A Simple and Low-Cost CRISPR/Cas9 Knockout System Widely Applicable to Insects.

The CRISPR/Cas9 gene-editing system is a standard technique in functional genomics, with widespread applications. However, the establishment of a CRISPR/Cas9 system is challenging. Previous studies have presented numerous methodologies for establishing a CRISPR/Cas9 system, yet detailed descriptions are limited. Additionally, the difficulties in obtaining the necessary plasmids have hindered the replication of CRISPR/Cas9 techniques in other laboratories. In this study, we share a detailed and simple CRISPR/Cas9 knockout system with optimized steps. The results of gene knockout experiments in vitro and in vivo show that this system successfully knocked out the target gene. By sharing detailed information on plasmid sequences, reagent codes, and methods, this study can assist researchers in establishing gene knockout systems.

Identification and function of the Pax gene Bmgsb in the silk gland of Bombyx mori.

Paired box (Pax) genes are highly conserved throughout evolution, and the Pax protein is an important transcription factor of embryonic development. The Pax gene Bmgsb is expressed in the silk glands of silkworm, but its biological functions remain unclear. This study aimed to investigate the expression pattern of Bmgsb in the silk gland and explore its functions using RNA interference (RNAi). Here, we identified eight Pax genes in Bombyx mori. Phylogenetic analysis showed that the B. mori Pax genes were highly homologous to the Pax genes in other insects and highly evolutionarily conserved. The tissue expression profile showed that Bmgsb was expressed in the anterior silk gland and anterior part of the middle silk gland (AMSG). RNAi of Bmgsb resulted in defective development of the AMSG, and the larvae were mostly unable to cocoon in the wandering stage. RNA-seq analysis showed that the fibroin genes fib-l, fib-h and p25, cellular heat shock response-related genes and phenol oxidase genes were considerably upregulated upon Bmgsb knockdown. Furthermore, quantitative reverse transcription-PCR results showed that the fibroin genes and ubiquitin proteolytic enzyme-related genes were significantly upregulated in the AMSG after Bmgsb knockdown. This study provides a foundation for future research on the biological functions of B. mori Pax genes. In addition, it demonstrates the important roles of Bmgsb in the transcriptional regulation of fibroin genes and silk gland development.

SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data.

The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcripts and a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.

Identification and Functions of JHE 6 Specifically Expressed in Bombyx mori Silk Gland.

Juvenile hormone esterase (JHE) is the specific enzyme that degrades juvenile hormone (JH) and regulates the JH titer in insects. JH also regulates the development of the silk gland and the synthesis and secretion of silk proteins in Bombyx mori. Here, we identified nine possible JHE family members, Bmjhe1-9. Notably, Bmjhe6 is specifically expressed in the silk gland. Using semi-quantitative, quantitative real-time RT-PCR and Western blot, it was confirmed that Bmjhe6 was specifically expressed in the middle silk gland (MSG) with high levels in the anterior region of the MSG (A-MSG). The immunofluorescence localization analysis revealed that Bmjhe6 is produced within cells, secreted into the gland lumen, and co-transported with silk proteins into the anterior silk gland (ASG). In vitro hormone induction experiments demonstrated that Bmjhe6 responds to a JH analog, increasing its expression after 12-24 h, whereas 20-hydroxyecdysone inhibited it. In addition, Bmjhe6 knockdown using dsBmjhe6 injections accelerated larval development, resulting in increased larval body and silk gland weight. This induced disordered sericin genes (Ser2, Ser3) expression, and key genes in the JH synthesis pathway (BmKr-h1 and BmMet1) were significantly upregulated along with the transcription factors (SGF-1 and Sage). These results indicate that Bmjhe6 plays an important role in silk gland growth and silk protein synthesis by modulating JH signal.

Dimmed gene knockout shortens larval growth and reduces silk yield in the silkworm, Bombyx mori.

