ArticleGenome biology2021
Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
- Identification of over ten thousand candidate structured RNAs in viruses and phages.Computational and structural biotechnology journal · 2023Article
- FindNonCoding: rapid and simple detection of non-coding RNAs in genomes.Bioinformatics (Oxford, England) · 2022Article
- Comparative Population Genetics in the Human Gut Microbiome.Genome biology and evolution · 2022Article
- Identifying candidate structured RNAs in CRISPR operons.RNA biology · 2022Article
- Structured RNA Contaminants in Bacterial Ribo-Seq.mSphere · 2020Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundStructured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations.
resultsWe sought to apply a large-scale, comparative genomics approach to these organisms to identify candidate structured RNAs. With a carefully constructed, though computationally intensive automated analysis, we identify 3161 conserved candidate structured RNAs in intergenic regions, as well as 2022 additional candidate structured RNAs that may overlap coding regions. We validate the RNA expression of 177 of these candidate structures by analyzing small fragment RNA-seq data from four human fecal samples.
conclusionsThis approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. Overall, our pipeline enables conservative predictions of thousands of novel candidate structured RNAs from human microbiomes.
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