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Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage [RNA-Seq]

ABSTRACT: Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage [RNA-Seq]

PROVIDER: PRJNA484636 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7646410.fastq.gz	Fastqsanger.gz
	SRR7646411.fastq.gz	Fastqsanger.gz
	SRR7646412.fastq.gz	Fastqsanger.gz
	SRR7646413.fastq.gz	Fastqsanger.gz

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Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage

Project description:Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage

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Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage [ChIP-Seq]

Project description:Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage [ChIP-Seq]

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Cell-type-specific transcriptome and histone modification dynamics during cellular reprogramming in the Arabidopsis stomatal lineage.

Project description:Plant cells maintain remarkable developmental plasticity, allowing them to clonally reproduce and to repair tissues following wounding; yet plant cells normally stably maintain consistent identities. Although this capacity was recognized long ago, our mechanistic understanding of the establishment, maintenance, and erasure of cellular identities in plants remains limited. Here, we develop a cell-type-specific reprogramming system that can be probed at the genome-wide scale for alterations in gene expression and histone modifications. We show that relationships among H3K27me3, H3K4me3, and gene expression in single cell types mirror trends from complex tissue, and that H3K27me3 dynamics regulate guard cell identity. Further, upon initiation of reprogramming, guard cells induce H3K27me3-mediated repression of a regulator of wound-induced callus formation, suggesting that cells in intact tissues may have mechanisms to sense and resist inappropriate dedifferentiation. The matched ChIP-sequencing (seq) and RNA-seq datasets created for this analysis also serve as a resource enabling inquiries into the dynamic and global-scale distribution of histone modifications in single cell types in plants.

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Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage

Project description:This SuperSeries is composed of the SubSeries listed below.

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Regulation of Stomatal Development by Stomatal Lineage miRNAs

Project description:Stomata in the plant epidermis play a vital role in growth and survival by controlling gas exchange and immunity to pathogens. A genetic frame of key transcriptional factors and cellular communication has been established, by which plants modulate stomatal cell fate and patterning. miRNAs contribute to functional and developmental plasticity in multicellular organisms. However, it remains very elusive as to whether miRNAs pitch in stomatal development. Here, we reveal dynamic miRNA expression profiles from stomatal lineage cells in a development stage-specific manner and show that stomatal lineage miRNAs positively and negatively regulate stomatal formation and pattern to avoid clustered and paired stomata. Target prediction of stomatal lineage miRNAs suggests potential cellular processes involved in stomatal development. Furthermore, dysregulation of stomatal lineage miRNAs and their target mRNAs disclose unexpected genetic pathways modulating stomatal development. Our study demonstrates that miRNAs constitute an additional layer in the complex regulatory mechanism of stomatal development.

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Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage [RNA-Seq]

Project description:Plants and plant cells exhibit extraordinary regenerative capacity, yet plant cells stably maintain their identities once acquired. Although this capacity was recognized more than 100 years ago, our mechanistic understanding of the establishment, maintenance, and erasure of cellular identities in plants remains limited. Here we develop a cell-type specific reprogramming system than can be probed at the genome-wide scale for alterations in gene expression and histone modifications before and during reprogramming. We show that the relationship between H3K27me3 and H3K4me3 and gene expression in a single cell type mirrors trends from more complex tissue, and that H3K27me3 dynamics is a critical regulator of guard cell identity. Further, guard cells can sense and resist inappropriate reprogramming, in part via regulation of the wounding response through H3K27me3. The matched single cell-type ChIP-seq and RNA-seq datasets created for this analysis also serve as a resource enabling inquiries into the dynamic and global-scale distribution of histone modifications.

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Project description:Regulation of Stomatal Development by Stomatal Lineage miRNAs

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Project description:Dynamic cell identities underlie flexible developmental programs. The stomatal lineages in the Arabidopsis leaf epidermis feature asynchronous and indeterminate divisions that can be modulated by environmental cues. The products of these lineages, stomatal guard cells and pavement cells, regulate plant-atmosphere exchanges, and the epidermis as a whole influences overall leaf growth. How flexibility is encoded in development of the stomatal lineage, and how cell fates are coordinated in the leaf are open questions. Here, we offer single-cell transcriptomes to uncover models of cell differentiation within Arabidopsis leaf tissue.

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