The bHLH domain transcription factor, Bombyx mori-derived dimmed (Bmdimm), is directly regulated by the JH-BmMet/BmSRC-BmKr-h1 pathway and plays a key role in regulating the expression of FibH, which codes the main component of silk protein. However, the other roles of Bmdimm in silk protein synthesis remain unclear. Here, we established a Bmdimm knockout (KO) line containing a 7-bp deletion via CRISPR/Cas9 system, which led to the absence of the bHLH domain. The expression level of silk protein genes and silk yield decreased significantly in the Bmdimm KO line. Moreover, knocking out Bmdimm led to shortened larval stages and significant weight loss in larvae and adults. Bmdimm was found to be highly expressed in the silk gland, but it was also expressed in the fat body. The expression level of Bmkr-h1 in the fat body was significantly downregulated in the Bmdimm KO line. Exogenous JHA treatment upregulated Bmkr-h1 and rescued the phenotype of larval growth in the Bmdimm KO line. In conclusion, knocking out Bmdimm led to a shortened larval stage via the inhibition of Bmkr-h1 expression, then reduced silk yield. These findings help to elucidate the regulatory mechanism of fibroin synthesis and larval development in silkworms.

Abnormal overexpression of SoxD enhances melanin synthesis in the Ursa mutant of Bombyx mori.

The pigment and structural color of insects play crucial roles in body protection, ecological adaptation, and signal communication. Epidermal melanization is a common and main coloring pattern, which results in broad phenotypic diversity. Melanin is one of the compounds contributing to dark brown-black pigmentation, which is synthesized from dopamine and tyrosine by the melanin metabolism pathway. The Ursa mutant of the silkworm Bombyx mori is a body-color mutant characterized by excessive melanin pigmentation in the larval epidermis. However, the exact gene responsible for this phenotype remains unclear. Here, we performed positional cloning of the gene responsible for Ursa, which was mapped to an 83-kb region on chromosome 14. The genomic region contains a protein-coding gene encoding a transcription factor, which was designated BmSoxD. The mutation site was determined by analysis of nucleotide sequences of the genomic region corresponding to BmSoxD, which identified a 449-bp transposable sequence similar to that of the B. mori transposon Helitron inserted into the sixth intron. BmSoxD was dramatically overexpressed in the epidermis of Ursa at the end of the molting stage compared with that of wild-type B. mori. Overexpression of BmSoxD led to upregulation of genes involved in the melanin metabolism pathway, whereas knocking down BmSoxD via small interfering RNAs blocked melanin pigment production in the larval epidermis. These data indicate that the mutation in BmSoxD is responsible for the Ursa mutant phenotype. We propose that the transposable sequence insertion causes abnormal overexpression of BmSoxD at the molting stage in the Ursa mutant, resulting in excessive melanin synthesis and its accumulation in epidermal cells.

Identification and location of sericin in silkworm with anti-sericin antibodies.

Sericin, as the main component of silkworm cocoon silk, surrounds and protects the silk fibroin. Sericin is a natural macromolecular protein complex encoded by the genes Ser1, Ser2, and Ser3. At present, there are no available antibodies against sericin that may be used to identify and locate it at the protein level, hindering the study of its secretion mechanism and materials application. Therefore, the development of effective antibodies against sericin is an urgent necessity. To address this problem, we prepared polyclonal antibodies against the Ser1, Ser2 and Ser3 proteins using synthesized peptides for the first time. The specificity of the antibodies was confirmed using dot blot, immunoblotting and mass spectrometry on the hybrid bands of the middle silk gland. The immunoblotting results of anti-sericin antibodies showed that sericin has different molecular weights in different regions of the middle silk gland and strains in the 5th instar. Through immunohistochemistry, anti-sericin antibodies revealed that sericin presented different distributions in the anterior part of the middle silk gland of 872 strain at the 7th day of 5th instar. In addition, the prepared antibodies not only detected intact sericin molecules, but also detected degraded sericin that was dissolved in five different solvents. In summary, this work prepared effective sericin antibodies for silk protein synthesis and secretion research and provides a possible molecular detection method for biological products containing silkworm sericin.

Sage controls silk gland development by regulating Dfd in Bombyx mori.

Silk gland is an organ that produces and secretes silk proteins. The development of the silk gland is essential for high silk production yield and silk quality. Although Sage reportedly plays a pivotal role in embryonic silk gland development, the mechanism underlying its action remains unclear. Our study aimed to determine the genes downstream of Sage through which it regulates the development of the silk gland. After chromatin immunoprecipitation and sequencing, Dfd was identified as a downstream target gene of Sage and it was confirmed that Sage could inhibit Dfd expression by competing with SGF1. When Dfd was knocked down through RNA interference (RNAi), the number of cells in the middle silk gland decreased, and the posterior silk gland was straightened. Simultaneously, the expression of Ser1 and silk fibroin genes was no longer strictly regional. These changes eventually led to an alteration in the composition of the Dfd RNAi cocoon. In conclusion, our research contributes to a deeper understanding of the development of silk glands.

