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Moore AN, McWatters DC, Hudson AJ, Russell AG. RNA-Seq employing a novel rRNA depletion strategy reveals a rich repertoire of snoRNAs in Euglena gracilis including box C/D and Ψ-guide RNAs targeting the modification of rRNA extremities. RNA Biol 2018; 15:1309-1318. [PMID: 30252600 PMCID: PMC6284569 DOI: 10.1080/15476286.2018.1526561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/21/2018] [Accepted: 09/16/2018] [Indexed: 01/06/2023] Open
Abstract
Previous mRNA transcriptome studies of Euglena gracilis have shown that this organism possesses a large and diverse complement of protein coding genes; however, the study of non-coding RNA classes has been limited. The natural extensive fragmentation of the E. gracilis large subunit ribosomal RNA presents additional barriers to the identification of non-coding RNAs as size-selected small RNA libraries will be dominated by rRNA sequences. In this study we have developed a strategy to significantly reduce rRNA amplification prior to RNA-Seq analysis thereby producing a ncRNA library allowing for the identification of many new E. gracilis small RNAs. Library analysis reveals 113 unique new small nucleolar (sno) RNAs and a large collection of snoRNA isoforms, as well as the first significant collection of nuclear tRNAs in this organism. A 3' end AGAUGN consensus motif and conserved structural features can now be defined for E. gracilis pseudouridine guide RNAs. snoRNAs of both classes were identified that target modification of the 3' extremities of rRNAs utilizing predicted base-pairing interactions with internally transcribed spacers (ITS), providing insight into the timing of steps in rRNA maturation. Cumulatively, this represents the most comprehensive analysis of small ncRNAs in Euglena gracilis to date.
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Affiliation(s)
- Ashley N. Moore
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - David C. McWatters
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Andrew J. Hudson
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Anthony G. Russell
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
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2
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Terns MP, Terns RM. Small nucleolar RNAs: versatile trans-acting molecules of ancient evolutionary origin. Gene Expr 2018; 10:17-39. [PMID: 11868985 PMCID: PMC5977530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The small nucleolar RNAs (snoRNAs) are an abundant class of trans-acting RNAs that function in ribosome biogenesis in the eukaryotic nucleolus. Elegant work has revealed that most known snoRNAs guide modification of pre-ribosomal RNA (pre-rRNA) by base pairing near target sites. Other snoRNAs are involved in cleavage of pre-rRNA by mechanisms that have not yet been detailed. Moreover, our appreciation of the cellular roles of the snoRNAs is expanding with new evidence that snoRNAs also target modification of small nuclear RNAs and messenger RNAs. Many snoRNAs are produced by unorthodox modes of biogenesis including salvage from introns of pre-mRNAs. The recent discovery that homologs of snoRNAs as well as associated proteins exist in the domain Archaea indicates that the RNA-guided RNA modification system is of ancient evolutionary origin. In addition, it has become clear that the RNA component of vertebrate telomerase (an enzyme implicated in cancer and cellular senescence) is related to snoRNAs. During its evolution, vertebrate telomerase RNA appears to have co-opted a snoRNA domain that is essential for the function of telomerase RNA in vivo. The unique properties of snoRNAs are now being harnessed for basic research and therapeutic applications.
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MESH Headings
- Animals
- Base Pairing
- Biological Transport
- Cell Nucleolus/metabolism
- Cell Nucleus/metabolism
- Eukaryotic Cells/metabolism
- Evolution, Molecular
- Methylation
- Prokaryotic Cells/metabolism
- Pseudouridine/metabolism
- RNA/metabolism
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Archaeal/genetics
- RNA, Archaeal/physiology
- RNA, Catalytic/metabolism
- RNA, Messenger/metabolism
- RNA, Ribosomal/biosynthesis
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/classification
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Small Nucleolar/physiology
- Ribonucleoproteins, Small Nucleolar/metabolism
- Ribosomes/metabolism
- Species Specificity
- Structure-Activity Relationship
- Telomerase/metabolism
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Affiliation(s)
- Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens 30602, USA.
