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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE118138 | GEO | 2019/10/08

REPOSITORIES: GEO

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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.

| S-EPMC6815143 | biostudies-literature

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.

2019-10-08 | GSE118137 | GEO

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

2019-10-08 | GSE118136 | GEO

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

| PRJNA484634 | ENA

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

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

| PRJNA484636 | ENA

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]

| PRJNA484637 | ENA

Regulation of stomatal opening and histone modification by photoperiod in Arabidopsis thaliana.

Project description:Stomatal movements are regulated by many environmental signals, such as light, CO2, temperature, humidity, and drought. Recently, we showed that photoperiodic flowering components have positive effects on light-induced stomatal opening in Arabidopsis thaliana. In this study, we determined that light-induced stomatal opening and increased stomatal conductance were larger in plants grown under long-day (LD) conditions than in those grown under short-day (SD) conditions. Gene expression analyses using purified guard cell protoplasts revealed that FT and SOC1 expression levels were significantly increased under LD conditions. Interestingly, the enhancement of light-induced stomatal opening and increased SOC1 expression in guard cells due to LD conditions persisted for at least 1 week after plants were transferred to SD conditions. We then investigated histone modification using chromatin immunoprecipitation-PCR, and observed increased trimethylation of lysine 4 on histone 3 (H3K4) around SOC1. We also found that LD-dependent enhancement of light-induced stomatal opening and H3K4 trimethylation in SOC1 were suppressed in the ft-2 mutant. These results indicate that photoperiod is an important environmental cue regulating stomatal opening, and that LD conditions enhance light-induced stomatal opening and epigenetic modification (H3K4 trimethylation) around SOC1, a positive regulator of stomatal opening, in an FT-dependent manner. Thus, this study provides novel insights into stomatal responses to photoperiod.

| S-EPMC6646381 | biostudies-literature

Histone acetylation orchestrates wound-induced transcriptional activation and cellular reprogramming in Arabidopsis.

Project description:Plant somatic cells reprogram and regenerate new tissues or organs when they are severely damaged. These physiological processes are associated with dynamic transcriptional responses but how chromatin-based regulation contributes to wound-induced gene expression changes and subsequent cellular reprogramming remains unknown. In this study we investigate the temporal dynamics of the histone modifications H3K9/14ac, H3K27ac, H3K4me3, H3K27me3, and H3K36me3, and analyze their correlation with gene expression at early time points after wounding. We show that a majority of the few thousand genes rapidly induced by wounding are marked with H3K9/14ac and H3K27ac before and/or shortly after wounding, and these include key wound-inducible reprogramming genes such as WIND1, ERF113/RAP2.6?L and LBD16. Our data further demonstrate that inhibition of GNAT-MYST-mediated histone acetylation strongly blocks wound-induced transcriptional activation as well as callus formation at wound sites. This study thus uncovered a key epigenetic mechanism that underlies wound-induced cellular reprogramming in plants.

| S-EPMC6828771 | biostudies-literature

Cell-type-specific genomics reveals histone modification dynamics in mammalian meiosis.

Project description:Meiosis is the specialized cell division during which parental genomes recombine to create genotypically unique gametes. Despite its importance, mammalian meiosis cannot be studied in vitro, greatly limiting mechanistic studies. In vivo, meiocytes progress asynchronously through meiosis and therefore the study of specific stages of meiosis is a challenge. Here, we describe a method for isolating pure sub-populations of nuclei that allows for detailed study of meiotic substages. Interrogating the H3K4me3 landscape revealed dynamic chromatin transitions between substages of meiotic prophase I, both at sites of genetic recombination and at gene promoters. We also leveraged this method to perform the first comprehensive, genome-wide survey of histone marks in meiotic prophase, revealing a heretofore unappreciated complexity of the epigenetic landscape at meiotic recombination hotspots. Ultimately, this study presents a straightforward, scalable framework for interrogating the complexities of mammalian meiosis.

| S-EPMC6707301 | biostudies-literature

Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification.

Project description:The photoreceptor UV RESISTANCE LOCUS 8 (UVR8) specifically mediates photomorphogenic responses to UV-B wavelengths. UVR8 acts by regulating transcription of a set of genes, but the underlying mechanisms are unknown. Previous research indicated that UVR8 can associate with chromatin, but the specificity and functional significance of this interaction are not clear. Here we show, by chromatin immunoprecipitation, that UV-B exposure of Arabidopsis increases acetylation of lysines K9 and/or K14 of histone H3 at UVR8-regulated gene loci in a UVR8-dependent manner. The transcription factors HY5 and/or HYH, which mediate UVR8-regulated transcription, are also required for this chromatin modification, at least for the ELIP1 gene. Furthermore, sequencing of the immunoprecipitated DNA revealed that all UV-B-induced enrichments in H3K9,14diacetylation across the genome are UVR8-dependent, and approximately 40 % of the enriched loci contain known UVR8-regulated genes. In addition, inhibition of histone acetylation by anacardic acid reduces the UV-B induced, UVR8 mediated expression of ELIP1 and CHS. No evidence was obtained in yeast 2-hybrid assays for a direct interaction between either UVR8 or HY5 and several proteins involved in light-regulated histone modification, nor for the involvement of these proteins in UVR8-mediated responses in plants, although functional redundancy between proteins could influence the results. In summary, this study shows that UVR8 regulates a specific chromatin modification associated with transcriptional regulation of a set of UVR8-target genes.

| S-EPMC5080334 | biostudies-literature

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