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Transcriptome-Wide Analysis of Uncapped mRNAs in Arabidopsis Reveals Regulation of mRNA Degradation

Jiao, Yuling and Riechmann, José Luis and Meyerowitz, Elliot M. (2008) Transcriptome-Wide Analysis of Uncapped mRNAs in Arabidopsis Reveals Regulation of mRNA Degradation. Plant Cell, 20 (10). pp. 2571-2585. ISSN 1040-4651. PMCID PMC2590717. doi:10.1105/tpc.108.062786. https://resolver.caltech.edu/CaltechAUTHORS:JIApc08

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Abstract

The composition of the transcriptome is determined by a balance between mRNA synthesis and degradation. An important route for mRNA degradation produces uncapped mRNAs, and this decay process can be initiated by decapping enzymes, endonucleases, and small RNAs. Although uncapped mRNAs are an important intermediate for mRNA decay, their identity and abundance have never been studied on a large scale until recently. Here, we present an experimental method for transcriptome-wide profiling of uncapped mRNAs that can be used in any eukaryotic system. We applied the method to study the prevalence of uncapped transcripts during the early stages of Arabidopsis thaliana flower development. Uncapped transcripts were identified for the majority of expressed genes, although at different levels. By comparing uncapped RNA levels with steady state overall transcript levels, our study provides evidence for widespread mRNA degradation control in numerous biological processes involving genes of varied molecular functions, implying that uncapped mRNA levels are dynamically regulated. Sequence analyses identified structural features of transcripts and cis-elements that were associated with different levels of uncapping. These transcriptome-wide profiles of uncapped mRNAs will aid in illuminating new regulatory mechanisms of eukaryotic transcriptional networks.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1105/tpc.108.062786DOIArticle
http://www.plantcell.org/cgi/content/abstract/20/10/2571PublisherArticle
http://www.plantcell.org/cgi/content/full/tpc.108.062786/DC1PublisherSupporting Information
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2590717/PubMed CentralArticle
ORCID:
AuthorORCID
Jiao, Yuling0000-0002-1189-1676
Meyerowitz, Elliot M.0000-0003-4798-5153
Additional Information:© 2008 American Society of Plant Biologists. Received August 21, 2008; revised September 26, 2008; accepted October 10, 2008; First published online October 24, 2008; 10.1105/tpc.108.062786 We thank Vijaya Kumar, Lorian Schaeffer, and Joanne Tan-Cabugao for assistance with microarray manufacture, David Mathog for advice on sequence analysis, and Zachary Nimchuk, Adrienne Roeder, and Kathrin Schrick for comments on the manuscript. This work was supported by National Science Foundation 2010 Project Grant 0520193 to J.L.R. and E.M.M. and by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at the California Institute of Technology. Accession Number: All raw microarray data from our analyses have been deposited in the Gene Expression Omnibus under accession number GSE12043. Online version contains Web-only data www.plantcell.org/cgi/doi/10.1105/tpc.108.062786 Supplemental Data: The following materials are available in the online version of this article. Supplemental Figure 1. Overview of the T4 RNA Ligase-Mediated Method for the Isolation of Uncapped mRNA. Supplemental Figure 2. Comparison of PCR Conditions for Second Strand Synthesis and Amplification.
Funders:
Funding AgencyGrant Number
NSFMCB-0520193
Caltech Millard and Muriel Jacobs Genetics and Genomics LaboratoryUNSPECIFIED
Subject Keywords:NATURAL ANTISENSE TRANSCRIPTS; REPEAT RECEPTOR KINASE; GENOME-WIDE; GENE-EXPRESSION; POSTTRANSCRIPTIONAL EVENTS; POSTEMBRYONIC DEVELOPMENT; TRANSLATIONAL INHIBITION; FLOWER DEVELOPMENT; DECAPPING COMPLEX; ENDOGENOUS SIRNA
Issue or Number:10
PubMed Central ID:PMC2590717
DOI:10.1105/tpc.108.062786
Record Number:CaltechAUTHORS:JIApc08
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:JIApc08
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:12976
Collection:CaltechAUTHORS
Deposited By:INVALID USER
Deposited On:15 Jan 2009 23:44
Last Modified:08 Nov 2021 22:34

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