Distinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates

Nat Commun. 2021 Jan 20;12(1):484. doi: 10.1038/s41467-020-20783-z.

Abstract

The tumor suppressor p53 integrates stress response pathways by selectively engaging one of several potential transcriptomes, thereby triggering cell fate decisions (e.g., cell cycle arrest, apoptosis). Foundational to this process is the binding of tetrameric p53 to 20-bp response elements (REs) in the genome (RRRCWWGYYYN0-13RRRCWWGYYY). In general, REs at cell cycle arrest targets (e.g. p21) are of higher affinity than those at apoptosis targets (e.g., BAX). However, the RE sequence code underlying selectivity remains undeciphered. Here, we identify molecular mechanisms mediating p53 binding to high- and low-affinity REs by showing that key determinants of the code are embedded in the DNA shape. We further demonstrate that differences in minor/major groove widths, encoded by G/C or A/T bp content at positions 3, 8, 13, and 18 in the RE, determine distinct p53 DNA-binding modes by inducing different Arg248 and Lys120 conformations and interactions. The predictive capacity of this code was confirmed in vivo using genome editing at the BAX RE to interconvert the DNA-binding modes, transcription pattern, and cell fate outcome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Apoptosis / genetics
  • Cell Cycle
  • Cell Cycle Checkpoints
  • Cell Differentiation / genetics*
  • Cell Differentiation / physiology*
  • Cell Line
  • DNA / chemistry
  • DNA-Binding Proteins
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Models, Molecular
  • Molecular Conformation
  • Protein Binding / genetics
  • Response Elements
  • Tumor Suppressor Protein p53 / genetics*
  • Tumor Suppressor Protein p53 / metabolism*

Substances

  • DNA-Binding Proteins
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • DNA