOI: 10.1016/j.jprot.2013.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/19/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023]
Abstract
The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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Falaleeva M, Sulsona CR, Zielke HR, Currey KM, de la Grange P, Aslanzadeh V, Driscoll DJ, Stamm S. Molecular characterization of a patient presumed to have prader-willi syndrome. CLINICAL MEDICINE INSIGHTS-CASE REPORTS 2013; 6:79-86. [PMID: 23700380 PMCID: PMC3656643 DOI: 10.4137/ccrep.s11510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Prader-Willi syndrome (PWS) is caused by the loss of RNA expression from an imprinted region on chromosome 15 that includes SNRPN, SNORD115, and SNORD116. Currently, there are no mouse models that faithfully reflect the human phenotype and investigations rely on human post-mortem material. During molecular characterization of tissue deposited in a public brain bank from a patient diagnosed with Prader-Willi syndrome, we found RNA expression from SNRPN, SNORD115, and SNORD116 which does not support a genetic diagnosis of Prader-Willi syndrome. The patient was a female, Caucasian nursing home resident with history of morbid obesity (BMI 56.3) and mental retardation. She died at age of 56 from pulmonary embolism. SNORD115 and SNORD116 are unexpectedly stable in post mortem tissue and can be used for post-mortem diagnosis. Molecular characterization of PWS tissue donors can confirm the diagnosis and identify those patients that have been misdiagnosed.
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Affiliation(s)
- Marina Falaleeva
- University of Kentucky, Department of Molecular and Cellular Biochemistry, South Limestone, Lexington, KY
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40
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Shen M, Bellaousov S, Hiller M, de La Grange P, Creamer TP, Malina O, Sperling R, Mathews DH, Stoilov P, Stamm S. Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure. Nucleic Acids Res 2013; 41:3819-32. [PMID: 23393189 PMCID: PMC3616728 DOI: 10.1093/nar/gkt063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/08/2013] [Accepted: 01/15/2013] [Indexed: 01/17/2023] Open
Abstract
The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2'-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5'-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A-U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch.
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MESH Headings
- Alternative Splicing/drug effects
- Base Sequence
- Exons
- HEK293 Cells
- High-Throughput Screening Assays
- Humans
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Pyrvinium Compounds/metabolism
- Pyrvinium Compounds/pharmacology
- RNA Editing
- RNA Precursors/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/drug effects
- RNA, Messenger/chemistry
- RNA, Messenger/drug effects
- RNA, Messenger/metabolism
- Receptor, Serotonin, 5-HT2C/genetics
- Receptor, Serotonin, 5-HT2C/metabolism
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Spliceosomes/metabolism
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Affiliation(s)
- Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Stanislav Bellaousov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Michael Hiller
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Pierre de La Grange
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Trevor P. Creamer
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Orit Malina
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Ruth Sperling
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - David H. Mathews
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Peter Stoilov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
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Falaleeva M, Stamm S. Processing of snoRNAs as a new source of regulatory non-coding RNAs: snoRNA fragments form a new class of functional RNAs. Bioessays 2012. [PMID: 23180440 DOI: 10.1002/bies.201200117] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recent experimental evidence suggests that most of the genome is transcribed into non-coding RNAs. The initial transcripts undergo further processing generating shorter, metabolically stable RNAs with diverse functions. Small nucleolar RNAs (snoRNAs) are non-coding RNAs that modify rRNAs, tRNAs, and snRNAs that were considered stable. We review evidence that snoRNAs undergo further processing. High-throughput sequencing and RNase protection experiments showed widespread expression of snoRNA fragments, known as snoRNA-derived RNAs (sdRNAs). Some sdRNAs resemble miRNAs, these can associate with argonaute proteins and influence translation. Other sdRNAs are longer, form complexes with hnRNPs and influence gene expression. C/D box snoRNA fragmentation patterns are conserved across multiple cell types, suggesting a processing event, rather than degradation. The loss of expression from genetic loci that generate canonical snoRNAs and processed snoRNAs results in diseases, such as Prader-Willi Syndrome, indicating possible physiological roles for processed snoRNAs. We propose that processed snoRNAs acquire new roles in gene expression and represent a new class of regulatory RNAs distinct from canonical snoRNAs.
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Affiliation(s)
- Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, KY, USA
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42
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Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci 2012; 13:528-41. [PMID: 22814587 DOI: 10.1038/nrn3234] [Citation(s) in RCA: 420] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel classes of small and long non-coding RNAs (ncRNAs) are being characterized at a rapid pace, driven by recent paradigm shifts in our understanding of genomic architecture, regulation and transcriptional output, as well as by innovations in sequencing technologies and computational and systems biology. These ncRNAs can interact with DNA, RNA and protein molecules; engage in diverse structural, functional and regulatory activities; and have roles in nuclear organization and transcriptional, post-transcriptional and epigenetic processes. This expanding inventory of ncRNAs is implicated in mediating a broad spectrum of processes including brain evolution, development, synaptic plasticity and disease pathogenesis.
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43
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Khanna A, Stamm S. Regulation of alternative splicing by short non-coding nuclear RNAs. RNA Biol 2010; 7:480-5. [PMID: 20657181 DOI: 10.4161/rna.7.4.12746] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recent results from deep-sequencing and tiling array studies indicated the existence of a large number of short, metabolically stable, non-coding RNAs. Some of these short RNAs derive from known RNA classes like snoRNA or tRNAs. There are intriguing similarities between short non-coding nuclear RNAs and oligonucleotides used to change alternative splicing events, which usually target a disease-relevant RNA. We review the current knowledge of this emerging class of RNAs and discuss evidence that some of these short RNAs could function in alternative splice site selection.
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Affiliation(s)
- Amit Khanna
- University of Kentucky, Molecular and Cellular Biochemistry, South Limestone, Lexington, KY, USA
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