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Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis

ABSTRACT: Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis

PROVIDER: PRJNA649530 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12344600.fastq.gz	Fastqsanger.gz
	SRR12344601.fastq.gz	Fastqsanger.gz
	SRR12344602.fastq.gz	Fastqsanger.gz
	SRR12344603.fastq.gz	Fastqsanger.gz
	SRR12344604.fastq.gz	Fastqsanger.gz

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Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [DNA methylation]

Project description:Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements, which is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilization. These distinct epigenetic reprogramming events rewire transcription through major reorganization of the regulatory epigenome to guide the alternation of generations in flowering plants.

2021-01-26 | GSE155367 | GEO

Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [RNA-Seq]

2021-01-26 | GSE155365 | GEO

Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [ATAC-Seq]

2021-01-26 | GSE155344 | GEO

Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [Small RNA-Seq]

Project description:Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements. This event is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilization. Hence, distinct epigenetic reprogramming events rewire transcription through major reorganization of the regulatory epigenome to guide the alternation of generations in flowering plants.

2021-01-26 | GSE155368 | GEO

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis.

Project description:Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements. This event is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilisation. Hence, distinct epigenetic reprogramming events rewire transcription through major reorganisation of the regulatory epigenome to guide the alternation of generations in flowering plants.

| S-EPMC7920552 | biostudies-literature

Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [RNA-Seq]

Project description:Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [RNA-Seq]

| PRJNA649527 | ENA

Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [ATAC-Seq]

Project description:Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [ATAC-Seq]

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Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis

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

2021-01-26 | GSE155369 | GEO

Defective germline reprogramming rewires the spermatogonial transcriptome

Project description:Defective germline reprogramming rewires the spermatogonial transcriptome

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Epigenetic reprogramming shapes the cellular landscape of schwannoma

Project description:Cell state evolution underlies tumor development and response to therapy1, but mechanisms specifying cancer cell states and intratumor heterogeneity are incompletely understood. Schwannomas are the most common tumors of the peripheral nervous system and are treated with surgery and ionizing radiation2–5. Schwannomas can oscillate in size for many years after radiotherapy6,7, suggesting treatment may reprogram schwannoma cells or the tumor microenvironment. Here we show epigenetic reprogramming shapes the cellular landscape of schwannomas. We find schwannomas are comprised of 2 molecular groups distinguished by reactivation of neural crest development pathways or misactivation of nerve injury mechanisms that specify cancer cell states and the architecture of the tumor immune microenvironment. Schwannoma molecular groups can arise independently, but ionizing radiation is sufficient for epigenetic reprogramming of neural crest to immune-enriched schwannoma by remodeling chromatin accessibility, gene expression, and metabolism to drive schwannoma cell state evolution and immune cell infiltration. To define functional genomic mechanisms underlying epigenetic reprograming of schwannomas, we develop a technique for simultaneous interrogation of chromatin accessibility and gene expression coupled with genetic and therapeutic perturbations in single-nuclei. Our results elucidate a framework for understanding epigenetic drivers of cancer evolution and establish a paradigm of epigenetic reprograming of cancer in response to radiotherapy.

2023-04-18 | PXD014798 | Pride

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