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

Shi, Dongbo; Jouannet, Virginie; Agustí, Javier; Kaul, Verena; Levitsky, Victor G.; Sánchez, Pablo; Миронова, В. В.; Greb, Thomas

doi:10.1093/plcell/koaa019

Cited by 62 publications

(78 citation statements)

References 100 publications

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“…1D). More specifically, cluster 1 corresponds to vascular stem cells, as marked by cambium (Sup Fig 2C) expressing markers genes such as PHLOEM INTERCALATED WITH XYLEM (PXY) and SMAX1-LIKE 5 (SMXL5) (Shi et al 2021) (Sup Fig 3). Cluster 12 contains cells that are associated with phloem, containing the marker genes ALTERED PHLOEM DEVELOPMENT ( APL ) (Shi et al 2021; Bonke et al 2003) (Sup Fig 3).…”

Section: Resultsmentioning

confidence: 99%

“…More specifically, cluster 1 corresponds to vascular stem cells, as marked by cambium (Sup Fig 2C) expressing markers genes such as PHLOEM INTERCALATED WITH XYLEM (PXY) and SMAX1-LIKE 5 (SMXL5) (Shi et al 2021) (Sup Fig 3). Cluster 12 contains cells that are associated with phloem, containing the marker genes ALTERED PHLOEM DEVELOPMENT ( APL ) (Shi et al 2021; Bonke et al 2003) (Sup Fig 3). Cluster 8 is enriched for vascular xylem parenchyma genes, for example CYTOCHROME P450, FAMILY 708 (CYP708A3) (Shi et al 2021) (Sup Fig 3), and shows signatures of cell expansion and cellulose biosynthesis.…”

Section: Resultsmentioning

confidence: 99%

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A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

Neumann

Smaczniak

et al. 2021

Preprint

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Identity and functions of plant cells are influenced by their precise cellular location within the plant body. Cellular heterogeneity in growth and differentiation trajectories results in organ patterning. Therefore, assessing this heterogeneity at molecular scale is a major question in developmental biology. Single-cell transcriptomics (scRNA-seq) allows to characterize and quantify gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during the scRNA-seq procedure. To recover the original location of cells is essential to link gene activity with cellular function and morphology. Here, we reconstruct genome-wide gene expression patterns of individual cells in a floral meristem by combining single-nuclei RNA-seq with 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the data are used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

Neumann

Smaczniak

et al. 2021

Preprint

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“…Heterogeneity of the transcriptome and epigenome among these different tissues and developmental stages are well characterized in A . thaliana plants [ 28 – 31 ]. During plant reproductive development, dynamic chromatin remodelling including the localizations of DNA methylation and specific histone species occurs [ 32 – 36 ].…”

Section: Introductionmentioning

confidence: 99%

De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome

et al. 2021

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The manner in which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines. Among them, we determined the individual LUC insertion loci in 76 lines and found that one-third of them were transcribed de novo even in the intergenic or inherently unexpressed regions. In the transcribed lines, transcription-related chromatin marks were detected across the newly activated transcribed regions. These results agreed with our previous findings in A. thaliana cultured cells under a similar experimental scheme. A comparison of the results of the T2-plant and cultured cell experiments revealed that the de novo-activated transcription concomitant with local chromatin remodelling was inheritable. During one-generation inheritance, it seems likely that the transcription activities of the LUC inserts trapped by the endogenous genes/transcripts became stronger, while those of de novo transcription in the intergenic/untranscribed regions became weaker. These findings may offer a clue for the elucidation of the mechanism by which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome.

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“…Heterogeneity of the transcriptome and epigenome among these different tissues and developmental stages are well characterized in A. thaliana plants [28][29][30][31]. During plant reproductive development, dynamic chromatin remodelling including the localizations of DNA methylation and specific histone species occurs [32][33][34][35][36].…”

Section: Introductionmentioning

confidence: 99%

De novoactivated transcription of inserted foreign coding sequences is inheritable in the plant genome

Hata

Takada

Hayakawa

et al. 2020

Preprint

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The manner in which newborn genes become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines. Among them, we determined the individual LUC insertion loci in 76 lines and found that one-third of them were transcribed de novo even in the intergenic or inherently unexpressed regions. In the transcribed lines, transcription-related epigenetic marks were detected across the newly activated transcribed regions. These results agreed with our previous findings in A. thaliana cultured cells under a similar experimental scheme. The comparison of the results of the T2-plant and cultured cell experiments revealed that the de novo-activated transcription caused by local chromatin remodelling was inheritable. During one-generation inheritance, it seems likely that the transcription activities of the LUC inserts trapped by the endogenous genes/transcripts became stronger, while those of de novo transcription in the intergenic/untranscribed regions became weaker. These findings may offer a clue for the elucidation of the mechanism via which newborn genes become transcriptionally activated and fixed in the plant genome.

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

Cited by 62 publications

References 100 publications

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome

De novoactivated transcription of inserted foreign coding sequences is inheritable in the plant genome

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