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

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

PROVIDER: PRJNA417673 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6269100_1.fastq.gz	Fastqsanger.gz
	SRR6269100_2.fastq.gz	Fastqsanger.gz
	SRR6269101_1.fastq.gz	Fastqsanger.gz
	SRR6269101_2.fastq.gz	Fastqsanger.gz
	SRR6269102_1.fastq.gz	Fastqsanger.gz

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Coordinated regulation of starch synthesis by microRNAs and DNA methylation

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

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

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Gene expression in cotton stems and roots accumulating starch

Project description:Cotton (Gossypium hirsutum L) is an important crop world wide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. These reserves are not available to produce seed and fiber when cotton is usually grown as an annual crop. Analysis of developing cotton plants indicated that starch levels peaked about the time of first anthesis then began to decline. An earlier peak of levels of starch was occasionally observed and in some greenhouse-grown samples starch increased 2 week after first bloom. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with carbohydrate metabolism, transcription activity and the proteasome. Genes associated with starch synthesis, starch degradation, sucrose metabolism, hexose metabolism, raffinose synthesis and trehalose synthesis increased in expression in starch accumulating tissues. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in relevant tissues. We propose that altering expressions of genes and pathways identified in this work could be used to more efficiently mobilize stored carbohydrate to fiber production. Keywords: starch accumulating, stem, root

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