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

RNA 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. Suc...

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Autores principales: Johnson, Nathan R, Larrondo, Luis F, Álvarez, José M, Vidal, Elena A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9757828/
https://www.ncbi.nlm.nih.gov/pubmed/36484778
http://dx.doi.org/10.7554/eLife.83691
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author Johnson, Nathan R
Larrondo, Luis F
Álvarez, José M
Vidal, Elena A
author_facet Johnson, Nathan R
Larrondo, Luis F
Álvarez, José M
Vidal, Elena A
author_sort Johnson, Nathan R
collection PubMed
description RNA 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 technologies. 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.
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spelling pubmed-97578282022-12-17 Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links Johnson, Nathan R Larrondo, Luis F Álvarez, José M Vidal, Elena A eLife Genetics and Genomics RNA 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 technologies. 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. eLife Sciences Publications, Ltd 2022-12-09 /pmc/articles/PMC9757828/ /pubmed/36484778 http://dx.doi.org/10.7554/eLife.83691 Text en © 2022, Johnson et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Genetics and Genomics
Johnson, Nathan R
Larrondo, Luis F
Álvarez, José M
Vidal, Elena A
Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links
title Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links
title_full Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links
title_fullStr Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links
title_full_unstemmed Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links
title_short Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links
title_sort comprehensive re-analysis of hairpin small rnas in fungi reveals loci with conserved links
topic Genetics and Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9757828/
https://www.ncbi.nlm.nih.gov/pubmed/36484778
http://dx.doi.org/10.7554/eLife.83691
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