PT  - JOURNAL ARTICLE
AU  - Collin B. Merrill
AU  - Miguel A. Pabon
AU  - Austin B. Montgomery
AU  - Aylin R. Rodan
AU  - Adrian Rothenfluh
TI  - An optimized protocol for neuronal assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation using <em>Drosophila melanogaster</em>
AID  - 10.1101/2021.05.05.442838
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.05.05.442838
4099  - http://biorxiv.org/content/early/2021/05/05/2021.05.05.442838.short
4100  - http://biorxiv.org/content/early/2021/05/05/2021.05.05.442838.full
AB  - Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is rapidly becoming the assay of choice to investigate chromatin-mediated gene regulation, largely because of low input requirements, a fast workflow, and the ability to interrogate the entire genome in an unbiased manner. Many studies using ATAC-seq use mammalian or human-derived tissues and the established protocols work well in these systems. However, ATAC-seq is not yet widely used in Drosophila model systems. Vinegar flies present several key advantages over mammalian systems that make them an excellent model for ATAC-seq studies. For example, there are abundant genetic tools in flies that are not available in mammalian models that allow straightforward targeting, transgene expression, and genetic manipulation. Because current ATAC-seq protocols are not optimized to use fly tissue as input, we developed an optimized workflow that accounts for several complicating factors present in Drosophila. We examined several parameters of library construction, including input size, freezing time, and washing, which specifically address the fly cuticle and possible confounds from retinal pigments. Then, we further optimized the enzymatic steps of library construction to account for the smaller genome size in flies. Finally, we used our optimized protocol to generate ATAC-seq libraries that displayed metrics indicating excellent library quality. Our optimized protocol will enable extensive ATAC-seq experiments in Drosophila, thereby leveraging the advantages of this powerful model system to understand chromatin-mediated gene regulation.Competing Interest StatementThe authors have declared no competing interest.