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Analysis of Myc Chromatin Binding by Calibrated ChIP-Seq Approach

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The Myc Gene

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2318))

Abstract

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.

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Acknowledgments

The computations and data storage were enabled by resources in project SNIC 2018/8-390 provided by the Swedish National Infrastructure for Computing (SNIC) at UPPMAX, partially funded by the Swedish Research Council through grant agreement no. 2018-05973.

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Author notes

  1. Donald P. Cameron and Vladislav Kuzin contributed equally with all other contributors.

Authors and Affiliations

  1. Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden

    Donald P. Cameron, Vladislav Kuzin & Laura Baranello

Authors
  1. Donald P. Cameron
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  2. Vladislav Kuzin
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  3. Laura Baranello
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Corresponding author

Correspondence to Laura Baranello .

Editor information

Editors and Affiliations

  1. Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain

    Laura Soucek

  2. Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain

    Jonathan Whitfield

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Cameron, D.P., Kuzin, V., Baranello, L. (2021). Analysis of Myc Chromatin Binding by Calibrated ChIP-Seq Approach. In: Soucek, L., Whitfield, J. (eds) The Myc Gene. Methods in Molecular Biology, vol 2318. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1476-1_8

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  • DOI: https://doi.org/10.1007/978-1-0716-1476-1_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1475-4

  • Online ISBN: 978-1-0716-1476-1

  • eBook Packages: Springer Protocols

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