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Pagès A, Dotu I, Pallarès-Albanell J, Martí E, Guigó R, Eyras E. The discovery potential of RNA processing profiles. Nucleic Acids Res 2018; 46:e15. [PMID: 29155959 PMCID: PMC5814818 DOI: 10.1093/nar/gkx1115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
Small non-coding RNAs (sncRNAs) are highly abundant molecules that regulate essential cellular processes and are classified according to sequence and structure. Here we argue that read profiles from size-selected RNA sequencing capture the post-transcriptional processing specific to each RNA family, thereby providing functional information independently of sequence and structure. We developed SeRPeNT, a new computational method that exploits reproducibility across replicates and uses dynamic time-warping and density-based clustering algorithms to identify, characterize and compare sncRNAs by harnessing the power of read profiles. We applied SeRPeNT to: (i) generate an extended human annotation with 671 new sncRNAs from known classes and 131 from new potential classes, (ii) show pervasive differential processing of sncRNAs between cell compartments and (iii) predict new molecules with miRNA-like behaviour from snoRNA, tRNA and long non-coding RNA precursors, potentially dependent on the miRNA biogenesis pathway. Furthermore, we validated experimentally four predicted novel non-coding RNAs: a miRNA, a snoRNA-derived miRNA, a processed tRNA and a new uncharacterized sncRNA. SeRPeNT facilitates fast and accurate discovery and characterization of sncRNAs at an unprecedented scale. SeRPeNT code is available under the MIT license at https://github.com/comprna/SeRPeNT.
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Affiliation(s)
- Amadís Pagès
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Ivan Dotu
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- IMIM—Hospital del Mar Medical Research Institute, E08003 Barcelona, Spain
| | - Joan Pallarès-Albanell
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Eulàlia Martí
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Roderic Guigó
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E08003 Barcelona, Spain
| | - Eduardo Eyras
- Pompeu Fabra University (UPF), E08003 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), E08010 Barcelona, Spain
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4
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Venkatesh T, Suresh PS, Tsutsumi R. Non-coding RNAs: Functions and applications in endocrine-related cancer. Mol Cell Endocrinol 2015; 416:88-96. [PMID: 26360585 DOI: 10.1016/j.mce.2015.08.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 01/25/2023]
Abstract
A significant fraction of the human genome is transcribed as non-coding RNAs (ncRNAs). This non-coding transcriptome has challenged the notion of the central dogma and its involvement in transcriptional and post-transcriptional regulation of gene expression is well established. Interestingly, several ncRNAs are dysregulated in cancer and current non-coding transcriptome research aims to use our increasing knowledge of these ncRNAs for the development of cancer biomarkers and anti-cancer drugs. In endocrine-related cancers, for which survival rates can be relatively low, there is a need for such advancements. In this review, we aimed to summarize the roles and clinical implications of recently discovered ncRNAs, including long ncRNAs, PIWI-interacting RNAs, tRNA- and Y RNA-derived ncRNAs, and small nucleolar RNAs, in endocrine-related cancers affecting both sexes. We focus on recent studies highlighting discoveries in ncRNA biology and expression in cancer, and conclude with a discussion on the challenges and future directions, including clinical application. ncRNAs show great promise as diagnostic tools and therapeutic targets, but further work is necessary to realize the potential of these unconventional transcripts.
