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Decoding the gene regulatory network of endosperm differentiation in maize [DAP-seq]

ABSTRACT: Decoding the gene regulatory network of endosperm differentiation in maize [DAP-seq]

PROVIDER: PRJNA956867 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24203700_1.fastq.gz	Fastqsanger.gz
	SRR24203700_2.fastq.gz	Fastqsanger.gz
	SRR24203701_1.fastq.gz	Fastqsanger.gz
	SRR24203701_2.fastq.gz	Fastqsanger.gz
	SRR24203702_1.fastq.gz	Fastqsanger.gz

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Decoding the gene regulatory network of endosperm differentiation in maize [DAP-seq]

Project description:Decoding the gene regulatory network of endosperm differentiation in maize [DAP-seq]

| PRJNA832702 | ENA

Decoding the gene regulatory network of endosperm differentiation in maize [DAP-seq]

Project description:The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. We delineate the temporal gene expression pattern from 6 to 7 days after pollination. We profile the genomic DNA binding sites of 161 transcription factors differentially expressed between cell clusters and constructed a gene regulatory network by combining the single-cell transcriptomic data with the direct DNA-binding profiles, identifying 181 regulons containing genes encoding transcription factors along with their high-confidence targets, Furthermore, we map the regulons to endosperm cell clusters, identify cell-cluster-specific essential regulators, and experimentally validated three predicted key regulators. This study provides a framework for understanding cereal endosperm development and function at single-cell resolution.

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DAP-seq Analysis of Transcription Factors Associated with Maize Endosperm Development

Project description:Transcription factors (TFs) play an important role in maize endosperm development regulation. The temporal RNA-seq and co-expression network analysis of maize endosperm reveals a hiararchical regulatory network architechture modulating the endosperm development. In the network, NKD1 and NKD2 are central regulators, and GBF1, HSFTF10, NACTF49 and HB115 are secondary regulators downstream of NKD1 and 2. To further test the relationship between these TFs, a DNA affinity purification and sequencing (DAP-seq) assay was performed. The result shows that the assay on NKD1 and NKD2 called 1,951 and 56,855 peaks, and 93 and 1,692 peaks are located within 3 kb distance to transcription starting site (TSS), respectively. And assays on GBF1, HSFTF10, NACTF49 and HB115 called 15,543; 38,147; 7,388 and 936 peaks, respectively.

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Decoding the gene regulatory network of endosperm differentiation in maize

Project description:Decoding the gene regulatory network of endosperm differentiation in maize

| PRJNA832700 | ENA