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Karaca M, Ince AG. Grafting based DNA methylation alteration of snoRNAs in upland cotton ( Gossypium L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:893-907. [PMID: 38974361 PMCID: PMC11222342 DOI: 10.1007/s12298-024-01469-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 07/09/2024]
Abstract
The effects of grafting in response to various biotic and abiotic stressors have been studied, however, the methylation status of small nucleolar RNA (snoRNA) genes in heterograft and homograft cotton needs investigation. This study was undertaken to determine grafting effects on DNA methylation of snoRNA genes in Upland cotton. Rootstocks used were Pima 3-79 (Gossypium barbadense acc. Pima 3-79) and Texas Marker-1 (G. hirsutum acc. TM-1), representing two different species with different fiber properties, adaptations, and morphologies. The methylation ratio and differently methylated cytosines (DMCs) of 10935 snoRNA genes in mature seeds of heterograft and homograft cotton samples were studied using the whole genome bisulfite sequencing method. Seedling vigor and seed weight were studied to investigate phenotype alterations that might be associated with altered methylation levels among grafts. Statistically significant DMC differences among gene elements of snoRNA genes and between homograft and heterograft cotton samples were identified in the absence of DNA sequence alterations. DNA methylation alterations of snoRNA genes associated with seedling vigor and 100 seed weight. The majority of snoRNA genes showed higher numbers of mCG + mCHG-DMCs with increased methylation levels in heterograft, while there were higher numbers of mCG + mCHG-DMCs with decreased methylation levels in homograft. Since snoRNAs regulate essential genes for plant growth and development and plant adaptation to different habitats or extreme environments, their altered methylation levels should be related with plant physiology.
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Affiliation(s)
- Mehmet Karaca
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07059 Antalya, Turkey
| | - Ayse Gul Ince
- Vocational School of Technical Sciences, Akdeniz University, 07059 Antalya, Turkey
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Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Comparative RNA Genomics. Methods Mol Biol 2024; 2802:347-393. [PMID: 38819565 DOI: 10.1007/978-1-0716-3838-5_12] [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] [Indexed: 06/01/2024]
Abstract
Over the last quarter of a century it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large-scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible non-coding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of non-coding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.
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Affiliation(s)
- Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
- Bioinformatics and Computational Biology research group, University of Vienna, Vienna, Austria
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany.
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
- Universidad National de Colombia, Bogotá, Colombia.
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria.
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.
- Santa Fe Institute, Santa Fe, NM, USA.
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3
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Niu Y, Liu L. RNA pseudouridine modification in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6431-6447. [PMID: 37581601 DOI: 10.1093/jxb/erad323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Pseudouridine is one of the well-known chemical modifications in various RNA species. Current advances to detect pseudouridine show that the pseudouridine landscape is dynamic and affects multiple cellular processes. Although our understanding of this post-transcriptional modification mainly depends on yeast and human models, the recent findings provide strong evidence for the critical role of pseudouridine in plants. Here, we review the current knowledge of pseudouridine in plant RNAs, including its synthesis, degradation, regulatory mechanisms, and functions. Moreover, we propose future areas of research on pseudouridine modification in plants.
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Affiliation(s)
- Yanli Niu
- Laboratory of Cell Signal Transduction, School of Basic Medical Sciences, Henan University, Kaifeng 475001, China
| | - Lingyun Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China
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4
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Cao Y, Wang J, Wu S, Yin X, Shu J, Dai X, Liu Y, Sun L, Zhu D, Deng XW, Ye K, Qian W. The small nucleolar RNA SnoR28 regulates plant growth and development by directing rRNA maturation. THE PLANT CELL 2022; 34:4173-4190. [PMID: 36005862 PMCID: PMC9614442 DOI: 10.1093/plcell/koac265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs (ncRNAs) that guide chemical modifications of structural RNAs, which are essential for ribosome assembly and function in eukaryotes. Although numerous snoRNAs have been identified in plants by high-throughput sequencing, the biological functions of most of these snoRNAs remain unclear. Here, we identified box C/D SnoR28.1s as important regulators of plant growth and development by screening a CRISPR/Cas9-generated ncRNA deletion mutant library in Arabidopsis thaliana. Deletion of the SnoR28.1 locus, which contains a cluster of three genes producing SnoR28.1s, resulted in defects in root and shoot growth. SnoR28.1s guide 2'-O-ribose methylation of 25S rRNA at G2396. SnoR28.1s facilitate proper and efficient pre-rRNA processing, as the SnoR28.1 deletion mutants also showed impaired ribosome assembly and function, which may account for the growth defects. SnoR28 contains a 7-bp antisense box, which is required for 2'-O-ribose methylation of 25S rRNA at G2396, and an 8-bp extra box that is complementary to a nearby rRNA methylation site and is partially responsible for methylation of G2396. Both of these motifs are required for proper and efficient pre-rRNA processing. Finally, we show that SnoR28.1s genetically interact with HIDDEN TREASURE2 and NUCLEOLIN1. Our results advance our understanding of the roles of snoRNAs in Arabidopsis.
