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The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [DAP-Seq]

ABSTRACT: The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [DAP-Seq]

PROVIDER: PRJNA1091355 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28431378_1.fastq.gz	Fastqsanger.gz
	SRR28431378_2.fastq.gz	Fastqsanger.gz
	SRR28431379_1.fastq.gz	Fastqsanger.gz
	SRR28431379_2.fastq.gz	Fastqsanger.gz
	SRR28431380_1.fastq.gz	Fastqsanger.gz

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The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [DAP-Seq]

Project description:Grain filling in maize (Zea mays L.) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1,744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130. In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA. Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.

2024-06-21 | GSE262337 | GEO

The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [ChIP-seq]

2024-06-21 | GSE262335 | GEO

The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [RNA-Seq]

2024-06-21 | GSE262336 | GEO

The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [RNA-Seq]

Project description:The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [RNA-Seq]

| PRJNA1091356 | ENA

The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [ChIP-seq]

Project description:The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [ChIP-seq]

| PRJNA1091354 | ENA

Expression analysis of barley glumes vs. endosperm between 0-24 days after pollination

Project description:During grain filling in barley reserves are remobilized from vegetative organs like glumes. In this expression analysis values from glumes and endosperm material were compared from 0 - 24 day after pollination (DAP). This study showed that glumes metabolism and development is adjusted to changing grain demands. Candidate genes are potentially involved in assimilate conversion and translocation.

2015-01-30 | E-MTAB-3040 | biostudies-arrayexpress

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.

2023-10-09 | GSE214166 | GEO

Expression data from early rice endosperm

Project description:We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of regulated genes during this process. Rice endosperm at 2 days after pollination(DAP) was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the endosperm expression profile at 2 DAP. To that end, we hand-selected endosperm according to morphological criteria at 2 DAP before cellularization.

2015-09-01 | E-GEOD-57615 | biostudies-arrayexpress

Genome-wide maps of DNA methylation state in rice embryo and endosperm

Project description:We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development. Rice embryo and endosperm were selected for DNA extraction and methylacytosine immunoprecipetation combined with Illumina sequencing. We sought to obtain the genome-wide DNA methylation profilings of embryo at 3,6,9 days after pollination(DAP) and endosperm at 2,3,6,9 DAP. To that end, we hand-selected embryo at 3,6,9 DAP and endosperm at 2,3,6,9 DAP according to morphological criteria.

2015-09-01 | E-GEOD-57706 | biostudies-arrayexpress

Auxin regulates endosperm cellularization in Arabidopsis

Project description:The endosperm is an ephemeral tissue that nourishes the developing embryo, similar to the placenta in mammals. In most angiosperms, endosperm development starts as a syncytium, in which nuclear divisions are not followed by cytokinesis. The timing of endosperm cellularization largely varies between species, and the event triggering this transition remains unknown. Here we show that increased auxin biosynthesis in the endosperm prevents its cellularization, leading to seed arrest. Auxin-overproducing seeds phenocopy paternal-excess triploid seeds derived from hybridizations of diploid maternal plants with tetraploid fathers. Concurrently, auxin-related genes are strongly overexpressed in triploid seeds, correlating with increased auxin activity. Reducing auxin biosynthesis and signaling reestablishes endosperm cellularization in triploid seeds and restores their viability, highlighting a causal role of increased auxin in preventing endosperm cellularization. We propose that auxin determines the time of endosperm cellularization, and thereby uncovered a central role of auxin in establishing hybridization barriers in plants.

2019-12-21 | GSE124108 | GEO

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