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MESH Headings
- Biomarkers, Tumor/classification
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Endocrine Gland Neoplasms/genetics
- Endocrine Gland Neoplasms/metabolism
- Endocrine Gland Neoplasms/therapy
- Female
- Gene Expression Regulation
- Humans
- Male
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Small Nucleolar/classification
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Transcriptome
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Affiliation(s)
- Thejaswini Venkatesh
- Nitte University Centre for Science Education and Research (NUCSER), Nitte University, Deralakatte, Mangalore 575 018, Karnataka, India
| | - Padmanaban S Suresh
- Department of Biosciences, Mangalore University, Mangalagangothri, Mangalore 574 199, Karnataka, India.
| | - Rie Tsutsumi
- Division of Nutrition and Metabolism, Institute of Biomedical Science, Tokushima University, Tokushima, Japan
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5
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Deschamps-Francoeur G, Garneau D, Dupuis-Sandoval F, Roy A, Frappier M, Catala M, Couture S, Barbe-Marcoux M, Abou-Elela S, Scott MS. Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency. Nucleic Acids Res 2014; 42:10073-85. [PMID: 25074380 PMCID: PMC4150776 DOI: 10.1093/nar/gku664] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are among the first discovered and most extensively studied group of small non-coding RNA. However, most studies focused on a small subset of snoRNAs that guide the modification of ribosomal RNA. In this study, we annotated the expression pattern of all box C/D snoRNAs in normal and cancer cell lines independent of their functions. The results indicate that C/D snoRNAs are expressed as two distinct forms differing in their ends with respect to boxes C and D and in their terminal stem length. Both forms are overexpressed in cancer cell lines but display a conserved end distribution. Surprisingly, the long forms are more dependent than the short forms on the expression of the core snoRNP protein NOP58, thought to be essential for C/D snoRNA production. In contrast, a subset of short forms are dependent on the splicing factor RBFOX2. Analysis of the potential secondary structure of both forms indicates that the k-turn motif required for binding of NOP58 is less stable in short forms which are thus less likely to mature into a canonical snoRNP. Taken together the data suggest that C/D snoRNAs are divided into at least two groups with distinct maturation and functional preferences.
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Affiliation(s)
- Gabrielle Deschamps-Francoeur
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Daniel Garneau
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Fabien Dupuis-Sandoval
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Audrey Roy
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Marie Frappier
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Mathieu Catala
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sonia Couture
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Mélissa Barbe-Marcoux
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou-Elela
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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6
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Soeno Y, Fujita K, Kudo T, Asagiri M, Kakuta S, Taya Y, Shimazu Y, Sato K, Tanaka-Fujita R, Kubo S, Iwakura Y, Nakamura Y, Mori S, Aoba T. Generation of a mouse model with down-regulated U50 snoRNA (SNORD50) expression and its organ-specific phenotypic modulation. PLoS One 2013; 8:e72105. [PMID: 23991050 PMCID: PMC3753356 DOI: 10.1371/journal.pone.0072105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 07/07/2013] [Indexed: 11/21/2022] Open
Abstract
Box C/D-type small nucleolar RNAs (snoRNAs) are functional RNAs responsible for mediating 2'-O-ribose methylation of ribosomal RNAs (rRNAs) within the nucleolus. In the past years, evidence for the involvement of human U50 snoRNA in tumorigenesis has been accumulating. We previously identified U50HG, a non-protein-coding gene that hosted a box C/D-type U50 snoRNA, in a chromosomal breakpoint in a human B-cell lymphoma. Mouse genome analysis revealed four mouse U50 (mU50) host-genes: three mU50HG-a gene variants that were clustered in the genome and an mU50HG-b gene that we supposed to be the U50HG ortholog. In this study, to investigate the physiological importance of mU50 snoRNA and its involvement in tumorigenesis, we eliminated mU50 snoRNA sequences from the mU50HG-b gene. The established mouse line (ΔmU50(HG-b)) showed a significant reduction of mU50 snoRNA expression without alteration of the host-gene length and exon-intron structure, and the corresponding target rRNA methylation in various organs was reduced. Lifelong phenotypic monitoring showed that the ΔmU50(HG-b) mice looked almost normal without accelerated tumorigenicity; however, a notable difference was the propensity for anomalies in the lymphoid organs. Transcriptome analysis showed that dozens of genes, including heat shock proteins, were differentially expressed in ΔmU50(HG-b) mouse lymphocytes. This unique model of a single snoRNA knockdown with intact host-gene expression revealed further new insights into the discrete transcriptional regulation of multiple mU50 host-genes and the complicated dynamics involved in organ-specific processing and maintenance of snoRNAs.
