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Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (csRNA-seq)

ABSTRACT: Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (csRNA-seq)

PROVIDER: PRJNA1053374 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27227832.fastq.gz	Fastqsanger.gz
	SRR27227833.fastq.gz	Fastqsanger.gz
	SRR27227834.fastq.gz	Fastqsanger.gz
	SRR27227835.fastq.gz	Fastqsanger.gz
	SRR27227836.fastq.gz	Fastqsanger.gz

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Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.

Project description:Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.

2024-02-01 | GSE250331 | GEO

Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (ATAC-seq)

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Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (csRNA-seq)

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Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (RNA-seq)

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Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.

Project description:Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.

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Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (ATAC-seq)

Project description:Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (ATAC-seq)

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Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (RNA-seq)

Project description:Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (RNA-seq)

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Project description:The expression levels of Arabidopsis thaliana (Col-0) genes in several developmental stages during the seed-to-seedling transition were measured by using high-density Affymetrix® arrays (Aragene.st1.1). We used a time-series of microarrays to gain temporal resolution and identify relevant genes in the seed-to-seedling transition.

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Project description:During the embryonic-to-vegetative transition in plants, many genes that were active in seeds become transcriptionally turned off. Recently, we reported a new transcriptional corepressor of the embryonic program, SEED DORMANCY 4-LIKE (AtSDR4L). Multiple lines of evidence suggest that AtSDR4L plays an essential role in regulating the transition from seed to seedling, possibly by collaborating with components of Polycomb Repressive Complexes (PRCs) and PRC-associated proteins VIVIPAROUS1/ABI3-LIKE (VAL) proteins. Through yeast-two-hybrid (Y2H) assays and genome-wide binding analysis, we demonstrated that AtSDR4L and DIG1 physically interact with VAL2 but not with VAL1. The interactions depend on the C-terminal halves of AtSDR4L and DIG1, and the N-terminal half of VAL2. AtSDR4L binds to target loci in germinating seeds, preceding reduced accumulation of H3K27me3 Atsdr4l seedlings at a few loci important for seed development. These findings suggest AtSDR4L, and potentially DIG1, facilitate the recruitment of PRC2 through VAL2 to inactivate seed development genes, thus promoting the seed-to-seedling transition.

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