Transgenic Ectopic Overexpression of Broad Complex (BrC-Z2) in the Silk Gland Inhibits the Expression of Silk Fibroin Genes of Bombyx mori.

Bombyx mori silk protein genes are strictly turned on and off in different developmental stages under the hormone periodically change. The broad complex (BrC) is a transcription factor mediating 20-hydroxyecdysone action, which plays important roles during metamorphosis. Here, we observed that two isoforms of BmBrC (BmBrC-Z2 and BmBrC-Z4) exhibited contrasting expression patterns with fibroin genes (FibH, FibL and P25) in the posterior silk gland (PSG), suggesting that BmBrC may negatively regulate fibroin genes. Transgenic lines were constructed to ectopically overexpress BmBrC-Z2 in the PSG. The silk protein genes in the transgenic line were decreased to almost half of that in the wild type. The silk yield was decreased significantly. In addition, the expression levels of regulatory factors (BmKr-h1 and BmDimm) response to juvenile hormone (JH) signal were inhibited significantly. Then exogenous JH in the BmBrC-Z2 overexpressed lines can inhibit the expression of BmBrC-Z2 and activate the expression of silk protein genes and restore the silk yield to the level of the wild type. These results indicated that BmBrC may inhibit fibroin genes by repressing the JH signal pathway, which would assist in deciphering the comprehensive regulation mechanism of silk protein genes.

Effects of Osiris9a on Silk Properties in Bombyx mori Determined by Transgenic Overexpression.

Osiris is an insect-specific gene family with multiple biological roles in development, phenotypic polymorphism, and protection. In the silkworm, we have previously identified twenty-five Osiris genes with high evolutionary conservation and remarkable synteny among several insects. Bombxy mori Osiris9a (BmOsi9a) is expressed only in the silk gland, particularly in the middle silk gland (MSG). However, the biological function of BmOsi9a is still unknown. In this study, we overexpressed BmOsi9a in the silk gland by germline transgene expression. BmOsi9a was overexpressed not only in the MSG but also in the posterior silk gland (PSG). Interestingly, BmOsi9a could be secreted into the lumen in the MSG but not in the PSG. In the silk fiber, overexpressed BmOsi9a interacted with Sericin1 in the MSG, as confirmed by a co-immunoprecipitation assay. The overexpression of BmOsi9a altered the secondary structure and crystallinity of the silk fiber, thereby changing the mechanical properties. These results provide insight into the mechanisms underlying silk proteins secretion and silk fiber formation.

Bombyx mori monocarboxylate transporter 9 (BmMCT9) is involved in the transport of uric acid in silkworm integument.

In Bombyx mori, there are more than 30 mutant strains exhibiting the translucent larval skin resulting from a decrease in the uric acid content in epidermal cell. Of these, the Chinese translucent (oc) mutant presents a moderately translucent larval skin. Previously, we narrowed the region linked to the oc phenotype to approximately 234 kb by positional cloning, and found that BmMCT9 was severely suppressed in the mutant. Here, we analyzed the mutation and potential molecular function of BmMCT9. Sequence analysis showed that a 2,624-bp fragment of BmMCT9 promoter region was replaced by a 22-bp sequence in the mutant. Luciferase reporter gene assay confirmed that BmMCT9 promoter activity in the mutant was significantly lower than that in the wild type. Knockdown of BmMCT9 caused a translucent phenotype in the first-instar silkworm larvae. Immunoblotting analysis showed that BmMCT9 expression was severely reduced in the mutant than in the wild type, and immunofluorescence showed that BmMCT9 existed mainly within the cytoplasm of epidermal cells. Together, our results suggest that reduced levels of BmMCT9 were responsible for the translucent phenotype of oc mutant, and that BmMCT9 might function in intracellular vesicles facing the cytoplasm including urate granules in silkworm integument.

Bmsage is involved in the determination of cell number in the silk gland of Bombyx mori.