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Affiliation(s)
- Yuuichi Soeno
- Department of Pathology, School of Life Dentistry, The Nippon Dental University, Tokyo, Japan
| | - Kazuya Fujita
- Department of Pathology, School of Life Dentistry, The Nippon Dental University, Tokyo, Japan
| | - Tomoo Kudo
- Department of Pathology, Hyogo College of Medicine, Hyogo, Japan
| | - Masataka Asagiri
- Innovation Center for Immunoregulation and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigeru Kakuta
- Department of Biomedical Science, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yuji Taya
- Department of Pathology, School of Life Dentistry, The Nippon Dental University, Tokyo, Japan
| | - Yoshihito Shimazu
- Department of Pathology, School of Life Dentistry, The Nippon Dental University, Tokyo, Japan
| | - Kaori Sato
- Department of Pathology, School of Life Dentistry, The Nippon Dental University, Tokyo, Japan
| | - Ritsuko Tanaka-Fujita
- Risk Assessment Division, Food Safety Commission Secretariat, Cabinet Office, Government of Japan, Tokyo, Japan
| | - Sachiko Kubo
- Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Division of Experimental Animal Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yoichiro Iwakura
- Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Division of Experimental Animal Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yoshikazu Nakamura
- Division of RNA Medical Science, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Ribomic Inc., Tokyo, Japan
| | - Shigeo Mori
- Kotobiken Medical Laboratories Inc., Tokyo, Japan
| | - Takaaki Aoba
- Department of Pathology, School of Life Dentistry, The Nippon Dental University, Tokyo, Japan
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7
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Goyal RK, Kumar V, Shukla V, Mattoo R, Liu Y, Chung SH, Giovannoni JJ, Mattoo AK. Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum). Planta 2012; 235:453-71. [PMID: 21947620 DOI: 10.1007/s00425-011-1518-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 09/05/2011] [Indexed: 05/03/2023]
Abstract
Physical clustering of genes has been shown in plants; however, little is known about gene clusters that have different functions, particularly those expressed in the tomato fruit. A class I 17.6 small heat shock protein (Sl17.6 shsp) gene was cloned and used as a probe to screen a tomato (Solanum lycopersicum) genomic library. An 8.3-kb genomic fragment was isolated and its DNA sequence determined. Analysis of the genomic fragment identified intronless open reading frames of three class I shsp genes (Sl17.6, Sl20.0, and Sl20.1), the Sl17.6 gene flanked by Sl20.1 and Sl20.0, with complete 5' and 3' UTRs. Upstream of the Sl20.0 shsp, and within the shsp gene cluster, resides a box C/D snoRNA cluster made of SlsnoR12.1 and SlU24a. Characteristic C and D, and C' and D', boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box 1, homol-E and homol-D box-like cis sequences, TM6 promoter, and an uncharacterized tomato EST. Molecular phylogenetic analysis revealed that this particular arrangement of shsps is conserved in tomato genome but is distinct from other species. The intronless genomic sequence is decorated with cis elements previously shown to be responsive to cues from plant hormones, dehydration, cold, heat, and MYC/MYB and WRKY71 transcription factors. Chromosomal mapping localized the tomato genomic sequence on the short arm of chromosome 6 in the introgression line (IL) 6-3. Quantitative polymerase chain reaction analysis of gene cluster members revealed differential expression during ripening of tomato fruit, and relatively different abundances in other plant parts.
