Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links

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dc.contributor.authorJohnson, Nathan R.
dc.contributor.authorLarrondo, Luis F.
dc.contributor.authorÁlvarez, José M.
dc.contributor.authorVidal, Elena A.
dc.date.accessioned2023-04-05T16:20:01Z
dc.date.available2023-04-05T16:20:01Z
dc.date.issued2022-12
dc.descriptionIndexación: Scopus.es
dc.description.abstractRNA interference is an ancient mechanism with many regulatory roles in eukaryotic genomes, with small RNAs acting as their functional element. While there is a wide array of classes of small-RNA-producing loci, those resulting from stem-loop structures (hairpins) have received profuse attention. Such is the case of microRNAs (miRNAs), which have distinct roles in plants and animals. Fungi also produce small RNAs, and several publications have identified miRNAs and miRNA-like (mi/milRNA) hairpin RNAs in diverse fungal species using deep sequencing technolo-gies. Despite this relevant source of information, relatively little is known about mi/milRNA features in fungi, mostly due to a lack of established criteria for their annotation. To systematically assess mi/milRNA characteristics and annotation confidence, we searched for publications describing mi/ milRNA loci and re-assessed the annotations for 41 fungal species. We extracted and normalized the annotation data for 1727 reported mi/milRNA loci and determined their abundance profiles, concluding that less than half of the reported loci passed basic standards used for hairpin RNA discovery. We found that fungal mi/milRNA are generally more similar in size to animal miRNAs and were frequently associated with protein-coding genes. The compiled genomic analyses identified 25 mi/milRNA loci conserved in multiple species. Our pipeline allowed us to build a general hierarchy of locus quality, identifying more than 150 loci with high-quality annotations. We provide a centralized annotation of identified mi/milRNA hairpin RNAs in fungi which will serve as a resource for future research and advance in understanding the characteristics and functions of mi/milRNAs in fungal organisms. © Johnson et al.es
dc.description.urihttps://elifesciences.org/articles/83691
dc.identifier.citationeLife, Volume 11December 2022 Article number e83691es
dc.identifier.doi10.7554/ELIFE.83691
dc.identifier.issn2050-084X
dc.identifier.urihttps://repositorio.unab.cl/xmlui/handle/ria/48245
dc.language.isoenes
dc.publishereLife Sciences Publications Ltdes
dc.rights.licenseAtribución 4.0 Internacional (CC BY 4.0)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/deed.es
dc.subjectAnimalses
dc.subjectFungies
dc.subjectGene Expression Regulationes
dc.subjectFungales
dc.subjectMicroRNAses
dc.subjectRNA Interferencees
dc.subjectRNAes
dc.subjectFungales
dc.titleComprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved linkses
dc.typeArtículoes
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