Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [DamID-seq]

Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. Overall design: We determined DamID scores for Polycomb, normalized by Dam only control, for Drosophila larval central brain, larval fat bodies and repo+ glial cells of larval central brain. All samples were performed with 2 biological replicates. In case of Dam only control for larval central brain, each biological replicate was performed with 3 technical replicates.

Dam鉴定（DamID）是一种可获取染色质蛋白结合全基因组图谱的高效技术。因其具备极高的灵敏度，该技术尤其适用于探究果蝇等模式生物小型组织样本内染色质蛋白的基因组相互作用。本研究报道了一种基于内含肽（intein）的方法，通过向果蝇饲料添加配体，可调控Dam及Dam融合蛋白在果蝇体内的表达水平，进而有效抑制Dam的毒性效应。此外，本研究还提出了一种可在复杂组织的特定细胞类型中实现Dam遗传调控表达的策略。我们通过在小型脑组织样本中构建多梳蛋白（Polycomb）的胶质细胞特异性结合图谱，验证了该策略的实用性。实验整体设计如下：我们针对果蝇幼虫中枢脑、幼虫脂肪体以及幼虫中枢脑内repo+胶质细胞，以仅表达Dam的样本作为对照，测定了多梳蛋白的DamID评分并完成标准化处理。所有样本均设置2次生物学重复；针对仅以Dam为对照的幼虫中枢脑样本，每一次生物学重复均搭配3次技术重复。