Global Inhibition with Specific Activation: How p53 and MYC Redistribute the Transcriptome in the DNA Double-Strand Break Response

Joshua R. Porter, Brian E. Fisher, Laura Baranello, Julia C. Liu, Diane M. Kambach, Zuqin Nie, Woo Seuk Koh, Ji Luo, Jayne M. Stommel, David Levens, Eric Batchelor

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

In response to stresses, cells often halt normal cellular processes, yet stress-specific pathways must bypass such inhibition to generate effective responses. We investigated how cells redistribute global transcriptional activity in response to DNA damage. We show that an oscillatory increase of p53 levels in response to double-strand breaks drives a counter-oscillatory decrease of MYC levels. Using RNA sequencing (RNA-seq) of newly synthesized transcripts, we found that p53-mediated reduction of MYC suppressed general transcription, with the most highly expressed transcripts reduced to a greater extent. In contrast, upregulation of p53 targets was relatively unaffected by MYC suppression. Reducing MYC during the DNA damage response was important for cell-fate regulation, as counteracting MYC repression reduced cell-cycle arrest and elevated apoptosis. Our study shows that global inhibition with specific activation of transcriptional pathways is important for the proper response to DNA damage; this mechanism may be a general principle used in many stress responses. Porter et al. report a mechanism by which p53 dynamics are coupled to MYC repression in response to DNA damage. The coupling generates MYC-dependent global transcription inhibition, but p53 targets bypass the inhibition. MYC repression during the damage response is important for proper regulation of the cell cycle and apoptosis.

Original languageEnglish (US)
Pages (from-to)1013-1025.e9
JournalMolecular Cell
Volume67
Issue number6
DOIs
StatePublished - Sep 21 2017

Bibliographical note

Funding Information:
We thank Jie Liu, Toren Finkel, Ying Zheng, Liqiang Xi, Mark Raffeld, and all members of the Batchelor lab and the Levens lab for their help through technical assistance and many useful discussions. We also thank Qizong Lao, Brian Larsen, Sohyoung Kim, and Saori Fujiwara for their generous help with ATAC-seq. S. pombe was kindly provided by Julie Cooper. We thank Charles Fulco for providing data from CRISPRi experiments in the vicinity of the MYC locus. RNA-seq, ATAC-seq, and ChIP-seq were performed by the Center for Cancer Research Sequencing Facility. We thank the ENCODE Consortium and the Peggy Farnham lab (USC) for data from ChIP-seq of H3K27ac in MCF-7 cells (GEO: GSM945854 and GSM945859 ). This work used computational resources of the NIH HPC Biowulf cluster ( https://hpc.nih.gov ) . This work was supported by the Intramural Research Program of the Center for Cancer Research, National Cancer Institute, NIH .

Keywords

  • DNA damage
  • MYC
  • apoptosis
  • cell cycle
  • p53
  • transcriptome

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