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Affiliation(s)
- Ravinder K Goyal
- US Department of Agriculture, The Henry A. Wallace Beltsville Agricultural Research Center, Agriculture Research Service, Beltsville, MD 20705-2350, USA
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8
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Wang PPS, Ruvinsky I. Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes. RNA 2010; 16:290-298. [PMID: 20038629 PMCID: PMC2811658 DOI: 10.1261/rna.1876210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 10/27/2009] [Indexed: 05/28/2023]
Abstract
Identification of small nucleolar RNAs (snoRNAs) in genomic sequences has been challenging due to the relative paucity of sequence features. Many current prediction algorithms rely on detection of snoRNA motifs complementary to target sites in snRNAs and rRNAs. However, recent discovery of snoRNAs without apparent targets requires development of alternative prediction methods. We present an approach that combines rule-based filters and a Bayesian Classifier to identify a class of snoRNAs (H/ACA) without requiring target sequence information. It takes advantage of unique attributes of their genomic organization and improved species-specific motif characterization to predict snoRNAs that may otherwise be difficult to discover. Searches in the genomes of Caenorhabditis elegans and the closely related Caenorhabditis briggsae suggest that our method performs well compared to recent benchmark algorithms. Our results illustrate the benefits of training gene discovery engines on features restricted to particular phylogenetic groups and the utility of incorporating diverse data types in gene prediction.
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Affiliation(s)
- Paul Po-Shen Wang
- Department of Ecology and Evolution , University of Chicago, Chicago, Illinois 60637, USA
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9
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Langenberger D, Bermudez-Santana CI, Stadler PF, Hoffmann S. Identification and classification of small RNAs in transcriptome sequence data. Pac Symp Biocomput 2010:80-7. [PMID: 19908360 DOI: 10.1142/9789814295291_0010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Current methods for high throughput sequencing (HTS) for the first time offer the opportunity to investigate the entire transcriptome in an essentially unbiased way. In many species, small non-coding RNAs with specific secondary structures constitute a significant part of the transcriptome. Some of these RNA classes, in particular microRNAs and snoRNAs, undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome specific patterns of short reads can be observed. These read patterns seem to reflect the processing and thus are specific for the RNA transcripts of which they are derived from. We explore here the potential of short read sequence data in the classification and identification of non-coding RNAs.
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Affiliation(s)
- D Langenberger
- University Leipzig, Interdisciplinary Center for Bioinformatics, Haertelstrasse 16-18, D-04107 Leipzig, Germany
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10
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Liu N, Xiao ZD, Yu CH, Shao P, Liang YT, Guan DG, Yang JH, Chen CL, Qu LH, Zhou H. SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights. BMC Genomics 2009; 10:515. [PMID: 19895704 PMCID: PMC2780460 DOI: 10.1186/1471-2164-10-515] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 11/08/2009] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND SnoRNAs represent an excellent model for studying the structural and functional evolution of small non-coding RNAs involved in the post-transcriptional modification machinery for rRNAs and snRNAs in eukaryotic cells. Identification of snoRNAs from Neurospora crassa, an important model organism playing key roles in the development of modern genetics, biochemistry and molecular biology will provide insights into the evolution of snoRNA genes in the fungus kingdom. RESULTS Fifty five box C/D snoRNAs were identified and predicted to guide 71 2'-O-methylated sites including four sites on snRNAs and three sites on tRNAs. Additionally, twenty box H/ACA snoRNAs, which potentially guide 17 pseudouridylations on rRNAs, were also identified. Although not exhaustive, the study provides the first comprehensive list of two major families of snoRNAs from the filamentous fungus N. crassa. The independently transcribed strategy dominates in the expression of box H/ACA snoRNA genes, whereas most of the box C/D snoRNA genes are intron-encoded. This shows that different genomic organizations and expression modes have been adopted by the two major classes of snoRNA genes in N. crassa . Remarkably, five gene clusters represent an outstanding organization of box C/D snoRNA genes, which are well conserved among yeasts and multicellular fungi, implying their functional importance for the fungus cells. Interestingly, alternative splicing events were found in the expression of two polycistronic snoRNA gene hosts that resemble the UHG-like genes in mammals. Phylogenetic analysis further revealed that the extensive separation and recombination of two functional elements of snoRNA genes has occurred during fungus evolution. CONCLUSION This is the first genome-wide analysis of the filamentous fungus N. crassa snoRNAs that aids in understanding the differences between unicellular fungi and multicellular fungi. As compared with two yeasts, a more complex pattern of methylation guided by box C/D snoRNAs in multicellular fungus than in unicellular yeasts was revealed, indicating the high diversity of post-transcriptional modification guided by snoRNAs in the fungus kingdom.
