Custers Stefan, Apel Erika, Suk Yujin, Venugopal Chitra, Singh Sheila K, Danis Etienne
Department of Biochemistry and Biomedical Sciences, Department of Surgery, McMaster Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada.
Department of Biochemistry and Biomedical Sciences, McMaster Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada.
Methods Mol Biol. 2025;2944:207-225. doi: 10.1007/978-1-0716-4654-0_17.
Cancer cell malignancy is regulated by a variety of mechanisms, collectively termed the hallmarks of cancer. At the core of these regulative processes are genetic and epigenetic perturbations that play an essential role in neoplasmic formation. Advances in molecular techniques have enabled the in-depth research of the epigenome by means of epigenetic profiling, a process that has been dominated by the chromatin immunoprecipitation (ChIP) method. Even though ChIP has dominated the field, the technique is hindered by limitations such as high background noise, requirement of a large number of cells, requirement of antibodies with high pull-down efficiency, and crosslinking and solubilization-induced artifacts (e.g., epitope masking). Cleavage Under Targets and Release Under Nuclease (CUT&RUN) is a recently developed epigenomic alternative method to ChIP, offering advantages designed to overcome limitations of the ChIP method. Despite its advantages, it is not always straightforward which technique is most suitable for the job at hand. This chapter aims to provide an in-depth guide in performing CUT&RUN.
癌细胞的恶性程度受多种机制调节，这些机制统称为癌症的标志。在这些调节过程的核心是基因和表观遗传扰动，它们在肿瘤形成中起着至关重要的作用。分子技术的进步使得通过表观遗传谱分析对表观基因组进行深入研究成为可能，这一过程一直由染色质免疫沉淀（ChIP）方法主导。尽管ChIP在该领域占据主导地位，但该技术受到诸如高背景噪声、需要大量细胞、需要具有高下拉效率的抗体以及交联和溶解诱导的假象（例如表位掩盖）等限制。靶向切割与核酸酶释放（CUT&RUN）是最近开发的一种替代ChIP的表观基因组方法，具有旨在克服ChIP方法局限性的优点。尽管它有优点，但要确定哪种技术最适合手头的工作并不总是那么简单。本章旨在提供一份关于进行CUT&RUN的深入指南。
