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:Analysis of transcriptomes from filling endosperms of zmnac128 zmnac130 mutants
| PRJNA1057451 | ENA
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 | GSE262337 | 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:Endosperms (with the embryo, aleurone, seed coat, and pericarp removed) at 5, 10, 15, 20, and 25 DPAs of the T. urartu accession PI 428198 were used for RNA-Seq analysis. Each sample had three independent biological replicates. The total RNA of endosperms was isolated and a library with an insert length of ~350 bp was sequenced using the Illumina HiSeq 2000 (San Diego, CA, USA). An integrated reference sequence of T. urartu PI 428198 was prepared by combining the annotated gene set (ftp://ftp.ensemblgenomes.org/pub/plants/release3 9/fasta/triticum_urartu) with cloned low-molecule-weight glutenin subunit genes and gliadin genes after gene redundancy removal. The relative transcript abundance of seed storage protein genes and the 41,507 predicted genes from genome sequences were calculated using the unique aligned reads as the expected number of fragments per kilobase of the transcript sequence per million base pairs sequenced (FPKM).
2021-02-01 | GSE165862 | GEO
Project description:Reproductive-stage heat stress reduces rice yield and grain appearance quality, even in modern heat-resilient cultivars. Although our previous work showed that green manure can lessen ripening heat damage in the widely grown but heat-susceptible Japanese cultivar Koshihikari, it remains unclear whether similar benefits occur in heat-resilient cultivars and how green manure influences source–sink molecular responses during ripening. Here, using the heat-resilient cultivar Nijinokirameki, we tested whether green manure alleviates ripening heat stress by modifying panicle thermal status, nitrogen assimilation, and early endosperm stress responses. Green manure increased flag-leaf size and tiller (panicle) number and enhanced ripening-stage heat resilience by lowering panicle temperature without a meaningful phenological shift. Consistent with reduced heat load at the target organ, endosperm RNA-seq at 5 days after flowering (DAF) revealed weaker induction of heat-responsive programs under green manure, accompanied by increased grain protein content and reduced chalkiness classes (e.g., white milky, and white belly and back kernels). In parallel, shoot nitrogen contents at panicle formation stage were increased and flag-leaf RNA-seq at 5 DAF showed upregulation of ASN1 and NADH-GOGAT2, suggesting contribution to nitrogen assimilation in source organs and nitrogen allocation to grains. Together, these results link a sustainable fertility practice to tissue-scale heat stress mitigation and coordinated source–sink transcriptional responses at ripening that reflects enhanced grain protein accumulation and appearance quality under green manure treatment.
2026-06-01 | GSE331540 | GEO
Project description:Previous study showed that there are more cell cycle active cardiomyocytes (CMs) in 3-month-old (3M) than1-year-old (1Y) human atria, and extracellular matrix (ECM) from mouse atria benefits neonatal CMs proliferation. We investigate the global changes of transcriptomes between 3M and 1Y human atria and whether ECM from 3M human atria improves myocardium infarct recovery. RNAseq results showed that the major changes between 3M and 1Y human atria were ECM. 3M –ECM increased CM cell cycle activities and rescue mouse heart from injury. We conclude that 3M-ECM hold a therapeutic effect on myocardium infarction.
2020-07-02 | PXD020148 |
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.
2011-09-15 | GSE30477 | GEO