UVB induces a genome-wide acting negative regulatory mechanism that operates at the level of transcription initiation in human cells

PLoS Genet. 2014 Jul 24;10(7):e1004483. doi: 10.1371/journal.pgen.1004483. eCollection 2014 Jul.

Abstract

Faithful transcription of DNA is constantly threatened by different endogenous and environmental genotoxic effects. Transcription coupled repair (TCR) has been described to stop transcription and quickly remove DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked transcription. This repair mechanism has been well characterized in the past using individual target genes. Moreover, numerous efforts investigated the fate of blocked RNA polymerase II (Pol II) during DNA repair mechanisms and suggested that stopped Pol II complexes can either backtrack, be removed and degraded or bypass the lesions to allow TCR. We investigated the effect of a non-lethal dose of UVB on global DNA-bound Pol II distribution in human cells. We found that the used UVB dose did not induce Pol II degradation however surprisingly at about 93% of the promoters of all expressed genes Pol II occupancy was seriously reduced 2-4 hours following UVB irradiation. The presence of Pol II at these cleared promoters was restored 5-6 hours after irradiation, indicating that the negative regulation is very dynamic. We also identified a small set of genes (including several p53 regulated genes), where the UVB-induced Pol II clearing did not operate. Interestingly, at promoters, where Pol II promoter clearance occurs, TFIIH, but not TBP, follows the behavior of Pol II, suggesting that at these genes upon UVB treatment TFIIH is sequestered for DNA repair by the TCR machinery. In agreement, in cells where the TCR factor, the Cockayne Syndrome B protein, was depleted UVB did not induce Pol II and TFIIH clearance at promoters. Thus, our study reveals a UVB induced negative regulatory mechanism that targets Pol II transcription initiation on the large majority of transcribed gene promoters, and a small subset of genes, where Pol II escapes this negative regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Damage / genetics
  • DNA Damage / radiation effects
  • DNA Repair / genetics
  • DNA Repair / radiation effects
  • DNA-Binding Proteins / genetics
  • Gene Expression Regulation / radiation effects*
  • Genome, Human / radiation effects*
  • Humans
  • MCF-7 Cells
  • Promoter Regions, Genetic*
  • RNA Polymerase II / genetics*
  • RNA Polymerase II / metabolism
  • TATA-Box Binding Protein
  • Transcription Factors, TFII / biosynthesis
  • Transcription Factors, TFII / metabolism
  • Transcription Termination, Genetic
  • Ultraviolet Rays

Substances

  • DNA-Binding Proteins
  • TATA-Box Binding Protein
  • Transcription Factors, TFII
  • RNA Polymerase II
  • transcription factor TFIIF

Grant support

ÁG was supported through a French-Hungarian Cotutelle program, and by fellowships from BAYGEN institute Szeged (Hungary), and from Fondation pour la Recherche Médicale en France (FRM). The work was supported by funds from CNRS LEA SKINCHROMA; Agence Nationale de la Recherche (ANR) (grant numbers: ANR-09-BLAN-0266; ANR-09-BLAN-0052) and European Community (EUTRRAC) grants to LT and New Hungary Development Plan Project TÁMOP-4.2.2.A-11/1/KONV-2012-0035 to IB and ZÚ. This study was also supported by the grant ANR-10-LABX-0030-INRT, under the frame programme Investissements ANR-10-IDEX-0002-02. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.