The number of cells in tissues is under strict genetic control, and research on the determination of cell number is of great importance to understand the growth and development of organs. Bmsage, a bHLH transcription factor, is involved in the development of the silk gland during the embryonic stage in Bombyx mori. However, the mechanism by which it influences silk gland development is unclear. In the present study, we determined via immunofluorescence staining during the embryonic stage of Bombyx mori that Bmsage is expressed in silk gland cells from the beginning of development of the silk gland until its complete formation. By comparing different silkworm strains, we found that Bmsage expression is positively correlated with the number of silk gland cells. Bmsage knockdown by RNAi resulted in shorter silk glands and lower cell numbers, especially in the posterior silk gland. The silk gland lumen also shriveled, and the silk protein content was significantly lower than that in the control. Further investigation revealed that all cyclins decreased after knock down of Bmsage, and cyclin B and cyclin 3 were significantly down-regulated. Bmsage may be involved in the regulation of the cyclin pathway to control silk gland development. Taken together, it can be concluded from our results that Bmsage is involved in the determination of cell number in silk glands. Our results help clarify the process of cell number determination in silk gland and identify a potential target for silkworm breeding.

Gene Expression Pattern and Regulatory Network of α-Toxin Treatment in Bombyx mori.

Bacillus bombyseptieus is a pathogen of Bombyx mori; it can cause bacterial septicemia in silkworm. One of the components of the parasporal crystal toxin of B. bombyseptieus, α-toxin, plays an important role in the process of infection in silkworm. In this study, we investigated the immune response of silkworm induced by α-toxin by using RNA-seq. We compared the changes in gene expression in the midgut, fatbody, and hemocytes of silkworm and in the B. mori embryonic cell line (BmE) after treatment with α-toxin and identified 952 differentially expressed genes and 353 differentially expressed long noncoding RNAs (lncRNAs). These regulated genes in different tissues were found to be enriched in different pathways. The upregulated genes in the midgut were mainly involved in peptidoglycan catabolic process and tyrosine kinase signaling pathway, whereas the downregulated genes were mainly involved in chitin metabolic pathways. The upregulated genes in fatbody were also involved in peptidoglycan catabolic process, but they were for a different peptidoglycan subtype. Further, genes encoding cecropins were enriched in the fatbody. The downregulated genes were mainly involved in the metabolic pathways of fundamental substances such as cellular protein metabolic process and nucleobase-containing compound metabolic process. These results suggest that α-toxin can induce various immune responses in silkworm, and further studies are warranted to understand the mechanism of α-toxin action in silkworm. Further, lncRNAs and differentially expressed genes were correlated using coexpression network analysis. Our findings revealed potential candidate genes and lncRNAs that might play important physiological functions in the immune response to α-toxins in silkworm.

Synergism of open chromatin regions involved in regulating genes in Bombyx mori.

The dynamic variability of transcription factors (TFs) and their binding sites makes it challenging to conduct genome-wide transcription regulation research. The silkworm Bombyx mori, which produces silk, is one of the most valuable model insects in the order Lepidoptera. The "opening" and "closing" of chromatin in different silk yield strains is associated with changes in silk production, making this insect a good model for studying the transcriptional regulation of genes. However, few studies have examined the open chromatin regions (OCRs) of silkworms, and studying OCR synergism and their function in silk production remains challenging. Here, we performed formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate OCRs from the silk glands of fifth-instar larvae of the DaZao and D872 strains. In total, 128,908 high confidence OCRs were identified and approximately 80% of OCRs were located in non-coding regions. OCRs upregulated adjacent genes and showed signal-dependent vulnerability to single-nucleotide polymorphisms. Mid- and low-signal OCRs were more likely to have single-nucleotide polymorphisms (SNP). Further, OCRs interacted with each other within a distance of 5 kb. We named the OCR interaction complex as the "cluster of related regions" (COREs). The functions of the CORE and its harbored OCRs showed some differences. Additionally, COREs enriched many silk protein synthesis-associated genes, some of which were upregulated. This study identified numerous high confidence regulation sites and synergistic regulatory modes of OCRs that affect adjacent genes. These results provide insight into silkworm transcriptional regulation and improve our understanding of cis-element cooperation.

Genome-wide annotation and comparative analysis of cuticular protein genes in the noctuid pest Spodoptera litura.