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Affiliation(s)
- Yuxin Cao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jiayin Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Wu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jia Shu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Dai
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Yannan Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
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5
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Gasińska K, Czop M, Kosior-Jarecka E, Wróbel-Dudzińska D, Kocki J, Żarnowski T. Small Nucleolar RNAs in Pseudoexfoliation Glaucoma. Cells 2022; 11:cells11172738. [PMID: 36078146 PMCID: PMC9454646 DOI: 10.3390/cells11172738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are small non-coding regulatory RNAs that have been investigated extensively in recent years. However, the relationship between snoRNA and glaucoma is still unknown. This study aims to analyze the levels of snoRNA expression in the aqueous humor (AH) of patients with pseudoexfoliation glaucoma (PEXG) compared to a control group and identify hypothetical snoRNA-dependent mechanisms contributing to PEXG. The AH was obtained from eighteen Caucasian patients, comprising nine PEXG and nine age-matched control patients. RNA was isolated, and a microarray system was used to determine the snoRNA expression profiles. Functional and enrichment analyses were performed. We identified seven snoRNAs, SNORD73B, SNORD58A, SNORD56, SNORA77, SNORA72, SNORA64, and SNORA32, in the AH of the PEXG and control group patients. Five snoRNAs showed statistically significantly lower expression in the PEXG group, and two snoRNAs had statistically significantly higher expression in the PEXG group compared to the control group. In addition, we identified two factors-CACNB3 for SNORA64 and TMEM63C for SNORA32, similar to PEX-related genes (CACNA1A and TMEM136). The enrichment analysis for four genes targeted by snoRNAs revealed possible mechanisms associated with glaucoma and/or PEX, but the direct role of snoRNAs in these biological processes was not proven.
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Affiliation(s)
- Karolina Gasińska
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, 20-079 Lublin, Poland
| | - Marcin Czop
- Department of Clinical Genetics, Medical University of Lublin, 20-080 Lublin, Poland
| | - Ewa Kosior-Jarecka
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, 20-079 Lublin, Poland
- Correspondence:
| | - Dominika Wróbel-Dudzińska
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, 20-079 Lublin, Poland
| | - Janusz Kocki
- Department of Clinical Genetics, Medical University of Lublin, 20-080 Lublin, Poland
| | - Tomasz Żarnowski
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, 20-079 Lublin, Poland
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6
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Nunn A, Rodríguez‐Arévalo I, Tandukar Z, Frels K, Contreras‐Garrido A, Carbonell‐Bejerano P, Zhang P, Ramos Cruz D, Jandrasits K, Lanz C, Brusa A, Mirouze M, Dorn K, Galbraith DW, Jarvis BA, Sedbrook JC, Wyse DL, Otto C, Langenberger D, Stadler PF, Weigel D, Marks MD, Anderson JA, Becker C, Chopra R. Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:944-963. [PMID: 34990041 PMCID: PMC9055812 DOI: 10.1111/pbi.13775] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/28/2021] [Accepted: 12/23/2021] [Indexed: 05/20/2023]
Abstract
Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
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Affiliation(s)
- Adam Nunn
- ecSeq Bioinformatics GmbHLeipzigGermany
- Department of Computer ScienceLeipzig UniversityLeipzigGermany
| | - Isaac Rodríguez‐Arévalo
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Zenith Tandukar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Katherine Frels
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
| | | | | | - Panpan Zhang
- Institut de Recherche pour le DéveloppementUMR232 DIADEMontpellierFrance
- Laboratory of Plant Genome and DevelopmentUniversity of PerpignanPerpignanFrance
| | - Daniela Ramos Cruz
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Katharina Jandrasits
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Christa Lanz
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Anthony Brusa
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Marie Mirouze
- Institut de Recherche pour le DéveloppementUMR232 DIADEMontpellierFrance
- Laboratory of Plant Genome and DevelopmentUniversity of PerpignanPerpignanFrance
| | - Kevin Dorn
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
