Chromatin Biology & Epigenetics Lab, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Erica Invernizzi" (INGM), Milan, Italy.
Methods Mol Biol. 2021;2318:187-208. doi: 10.1007/978-1-0716-1476-1_9.
MYC is a transcription factor playing multiple functions both in physiological and pathological settings. Biochemical characterizations, combined with the analyses of MYC chromatin binding, have shown that its pleiotropic activity depends on the chromatin context and its protein-protein interactions with different cofactors. In order to determine the contribution of MYC in a certain biological condition, it would be relevant to analyze the concomitant binding of MYC and its associated proteins, in relationship to the chromatin environment. To this end, we here provide a simple method to parallel map the genome-wide binding of MYC-associated proteins, together with the chromatin profiling of multiple histone modifications. We detail the procedure to perform high-throughput ChIP-seq (HT-ChIP-seq) with a variety of biological samples. In addition, we describe simple bioinformatic steps to determine the distribution of MYC binding with respect to the chromatin context and the association of its cofactors. The described approach will permit the reproducible characterization of MYC activity in different biological contexts.
MYC 是一种转录因子，在生理和病理环境中发挥多种功能。生化特性分析，结合 MYC 染色质结合的分析，表明其多效性活性取决于染色质环境及其与不同辅助因子的蛋白质-蛋白质相互作用。为了确定 MYC 在特定生物条件下的作用，分析 MYC 与其相关蛋白的伴随结合，以及与染色质环境的关系，将是相关的。为此，我们在此提供了一种简单的方法来平行绘制 MYC 相关蛋白的全基因组结合，以及多种组蛋白修饰的染色质特征分析。我们详细介绍了使用各种生物样本进行高通量 ChIP-seq（HT-ChIP-seq）的过程。此外，我们还描述了简单的生物信息学步骤，以确定 MYC 结合相对于染色质环境的分布及其辅助因子的关联。所描述的方法将允许在不同的生物环境中重复表征 MYC 的活性。