Insect cuticle is considered an adaptable and versatile building material with roles in the construction and function of exoskeleton. Its physical properties are varied, as the biological requirements differ among diverse structures and change during the life cycle of the insect. Although the bulk of cuticle consists basically of cuticular proteins (CPs) associated with chitin, the degree of cuticular sclerotization is an important factor in determining its physical properties. Spodoptera litura, the tobacco cutworm, is an important agricultural pest in Asia. Compared to the domestic silkworm, Bombyx mori, another lepidopteran whose CP genes have been well annotated, S. litura has a shorter life cycle, hides in soil during daytime beginning in the 5th instar and is exposed to soil in the pupal stage without the protection of a cocoon. In order to understand how the CP genes may have been adapted to support the characteristic life style of S. litura, we searched its genome and found 287 putative cuticular proteins that can be classified into 9 CP families (CPR with three groups (RR-1, RR-2, RR-3), CPAP1, CPAP3, CPF, CPFL, CPT, CPG, CPCFC and CPLCA), and a collection of unclassified CPs named CPH. There were also 112 cuticular proteins enriched in Histidine residues with content varying from 6% to 30%, comprising many more His-rich cuticular proteins than B. mori. A phylogenetic analysis between S. litura, M. sexta and B. mori uncovered large expansions of RR-1 and RR-2 CPs, forming large gene clusters in different regions of S. litura chromosome 9. We used RNA-seq analysis to document the expression profiles of CPs in different developmental stages and tissues of S. litura. The comparative genomic analysis of CPs between S. litura and B. mori integrated with the unique behavior and life cycle of the two species offers new insights into their contrasting ecological adaptations.

Distinct Functions of Bombyx mori Peptidoglycan Recognition Protein 2 in Immune Responses to Bacteria and Viruses.

Peptidoglycan recognition protein (PGRP) is an important pattern recognition receptor in innate immunity that is vital for bacterial recognition and defense in insects. Few studies report the role of PGRP in viral infection. Here we cloned two forms of PGRP from the model lepidopteran Bombyx mori: BmPGRP2-1 is a transmembrane protein, whereas BmPGRP2-2 is an intracellular protein. BmPGRP2-1 bound to diaminopimelic acid (DAP)-type peptidoglycan (PGN) to activate the canonical immune deficiency (Imd) pathway. BmPGRP2-2 knockdown reduced B. mori nucleopolyhedrovirus (BmNPV) multiplication and mortality in cell lines and in silkworm larvae, while its overexpression increased viral replication. Transcriptome and quantitative PCR (qPCR) results confirmed that BmPGRP2 negatively regulated phosphatase and tensin homolog (PTEN). BmPGRP2-2 expression was induced by BmNPV, and the protein suppressed PTEN-phosphoinositide 3-kinase (PI3K)/Akt signaling to inhibit cell apoptosis, suggesting that BmNPV modulates BmPGRP2-2-PTEN-PI3K/Akt signaling to evade host antiviral defense. These results demonstrate that the two forms of BmPGRP2 have different functions in host responses to bacteria and viruses.

Genome-wide patterns of copy number variations in Spodoptera litura.

Spodoptera litura is a polyphagous pest and can feed on more than 100 species of plants, causing great damage to agricultural production. The SNP results showed that there were gene exchanges between different regions. To explore the variations of larger segments in S. litura genome, we used genome resequencing samples from 14 regions of China, India, and Japan to study the copy number variations (CNVs). We identified 3976 CNV events and 1581 unique copy number variation regions (CNVRs) occupying the 108.5 Mb genome of S. litura. A total of 5527 genes that overlapped with CNVRs were detected. Selection signal analysis identified 19 shared CNVRs and 105 group-specific CNVRs, whose related genes were involved in various biological processes in S. litura. We constructed the first CNVs map in S. litura genome, and our findings will be valuable for understanding the genomic variations and population differences of S. litura.

[Interaction of Bombyx mori aminopeptidase N and cadherin-like protein with Bacillus thuringiensis Cry1Ac toxin].

