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| Status |
Public on Nov 04, 2020 |
| Title |
Coordinated regulation of starch synthesis by microRNAs and DNA methylation [miRNA-seq] |
| Organism |
Zea mays |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
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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| Overall design |
Maize miRNA profiles of two stages of whole kernels (3 and 5 DAP) and eight stages of isolated endosperm (7, 9, 10, 11,13, 15, 20 and 25 DAP) of the Mo17 inbred line were generated by Illumina NextSeq 500, 13 DAP ear leaf was selected as a control.
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| Contributor(s) |
Huang Y, Hu Y, Liu H, Zhang J, Li Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Nov 07, 2017 |
| Last update date |
Nov 04, 2020 |
| Contact name |
dong chen |
| Organization name |
ablife
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| Street address |
GaoXin 2nd Road
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| City |
wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430064 |
| Country |
China |
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| Platforms (1) |
| GPL13977 |
Illumina Genome Analyzer IIx (Zea mays) |
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| Samples (11)
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| This SubSeries is part of SuperSeries: |
| GSE106686 |
Coordinated regulation of starch synthesis by microRNAs and DNA methylation |
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| Relations |
| BioProject |
PRJNA417672 |
| SRA |
SRP124623 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE106627_expressed_mature_miRNA_TPM.txt.gz |
6.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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