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Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

Jiao, Yuling and Meyerowitz, Elliot M. (2010) Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Molecular Systems Biology, 6 . Art. No. 419. ISSN 1744-4292. PMCID PMC2990639. https://resolver.caltech.edu/CaltechAUTHORS:20101130-093613906

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Abstract

Determining both the expression levels of mRNA and the regulation of its translation is important in understanding specialized cell functions. In this study, we describe both the expression profiles of cells within spatiotemporal domains of the Arabidopsis thaliana flower and the post-transcriptional regulation of these mRNAs, at nucleotide resolution. We express a tagged ribosomal protein under the promoters of three master regulators of flower development. By precipitating tagged polysomes, we isolated cell type specific mRNAs that are probably translating, and quantified those mRNAs through deep sequencing. Cell type comparisons identified known cell-specific transcripts and uncovered many new ones, from which we inferred cell type-specific hormone responses, promoter motifs and coexpressed cognate binding factor candidates, and splicing isoforms. By comparing translating mRNAs with steady-state overall transcripts, we found evidence for widespread post-transcriptional regulation at both the intron splicing and translational stages. Sequence analyses identified structural features associated with each step. Finally, we identified a new class of noncoding RNAs associated with polysomes. Findings from our profiling lead to new hypotheses in the understanding of flower development.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/msb.2010.76 DOIArticle
http://www.nature.com/msb/journal/v6/n1/full/msb201076.htmlPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990639/PubMed CentralArticle
ORCID:
AuthorORCID
Jiao, Yuling0000-0002-1189-1676
Meyerowitz, Elliot M.0000-0003-4798-5153
Additional Information:© 2010 EMBO and Macmillan Publishers Limited. Molecular Systems Biology is an open-access journal published by European Molecular Biology Organization and Nature Publishing Group. This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License. Received 19.3.10; accepted 27.8.2010. published online 5 October 2010. We thank J Bailey-Serres, T Laux, I Moore, and F Wellmer for seeds and constructs; X Zhang and S-O Shan for invaluable help during polysome isolation; A Mortazavi, B Williams, B Wold, and H Jiang for advice on deep sequencing and data processing; H Amrhein, L Schaeffer, and D Trout for professional technical assistance; and W Li, A Roeder, K Sugimoto, and other members of the Meyerowitz lab for comments on the paper. This study was supported by the Edelman Discovery Fund of the California Institute of Technology (CIT) to EMM, by NSF 2010 Project grant MCB-0929349 to EMM and YJ, and by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at CIT. The authors declare that they have no conflict of interest.
Funders:
Funding AgencyGrant Number
Caltech Edelman Discovery FundUNSPECIFIED
NSFMCB-0929349
Caltech Millard and Muriel Jacobs Genetics and Genomics LaboratoryUNSPECIFIED
Subject Keywords:Arabidopsis; flower; intron; transcriptome; translation
PubMed Central ID:PMC2990639
Record Number:CaltechAUTHORS:20101130-093613906
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20101130-093613906
Usage Policy:This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License.
ID Code:21055
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:04 Dec 2010 00:52
Last Modified:03 Oct 2019 02:19

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