ArticleNucleic acids research2009
Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 32 citations in OpenAlex.
- RNA regulation in plants.Science China. Life sciences · 2026Review
- Epitranscriptomic modifications in plant RNAs.RNA biology · 2025Review
- RNA processing/modifying enzymes play key roles in the response to thermospermine in Arabidopsis thaliana.The Plant journal : for cell and molecular biology · 2025Article
- SnoBIRD: a tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes.Nucleic acids research · 2025Article
- Cajal bodies: Evolutionarily conserved nuclear biomolecular condensates with properties unique to plants.The Plant cell · 2023Review
- The plant epitranscriptome: revisiting pseudouridine and 2'-O-methyl RNA modifications.Plant biotechnology journal · 2022Review
- Mapping rRNA 2'-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants.RNA biology · 2021Article
- Profiling of RNA ribose methylation in Arabidopsis thaliana.Nucleic acids research · 2021Article
- The Arabidopsis 2'-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast.Frontiers in plant science · 2021Review
- The Existence and Localization of Nuclear snoRNAs inPlants (Basel, Switzerland) · 2020Article
- Transcriptome-wide analysis of pseudouridylation of mRNA and non-coding RNAs in Arabidopsis.Journal of experimental botany · 2019Article
- Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors.The Plant cell · 2019Review
- High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq.Nucleic acids research · 2017Article
- The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages.Scientific reports · 2017Article
- Transfer RNA Derived Small RNAs Targeting Defense Responsive Genes Are Induced during Phytophthora capsici Infection in Black Pepper (Piper nigrum L.).Frontiers in plant science · 2016Article
- Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.BMC genomics · 2015Article
- Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data.BMC genomics · 2014Article
- Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.Nature structural & molecular biology · 2012Article
- Article
- Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli.Nucleic acids research · 2010Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs that direct 2'-O-methylation or pseudouridylation on ribosomal RNAs or spliceosomal small nuclear RNAs. These modifications are needed to modulate the activity of ribosomes and spliceosomes. A comprehensive repertoire of snoRNAs is needed to expand the knowledge of these modifications. The sequences corresponding to snoRNAs in 18-26-nt small RNA sequencing data have been rarely explored and remain as a hidden treasure for snoRNA annotation. Here, we showed the enrichment of small RNAs at Arabidopsis snoRNA termini and developed a computational approach to identify snoRNAs on the basis of this characteristic. The approach successfully uncovered the full-length sequences of 144 known Arabidopsis snoRNA genes, including some snoRNAs with improved 5'- or 3'-end annotation. In addition, we identified 27 and 17 candidates for novel box C/D and box H/ACA snoRNAs, respectively. Northern blot analysis and sequencing data from parallel analysis of RNA ends confirmed the expression and the termini of the newly predicted snoRNAs. Our study especially expanded on the current knowledge of box H/ACA snoRNAs and snoRNA species targeting snRNAs. In this study, we demonstrated that the use of small RNA sequencing data can increase the complexity and the accuracy of snoRNA annotation.
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