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A gene expression map of shoot domains reveals regulatory mechanisms

Tian, Caihuan and Wang, Ying and Yu, Haopeng and He, Jun and Wang, Jin and Shi, Bihai and Du, Qingwei and Provart, Nicholas J. and Meyerowitz, Elliot M. and Jiao, Yuling (2019) A gene expression map of shoot domains reveals regulatory mechanisms. Nature Communications, 10 . Art. No. 141. ISSN 2041-1723. PMCID PMC6329838. doi:10.1038/s41467-018-08083-z. https://resolver.caltech.edu/CaltechAUTHORS:20190122-110956273

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Abstract

Gene regulatory networks control development via domain-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from the SAM peripheral zone. After initiation, leaves develop polarity patterns to form a planar shape. Here we compare translating RNAs among SAM and leaf domains. Using translating ribosome affinity purification and RNA sequencing to quantify gene expression in target domains, we generate a domain-specific translatome map covering representative vegetative stage SAM and leaf domains. We discuss the predicted cellular functions of these domains and provide evidence that dome seemingly unrelated domains, utilize common regulatory modules. Experimental follow up shows that the RABBIT EARS and HANABA TARANU transcription factors have roles in axillary meristem initiation. This dataset provides a community resource for further study of shoot development and response to internal and environmental signals.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41467-018-08083-zDOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329838/PubMed CentralArticle
ORCID:
AuthorORCID
Tian, Caihuan0000-0002-0794-5037
Yu, Haopeng0000-0003-0525-3157
Wang, Jin0000-0002-4924-1716
Provart, Nicholas J.0000-0001-5551-7232
Meyerowitz, Elliot M.0000-0003-4798-5153
Jiao, Yuling0000-0002-1189-1676
Additional Information:© 2019 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Received 06 August 2018; Accepted 18 December 2018; Published 11 January 2019. Data availability: TRAP-seq data have been deposited in the NCBI Short Read Archive with accession number SRP145572. The expression patterns of different domains were implemented in a web based genome browser available at http://bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpWeb.cgi?dataSource=Shoot_Apex. The source data underlying Figs. 1c-d, 2a, 3b, Supplementary Figs. 5, 7a, and Supplementary Data 1, 2, 4-6, 9-11 are provided as a Source Data file. The authors declare that all other data supporting the findings of this study are available within the manuscript and its Supplementary files or are available from the corresponding author upon request. We thank Drs. Yuval Eshed, Tengbo Huang, Thomas Laux, David Smyth, and Hirokazu Tsukaya for seeds. This work was supported by National Natural Science Foundation of China (NSFC) Grants 31430010, 31825002, 31861143021, and 31861130355, National Basic Research Program of China (973 Program) Grant 2014CB943500, and a Royal Society Newton Advanced Fellowship (award NAF/R1/180125) to Y.J., by the National Transgenic Science and Technology Program Grant 2016ZX08010-002, NSFC Grant 31770311, and Youth Innovation Promotion Association of CAS (2017139) to C.T., by NSFC Grant 31871245, University of CAS (Grant 110601M206), and the Beijing NOVA Program (Z161100004916107) to Y.W., and by the US NSF 2010 Project Grant MCB-0929349 to E.M.M. and Y.J. The Meyerowitz Laboratory is also supported by the Howard Hughes Medical Institute.
Funders:
Funding AgencyGrant Number
National Natural Science Foundation of China31430010
National Natural Science Foundation of China31825002
National Natural Science Foundation of China31861143021
National Natural Science Foundation of China31861130355
National Basic Research Program of China2014CB943500
Royal SocietyNAF/R1/180125
National Transgenic Science and Technology Program2016ZX08010-002
National Natural Science Foundation of China31770311
Chinese Academy of Sciences2017139
National Natural Science Foundation of China31871245
Chinese Academy of Sciences110601M206
Beijing NOVA ProgramZ161100004916107
NSFMCB-0929349
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
PubMed Central ID:PMC6329838
DOI:10.1038/s41467-018-08083-z
Record Number:CaltechAUTHORS:20190122-110956273
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190122-110956273
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:92394
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:22 Jan 2019 21:12
Last Modified:16 Nov 2021 03:50

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