Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Nat Commun. 2023 Sep 22;14(1):5930. doi: 10.1038/s41467-023-41666-z.
For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
一个多世纪以来，福尔马林固定石蜡包埋（FFPE）样本制备一直是长期保存生物材料的首选方法。然而，由于长时间暴露在高浓度甲醛中导致染色质受损，FFPE 样本在表观基因组研究中的应用一直存在困难。之前，我们引入了靶向可及染色质切割（CUTAC），这是一种基于 CUT&Tag 的抗体靶向染色质可及性图谱绘制协议。在这里，我们展示了对我们的 CUTAC 方案进行简单的修改，无论是在单个管中还是直接在载玻片上进行，都可以使用 FFPE 样本生成增强子和启动子处暂停 RNA 聚合酶 II 的高分辨率图谱。我们发现，由 FFPE-CUTAC 产生的转录调控元件差异可以区分小鼠脑肿瘤，并以高置信度和精度识别和绘制调控元件标记物，包括 RNA-seq 无法检测到的 microRNAs。我们的简单工作流程使得对存档生物样本进行经济实惠的表观基因组分析成为可能，用于生物标志物鉴定、临床应用和回顾性研究。