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Affiliation(s)
- Na Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhen-Dong Xiao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chun-Hong Yu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Peng Shao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yin-Tong Liang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Dao-Gang Guan
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chun-Long Chen
- Centre National de la Recherche Scientifique (CNRS), UPR 2167, CGM, Gif sur Yvette, 91198, France
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Hui Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
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Makarova IA, Kramerov DA. [Small nucleolar RNAs]. Mol Biol (Mosk) 2007; 41:246-59. [PMID: 17514894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are an abundant class of non-protein-coding RNAs. In association with proteins they perform two most frequent nucleotide modifications in rRNAs and some other cellular RNAs: 2'-O-ribose methylation and pseudouridylation. SnoRNAs also participate in pre-rRNA cleavage and telomerase functions. Most snoRNAs fall into two families, box C/D and H/ACA, distinguished by the presence of conserved sequence boxes. Although C/D and H/ACA snoRNP proteins contain homologous regions, the assembly of these RNPs significantly differ. In addition, snoRNAs include the RNA component of RNAses P and MRP. The structure and function of small RNPs from Cajal bodies (small organelles associated with nucleoli) similar to snoRNP are also discussed.
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Abstract
In contrast to mRNAs, which are templates for translating proteins, non-protein coding (npc) RNAs (also known as ‘non-coding’ RNA, ncRNA), exhibit various functions in different compartments and developmental stages of the cell. Small nucleolar RNAs (snoRNAs), one of the largest classes of npcRNAs, guide post-transcriptional modifications of other RNAs that are crucial for appropriate RNA folding as well as for RNA–RNA and RNA–protein interactions. Although snoRNA genes comprise a significant fraction of the eutherian genome, identifying and characterizing large numbers of them is not sufficiently accessible by classical computer searches alone. Furthermore, most previous investigations of snoRNAs yielded only limited indications of their evolution. Using data obtained by a combination of high-throughput cDNA library screening and computational search strategies based on a modified DNAMAN program, we characterized 151 npcRNAs, and in particular 121 snoRNAs, from Caenorhabditis elegans and extensively compared them with those in the related, Caenorhabditis briggsae. Detailed comparisons of paralog snoRNAs in the two nematodes revealed, in addition to trans-duplication, a novel, cis-duplication distribution strategy with insertions near to the original loci. Some snoRNAs coevolved with their modification target sites, demonstrating the close interaction of complementary regions. Some target sites modified by snoRNAs were changed, added or lost, documenting a high degree of evolutionary plasticity of npcRNAs.
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MESH Headings
- Animals
- Caenorhabditis/genetics
- Caenorhabditis elegans/genetics
- Computational Biology
- Evolution, Molecular
- Gene Duplication
- Gene Library
- Phylogeny
- RNA, Helminth/chemistry
- RNA, Helminth/classification
- RNA, Helminth/genetics
- RNA, Ribosomal/chemistry
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/classification
- RNA, Small Nucleolar/genetics
- RNA, Untranslated/classification
- RNA, Untranslated/genetics
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Affiliation(s)
- Anja Zemann
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
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Abstract
Small non-messenger RNAs (snmRNAs) are a heterogeneous group of non-coding RNAs with a variety of regulatory functions including regulation of protein expression and guidance in RNA modifications. They are actively being investigated in Archaebacteria, yeast, invertebrates and mammals. Brain-specific snmRNAs have been identified in mammals and they seem to contribute to neuronal differentiation during development and to brain functions subserving learning and memory. Here we review the current knowledge of the properties, expression and functions of three groups of brain-specific snmRNAs: small nucleolar RNAs, BC1/BC200 RNAs and microRNAs.
