Mapping rRNA 2’-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants

Azevedo-Favory, Jacinthe; Gaspin, Christine; Ayadi, Lilia; Montacié, Charlotte; Marchand, Virginie; Jobet, Edouard; Rompais, Magali; Carapito, Christine; Motorin, Yuri; Sáez‐Vasquez, Julio

doi:10.1080/15476286.2020.1869892

Cited by 29 publications

(37 citation statements)

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“…However, future studies are required to explore whether this is a unique modification or whether ITS1, ITS2 and the ETS regions are generally modified, and to understand the role of modifications of the pre-rRNA. A complementary analysis using RiboMethSeq for detection of 2′-O-ribose-me modifications yielded novel modification sites as well ( Azevedo-Favory et al, 2020 ).…”

Section: The Rrna Modification In Plantsmentioning

confidence: 99%

“…Different approaches exploring the modifications of the rRNA in Arabidopsis yielded a total of 321 rRNA modification sites ( Barneche et al, 2001 ; Qu et al, 2001 ; Chen and Wu, 2009 ; Kim et al, 2010 ; Sun et al, 2019 ; Azevedo-Favory et al, 2020 ; Streit et al, 2020 ). A total of 79 2′-O-ribose-me and 43 pseudouridylation sites were assigned for the 18S rRNA, of which 44 2′-O-ribose-me and 28 pseudouridylation sites were experimentally confirmed.…”

Section: The Rrna Modification In Plantsmentioning

confidence: 99%

“…Analyses were conducted by using the snoRNA databases snOPY ( Yoshihama et al, 2013 ) and the plant snoRNA DB ( Brown et al, 2003 ). Predicted and verified positions for 2′-O-ribose-methylations and pseudouridylations were obtained from Barneche et al (2001) , Brown et al (2001) , Qu et al (2001) , Sun et al (2019) , Azevedo-Favory et al (2020) . Every tenth nucleotide is marked in red and every 50th nucleotide is labeled with the according number.…”

Section: A View On the Rrna Modification Sites And Snornas In Arabidopsis Thalianamentioning

confidence: 99%

“…To date, more than 200 RBFs and more than 200 snoRNAs were described to regulate ribosome maturation. In plants, the inventory for both has been established by a combination of experimental evidence and bioinformatics prediction ( Barneche et al, 2001 ; Brown et al, 2001 ; Qu et al, 2001 ; Chen C. L. et al, 2003 ; Chen and Wu, 2009 ; Kim et al, 2010 ; Liu et al, 2013 ; Palm et al, 2016 ; Azevedo-Favory et al, 2020 ). Considering the importance of rRNA modifications for proper processing and maturation of rRNA but also for the function of ribosomes, we discuss in the following the current knowledge on the rRNA modifications and snoRNAs in Arabidopsis and compare these with the human and yeast modifications sites.…”

Section: Introductionmentioning

confidence: 99%

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The Arabidopsis 2′-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast

Streit

Schleiff

2021

Front. Plant Sci.

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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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Section: The Rrna Modification In Plantsmentioning

confidence: 99%

Section: The Rrna Modification In Plantsmentioning

confidence: 99%

Section: A View On the Rrna Modification Sites And Snornas In Arabidopsis Thalianamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The Arabidopsis 2′-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast

Streit

Schleiff

2021

Front. Plant Sci.

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“…The snoRNAs identified here are all C/D-box members. Prediction and experimental identification of their targets (Table 1; Azevedo-Favory et al, 2021;Lowe and Eddy, 1999;Van Bel et al, 2018;Wu et al, 2021;Yoshihama et al, 2013) has suggested an involvement of RBP45D in 18S and 25S rRNA Nm. However, reverse transcription at low dNTP levels, followed by PCR (RTL-P; Dong et al, 2012), suggested that Nm of A1731 and A1735 of 18S rRNA and A945 of 25S rRNA (targets of snoR6-3, snoR6-2 and snoR12-1a, respectively) was not significantly altered in rpb-ko and rls6 mutants compared to their WT (Figure S6C,D), nor was the 18S or 25S rRNA maturation pattern (Figure S6E).…”

Section: Rbp45d Is a Nuclear Protein That Binds To Snrnas And Snornasmentioning

confidence: 99%

The RNA-binding protein RBP45D of Arabidopis plays a role in epigenetic control of flowering time and DCL3-independent RNA-directed DNA methylation

Wang

D²,

Scharf³

et al. 2021

Preprint

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RNA-directed DNA methylation (RdDM) helps to defend plants against invasive nucleic acids. In the canonical form of RdDM, 24-nt small interfering RNAs (siRNAs) are produced by DICER-LIKE 3 (DCL3). Here, we describe the Arabidopsis thaliana prors1 (LUC) transgenic system, in which transcriptional gene silencing (TGS) is independent of DLC3. A forward genetics screen performed with this system identified both known components of RdDM, and the RNA-binding protein RBP45D. RBP45D promotes DNA methylation, and its loss delays flowering, especially at high temperature, presumably mediated by elevated FLC levels. RBP45D is localized to the nucleus, where it is associated with snRNAs and snoRNAs. RBP45D maintains siRNA production originating from the LUC transgene, but does not alter mRNA levels or affect processing of transcripts of known RdDM genes. We suggest that RBPD45 facilitates DCL3-independent siRNA production by stabilising either the precursor RNA or the as yet unidentified slicer protein.

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Current technical advancements in plant epitranscriptomic studies

et al. 2023

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The growth and development of plants are the result of the interplay between the internal developmental programming and plant–environment interactions. Gene expression regulations in plants are made up of multi‐level networks. In the past few years, many studies were carried out on co‐ and post‐transcriptional RNA modifications, which, together with the RNA community, are collectively known as the “epitranscriptome.” The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third‐generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant–environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi‐omics investigations using the recent technical advancements.

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Mapping rRNA 2’-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants

Cited by 29 publications

References 75 publications

The Arabidopsis 2′-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast

The Arabidopsis 2′-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast

The RNA-binding protein RBP45D of Arabidopis plays a role in epigenetic control of flowering time and DCL3-independent RNA-directed DNA methylation

Current technical advancements in plant epitranscriptomic studies

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