ArticleNucleic acids research2021
Discovery of 17 conserved structural RNAs in fungi.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Article
- Genome-wide discovery and phenotyping of non-coding transcripts in A. fumigatus reveals lncRNAs with a role in antifungal drug sensitivity.Nature communications · 2026Article
- Article
- Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo.Nature structural & molecular biology · 2025Article
- AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction.bioRxiv : the preprint server for biology · 2025Article
- Autoregulation of RPL7B by inhibition of a structural splicing enhancer.Nucleic acids research · 2025Article
- RNAhub-an automated pipeline to search and align RNA homologs with secondary structure assessment.Nucleic acids research · 2025Article
- Tick-borne flavivirus exoribonuclease-resistant RNAs contain a double loop structure.Nature communications · 2025Article
- Thirteen dubious ways to detect conserved structural RNAs.IUBMB life · 2023Article
- GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context.GigaScience · 2022Article
- Advances and opportunities in RNA structure experimental determination and computational modeling.Nature methods · 2022Review
- Advances in Non-Coding RNA Sequencing.Non-coding RNA · 2021Review
- Machine Learning to Enhance Biophysical Models for Riboswitch Discovery.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Many non-coding RNAs with known functions are structurally conserved: their intramolecular secondary and tertiary interactions are maintained across evolutionary time. Consequently, the presence of conserved structure in multiple sequence alignments can be used to identify candidate functional non-coding RNAs. Here, we present a bioinformatics method that couples iterative homology search with covariation analysis to assess whether a genomic region has evidence of conserved RNA structure. We used this method to examine all unannotated regions of five well-studied fungal genomes (Saccharomyces cerevisiae, Candida albicans, Neurospora crassa, Aspergillus fumigatus, and Schizosaccharomyces pombe). We identified 17 novel structurally conserved non-coding RNA candidates, which include four H/ACA box small nucleolar RNAs, four intergenic RNAs and nine RNA structures located within the introns and untranslated regions (UTRs) of mRNAs. For the two structures in the 3' UTRs of the metabolic genes GLY1 and MET13, we performed experiments that provide evidence against them being eukaryotic riboswitches.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.