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BackgroundAccurate regulation of tissue- and stage-specific expression of genes is prerequisite for normal development in organisms. DNA methylation plays an important role in modulating gene expression in mammals and plants. However, there is no direct evidence showing how DNA methylation regulates gene transcription in insects.ResultsDuring the development of Bombyx mori wing, the expression level of DNA methyltransferase 1 (BmDnmt1) gradually declined and became stationary at pupal stage, resulting in a lower methylation rate of the intragenic promoter of the mid-pupal wing-specific gene BmCHSA-2b, an epidermal chitin synthase controlling mid-pupal wing development in B. mori. The higher methylation rate of the promoter in the pupal epidermis was decreased and BmCHSA-2b transcription was significantly increased by the treatment with the DNA methylation inhibitor, 5-azacytidine-2′-deoxycytidine, suggesting that DNA methylation regulates the tissue-specific expression of BmCHSA-2b. Pupa-specific transcription factor BmDEAF1 bound to the unmethylated intragenic promoter and activated the BmCHSA-2b transcription in the mid-pupal wing. BmDnmt1 and BmDeaf1 influenced the BmCHSA-2b transcription by binding competitively to the CpG island in the promoter.ConclusionsAll the data together demonstrate that the cooperation between the down-regulation of BmDnmt1 and increased stage-specific expression of BmDeaf1 enhances BmCHSA-2b tissue- and stage-specific transcription to ensure mid-wing development in B. mori. This study highlights an elaborate regulation mechanism how tissue- and stage-specific gene expression is regulated through promoter methylation in insect development.Electronic supplementary materialThe online version of this article (10.1186/s13072-018-0202-4) contains supplementary material, which is available to authorized users.

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Bombyx mori has been extensively studied but the gene expression control of its embryonic development is unclear. In this study, we performed transcriptome profiling of six stages of B. mori embryonic development using RNA sequencing (RNA‐seq). A total of 12 894 transcripts were obtained from the embryos. Of these, 12 456 transcripts were shared among the six stages, namely, fertilized egg, blastoderm, germ‐band, organogenesis, reversal period, and youth period stages. There were 111, 48, 41, 54, 77, and 107 transcripts specifically expressed during the six stages, respectively. By analyzing weighted gene correlation networks and differently expressed genes, we found that during embryonic development, many genes related to DNA replication, transcription, protein synthesis, and epigenetic modifications were upregulated in the early embryos. Genes of cuticle proteins, chitin synthesis‐related proteins, and neuropeptides were more abundant in the late embryos. Although pathways of juvenile hormone and the ecdysteroid 20‐hydroxyecdysone, and transcription factors were expressed throughout the embryonic development stages, more regulatory pathways were highly expressed around the organogenesis stage, suggesting more gene expression for organogenesis. The results of RNA‐seq were confirmed by quantitative real‐time polymerase chain reaction of 16 genes of different pathways. Nucleic acid methylation and seven sites in histone H3 modifications were confirmed by dot blot and western blot. This study increases the understanding of the molecular mechanisms of the embryonic developmental process and information on the regulation of B. mori development.