- USDA‐ARSSoil Management and Sugarbeet ResearchFort CollinsCOUSA
| | - David W Galbraith
- BIO5 InstituteArizona Cancer CenterDepartment of Biomedical EngineeringUniversity of ArizonaSchool of Plant SciencesTucsonAZUSA
| | - Brice A. Jarvis
- School of Biological SciencesIllinois State UniversityNormalILUSA
| | - John C. Sedbrook
- School of Biological SciencesIllinois State UniversityNormalILUSA
| | - Donald L. Wyse
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | | | | | - Peter F. Stadler
- Department of Computer ScienceLeipzig UniversityLeipzigGermany
- Max Planck Institute for Mathematics in the SciencesLeipzigGermany
| | - Detlef Weigel
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - M. David Marks
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
| | - James A. Anderson
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Claude Becker
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Ratan Chopra
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
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7
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Small nucleolar RNA 42 promotes the growth of hepatocellular carcinoma through the p53 signaling pathway. Cell Death Discov 2021; 7:347. [PMID: 34759267 PMCID: PMC8581050 DOI: 10.1038/s41420-021-00740-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 01/15/2023] Open
Abstract
Recent studies show that small nucleolar RNAs (snoRNAs) play an important role in tumorigenesis. SNORA42 is a potential therapeutic target and prognostic biomarker for various cancers, and the aim of the present study was to investigate the function and clinical relevance of SNORA42 in hepatocellular carcinoma (HCC). We detected the expression levels of SNORA42 in HCC and normal liver tissue samples, as well as in tumor and hepatocyte-derived cell lines. SNORA42 was significantly upregulated in the HCC tissues and cells compared to the adjacent liver tissues and normal hepatocytes. Furthermore, overexpression of SNORA42 correlated with poor prognosis in the HCC patients. Knocking down SNORA42 in HCC cell lines decreased their proliferation, migration and invasion in vitro, and inhibited tumor growth and metastasis in vivo. In contrast, ectopic expression of SNORA42 promoted HCC cell proliferation and inhibited apoptosis. Mechanistically, SNORA42 exerted its oncogenic effects by targeting the p53 signaling pathway and cell cycle transition. In conclusion, SNORA42 acted as an oncogene in HCC and was a potential prognostic biomarker and therapeutic target.
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8
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Streit D, Schleiff E. The Arabidopsis 2'-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast. FRONTIERS IN PLANT SCIENCE 2021; 12:684626. [PMID: 34381476 PMCID: PMC8351944 DOI: 10.3389/fpls.2021.684626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/16/2021] [Indexed: 05/25/2023]
Abstract
Eukaryotic ribosome assembly starts in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into the 35S pre-ribosomal RNA (pre-rRNA). More than two-hundred ribosome biogenesis factors (RBFs) and more than two-hundred small nucleolar RNAs (snoRNA) catalyze the processing, folding and modification of the rRNA in Arabidopsis thaliana. The initial pre-ribosomal 90S complex is formed already during transcription by association of ribosomal proteins (RPs) and RBFs. In addition, small nucleolar ribonucleoprotein particles (snoRNPs) composed of snoRNAs and RBFs catalyze the two major rRNA modification types, 2'-O-ribose-methylation and pseudouridylation. Besides these two modifications, rRNAs can also undergo base methylations and acetylation. However, the latter two modifications have not yet been systematically explored in plants. The snoRNAs of these snoRNPs serve as targeting factors to direct modifications to specific rRNA regions by antisense elements. Today, hundreds of different sites of modifications in the rRNA have been described for eukaryotic ribosomes in general. While our understanding of the general process of ribosome biogenesis has advanced rapidly, the diversities appearing during plant ribosome biogenesis is beginning to emerge. Today, more than two-hundred RBFs were identified by bioinformatics or biochemical approaches, including several plant specific factors. Similarly, more than two hundred snoRNA were predicted based on RNA sequencing experiments. Here, we discuss the predicted and verified rRNA modification sites and the corresponding identified snoRNAs on the example of the model plant Arabidopsis thaliana. Our summary uncovers the plant modification sites in comparison to the human and yeast modification sites.