Bacillus thuringiensis (Bt) produces Cry toxins that are widely used as insecticides in agriculture and forestry. Receptors are important to elucidate the mode of interaction with Cry toxins and toxicity in lepidopteran insects. Here, we purified the Cry toxin from Bt and identified this toxin by flight mass spectrometry as Cry1Ac, and then recombinantly expressed aminopeptidase N (BmAPN6) and repeat domains of cadherin-like protein (CaLP) of B. mori. Using co-immunoprecipitation (co-IP), Far-Western blotting, and enzyme-linked immunosorbent assays (ELISAs), we identified the interaction between Cry1Ac and BmAPN6. Furthermore, analysis of the cytotoxic activity of Cry1Ac toxin in Sf9 cells showed that BmAPN6 directly interacted with Cry1Ac toxin to induce morphological aberrations and cell lysis. We also used co-IP, Far-Western blotting and ELISAs to analyze the interactions of Cry1Ac with three binding sites corresponding to cadherin repeat (CR) 7 CR11, and CR12 of CaLP. Notably, the three repeat domains were essential Cry1Ac binding components in CaLP. These results indicated that BmAPN6 and CaLP served as a functional receptor involved in Bt Cry1Ac toxin pathogenicity. These findings represent an important advancement in our understanding of the mechanisms of Cry1Ac toxicity and provide promising candidate targets for gene editing to enhance resistance to pathogens and increase the economic value of B. mori.

Transcriptome analysis of the response of silkworm to drastic changes in ambient temperature.

Bombyx mori is a poikilothermic insect and is economically important for silk production. Drastic changes in the ambient temperature have a negative impact on sericulture. However, the reason as to why high temperature is associated with the occurrence of diseases in silkworm and the response of silkworm to low temperature remain unclear and were the focus of the present study. Dazao silkworm exposed to 13 °C (DZ-13), 25 °C (DZ-25), and 37 °C (DZ-37) were used for RNA-seq analysis. There were 478 and 194 upregulated differentially expressed genes (DEGs) in DZ-13 and DZ-37 while 49 and 273 downregulated DEGs in DZ-13 and DZ-37, respectively. Eight DEGs were co-upregulated, in which seven genes were for heat shock proteins (Hsps), implying that Hsps play important roles in the tolerance of silkworm to high and low temperature. Gene ontology analysis revealed that the developmental process was downregulated in DZ-13. All the DEGs in the oxidative phosphorylation and insulin signaling pathways were upregulated in DZ-13. Several cuticular proteins and ATP synthesis-related genes were upregulated in DZ-13, suggesting that thickening of the cuticle and increase in the ATPase expression would help silkworms to protect themselves from low temperature-induced stress. Several immune-related genes, such as BmRel and BmSerpin-2, were downregulated in DZ-37, revealing that the resistance of silkworm is decreased under high temperature shock resulting in susceptibility to pathogens. Thus, the increase in the thermo-tolerance of silkworm should be related to the enhancement in the pathogen resistance.

The genome-wide transcriptional regulatory landscape of ecdysone in the silkworm.

BACKGROUND: The silkworm, Bombyx mori, a typical representative of metamorphic insects, is of great agricultural and economic importance. The steroid hormone ecdysone (20-hydroxyecdysone, 20E) is the central regulator of insect developmental transitions, and its nuclear receptors are crucial for numerous biological processes, including reproduction, metabolism, and immunity. However, genome-wide DNA regulatory elements and the ecdysone receptor (EcR) that control these programs of gene expression are not well defined. RESULTS: In this study, we investigated the alterations in three types of histone modification in silkworm embryonic cells treated with 20E by chromatin immunoprecipitation sequencing (ChIP-seq). We identified enhancers using histone modifications and derived genome-wide ecdysone-dependent enhancer activity maps in the silkworm. We found enhancers enriched for monomethylation of histone H3 Lys4 (H3K4me1) that showed dynamic changes in acetylation of histone H3 Lys27 (H3K27ac) after 20E treatment and functioned to regulate the transcription of specific genes. EcR regulated transcription by binding not only to proximal promoters but also to the distal enhancers of target genes. Moreover, only 52.65% EcR peaks contained ecdysone response element (EcRE) motif, suggesting that EcR regulates the expression of target genes not only by binding directly to EcRE, but also by binding with other transcription factor. CONCLUSIONS: Our findings provide novel insights into the complex regulatory landscape of hormone-responsive cell activity and a basis for understanding the complex transcriptional regulatory processes of ecdysone.