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Affiliation(s)
- Boris Rogelj
- Department of Neuroscience, Institute of Psychiatry, King's College London, UK.
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Abstract
MOTIVATION Noncoding RNA genes produce functional RNA molecules rather than coding for proteins. One such family is the H/ACA snoRNAs. Unlike the related C/D snoRNAs these have resisted automated detection to date. RESULTS We develop an algorithm to screen the yeast genome for novel H/ACA snoRNAs. To achieve this, we introduce some new methods for facilitating the search for noncoding RNAs in genomic sequences which are based on properties of predicted minimum free-energy (MFE) secondary structures. The algorithm has been implemented and can be generalized to enable screening of other eukaryote genomes. We find that use of primary sequence alone is insufficient for identifying novel H/ACA snoRNAs. Only the use of secondary structure filters reduces the number of candidates to a manageable size. From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened.
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Affiliation(s)
- Sverker Edvardsson
- Department of Information Technology, Mid Sweden University, S-851 70, Sundsvall, Sweden
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Barneche F, Gaspin C, Guyot R, Echeverría M. Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2'-O-methylation sites. J Mol Biol 2001; 311:57-73. [PMID: 11469857 DOI: 10.1006/jmbi.2001.4851] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dozens of box C/D small nucleolar RNAs (snoRNAs) have recently been found in eukaryotes (vertebrates, yeast), ancient eukaryotes (trypanosomes) and archae, that specifically target ribosomal RNA sites for 2'-O-ribose methylation. Although early biochemical data revealed that plant rRNAs are among the most highly ribomethylated in eukaryotes, only a handful of methylation guide snoRNAs have been characterized in this kingdom. We report 66 novel box C/D snoRNAs identified by computational screening of Arabidopsis genomic sequences that are expressed in vivo from either single genes, 17 different clusters or three introns. At the structural level, many box C/D snoRNAs have dual antisense elements often matching rRNA regions close to each other on the rRNA secondary structure, which is reminiscent of their archaeal counterparts. Remarkable specimens are found that display two antisense elements having the potential to form an extended snoRNA-rRNA duplex of 23 to 30 nt, in line with the hypothetical function of box C/D snoRNAs in pre-rRNA folding or chaperoning. In contrast to other species, many Arabidopsis snoRNAs are found in multiple isoforms mainly resulting from two different mechanisms: large chromosomal duplications and small tandem duplications producing polycistronic genes. The discovery of numerous different snoRNAs, some of them arising from common ancestors, provide new insights to understand snoRNAs evolution and the birth of new rRNA methylation sites in plants and other organisms.
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MESH Headings
- Arabidopsis/genetics
- Base Sequence
- Chromosomes/genetics
- Computational Biology
- Evolution, Molecular
- Gene Duplication
- Genes, Duplicate/genetics
- Genes, Plant/genetics
- Genetic Variation/genetics
- Methylation
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Antisense/chemistry
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/classification
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Ribose/chemistry
- Ribose/metabolism
- Ribosomal Proteins/metabolism
- Tandem Repeat Sequences/genetics
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Affiliation(s)
- F Barneche
- Laboratoire Génome et Développement des Plantes, Université de Perpignan, UMR CNRS 5096, 52 Avenue de Villeneuve, Perpignan Cedex, 66860, France
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Affiliation(s)
- W Filipowicz
- Friedrich Miescher Institute, P.O. Box 2543, CH-4002 Basel, Switzerland.
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