Insect ChIP-Seq

Insects are the most diverse and numerous of the animal kingdom. They are found in almost every corner of the world and significantly impact agricultural production and human health. Insects are easy to breed, have a short life cycle, and can obtain a large number of individuals in a short period of time; they are open-cycle animals, and transplantation of organs and endocrine glands is relatively easy, and many physiological problems of invertebrates are studied using insects as experimental materials.

With the development of sequencing technologies and the reduction of sequencing prices, more and more insect genomes are being decoded, which provides the basis for developing insect epigenetic sequencing technologies, such as CHIP-seq. As scientists continue to expand the scope of insect research, the application of CHIP-seq in insects is becoming more and more common, providing new ideas and methods for studying the entire range of biological laws, such as development, ecology, and genetics.

Lifeasible has a mature platform and extensive experience in insect sequencing and can provide customers with insect ChIP-Seq solutions for a wide range of species, such as silkworms, drosophila, and mosquito.

Our Insect ChIP-Seq Service Content

We use antibodies specific to histone-specific modifications or DNA binding proteins, or transcription factor-specific antibodies to enrich for DNA fragments bound to them, then build libraries and sequence them. This service combines second-generation sequencing to search for genome-wide binding sites for transcription factors, epitope-modifying enzymes, or DNA-binding proteins.

• Analysis of transcription factors of silkworm by ChIP-Seq

To decipher the regulatory role of the transcription factor Broad Complex (BR-C) in insect growth and development, we performed whole-genome sequencing of BR-C target genes in silkworm (Bombyx mori) using ChIP-seq. The results showed that BR-C was enriched in pathways related to biosynthesis, metabolism, and development.

• Characterization of long non-coding RNAs (lncRNAs) in Drosophila melanogaster by ChIP-seq

To characterize lncRNAs in Drosophila melanogaster, we developed a novel protocol to detect active transcription of lncRNAs using ChIP-seq data (H3K4me3, H3K36me3, and Pol II). This study provides a basis for exploring the function of lncRNAs in Drosophila melanogaster.

Figure 1. Analysis of chromatin signatures (Pol II, H3K36me3, and H3K4me3) in the curated lncRNA genes. (Chen, M. J, et al. 2016)

• Chromatin analysis of Anopheles gambiae infected with Plasmodium falciparum by ChIP-seq

To investigate the potential mechanisms underlying the changes in vector competence induced by malaria infection in mosquitoes, we used ChIP-seq to sequence H3K27ac, H3K9ac, H3K9me3, and H3K4me3 at the whole genome level. The results of the data analysis helped us to analyze the regulatory elements and genes of mosquitoes in response to P. falciparum infection.

Figure 2. Analysis of histone ChIP-seq data. (Ruiz, J. L, et al. 2019)

Technical Route of Insect ChIP-Seq

Sample Requirements

• Sample type: DNA sample, cell, or tissue.
• Total sample volume: ≥ 10 ng of ChIPed DNA or ≥ 10⁷ of cell volume or 2 g of tissue.
• DNA samples: OD260/280 values should be between 1.8 and 2.0.
• Preservation solvent for DNA: in H₂O or TE (pH 8.0).
• Sample transport: choose the fastest transport method to avoid sample degradation. Please seal the tube mouth with parafilm during transport to prevent contamination.

It is recommended to provide two sample preparations, if possible, to ensure the quality and continuity of the experiment.

Bioinformatics Analysis Content

• Sequencing data quality assessment (QC)
• Comparison to reference genomes and data statistics
• Genome distribution statistics
• Peak calling analysis
• Peak cis-regulatory element distribution
• Peak region gene annotation
• Peak difference analysis
• Peak-associated gene GO annotation
• KEGG annotation of Peak-related genes
• Motif analysis of transcription binding sites (for transcription factors only)

Lifeasible's animal-oriented sequencing technology platform can provide complete insect ChIP-seq services to our customers. We are committed to meeting all of our customer's needs, and we guarantee to obtain high-quality reads and perform comprehensive bioinformatic analysis. Please feel free to contact us for any questions, inquiries, or cooperation.