In Vivo Determination of Direct Targets of the Nonsense-Mediated Decay Pathway in Drosophila

Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a mRNA degradation pathway that regulates a significant portion of the transcriptome. The expression levels of numerous genes are known to be altered in NMD mutants, but it is not known which of these transcripts is a direct pathway target. Here,...

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Main Authors:	Chapin, Alex, Hu, Hao, Rynearson, Shawn G., Hollien, Julie, Yandell, Mark, Metzstein, Mark M.
Format:	Online
Language:	English
Published:	Genetics Society of America 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962487/

id	pubmed-3962487
recordtype	oai_dc
spelling	pubmed-39624872014-03-24 In Vivo Determination of Direct Targets of the Nonsense-Mediated Decay Pathway in Drosophila Chapin, Alex Hu, Hao Rynearson, Shawn G. Hollien, Julie Yandell, Mark Metzstein, Mark M. Investigations Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a mRNA degradation pathway that regulates a significant portion of the transcriptome. The expression levels of numerous genes are known to be altered in NMD mutants, but it is not known which of these transcripts is a direct pathway target. Here, we present the first genome-wide analysis of direct NMD targeting in an intact animal. By using rapid reactivation of the NMD pathway in a Drosophila melanogaster NMD mutant and globally monitoring of changes in mRNA expression levels, we can distinguish between primary and secondary effects of NMD on gene expression. Using this procedure, we identified 168 candidate direct NMD targets in vivo. Remarkably, we found that 81% of direct target genes do not show increased expression levels in an NMD mutant, presumably due to feedback regulation. Because most previous studies have used up-regulation of mRNA expression as the only means to identify NMD-regulated transcripts, our results provide new directions for understanding the roles of the NMD pathway in endogenous gene regulation during animal development and physiology. For instance, we show clearly that direct target genes have longer 3′ untranslated regions compared with nontargets, suggesting long 3′ untranslated regions target mRNAs for NMD in vivo. In addition, we investigated the role of NMD in suppressing transcriptional noise and found that although the transposable element Copia is up-regulated in NMD mutants, this effect appears to be indirect. Genetics Society of America 2014-01-15 /pmc/articles/PMC3962487/ /pubmed/24429422 http://dx.doi.org/10.1534/g3.113.009357 Text en Copyright © 2014 Chapin et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Chapin, Alex Hu, Hao Rynearson, Shawn G. Hollien, Julie Yandell, Mark Metzstein, Mark M.
spellingShingle	Chapin, Alex Hu, Hao Rynearson, Shawn G. Hollien, Julie Yandell, Mark Metzstein, Mark M. In Vivo Determination of Direct Targets of the Nonsense-Mediated Decay Pathway in Drosophila
author_facet	Chapin, Alex Hu, Hao Rynearson, Shawn G. Hollien, Julie Yandell, Mark Metzstein, Mark M.
author_sort	Chapin, Alex
title	In Vivo Determination of Direct Targets of the Nonsense-Mediated Decay Pathway in Drosophila
title_short	In Vivo Determination of Direct Targets of the Nonsense-Mediated Decay Pathway in Drosophila
title_full	In Vivo Determination of Direct Targets of the Nonsense-Mediated Decay Pathway in Drosophila
title_fullStr	In Vivo Determination of Direct Targets of the Nonsense-Mediated Decay Pathway in Drosophila
title_full_unstemmed	In Vivo Determination of Direct Targets of the Nonsense-Mediated Decay Pathway in Drosophila
title_sort	in vivo determination of direct targets of the nonsense-mediated decay pathway in drosophila
description	Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a mRNA degradation pathway that regulates a significant portion of the transcriptome. The expression levels of numerous genes are known to be altered in NMD mutants, but it is not known which of these transcripts is a direct pathway target. Here, we present the first genome-wide analysis of direct NMD targeting in an intact animal. By using rapid reactivation of the NMD pathway in a Drosophila melanogaster NMD mutant and globally monitoring of changes in mRNA expression levels, we can distinguish between primary and secondary effects of NMD on gene expression. Using this procedure, we identified 168 candidate direct NMD targets in vivo. Remarkably, we found that 81% of direct target genes do not show increased expression levels in an NMD mutant, presumably due to feedback regulation. Because most previous studies have used up-regulation of mRNA expression as the only means to identify NMD-regulated transcripts, our results provide new directions for understanding the roles of the NMD pathway in endogenous gene regulation during animal development and physiology. For instance, we show clearly that direct target genes have longer 3′ untranslated regions compared with nontargets, suggesting long 3′ untranslated regions target mRNAs for NMD in vivo. In addition, we investigated the role of NMD in suppressing transcriptional noise and found that although the transposable element Copia is up-regulated in NMD mutants, this effect appears to be indirect.
publisher	Genetics Society of America
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962487/
_version_	1612070389569028096

In Vivo Determination of Direct Targets of the Nonsense-Mediated Decay Pathway in Drosophila

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