Cargando…

RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis

In plants, cytoplasmic mRNA decay is critical for posttranscriptionally controlling gene expression and for maintaining cellular RNA homeostasis. Arabidopsis DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a cytoplasmic mRNA decay factor that interacts with proteins involved in mRNA decapping and n...

Descripción completa

Detalles Bibliográficos
Autores principales: Nagarajan, Vinay K, Stuart, Catherine J, DiBattista, Anna T, Accerbi, Monica, Caplan, Jeffrey L, Green, Pamela J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10226599/
https://www.ncbi.nlm.nih.gov/pubmed/37070465
http://dx.doi.org/10.1093/plcell/koad085
_version_ 1785050606410399744
author Nagarajan, Vinay K
Stuart, Catherine J
DiBattista, Anna T
Accerbi, Monica
Caplan, Jeffrey L
Green, Pamela J
author_facet Nagarajan, Vinay K
Stuart, Catherine J
DiBattista, Anna T
Accerbi, Monica
Caplan, Jeffrey L
Green, Pamela J
author_sort Nagarajan, Vinay K
collection PubMed
description In plants, cytoplasmic mRNA decay is critical for posttranscriptionally controlling gene expression and for maintaining cellular RNA homeostasis. Arabidopsis DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a cytoplasmic mRNA decay factor that interacts with proteins involved in mRNA decapping and nonsense-mediated mRNA decay (NMD). There is limited information on the functional role of DNE1 in RNA turnover, and the identities of its endogenous targets are unknown. In this study, we utilized RNA degradome approaches to globally investigate DNE1 substrates. Monophosphorylated 5′ ends, produced by DNE1, should accumulate in mutants lacking the cytoplasmic exoribonuclease XRN4, but be absent from DNE1 and XRN4 double mutants. In seedlings, we identified over 200 such transcripts, most of which reflect cleavage within coding regions. While most DNE1 targets were NMD-insensitive, some were upstream ORF (uORF)-containing and NMD-sensitive transcripts, indicating that this endoribonuclease is required for turnover of a diverse set of mRNAs. Transgenic plants expressing DNE1 cDNA with an active-site mutation in the endoribonuclease domain abolished the in planta cleavage of transcripts, demonstrating that DNE1 endoribonuclease activity is required for cleavage. Our work provides key insights into the identity of DNE1 substrates and enhances our understanding of DNE1-mediated mRNA decay.
format Online
Article
Text
id pubmed-10226599
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-102265992023-05-30 RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis Nagarajan, Vinay K Stuart, Catherine J DiBattista, Anna T Accerbi, Monica Caplan, Jeffrey L Green, Pamela J Plant Cell Research Article In plants, cytoplasmic mRNA decay is critical for posttranscriptionally controlling gene expression and for maintaining cellular RNA homeostasis. Arabidopsis DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a cytoplasmic mRNA decay factor that interacts with proteins involved in mRNA decapping and nonsense-mediated mRNA decay (NMD). There is limited information on the functional role of DNE1 in RNA turnover, and the identities of its endogenous targets are unknown. In this study, we utilized RNA degradome approaches to globally investigate DNE1 substrates. Monophosphorylated 5′ ends, produced by DNE1, should accumulate in mutants lacking the cytoplasmic exoribonuclease XRN4, but be absent from DNE1 and XRN4 double mutants. In seedlings, we identified over 200 such transcripts, most of which reflect cleavage within coding regions. While most DNE1 targets were NMD-insensitive, some were upstream ORF (uORF)-containing and NMD-sensitive transcripts, indicating that this endoribonuclease is required for turnover of a diverse set of mRNAs. Transgenic plants expressing DNE1 cDNA with an active-site mutation in the endoribonuclease domain abolished the in planta cleavage of transcripts, demonstrating that DNE1 endoribonuclease activity is required for cleavage. Our work provides key insights into the identity of DNE1 substrates and enhances our understanding of DNE1-mediated mRNA decay. Oxford University Press 2023-04-18 /pmc/articles/PMC10226599/ /pubmed/37070465 http://dx.doi.org/10.1093/plcell/koad085 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Nagarajan, Vinay K
Stuart, Catherine J
DiBattista, Anna T
Accerbi, Monica
Caplan, Jeffrey L
Green, Pamela J
RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis
title RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis
title_full RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis
title_fullStr RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis
title_full_unstemmed RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis
title_short RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis
title_sort rna degradome analysis reveals dne1 endoribonuclease is required for the turnover of diverse mrna substrates in arabidopsis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10226599/
https://www.ncbi.nlm.nih.gov/pubmed/37070465
http://dx.doi.org/10.1093/plcell/koad085
work_keys_str_mv AT nagarajanvinayk rnadegradomeanalysisrevealsdne1endoribonucleaseisrequiredfortheturnoverofdiversemrnasubstratesinarabidopsis
AT stuartcatherinej rnadegradomeanalysisrevealsdne1endoribonucleaseisrequiredfortheturnoverofdiversemrnasubstratesinarabidopsis
AT dibattistaannat rnadegradomeanalysisrevealsdne1endoribonucleaseisrequiredfortheturnoverofdiversemrnasubstratesinarabidopsis
AT accerbimonica rnadegradomeanalysisrevealsdne1endoribonucleaseisrequiredfortheturnoverofdiversemrnasubstratesinarabidopsis
AT caplanjeffreyl rnadegradomeanalysisrevealsdne1endoribonucleaseisrequiredfortheturnoverofdiversemrnasubstratesinarabidopsis
AT greenpamelaj rnadegradomeanalysisrevealsdne1endoribonucleaseisrequiredfortheturnoverofdiversemrnasubstratesinarabidopsis