SRP124624 PRJNA417673 GSE106642 Coordinated regulation of starch synthesis by microRNAs and DNA methylation [BiSulfite-seq] 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. Overall design: Maize global genomic methylation 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 HiSeq 2000, 13 DAP ear leaf was selected as a control. GSE106642 parent_bioproject PRJNA417678