ArticleThe Plant cell2021
Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures.
Article in The Plant cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 87 citations in OpenAlex.
- Transcriptomic Data Meta-Analysis Sheds Light on High Light Response inInternational journal of molecular sciences · 2022Pooled it
- Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem.Science advances · 2026Article
- Plant hormone and peptide signaling converge in the genetic network regulating cambium activation in Arabidopsis roots.The Plant cell · 2026Article
- Co-extraction of Small RNAs and Total RNA from Arbuscular Mycorrhizal Roots Using Laser Microdissection.Methods in molecular biology (Clifton, N.J.) · 2026Article
- SUPPRESSOR OF LAZY QUADRUPLE 1 acts at ER-plasma membrane contact sites to control a gravitropism pathway in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Intercellular compartmentation of trehalose 6-phosphate metabolism in Setaria viridis leaves.Journal of experimental botany · 2025Article
- Companion cells with high florigen production express other small proteins and reveal a nitrogen-sensitiveeLife · 2025Article
- Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks.Genome biology · 2025Article
- Companion cells with high florigen production express other small proteins and reveal a nitrogen-sensitivebioRxiv : the preprint server for biology · 2025Article
- A cytokinin response maximum induces and activates bifacial stem cells for radial growth.Nature plants · 2025Article
- Advances in Small RNA Regulation of Female Gametophyte Development in Flowering Plants.Plants (Basel, Switzerland) · 2025Review
- GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte.The Plant journal : for cell and molecular biology · 2025Article
- ACT2.6: Global Gene Coexpression Network inGenes · 2025Article
- A gene expression atlas ofFrontiers in plant science · 2025Article
- Spatial transcriptome analysis reveals de novo regeneration of poplar roots.Horticulture research · 2024Article
- ggPlantmap: an open-source R package for the creation of informative and quantitative ggplot maps derived from plant images.Journal of experimental botany · 2024Article
- Analysis of Xylem Cells by Nucleus-Based Transcriptomics and Chromatin Profiling.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Cell-type-specific control of secondary cell wall formation by Musashi-type translational regulators ineLife · 2023Article
- Photoperiodic flowering in Arabidopsis: Multilayered regulatory mechanisms of CONSTANS and the florigen FLOWERING LOCUS T.Plant communications · 2023Review
- Dosage balance acts as a time-dependent selective barrier to subfunctionalization.BMC ecology and evolution · 2023Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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/.
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