Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
Methods Mol Biol. 2021;2318:161-185. doi: 10.1007/978-1-0716-1476-1_8.
Here, we present a strategy to map and quantify the interactions between Myc and chromatin using a calibrated Myc ChIP-seq approach. We recommend the use of an internal spike-in control for post-sequencing normalization to enable detection of broad changes in Myc binding as can occur under conditions with varied Myc abundance. We also highlight a range of bioinformatic analyses that can dissect the downstream effects of Myc binding. These methods include peak calling, mapping Myc onto an integrated metagenome, juxtaposing ChIP-seq data with matching RNA-seq data, and identifying gene ontologies enriched for genes with high Myc binding. Our aim is to provide a guided strategy, from cell harvest through to bioinformatic analysis, to elucidate the global effects of Myc on transcription.
在这里，我们提出了一种使用经过校准的 Myc ChIP-seq 方法来绘制和量化 Myc 与染色质之间相互作用的策略。我们建议在测序后使用内部 Spike-in 对照进行归一化，以能够检测到 Myc 结合的广泛变化，这种变化可能发生在 Myc 丰度不同的条件下。我们还强调了一系列可以剖析 Myc 结合下游效应的生物信息学分析。这些方法包括峰调用、将 Myc 映射到整合的宏基因组上、将 ChIP-seq 数据与匹配的 RNA-seq 数据并列以及识别富含高 Myc 结合基因的基因本体论。我们的目的是提供一种从细胞收获到生物信息学分析的指导策略，以阐明 Myc 对转录的全局影响。