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Affiliation(s)
- Deniz Streit
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
- Frankfurt Institute for Advanced Studies (FIAS), Frankfurt, Germany
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9
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Bergeron D, Laforest C, Carpentier S, Calvé A, Fafard-Couture É, Deschamps-Francoeur G, Scott MS. SnoRNA copy regulation affects family size, genomic location and family abundance levels. BMC Genomics 2021; 22:414. [PMID: 34090325 PMCID: PMC8178906 DOI: 10.1186/s12864-021-07757-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/26/2021] [Indexed: 12/03/2022] Open
Abstract
Background Small nucleolar RNAs (snoRNAs) are an abundant class of noncoding RNAs present in all eukaryotes and best known for their involvement in ribosome biogenesis. In mammalian genomes, many snoRNAs exist in multiple copies, resulting from recombination and retrotransposition from an ancestral snoRNA. To gain insight into snoRNA copy regulation, we used Rfam classification and normal human tissue expression datasets generated using low structure bias RNA-seq to characterize snoRNA families. Results We found that although box H/ACA families are on average larger than box C/D families, the number of expressed members is similar for both types. Family members can cover a wide range of average abundance values, but importantly, expression variability of individual members of a family is preferred over the total variability of the family, especially for box H/ACA snoRNAs, suggesting that while members are likely differentially regulated, mechanisms exist to ensure uniformity of the total family abundance across tissues. Box C/D snoRNA family members are mostly embedded in the same host gene while box H/ACA family members tend to be encoded in more than one different host, supporting a model in which box C/D snoRNA duplication occurred mostly by cis recombination while box H/ACA snoRNA families have gained copy members through retrotransposition. And unexpectedly, snoRNAs encoded in the same host gene can be regulated independently, as some snoRNAs within the same family vary in abundance in a divergent way between tissues. Conclusions SnoRNA copy regulation affects family sizes, genomic location of the members and controls simultaneously member and total family abundance to respond to the needs of individual tissues. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07757-1.
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Affiliation(s)
- Danny Bergeron
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Cédric Laforest
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Stacey Carpentier
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Annabelle Calvé
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Étienne Fafard-Couture
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
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10
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Czekay DP, Kothe U. H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes. Front Microbiol 2021; 12:654370. [PMID: 33776984 PMCID: PMC7991803 DOI: 10.3389/fmicb.2021.654370] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/18/2021] [Indexed: 01/04/2023] Open
Abstract
During ribosome synthesis, ribosomal RNA is modified through the formation of many pseudouridines and methylations which contribute to ribosome function across all domains of life. In archaea and eukaryotes, pseudouridylation of rRNA is catalyzed by H/ACA small ribonucleoproteins (sRNPs) utilizing different H/ACA guide RNAs to identify target uridines for modification. H/ACA sRNPs are conserved in archaea and eukaryotes, as they share a common general architecture and function, but there are also several notable differences between archaeal and eukaryotic H/ACA sRNPs. Due to the higher protein stability in archaea, we have more information on the structure of archaeal H/ACA sRNPs compared to eukaryotic counterparts. However, based on the long history of yeast genetic and other cellular studies, the biological role of H/ACA sRNPs during ribosome biogenesis is better understood in eukaryotes than archaea. Therefore, this review provides an overview of the current knowledge on H/ACA sRNPs from archaea, in particular their structure and function, and relates it to our understanding of the roles of eukaryotic H/ACA sRNP during eukaryotic ribosome synthesis and beyond. Based on this comparison of our current insights into archaeal and eukaryotic H/ACA sRNPs, we discuss what role archaeal H/ACA sRNPs may play in the formation of ribosomes.
