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piRNA-like small RNAs mark extended 3’UTRs present in germ and somatic cells

BACKGROUND: Piwi-interacting RNAs (piRNAs) are a class of small RNAs; distinct types of piRNAs are expressed in the mammalian testis at different stages of development. The function of piRNAs expressed in the adult testis is not well established. We conducted a detailed characterization of piRNAs al...

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Autores principales: Yamtich, Jennifer, Heo, Seok-Jin, Dhahbi, Joseph, Martin, David IK, Boffelli, Dario
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4469462/
https://www.ncbi.nlm.nih.gov/pubmed/26076733
http://dx.doi.org/10.1186/s12864-015-1662-6
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author Yamtich, Jennifer
Heo, Seok-Jin
Dhahbi, Joseph
Martin, David IK
Boffelli, Dario
author_facet Yamtich, Jennifer
Heo, Seok-Jin
Dhahbi, Joseph
Martin, David IK
Boffelli, Dario
author_sort Yamtich, Jennifer
collection PubMed
description BACKGROUND: Piwi-interacting RNAs (piRNAs) are a class of small RNAs; distinct types of piRNAs are expressed in the mammalian testis at different stages of development. The function of piRNAs expressed in the adult testis is not well established. We conducted a detailed characterization of piRNAs aligning at or near the 3’ UTRs of protein-coding genes in a deep dataset of small RNAs from adult mouse testis. RESULTS: We identified 2710 piRNA clusters associated with 3’ UTRs, including 1600 that overlapped genes not previously associated with piRNAs. 35 % of the clusters extend beyond the annotated transcript; we find that these clusters correspond to, and are likely derived from, novel polyadenylated mRNA isoforms that contain previously unannotated extended 3’UTRs. Extended 3’ UTRs, and small RNAs derived from them, are also present in somatic tissues; a subset of these somatic 3’UTR small RNA clusters are absent in mice lacking MIWI2, indicating a role for MIWI2 in the metabolism of somatic small RNAs. CONCLUSIONS: The finding that piRNAs are processed from extended 3’ UTRs suggests a role for piRNAs in the remodeling of 3’ UTRs. The presence of both clusters and extended 3’UTRs in somatic cells, with evidence for involvement of MIWI2, indicates that this pathway is more broadly distributed than currently appreciated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1662-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-44694622015-06-18 piRNA-like small RNAs mark extended 3’UTRs present in germ and somatic cells Yamtich, Jennifer Heo, Seok-Jin Dhahbi, Joseph Martin, David IK Boffelli, Dario BMC Genomics Research Article BACKGROUND: Piwi-interacting RNAs (piRNAs) are a class of small RNAs; distinct types of piRNAs are expressed in the mammalian testis at different stages of development. The function of piRNAs expressed in the adult testis is not well established. We conducted a detailed characterization of piRNAs aligning at or near the 3’ UTRs of protein-coding genes in a deep dataset of small RNAs from adult mouse testis. RESULTS: We identified 2710 piRNA clusters associated with 3’ UTRs, including 1600 that overlapped genes not previously associated with piRNAs. 35 % of the clusters extend beyond the annotated transcript; we find that these clusters correspond to, and are likely derived from, novel polyadenylated mRNA isoforms that contain previously unannotated extended 3’UTRs. Extended 3’ UTRs, and small RNAs derived from them, are also present in somatic tissues; a subset of these somatic 3’UTR small RNA clusters are absent in mice lacking MIWI2, indicating a role for MIWI2 in the metabolism of somatic small RNAs. CONCLUSIONS: The finding that piRNAs are processed from extended 3’ UTRs suggests a role for piRNAs in the remodeling of 3’ UTRs. The presence of both clusters and extended 3’UTRs in somatic cells, with evidence for involvement of MIWI2, indicates that this pathway is more broadly distributed than currently appreciated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1662-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-06-16 /pmc/articles/PMC4469462/ /pubmed/26076733 http://dx.doi.org/10.1186/s12864-015-1662-6 Text en © Yamtich et al. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Yamtich, Jennifer
Heo, Seok-Jin
Dhahbi, Joseph
Martin, David IK
Boffelli, Dario
piRNA-like small RNAs mark extended 3’UTRs present in germ and somatic cells
title piRNA-like small RNAs mark extended 3’UTRs present in germ and somatic cells
title_full piRNA-like small RNAs mark extended 3’UTRs present in germ and somatic cells
title_fullStr piRNA-like small RNAs mark extended 3’UTRs present in germ and somatic cells
title_full_unstemmed piRNA-like small RNAs mark extended 3’UTRs present in germ and somatic cells
title_short piRNA-like small RNAs mark extended 3’UTRs present in germ and somatic cells
title_sort pirna-like small rnas mark extended 3’utrs present in germ and somatic cells
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4469462/
https://www.ncbi.nlm.nih.gov/pubmed/26076733
http://dx.doi.org/10.1186/s12864-015-1662-6
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