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Coordinated regulation of starch synthesis by microRNAs and DNA methylation [miRNA-seq]

ABSTRACT: Coordinated regulation of starch synthesis by microRNAs and DNA methylation [miRNA-seq]

PROVIDER: PRJNA417672 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6269090.fastq.gz	Fastqsanger.gz
	SRR6269091.fastq.gz	Fastqsanger.gz
	SRR6269092.fastq.gz	Fastqsanger.gz
	SRR6269093.fastq.gz	Fastqsanger.gz
	SRR6269094.fastq.gz	Fastqsanger.gz

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Coordinated regulation of starch synthesis by microRNAs and DNA methylation

Project description:Coordinated regulation of starch synthesis by microRNAs and DNA methylation

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Coordinated regulation of starch synthesis by microRNAs and DNA methylation [miRNA-seq]

Project description:Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. Expression pattern analysis establishes a comprehensive network between starch synthesis genes and transcription factors. MiRNAs negatively regulating TF expression were extensively downregulated during maize endosperm development. We showed that TF ZmMYB33 and ZmMYB65 promotes the transcription of the GUS reporter under the control of Wx and Sbe2b/Bt2 gene promoters containing their binding motifs, respectively. We further showed that the abundantly expressed miR159k-3p negatively regulate the expression of these two transcription factors, suggesting that miRNAs are important regulators of starch synthesis. In addition, we showed that both starch synthesis genes and miRNAs are globally repressed by DNA methylation, while transcription factors are not. Taken together, the presented results establish the regulatory functions of miRNAs and DNA methylation in starch synthesis, and indicates DNA methylation as the master switch.

2020-11-04 | GSE106627 | GEO

Coordinated regulation of starch synthesis by microRNAs and DNA methylation [BiSulfite-seq]

Project description:Coordinated regulation of starch synthesis by microRNAs and DNA methylation [BiSulfite-seq]

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Project description:Coordinated regulation of starch synthesis by microRNAs and DNA methylation [RNA-seq]

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2020-11-04 | GSE106642 | GEO

Coordinated regulation of starch synthesis by microRNAs and DNA methylation [RNA-seq]

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Coordinated regulation of starch synthesis by microRNAs and DNA methylation

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-11-04 | GSE106686 | GEO

ISD-starch (initiation, synthesis, and degradation): an integrated approach toward the understanding of starch metabolism and formation in plants

Project description:gnp06-02_starch - isd-starch - What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves. - comparison between several mutant of the starch biosynthesis and the WT, at the end of the day and at the end of the night Keywords: gene knock out 48 dye-swap - CATMA arrays

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isd-starch-Initiation synthesis and degradation : an integrated approach toward the understanding of starch metabolism and formation in plants

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Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response

Project description:Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, miRNAs, and RNA-binding proteins. Here, we present Bru-Seq and BruChase-Seq to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeostasis and after exposure to the proinflammatory TNF. The inflammatory response in human cells involves rapid and dramatic changes in gene expression, and the Bru-Seq and BruChase-Seq techniques revealed a coordinated and complex regulation of gene expression both at the transcriptional and posttranscriptional levels. The combinatory analysis of both RNA synthesis and stability using Bru-Seq and BruChase-Seq allows for a much deeper understanding of mechanisms of gene regulation than afforded by the analysis of steadystate total RNA and should be useful in many biological settings. Analysis of the effect of TNF exposure in nascent gene expression and in transcript stability

2013-01-29 | E-GEOD-43440 | biostudies-arrayexpress

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