Role of Histone Variant H2A.J in Fine-Tuning Chromatin Organization for the Establishment of Ionizing Radiation-Induced Senescence

Cells. 2023 Mar 16;12(6):916. doi: 10.3390/cells12060916.


Purpose: Radiation-induced senescence is characterized by profound changes in chromatin organization with the formation of Senescence-Associated-Heterochromatin-Foci (SAHF) and DNA-Segments-with-Chromatin-Alterations-Reinforcing-Senescence (DNA-SCARS). Importantly, senescent cells also secrete complex combinations of pro-inflammatory factors, referred as Senescence-Associated-Secretory-Phenotype (SASP). Here, we analyzed the epigenetic mechanism of histone variant H2A.J in establishing radiation-induced senescence.

Experimental design: Primary and genetically-modified lung fibroblasts with down- or up-regulated H2A.J expression were exposed to ionizing radiation and were analyzed for the formation of SAHF and DNA-SCARS by immunofluorescence microscopy. Dynamic changes in chromatin organization and accessibility, transcription factor recruitment, and transcriptome signatures were mapped by ATAC-seq and RNA-seq analysis. The secretion of SASP factors and potential bystander effects were analyzed by ELISA and RT-PCR. Lung tissue of mice exposed to different doses were analyzed by the digital image analysis of H2A.J-immunohistochemistry.

Results: Differential incorporation of H2A.J has profound effects on higher-order chromatin organization and on establishing the epigenetic state of senescence. Integrative analyses of ATAC-seq and RNA-seq datasets indicate that H2A.J-associated changes in chromatin accessibility of regulatory regions decisively modulates transcription factor recruitment and inflammatory gene expression, resulting in an altered SASP secretome. In lung parenchyma, pneumocytes show dose-dependent H2A.J expression in response to radiation-induced DNA damage, therefore contributing to pro-inflammatory tissue reactions.

Conclusions: The fine-tuned incorporation of H2A.J defines the epigenetic landscape for driving the senescence programme in response to radiation-induced DNA damage. Deregulated H2A.J deposition affects chromatin remodeling, transcription factor recruitment, and the pro-inflammatory secretome. Our findings provide new mechanistic insights into DNA-damage triggered epigenetic mechanisms governing the biological processes of radiation-induced injury.

Keywords: DNA-Segments with Chromatin Alterations Reinforcing Senescence (DNA-SCARS); Senescence-Associated Heterochromatin Foci (SAHF); Senescence-Associated Secretory Phenotype (SASP); histone variant H2A.J; ionizing radiation; radiation-induced senescence.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin
  • Cicatrix*
  • Heterochromatin
  • Histones* / metabolism
  • Mice
  • Radiation, Ionizing
  • Transcription Factors / metabolism


  • Histones
  • Chromatin
  • Heterochromatin
  • Transcription Factors

Grants and funding

C.E.R. received funding from the German Research Foundation (Deutsche Forschungsgemeinschaft; grant number RU821/8-1), the German Cancer Aid (Deutsche Krebshilfe; grant number 70113135), and the Federal Ministry of Education and Research (BMBF; 02NUK035A; 02NUK058B). C.M. was supported by grants from the ANR (ANR-17-CE12-0008) and the CEA radiobiology program.