Analysis of Myc Chromatin Binding by Calibrated ChIP-Seq Approach.

Donald P Cameron, Vladislav Kuzin, Laura Baranello

Methods in molecular biology (Clifton, N.J.) 2021

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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.

Citation

Donald P Cameron, Vladislav Kuzin, Laura Baranello. Analysis of Myc Chromatin Binding by Calibrated ChIP-Seq Approach. Methods in molecular biology (Clifton, N.J.). 2021;2318:161-185