Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures.
Arabidopsis
/ genetics
Binding Sites
Cell Nucleus
/ metabolism
Databases, Genetic
Gene Expression Profiling
Gene Expression Regulation, Plant
Green Fluorescent Proteins
/ metabolism
Inflorescence
/ genetics
Organ Specificity
/ genetics
Phloem
/ metabolism
Plant Stems
/ genetics
Promoter Regions, Genetic
/ genetics
RNA, Messenger
/ genetics
RNA-Seq
Species Specificity
Transcription Factors
/ metabolism
Transgenes
Wood
/ genetics
Journal
The Plant cell
ISSN: 1532-298X
Titre abrégé: Plant Cell
Pays: England
ID NLM: 9208688
Informations de publication
Date de publication:
17 04 2021
17 04 2021
Historique:
received:
05
10
2020
accepted:
02
11
2020
pubmed:
15
2
2021
medline:
16
7
2021
entrez:
14
2
2021
Statut:
ppublish
Résumé
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/.
Identifiants
pubmed: 33582756
pii: 6017181
doi: 10.1093/plcell/koaa019
pmc: PMC8136906
doi:
Substances chimiques
RNA, Messenger
0
Transcription Factors
0
Green Fluorescent Proteins
147336-22-9
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
200-223Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of American Society of Plant Biologists.
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