TY - JOUR

T1 - Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures

AU - Shi, Dongbo

AU - Jouannet, Virginie

AU - Agustí, Javier

AU - Kaul, Verena

AU - Levitsky, Victor

AU - Sanchez, Pablo

AU - Mironova, Victoria V.

AU - Greb, Thomas

N1 - Funding Information: This work was supported by the European Research Council (ERC) through an ERC Consolidator grant [647148, PLANTSTEMS to T.G.], the Deutsche Forschungsgemeinschaft [DFG, through a Heisenberg Professorship GR2104/5-2 and the SFB1101 to T.G.], a postdoctoral fellowship of the Alexander von Humboldt-Stiftung [3.5-JPN –1164674-HFST-P to D.S.], the Japan Society for the Promotion of Science [JSPS Overseas Research Fellowships 201960008 to D.S.], a postdoctoral fellowship of the European Molecular Biology Organization [EMBO, ALTF 342-2012 to V.J.], the Russian Foundation for Basic Research and the Deutsche Forschungsgemeinschaft [RFBR-DFG 19-54-12013 for the co-operation of Russian and German teams], and the Russian Budget project [0259-2021-0009 to V.V.M and V.L]. Publisher Copyright: © The Author(s) 2020. Published by Oxford University Press on behalf of American Society of Plant Biologists. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/4/17

Y1 - 2021/4/17

N2 - Genome-wide gene expression maps with a high spatial resolution have substantially accelerated plant molecular science. However, the number of characterized tissues and growth stages is still small due to the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next-generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibers, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. By determining overrepresented transcription factor binding regions in the promoters of differentially expressed genes, we identified candidate tissue-specific transcriptional regulators. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrate that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling. Tissue-specific gene expression values can be accessed online at https://arabidopsis-stem.cos.uni-heidelberg.de/.

AB - Genome-wide gene expression maps with a high spatial resolution have substantially accelerated plant molecular science. However, the number of characterized tissues and growth stages is still small due to the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next-generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibers, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. By determining overrepresented transcription factor binding regions in the promoters of differentially expressed genes, we identified candidate tissue-specific transcriptional regulators. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrate that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling. Tissue-specific gene expression values can be accessed online at https://arabidopsis-stem.cos.uni-heidelberg.de/.

UR - http://www.scopus.com/inward/record.url?scp=85105689042&partnerID=8YFLogxK

U2 - 10.1093/plcell/koaa019

DO - 10.1093/plcell/koaa019

M3 - Article

C2 - 33582756

AN - SCOPUS:85105689042

VL - 33

SP - 200

EP - 223

JO - The Plant cell

JF - The Plant cell

SN - 1040-4651

IS - 2

ER -