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Affiliation(s)
- Dominic P Czekay
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Ute Kothe
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
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11
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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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12
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Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora. Noncoding RNA 2020; 6:ncrna6030039. [PMID: 32932872 PMCID: PMC7549347 DOI: 10.3390/ncrna6030039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 12/25/2022] Open
Abstract
Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the C. canephora genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity.
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13
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Streit D, Shanmugam T, Garbelyanski A, Simm S, Schleiff E. The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1016. [PMID: 32806552 PMCID: PMC7464842 DOI: 10.3390/plants9081016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
Ribosome biogenesis is one cell function-defining process. It depends on efficient transcription of rDNAs in the nucleolus as well as on the cytosolic synthesis of ribosomal proteins. For newly transcribed rRNA modification and ribosomal protein assembly, so-called small nucleolar RNAs (snoRNAs) and ribosome biogenesis factors (RBFs) are required. For both, an inventory was established for model systems like yeast and humans. For plants, many assignments are based on predictions. Here, RNA deep sequencing after nuclei enrichment was combined with single molecule species detection by northern blot and in vivo fluorescence in situ hybridization (FISH)-based localization studies. In addition, the occurrence and abundance of selected snoRNAs in different tissues were determined. These approaches confirm the presence of most of the database-deposited snoRNAs in cell cultures, but some of them are localized in the cytosol rather than in the nucleus. Further, for the explored snoRNA examples, differences in their abundance in different tissues were observed, suggesting a tissue-specific function of some snoRNAs. Thus, based on prediction and experimental confirmation, many plant snoRNAs can be proposed, while it cannot be excluded that some of the proposed snoRNAs perform alternative functions than are involved in rRNA modification.
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Affiliation(s)
- Deniz Streit
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
| | - Thiruvenkadam Shanmugam
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
| | - Asen Garbelyanski
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
| | - Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
- Institute of Bioinformatics, University Medicine Greifswald, D-17475 Greifswald, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany; (D.S.); (T.S.); (A.G.); (S.S)
- Frankfurt Institute of Advanced Studies (FIAS), D-60438 Frankfurt am Main, Germany
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14
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Deryusheva S, Talhouarne GJS, Gall JG. "Lost and Found": snoRNA Annotation in the Xenopus Genome and Implications for Evolutionary Studies. Mol Biol Evol 2020; 37:149-166. [PMID: 31553476 PMCID: PMC6984369 DOI: 10.1093/molbev/msz209] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) function primarily as guide RNAs for posttranscriptional modification of rRNAs and spliceosomal snRNAs, both of which are functionally important and evolutionarily conserved molecules. It is commonly believed that snoRNAs and the modifications they mediate are highly conserved across species. However, most relevant data on snoRNA annotation and RNA modification are limited to studies on human and yeast. Here, we used RNA-sequencing data from the giant oocyte nucleus of the frog Xenopus tropicalis to annotate a nearly complete set of snoRNAs. We compared the frog data with snoRNA sets from human and other vertebrate genomes, including mammals, birds, reptiles, and fish. We identified many Xenopus-specific (or nonhuman) snoRNAs and Xenopus-specific domains in snoRNAs from conserved RNA families. We predicted that some of these nonhuman snoRNAs and domains mediate modifications at unexpected positions in rRNAs and snRNAs. These modifications were mapped as predicted when RNA modification assays were applied to RNA from nine vertebrate species: frogs X. tropicalis and X. laevis, newt Notophthalmus viridescens, axolotl Ambystoma mexicanum, whiptail lizard Aspidoscelis neomexicana, zebrafish Danio rerio, chicken, mouse, and human. This analysis revealed that only a subset of RNA modifications is evolutionarily conserved and that modification patterns may vary even between closely related species. We speculate that each functional domain in snoRNAs (half of an snoRNA) may evolve independently and shuffle between different snoRNAs.
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Affiliation(s)
| | | | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
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15
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Abstract
Over the last two decades it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of noncoding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.
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Affiliation(s)
- Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany.,Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Ivo L Hofacker
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.,Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.,Bioinformatics and Computational Biology Research Group, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
| | - Peter F Stadler
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark. .,Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria. .,Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany. .,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany. .,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany. .,Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA.
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