Chromatin accessibility-based epigenetic landscape in osteoclastogenesis [ATAC-seq]

In this study, we showed chromatin accessibility-based epigenetic landscape in osteoclastogenesis. To reveal chromatin accessibility landscape throughout osteoclastogenesis, we conducted Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) with BMM (D0), OC precursors day 1 (D1), OC precursor day 2 (D2), and OC (D3). Overall design: Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) was conducted during osteoclastogenesis. We treated BMMs with RANKL for three days to differentiate them into osteoclasts (OCs). Cells in each day were subjected to ATAC-seq. Each sample was named as D0 (BMM), D1 (OC precursors day 1), D2 (OC precursor day 2), and D3 (OC), according to the day at which the cells were collected for the assay.

本研究揭示了破骨细胞生成过程中基于染色质开放状态的表观遗传图谱。为全面解析破骨细胞生成全程的染色质开放状态图谱，我们对骨髓来源巨噬细胞（bone marrow-derived macrophage, BMM）、第1天破骨细胞前体细胞（D1）、第2天破骨细胞前体细胞（D2）以及成熟破骨细胞（osteoclast, OC，D3）开展了转座酶可及性染色质高通量测序（Assay for Transposase Accessible Chromatin with high-throughput sequencing, ATAC-seq）。实验整体设计如下：本研究在破骨细胞生成进程中实施转座酶可及性染色质高通量测序（ATAC-seq）。我们通过核因子κB受体活化因子配体（Receptor Activator of Nuclear Factor κB Ligand, RANKL）处理骨髓来源巨噬细胞，诱导其连续分化3天以形成成熟破骨细胞；每日收集对应时间点的细胞进行ATAC-seq测序。各样本根据其用于测序的细胞收集时间节点命名，分别为D0（骨髓来源巨噬细胞，BMM）、D1（第1天破骨细胞前体细胞）、D2（第2天破骨细胞前体细胞）以及D3（成熟破骨细胞，OC）。