Construction of Drosophila chromatin accessibility landscape at a single-cell level using CH-ATAC-seq

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) at single-cell level can provide different perspectives of regulatory patterns based on cell type-specific accessible regions. While human genomic elements have been well studied, understanding how nuclear acid sequence regulates the expression of target genes in a genome-wide level in other organisms remains a major challenge. Batch effects, expensive machines are still constraints nowadays to build a cross-species landscape for further analysis, a platform with high throughput and low cost will be extremely required.Here, we constructed a cross-species accessible chromatin landscape by combinatorial-hybridization-based single-cell ATAC-seq, a single-cell ATAC-seq platform with high throughput and signal-noise ratio using fresh nuclei as input. Whole bodies of wild-type w1118 strain of Drosophila melanogaster at 10 days were dissociated into single-nucleus suspensions, followed by single-cell DNA library construction, high-throughput sequencing, and bioinformatics analysis.

单细胞水平转座酶可及性染色质测序（assay for transposase-accessible chromatin using sequencing, ATAC-seq）可基于细胞类型特异性可及染色质区域，从多维度揭示基因调控模式。尽管人类基因组元件已得到充分研究，但在其他生物体中，解析核酸序列如何在全基因组层面调控靶基因表达仍是一项核心挑战。当前，批次效应与昂贵的实验设备仍是构建跨物种染色质可及性图谱以开展后续分析的主要限制因素，因此亟需开发兼具高通量与低成本优势的技术平台。本研究通过基于组合杂交的单细胞ATAC-seq技术构建了跨物种染色质可及性图谱；该技术以新鲜细胞核为起始材料，具备高通量与高信噪比特性。本研究以羽化10天的野生型w1118品系黑腹果蝇（Drosophila melanogaster）的整体组织为材料，解离得到单细胞核悬液，随后完成单细胞DNA文库构建、高通量测序与生物信息学分析。