DAP-seq Analysis of Transcription Factors Associated with Maize Endosperm Development
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PROVIDER: PRJNA884295 | ENA |
REPOSITORIES: ENA
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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
Project description:In angiosperms, the endosperm provides nutrients for embryogenesis or seed germination and is the primary tissue where gene imprinting occurs. To map the imprintome of the early developing endosperm in maize, we performed high-throughput transcriptome sequencing of the kernels at 0, 3, 5 days after pollination (DAP) and the endosperms at 7, 10, and 15 DAP produced from the B73 and Mo17 reciprocal crosses. We observed a gradual increase of paternal gene mRNAs in the 3- and 5-DAP kernels. In the 7-DAP endosperm, the majority of the tested genes reached a ratio of 2m:1p suggesting that paternal genes were nearly fully activated by 7 DAP. A total of 116, 234 and 63 imprinted genes exhibiting parent-specific expression were identified in the 7-, 10-, and 15-DAP endosperms, respectively. The highest amount of paternally expressed genes (PEGs) was found at 7 DAP mainly due to the significantly deviated parental allele expression ratio of these genes at this stage, while nearly 80% of the maternally expressed genes (MEGs) were specific to 10 DAP which were primarily attributed to the sharply increased expression levels compared to the other stages. GO enrichment analysis of the imprinted genes indicated the 10-DAP-specific MEGs were involved in the nutrient uptake and allocation through auxin signaling pathway in the maize endosperm coincident with the endosperm developmental stage associated with the beginning of starch and storage protein accumulation
2013-06-29 | GSE48425 | GEO
Project description:In angiosperms, the endosperm provides nutrients for embryogenesis or seed germination and is the primary tissue where gene imprinting occurs. To map the imprintome of the early developing endosperm in maize, we performed high-throughput transcriptome sequencing of the kernels at 0, 3, 5 days after pollination (DAP) and the endosperms at 7, 10, and 15 DAP produced from the B73 and Mo17 reciprocal crosses. We observed a gradual increase of paternal gene mRNAs in the 3- and 5-DAP kernels. In the 7-DAP endosperm, the majority of the tested genes reached a ratio of 2m:1p suggesting that paternal genes were nearly fully activated by 7 DAP. A total of 116, 234 and 63 imprinted genes exhibiting parent-specific expression were identified in the 7-, 10-, and 15-DAP endosperms, respectively. The highest amount of paternally expressed genes (PEGs) was found at 7 DAP mainly due to the significantly deviated parental allele expression ratio of these genes at this stage, while nearly 80% of the maternally expressed genes (MEGs) were specific to 10 DAP which were primarily attributed to the sharply increased expression levels compared to the other stages. GO enrichment analysis of the imprinted genes indicated the 10-DAP-specific MEGs were involved in the nutrient uptake and allocation through auxin signaling pathway in the maize endosperm coincident with the endosperm developmental stage associated with the beginning of starch and storage protein accumulation The unpollinated kernels (0 DAP), the kernels of 3, 5 DAP and endosperms of 7 10, 15 DAP from the B73 and Mo17 reciprocal crosses were used to perform high-throughput sequencing using the Illumina HiSeq2000 platform
2013-06-29 | E-GEOD-48425 | biostudies-arrayexpress
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.
2023-11-29 | GSE229946 | GEO
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.
2023-11-29 | GSE201700 | GEO
Project description:Endosperm is a product of double fertilization and functions as a nutritive tissue in the angiosperm seed to support the growth of the embryo or the germinating seedling. In cereal grains, endosperm comprises a large proportion of the mature seed and contains large amounts of carbohydrates and proteins. To identify a high-resolution temporal transcriptome of the earliest stages of endosperm development, we used laser-capture microdissection to isolate and profile mRNA populations of a developmental series of the endosperm from 0 to 4 DAP in maize inbred B73. These stages comprise the initial period of proliferation of the triploid endosperm coenocyte through cellularized endosperm that shows an overall polarity and indications of early cell differentiation. Using computational tools, we identified distinct temporal co-expression modules during this period of development. Analysis of the co-expressed transcription-factor genes and the associated cis-regulatory elements allowed us to hypothesize gene regulatory networks involved in early endosperm development in maize.
2021-12-30 | GSE69784 | GEO
Project description:The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm developent. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology.
2015-01-28 | GSE61057 | GEO
Project description:In angiosperms, endosperm plays a crucial role in coordinating seed development through genetic balance and molecular interaction, and is the primary tissue where genomic imprinting occurs. To identify small interfering RNA (siRNA) “imprintome” and its paternal transcriptome activation in early developing maize endosperms, we performed high-throughput small RNA sequencing of whole kernels at 0, 3 and 5 days after pollination (DAP) and endosperms at 7, 10 and 15 DAP, using B73 by Mo17 reciprocal crosses. We observed gradually increased expression of paternal siRNAs in 3- and 5-DAP kernels and balanced contribution of parental siRNA transcriptome in 7-DAP endosperm, followed by identification 460 imprinted siRNA loci with majority (456/460, 99.1%) being maternally expressed that occurred at 10 DAP. Genome-wide scanning found 13 imprinted genes harboring imprinted siRNA loci within their 2-Kb flanking regions, which was significantly different from random probability based on simulation analysis. Finally, gene ontology categories of “response to auxin stimulus”, “response to brassinosteroid stimulus” and “regulation of gene expression” for genes harboring 10-DAP specific siRNAs and “nutrient reservoir activity”, “protein localization to vacuole” and “secondary metabolite biosynthetic process” for genes harboring 15-DAP specific siRNAs indicated that siRNAs could be involved in influencing specific cellular or biochemical processes that are essential for endosperm development, e.g. nutrient uptake and allocation. Although the mechanism of how these siRNAs regulating endosperm key events remains unclear, this study provided us an alternative perspective of siRNA function in plant.
2013-11-26 | GSE52726 | GEO
Project description:The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm development. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology. We performed RNA seq analysis of mid-mature (15DAP) endosperm in two cell types [aleurone (A) and starchy endosperm (S)] of wild type B73 (B) and nkd mutant (N) kernels with three independent biological replicates.
2015-01-28 | E-GEOD-61057 | biostudies-arrayexpress
Project description:The cereal endosperm consists of starchy endosperm (ST) cells, which accumulate storage proteins and starch, the peripheral aleurone (AL) cells, which mobilize these storage compounds during germination, and transfer cells in contact with the maternal vascular tissues, and the embryo-surrounding region. We conducted RNA-sequencing and analyzed transcript profiles of AL and ST tissues at 18 and 22 days after pollination (DAP), when storage compounds such as proteins, starch, triacylglycerols, specialized metabolites, and minerals are actively synthesized in the maize endosperm. We combined published RNA-seq datasets from other kernel tissues at different developmental stages to analyze gene expression connected to synthesis and accumulation of storage compounds and metabolites. Using weighted correlation network analysis (WGCNA), we identified gene modules associated with metabolic pathways related to nutritional properties of the maize endosperm. We also provide information of novel marker genes specifically expressed in AL and ST, at either early or late developmental stages. This study is important for understanding maize endosperm development and for developing strategies to improve nutritional quality of maize kernels.
2017-05-02 | GSE95678 | GEO