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The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection

ABSTRACT: The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection

PROVIDER: PRJNA689568 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13349172.fastq.gz	Fastqsanger.gz
	SRR13349173.fastq.gz	Fastqsanger.gz
	SRR13349174.fastq.gz	Fastqsanger.gz
	SRR13349175.fastq.gz	Fastqsanger.gz
	SRR13349176.fastq.gz	Fastqsanger.gz

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The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection

Project description:The flowering plant life cycle consists of alternating haploid (gametophyte) and diploid (sporophyte) generations, where the sporophytic generation begins with fertilization of haploid gametes. In Arabidopsis, genome-wide DNA demethylation is required for normal development, catalyzed by the DEMETER (DME) DNA demethylase in the gamete companion cells of male and female gametophytes. In the sporophyte, postembryonic growth and development are largely dependent on the activity of numerous stem cell niches, or meristems. Analyzing Arabidopsis plants homozygous for a loss-of-function dme-2 allele, we show that DME influences many aspects of sporophytic growth and development. dme-2 mutants exhibited delayed seed germination, variable root hair growth, aberrant cellular proliferation and differentiation followed by enhanced de novo shoot formation, dysregulation of root quiescence and stomatal precursor cells, and inflorescence meristem (IM) resurrection. We also show that sporophytic DME activity exerts a profound effect on the transcriptome of developing Arabidopsis plants, including discrete groups of regulatory genes that are misregulated in dme-2 mutant tissues, allowing us to potentially link phenotypes to changes in specific gene expression pathways. These results show that DME plays a key role in sporophytic development and suggest that DME-mediated active DNA demethylation may be involved in the maintenance of stem cell activities during the sporophytic life cycle in Arabidopsis.

2021-01-05 | GSE164217 | GEO

The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection.

| S-EPMC8307533 | biostudies-literature

Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem

Project description:To generate a de novo transcriptome assembly from three different parts of the Ceratopteris richardii young sporophyte (Hn-n cultivar). We then performed a differential gene expression analysis between the different plant segments, while trying to understand the expressed genes for each Ceratopteris part.

2022-08-15 | GSE207873 | GEO

Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens

2013-07-29 | GSE32928 | GEO

A Physcomitrella protein acts in spermatogenesis and sporophyte abortion

Project description:Functional targeting of PpPINC gene in Physcomitrella, researching it's role during gametangia and sporophyte development.

2022-06-19 | GSE205257 | GEO

Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens

Project description:Bryophytes are the most basal of the extant land plants. A major feature of these plants is the biphasic alteration of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. To analyse the differences in the transcriptome of the early gametophyte (protonema) and early and mid-sporophyte phases of the moss Physcomitrella patens, microarray gene expression profiles were performed using dissected sporophyte tissue. Through further analysis the early and mid-sporophyte phases were compared. RNA isolated from the Gametophytic protonemal tissue was hybridised to six microarrays. Each microarray was hybridised with RNA from a separate biological replicate. Three of these microarrays were co-hybridised with RNA isolated from early sporophytes. With the third gametophyte biological replicate and early sporophyte replicate a dye swap was carried out. The remaining three microarrays hybridised with RNA from the gametophytes were co-hybridised with RNA from mid-sporophytic tissue. A dye swap was carried out on the sixth gametophyte replicate and third mid-sporophyte replicate.To meet the quality requirements for the microarray experiment, at least 400 sporophytes were used per extraction. Three or four RNA extracts were then pooled for further precipitation to maximise purity and concentration. Up to 1600 sporophytes were harvested to prepare sufficient RNA for each microarray replicate. In bioinformatic analysis the channels were split into individual channels and the early and mid-sporophyte were compared.

2013-07-29 | E-GEOD-32928 | biostudies-arrayexpress

Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem

Project description:Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem

| PRJNA857489 | ENA

Altered expression of SELF-PRUNING disrupts meristem homeostasis and facilitates delivery of signals to the meristem

Project description:Meristem maintenance, achieved through the highly conserved CLAVATA-WUSCHEL (CLV-WUS) regulatory circuit, is fundamental in balancing stem cell proliferation with cellular differentiation. Disruptions to meristem homeostasis can alter meristem size, leading to enlarged organs. Cotton, the world’s most important fiber crop, shows inherent variation in fruit size. Leveraging meristem regulation could benefit cotton agriculture and increase yields of high-quality fibers. Using virus-based gene manipulation in cotton, we altered expression of genes functioning in the CLV-WUS circuit to perturb meristem regulation and increase fruit size. Targeted alteration of individual components of the CLV-WUS circuit only modestly fasciated flowers and fruits. Unexpectedly, controlled expression of meristem regulator SELF-PRUNING (SP) dramatically increased the impacts of altered CLV-WUS expression on flower and fruit fasciation. Meristem transcriptomics show SP and genes of the CLV-WUS circuit are expressed independently from each other, suggesting these gene products are not acting in the same path. Virus-induced silencing of GhSP facilitated delivery of other signals to the meristem to dramatically alter organ specification. SELF-PRUNING has a role in cotton meristem homeostasis, and changes in GhSP expression increased access of virus-based signals to the meristem.

2023-03-01 | GSE206189 | GEO

Bulk RNA-sequencing of wild-type (Ler) and dme-2 calli harvested 7 days after incubation on callus-inducing medium and of de novo regenerated shoots harvested 14 days after incubation on shoot-inducing medium

Project description:Plants possess high potential for somatic cell reprogramming. Despite extensive studies on the molecular network and key genetic factors during regeneration, the underlying epigenetic landscape remains incompletely understood. Here, we explored methylome and transcriptome dynamics during two-step plant regeneration. During leaf-to-callus transition, genic CG methylation shifts, while pericentromeric regions undergo substantial CG and extensive CHH hypomethylation. Upon shoot regeneration, methylation increases across all cytosine contexts, particularly in pericentromeric regions, coinciding with RNA-directed DNA methylation (RdDM) pathway activation. However, the DEMETER (DME)-deficient dme-2 mutant exhibited significant genic CG redistribution and global non-CG hypomethylation, partly due to RdDM downregulation. The dme-2 mutant affects gene expression in pluripotency and shoot meristem development, promoting regeneration through a reprogrammed state by pericentromeric hypomethylation. Our study demonstrates the intimate linkage between DME demethylase and RdDM underlying pericentromeric non-CG methylation maintenance, providing insight into the epigenetic mechanisms balancing pluripotency states and genome stability during plant regeneration.

2024-10-25 | GSE269609 | GEO

Transcription profiling by high throughput sequencing of Funaria hygrometrica sporophyte and gametophyte tissue

Project description:Funaria hygrometrica sporophyte/gametophyte gene expression

2011-10-01 | E-MTAB-284 | biostudies-arrayexpress