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Investigation of Gene Network of NKD1, NKD2 and OPAQUE-2 Associated with Maize Endosperm Development

ABSTRACT: The transcriptomic analysis of nkd1, nkd2 and o2 homozygous mutant set (including 1 WT, 3 single mutants, 3 double mutants and 1 triple mutant) at 8, 12 and 16 DAP revealed temporal regulatory landscape in endosperm grain-filling stage. The data also showed NKD1, NKD2 and O2 interactively regulate gene network overtime in several processes, such as hormone response, cell wall organization, nutrient storage and endoreduplication, etc.

ORGANISM(S): Zea mays

PROVIDER: GSE174059 | GEO | 2023/10/09

REPOSITORIES: GEO

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Effect of NKD1, NKD2 and O2 on Chromatin Accessible Regions

Project description:NKD1, 2 and O2 are key transcription factors interactively regulating endosperm development. Their mutation combinations may diversely alter the global gene regulatory landscape. To investigate how interactions between NKD1, 2 and O2 affect endosperm regulatome, which is indicated by accessible regions for regulators on chromatins, Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed for 16 DAP endosperms of all 8 genotype combinations (2 biological replicate per genotype). Among 16 sequenced samples, 20,478 to 49,640 (mean: 34,766) peaks were called, and these peaks represent potential chromatin accessible regions. Distribution of the peaks on chromatins varies among samples: 54.35% - 66.73% peaks are located at distal intergenic region (>3kb upstream and >300 bp downstream of a gene) and 6.7% - 12.1% are located at promoter region (within 3 kb flanking transcription starting site), and 4.62% - 8.88% peaks are located within 1kb flanking transcription starting site. Also, in WT background, nkd1 and nkd2 single mutants have overall greater number of opening regions (upregulated peaks) than closing regions (downregulated peaks), whereas nkd1,2 double mutant has similar number of opening and closing regions. In contrast, in o2-background, all nkd1, nkd2 and nkd1,2 mutants have greater number of closing than opening regions. This indicates that o2 may alter differential accessibility of nkd1, nkd2 single or nkd1,2 double mutants.

2023-10-09 | GSE214415 | GEO

Opaque-2 regulates a complex gene network associated with cell differentiation and storage function of maize endosperm

Project description:Development of the cereal endosperm involves cell differentiation processes that enable nutrient uptake from the maternal plant, accumulation of storage products and their utilization during germination. However, little is known about the regulatory mechanisms that link cell differentiation processes with those controlling storage product synthesis and deposition, including the activation of zein genes by the maize (Zea mays) bZIP transcription factor Opaque-2 (O2). In this study, we mapped in vivo binding sites of O2 in B73 endosperm, and compared the results with genes differentially expressed in B73 and B73o2. We identified 186 putative direct O2 targets and 1,677 indirect targets, encoding a broad set of gene functionalities. Examination of the temporal expression patterns of O2 targets using real-time RT-PCR experiments revealed at least two distinct modes of O2-mediated gene activation. We also showed that two O2-activated genes, bZIP17 and NAKED ENDOSPERM2 (NKD2) encoded transcription factors, which can in turn co-activate other O2-network genes with O2. NKD2 (with its paralog NKD1) was previously shown to be involved in regulation of aleurone development. Collectively, our results provide novel insights into the complexity of the O2-regulated network and its role in regulation of endosperm cell differentiation and function.

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Transcriptome analysis of nkd1 and nkd2 mutants in W22 maize endosperm

Project description:The maize NAKED ENDOSPERM (NKD) genes Nkd1 and Nkd2 encode paralogous INDETERMINATE DOMAIN (IDD) transcription factors (TFs) that have previously been shown to play critical roles in regulating endosperm gene expression and development. However, the function of each individual NKD protein is unclear. To elucidate this, we performed a transcriptome analysis for nkd1-Ds and nkd2-Ds single mutant endosperm. We found that in nkd1-Ds single mutant, nkd2 gene expression is significantly lower than WT, and similar to the nkd2-Ds mutant.

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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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Effect of NKD1, NKD2 and O2 on Chromatin Accessible Regions

Project description:Effect of NKD1, NKD2 and O2 on Chromatin Accessible Regions

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Investigation of Gene Network of NKD1, NKD2 and OPAQUE-2 Associated with Maize Endosperm Development

Project description:Investigation of Gene Network of NKD1, NKD2 and OPAQUE-2 Associated with Maize Endosperm Development

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Loss of Nkd1 is dominant over loss of Axin2 in regulating Wnt signaling.

Project description:Wnt signaling is a crucial developmental pathway involved in early development as well as stem cell maintenance in adults and its misregulation leads to numerous diseases. Thus, understanding the regulation of this pathway becomes vitally important. Axin2 and Nkd1 are widely utilized negative feedback regulators in Wnt signaling where Axin2 functions to destabilize cytoplasmic β-catenin, and Nkd1 functions to inhibit the nuclear localization of β-catenin. Here, we set out to further understand how Axin2 and Nkd1 regulate Wnt signaling by creating axin2-/-, nkd1-/- single mutants and axin2-/-;nkd1-/- double mutant zebrafish using sgRNA/Cas9. All three Wnt regulator mutants were viable and had impaired heart looping, neuromast migration defects, and behavior abnormalities in common, but there were no signs of synergy in the axin2-/-;nkd1-/- double mutants. Further, Wnt target gene expression by qRT-PCR, and RNA-seq analysis and protein expression by mass spec demonstrated that the double axin2-/-;nkd1-/- mutant resembled the nkd1-/- phenotype demonstrating that Axin functions upstream of Nkd1 and that loss of Nkd1 is dominant over the loss of Axin2. In support of this, the data further demonstrates that Axin2 uniquely alters the properties of β-catenin-dependent transcription having novel readouts of Wnt activity compared to nkd1-/- or the axin2-/-;nkd1-/- double mutant. We also tested the sensitivity of the Wnt regulator mutants to exacerbated Wnt signaling, where the single mutants displayed characteristic heightened Wnt sensitivity, resulting in an eyeless phenotype. Surprisingly, this phenotype was rescued in the double mutant, where we speculate that cross-talk between Wnt/β-catenin and Wnt/Planar Cell Polarity pathways could lead to altered Wnt signaling in some scenarios. Collectively, the data emphasizes both the commonality and the complexity in the feedback regulation of Wnt signaling.

2023-11-07 | GSE246858 | GEO

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Project description:High temperature during the grain-filling stage causes deleterious effects on storage material accumulation and grain quality. But it is still unclear how high temperature affects storage materials accumulation. In this study, we systemically analyzed the expression pattern of rice genes under high temperture during the grain-filling stage.

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