Insect ATAC-Seq

Insects are the most diverse and ancient group of living organisms. Insects are relevant to humans, as pests that cause great production and health hazards and as taxa that provide key service functions to agroecosystems.

With the rapid development of sequencing and analysis technologies, entomological research has also moved into the genomic era. Entomologists use various omics research tools, such as genome, transcriptome, and proteome, to solve problems in entomological research from the perspective of systems biology. Epigenetics, which studies chromatin conformation and gene expression, has received much attention from scientists in recent years. Therefore, ATAC-seq is widely used as a mainstream tool for chromatin conformation studies in insects.

Lifeasible has been in insect sequencing for many years and provides entomologists with innovative, flexible, and customizable insect ATAC-seq solutions. Our epigenome sequencing solutions bring new perspectives to entomological research, helping our customers gain insight into the genes that regulate insect growth, development, metamorphosis, rhythm, evolution, and reproduction.

Our Insect ATAC-Seq Service Content

• Analysis of open chromatin regions at specific developmental stages in butterflies using ATAC-seq technology

Taking butterflies as the research object, we randomly inserted and cleaved the exposed chromatin DNA in the nucleus using the super-active Tn5 transposase and then ligated it with specific sequencing adaptors. DNA fragments linked to adaptors were isolated for high-throughput sequencing and analysis, yielding information on genome-wide open chromatin regions at specific developmental stages and potentially active transcription factors and their target genes.

• Identification of accessible chromatin in bumblebees of different developmental states using ATAC-seq

To gain a comprehensive understanding of the open chromatin regions of the bumblebee genome and to detect regulatory elements at the genome-wide level, we performed ATAC-seq on Bombus terrestris samples at four developmental stages: egg, larva, pupa, and adult. 36,390 chromatin-accessible regions, including shared and specific stages, were finally identified, contributing to the understanding of bumblebees. The chromatin conformation throughout development was determined.

Figure 1. Flow chart for identification of bumblebee chromatin accessibility by ATAC-seq. (Zhao, X, et al. 2020)

• Analysis of regional differences in enhancer accessibility during Drosophila blastoderm development using ATAC-seq

Development of the Drosophila embryo is controlled by gene regulatory networks (GRNs) that unfold along the anterior-posterior (AP) and dorsoventral (DV) axes. Their different concentrations along the body axis provide location-specific information that translates into different transcriptional outputs in each cell. We determined chromatin accessibility at spatial and temporal resolution using ATAC-seq. The results suggest a positive interaction between regulatory mechanisms and the local chromatin environment of the axis patterning enhancers.

Figure 2. Regional differences in chromatin accessibility. (Bozek, M, et al. 2019)

Technical Route of Insect ATAC-Seq

Sample Requirements

• Cells: > 2 × 10⁵
• Tissue: 50 mg/serving
• Take cells in a good growth state for trypsin digestion counting to ensure cell viability of 85% or more.
• Resuspend the cells in the cryopreservation solution and add 80-100,000 cells per cryopreservation tube. (Basic freezing solution recipe: 50% FBS + 40% complete medium + 10% DMSO)

Please note: Ensure sufficient dry ice when transporting samples to avoid temperature rise to destroy cell activity.

Bioinformatics Analysis Content

• Raw data collation, filtering, and quality assessment
• Reference genome annotation collation and statistics
• Reference sequence alignment analysis
• Peak calling
• Peak-associated gene GO annotation
• KEGG annotation of Peak-related genes
• Sample-to-sample differential Peak analysis
• Differential Peak-related gene GO enrichment analysis
• Differential Peak-related gene KEGG pathway enrichment analysis
• Nucleosome localization
• Genome-wide chromatin open mapping

Lifeasible's animal-oriented sequencing technology platform can provide insect ATAC-seq services to meet our client's needs. Our extensive project experience, scientific protocol design, and strict quality control management ensure that every step of the process is completed with excellence. Please feel free to contact us for questions, inquiries, or collaboration.