Genome-wide characterization of cis-acting DNA targets of Opaque11 in maize
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays subsp. mays
PROVIDER: GSE97458 | GEO | 2017/10/01
SECONDARY ACCESSION(S): PRJNA381885
REPOSITORIES: GEO
Similar Datasets
Project description:Opaque11 (O11) is a bHLH transcription factor that plays important roles in maize endosperm development, nutrient metabolism, and stress response.
2018-04-09 | GSE102051 | GEO
Project description:Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds, but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). ChIP-Seq analysis detected 1,686 O2 DNA binding sites distributed over 1,143 genes. We identified 4 new O2 binding motifs; among them, TGACGTGG appears to be the most conserved and strongest. We confirmed that, except for the 16 kD and 18 kD zeins, O2 directly regulates expression of all other zeins. O2 directly regulates two transcription factors, genes linked to carbon and amino acid metabolism and abiotic stress resistance. Examination of 15 days after pollination(DAP) wild type maize endosperm with O2 specific antibody and IgG serves as control.
2015-03-06 | E-GEOD-63991 | biostudies-arrayexpress
Project description:Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds, but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). ChIP-Seq analysis detected 1,686 O2 DNA binding sites distributed over 1,143 genes. We identified 4 new O2 binding motifs; among them, TGACGTGG appears to be the most conserved and strongest. We confirmed that, except for the 16 kD and 18 kD zeins, O2 directly regulates expression of all other zeins. O2 directly regulates two transcription factors, genes linked to carbon and amino acid metabolism and abiotic stress resistance.
2015-03-06 | GSE63991 | GEO
Project description:OsNF-YB1 is a transcription factor that plays important roles during rice grain filling. OsNF-YB1 is specifically expressed in aleurone layer of developing endosperm and OsNF-YB1 RNAi lines showed retardation in grain filling and produced small grains with chalky endosperm as well as the altered starch quality. To reveal the transcriptional regulatory framework of OsNF-YB1, we determined OsNF-YB1 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). ChIP-Seq analysis detected 933 binding peaks distributed 743 neighbor genes. OsNF-YB1 directly regulates genes involved in nutrient transport including sugar and amino acids, and interestingly, different from the reported binding site of NF-Y complex, the GCC-box (a binding motif of ERF transcription factors) was enriched in the binding peaks of OsNF-YB1.
2016-12-16 | GSE72186 | GEO
Project description:Epigenetic modification plays important roles in plant and animal development. DNA methylation can impact the transposable element (TE) silencing, gene imprinting and regulate gene expression.Through a genome-wide analysis, DNA methylation peaks were respectively characterized and mapped in maize embryo and endosperm genome. Distinct methylation level across maize embryo and endosperm was observed. The maize embryo genome contained more DNA methylation peaks than endosperm. However, the endosperm chloroplast genome contained more DNA methylation peaks to compare with the embryo chloroplast genome. DNA methylation regions were characterized and mapped in genome. More CG island (CGI) shore are methylated than CGI in maize suggested that DNA methylation level is not positively correlated with CpG density. The DNA methylation occurred more frequently in the promoter sequence and transcriptional termination region (TTR) than other regions of the genes. The result showed that 99% TEs we characterized are methylated in maize embryo, but some (34.8%) of them are not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated two regions between embryo and endosperm are High CpG content promoters (HCPs) and high CpG content TTRs (HCTTRs). DNA methylation peaks distinction of mitochondria and chloroplast DNA were less than the nucleus DNA. Our results indicated that DNA methylation is associated with the gene silencing or gene activation in maize endosperm and embryo. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 17 endosperm-specific expressed imprinting genes were hypomethylated in endosperm and were hypermethylated in embryo. The expression of a maize DEMETER -like (DME-like) gene and MBD101 gene (MBD4 homolog) which direct bulk genome DNA demethylation were higher in endosperm than in embryo. These two genes may be associated with the distinct methylation level across maize embryo and endosperm.The methylomes of maize embryo and endosperm was obtained by MeDIP-seq method. The global mapping of maize embryo and endosperm methylation in this study broadened our knowledge of DNA methylation patterns in maize genome, and provided useful information for future studies on maize seed development and regulation of metabolic pathways in different seed tissues.
2014-06-17 | GSE58549 | GEO
Project description:Genome-wide characterization of cis-acting DNA targets of ZmbZIP22 in maize
| PRJNA449500 | ENA
Project description:Epigenetic modification plays important roles in plant and animal development. DNA methylation can impact the transposable element (TE) silencing, gene imprinting and regulate gene expression.Through a genome-wide analysis, DNA methylation peaks were respectively characterized and mapped in maize embryo and endosperm genome. Distinct methylation level across maize embryo and endosperm was observed. The maize embryo genome contained more DNA methylation peaks than endosperm. However, the endosperm chloroplast genome contained more DNA methylation peaks to compare with the embryo chloroplast genome. DNA methylation regions were characterized and mapped in genome. More CG island (CGI) shore are methylated than CGI in maize suggested that DNA methylation level is not positively correlated with CpG density. The DNA methylation occurred more frequently in the promoter sequence and transcriptional termination region (TTR) than other regions of the genes. The result showed that 99% TEs we characterized are methylated in maize embryo, but some (34.8%) of them are not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated two regions between embryo and endosperm are High CpG content promoters (HCPs) and high CpG content TTRs (HCTTRs). DNA methylation peaks distinction of mitochondria and chloroplast DNA were less than the nucleus DNA. Our results indicated that DNA methylation is associated with the gene silencing or gene activation in maize endosperm and embryo. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 17 endosperm-specific expressed imprinting genes were hypomethylated in endosperm and were hypermethylated in embryo. The expression of a maize DEMETER -like (DME-like) gene and MBD101 gene (MBD4 homolog) which direct bulk genome DNA demethylation were higher in endosperm than in embryo. These two genes may be associated with the distinct methylation level across maize embryo and endosperm.The methylomes of maize embryo and endosperm was obtained by MeDIP-seq method. The global mapping of maize embryo and endosperm methylation in this study broadened our knowledge of DNA methylation patterns in maize genome, and provided useful information for future studies on maize seed development and regulation of metabolic pathways in different seed tissues. Examination of DNA methylated modifications in 2 maize tissues.
2014-06-17 | E-GEOD-58549 | biostudies-arrayexpress
Project description:A new factor binds to the 27-kD γ-zein gene promoter was identified through probe affinity purification and mass spectrometry analysis. This new factor belongs to bZIP type TF (hence named as ZmbZIP22). Chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq) analysis with two biological replicates was performed to determine the DNA binding targets of ZmbZIP22. ChIP-Seq analysis detected 1,550 DNA binding sites distributed over 514 genes. We identified ACAGCTCA as the most conserved ZmbZIP22 binding motif. We confirmed that ZmbZIP22 binds the 27-kD γ-zein gene promoter in vivo, and also identified additional direct targets of ZmbZIP22.
2018-10-12 | GSE112917 | GEO
Project description:Transcriptomics at maize embryo/endosperm interfaces identifies a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)
2020-02-04 | GSE110060 | 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