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Core promoterome of barley embryo [CAGE]

ABSTRACT: Core promoterome of barley embryo [CAGE]

PROVIDER: PRJNA944156 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23829223_1.fastq.gz	Fastqsanger.gz
	SRR23829223_2.fastq.gz	Fastqsanger.gz
	SRR23829224_1.fastq.gz	Fastqsanger.gz
	SRR23829224_2.fastq.gz	Fastqsanger.gz
	SRR23829225_1.fastq.gz	Fastqsanger.gz

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Core promoterome of barley embryo

Project description:Core promoterome of barley embryo

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Core promoterome of barley embryo [CAGE]

Project description:We define the promotoreome sequence and epigenetic architecture in barley embryos to both put it into evolutionary perspective and to serve as a reference for agricultural and research biotechnology in cereals.

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Project description:5'Cap-Analysis of Gene Expression (5' CAGE) from mesodermal and whole embryo RNA at three different time intervals during development.

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Core promoterome of barley embryo.

Project description:Precise localization and dissection of gene promoters are key to understanding transcriptional gene regulation and to successful bioengineering applications. The core RNA polymerase II initiation machinery is highly conserved among eukaryotes, leading to a general expectation of equivalent underlying mechanisms. Still, less is known about promoters in the plant kingdom. In this study, we employed cap analysis of gene expression (CAGE) at three embryonic developmental stages in barley to accurately map, annotate, and quantify transcription initiation events. Unsupervised discovery of de novo sequence clusters grouped promoters based on characteristic initiator and position-specific core-promoter motifs. This grouping was complemented by the annotation of transcription factor binding site (TFBS) motifs. Integration with genome-wide epigenomic data sets and gene ontology (GO) enrichment analysis further delineated the chromatin environments and functional roles of genes associated with distinct promoter categories. The TATA-box presence governs all features explored, supporting the general model of two separate genomic regulatory environments. We describe the extent and implications of alternative transcription initiation events, including those that are specific to developmental stages, which can affect the protein sequence or the presence of regions that regulate translation. The generated promoterome dataset provides a valuable genomic resource for enhancing the functional annotation of the barley genome. It also offers insights into the transcriptional regulation of individual genes and presents opportunities for the informed manipulation of promoter architecture, with the aim of enhancing traits of agronomic importance.

| S-EPMC10762323 | biostudies-literature

Barley seed developmental series

Project description:To provide comprehensive spatiotemporal information about biological processes in developing grains of cultivated barley (Hordeum vulgare subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from 4 to 32 days after pollination.

2023-07-26 | GSE233316 | GEO

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