Analysis of transcriptomes from filling endosperms of zmnac128 zmnac130 mutants
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE252297 | GEO | 2024/01/10
REPOSITORIES: GEO
Similar Datasets
Project description:We report the transcriptome profile of the developing maize endosperm of nacRNAi. The nacRNAi is the transgenic maize which knocks down the expression of both ZmNAC128 and ZmNAC130 in the developing endosperm.ZmNAC128 and ZmNAC130 are the two maize endosperm-specific NAC-type transcription factors. This study finds that nacRNAi has a broad effect on the accumulation of starch and protein by regulating their main synthetic genes.
2019-05-04 | GSE127525 | GEO
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 | GSE262336 | GEO
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 | GSE262335 | GEO
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
Project description:In flowering plants, the male gametophyte, the pollen, develops in the anther. Complex patterns of gene expression in both the gametophytic and sporophytic tissues of the anther regulate this process. The gene expression profiles of the microspore/pollen and the sporophytic tapetum are of particular interest. In this study, a microarray technique combined with laser microdissection (44K LM-microarray) was developed and used to characterize separately the transcriptomes of the microspore/pollen and tapetum in rice. Expression profiles of 11 known tapetum specific-genes were consistent with previous reports. Based on the spatiotemporal expression patterns and gene ontology (GO) categories of anther-expressed genes, some noteworthy expression patterns are discussed in connection with various important biological events of anther development. The separated transcriptomes of rice microspore/pollen and tapetum were measured at the premeiosis, meiosis, tetrad, uninuclear, bicellular, and tricelluar stages by using laser microdissection (LM)-mediated microarray.
2011-05-12 | E-GEOD-29217 | biostudies-arrayexpress
Project description:This study describes the combined sequencing of the genomes and transcriptomes of single blastomeres from mouse 8-cell stage embryos.
2015-04-20 | E-ERAD-381 | biostudies-arrayexpress
Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes. Wild type accessions Col-0, Bur-0 and C24 were grown on soil at 23M-BM-0C with a 16 hour light period. Inflorescence tissue up to floral stage 14 was used for RNA extraction. Samples were collected 7-8 hours into the light period, with tissue from five plants pooled for each sample. RNA samples were converted into double stranded and hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0RM-BM-.). Three biological replicates were performed for each accession.
2012-03-12 | E-GEOD-24669 | biostudies-arrayexpress
Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes. Wild type accessions Col-0 were grown on soil at 16M-BM-0C with a 16 hour light period. Inflorescence tissue up to floral stage 14 was used for RNA extraction. Samples were collected 7-8 hours into the light period, with tissue from five plants pooled for each sample. RNA samples were converted into double stranded and hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0RM-BM-.). Three biological replicates were performed for each accession.
2012-05-21 | E-GEOD-38109 | biostudies-arrayexpress
Project description:In flowering plants, the male gametophyte, the pollen, develops in the anther. Complex patterns of gene expression in both the gametophytic and sporophytic tissues of the anther regulate this process. The gene expression profiles of the microspore/pollen and the sporophytic tapetum are of particular interest. In this study, a microarray technique combined with laser microdissection (44K LM-microarray) was developed and used to characterize separately the transcriptomes of the microspore/pollen and tapetum in rice. Expression profiles of 11 known tapetum specific-genes were consistent with previous reports. Based on the spatiotemporal expression patterns and gene ontology (GO) categories of anther-expressed genes, some noteworthy expression patterns are discussed in connection with various important biological events of anther development.
2011-05-12 | GSE29217 | GEO
Project description:rs10-04_mad - comparison of transcriptomes in mad mutants - What gene sets are differentially expressed in mad mutants? - Seeds of GFP171.1 (parental line), mad1, mad2, mad3, mad6 and dcl1-12 were sterilized and germinated on Murashige/Skoog medium with 0.9% agar. Plates were stratified at 4C in the dark for 4 days. The plates were then transferred to a growth cabinet at 21C under a 16h light/8h darkness light regime, and the seedlings were harvested 18 days after transfer to the growth cabinet.
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