Dose rate dependent reduction in chromatin accessibility at transcriptional start sites long time after exposure to gamma radiation

ABSTRACT Ionizing radiation (IR) impact cellular and molecular processes that require chromatin remodelling relevant for cellular integrity. However, the cellular implications of ionizing radiation (IR) delivered per time unit (dose rate) are still debated. This study investigates whether the dose rate is relevant for inflicting changes to the epigenome, represented by chromatin accessibility, or whether it is the total dose that is decisive. CBA/CaOlaHsd mice were whole-body exposed to either chronic low dose rate (2.5 mGy/h for 54 d) or the higher dose rates (10 mGy/h for 14 d and 100 mGy/h for 30 h) of gamma radiation (60Co, total dose: 3 Gy). Chromatin accessibility was analysed in liver tissue samples using Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-Seq), both one day after and over three months post-radiation (>100 d). The results show that the dose rate contributes to radiation-induced epigenomic changes in the liver at both sampling timepoints. Interestingly, chronic low dose rate exposure to a high total dose (3 Gy) did not inflict long-term changes to the epigenome. In contrast to the acute high dose rate given to the same total dose, reduced accessibility at transcriptional start sites (TSS) was identified in genes relevant for the DNA damage response and transcriptional activity. Our findings link dose rate to essential biological mechanisms that could be relevant for understanding long-term changes after ionizing radiation exposure. However, future studies are needed to comprehend the biological consequence of these findings.

[1]  Hae-June Lee,et al.  Differential Effects of Low and High Radiation Dose Rates on Mouse Spermatogenesis , 2021, International Journal of Molecular Sciences.

[2]  Chaohui Yu,et al.  Radiation-induced liver injury and hepatocyte senescence , 2021, Cell death discovery.

[3]  N. Duale,et al.  Perturbed transcriptional profiles after chronic low dose rate radiation in mice , 2021, PloS one.

[4]  M. Spivakov,et al.  Transcriptional enhancers and their communication with gene promoters , 2021, Cellular and Molecular Life Sciences.

[5]  P. Zhou,et al.  DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy , 2021, Signal Transduction and Targeted Therapy.

[6]  Robert J. Schmitz,et al.  Chromatin accessibility profiling methods , 2021, Nature Reviews Methods Primers.

[7]  Y. Socol,et al.  Low-dose ionizing radiation as a hormetin: experimental observations and therapeutic perspective for age-related disorders , 2021, Biogerontology.

[8]  T. Paunesku,et al.  Effects of low dose and low dose rate low linear energy transfer radiation on animals – review of recent studies relevant for carcinogenesis , 2020, International journal of radiation biology.

[9]  M. Little,et al.  Ionizing radiation-induced circulatory and metabolic diseases. , 2020, Environment international.

[10]  A. Adewoye,et al.  The long-term effects of exposure to ionising radiation on gene expression in mice. , 2020, Mutation research.

[11]  M. Belli,et al.  Ionizing Radiation-Induced Epigenetic Modifications and Their Relevance to Radiation Protection , 2020, International journal of molecular sciences.

[12]  A. Gospodinov,et al.  The Chromatin Response to Double-Strand DNA Breaks and Their Repair , 2020, Cells.

[13]  M. Bianchi,et al.  Nucleosomes effectively shield DNA from radiation damage in living cells , 2020, Nucleic acids research.

[14]  R. Huo,et al.  Characterization of epigenetic and transcriptional landscape in infantile hemangiomas with ATAC-seq and RNA-seq. , 2020, Epigenomics.

[15]  Philip A. Ewels,et al.  The nf-core framework for community-curated bioinformatics pipelines , 2020, Nature Biotechnology.

[16]  N. Duale,et al.  Using prediction models to identify miRNA-based markers of low dose rate chronic stress. , 2020, The Science of the total environment.

[17]  Gary S. Caldwell,et al.  Integrative assessment of low-dose gamma radiation effects on Daphnia magna reproduction: Toxicity pathway assembly and AOP development. , 2019, The Science of the total environment.

[18]  Astrid Gall,et al.  Ensembl 2020 , 2019, Nucleic Acids Res..

[19]  D. Clark,et al.  Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation , 2019, Genome research.

[20]  K. Zibara,et al.  The AP-1 transcriptional complex: Local switch or remote command? , 2019, Biochimica et biophysica acta. Reviews on cancer.

[21]  Alireza Hadj Khodabakhshi,et al.  Metascape provides a biologist-oriented resource for the analysis of systems-level datasets , 2019, Nature Communications.

[22]  Rebekah R. Starks,et al.  Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks , 2019, Epigenetics & Chromatin.

[23]  D. Oughton,et al.  Gamma radiation induces locus specific changes to histone modification enrichment in zebrafish and Atlantic salmon , 2019, PloS one.

[24]  A. Hida,et al.  Epidemiological studies of atomic bomb radiation at the Radiation Effects Research Foundation , 2019, International journal of radiation biology.

[25]  Sandy L. Klemm,et al.  Chromatin accessibility and the regulatory epigenome , 2019, Nature Reviews Genetics.

[26]  D. Sinclair,et al.  Epigenetic changes during aging and their reprogramming potential , 2019, Critical reviews in biochemistry and molecular biology.

[27]  M. Santos,et al.  Histone modifications and the DNA double-strand break response , 2018, Cell cycle.

[28]  Mauro A. A. Castro,et al.  The chromatin accessibility landscape of primary human cancers , 2018, Science.

[29]  O. Lind,et al.  The NMBU FIGARO low dose irradiation facility , 2018, International journal of radiation biology.

[30]  L. Migliore,et al.  Ionizing Radiation and Human Health: Reviewing Models of Exposure and Mechanisms of Cellular Damage. An Epigenetic Perspective , 2018, International journal of environmental research and public health.

[31]  M. Little Evidence for dose and dose rate effects in human and animal radiation studies , 2018, Annals of the ICRP.

[32]  Shiwei Zheng,et al.  Molecular transitions in early progenitors during human cord blood hematopoiesis , 2018, Molecular systems biology.

[33]  A. Wieczorek,et al.  Long-term effects of low-dose mouse liver irradiation involve ultrastructural and biochemical changes in hepatocytes that depend on lipid metabolism , 2018, Radiation and Environmental Biophysics.

[34]  Brandon J Thomas,et al.  IL-10 Signaling Remodels Adipose Chromatin Architecture to Limit Thermogenesis and Energy Expenditure , 2018, Cell.

[35]  D. Geschwind,et al.  The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis , 2018, Cell.

[36]  V. Jain,et al.  Global transcriptome profile reveals abundance of DNA damage response and repair genes in individuals from high level natural radiation areas of Kerala coast , 2017, PloS one.

[37]  G. Brunborg,et al.  Genotoxic effects of high dose rate X‐ray and low dose rate gamma radiation in ApcMin/+ mice , 2017, Environmental and molecular mutagenesis.

[38]  Nicholas A. Sinnott-Armstrong,et al.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues , 2017, Nature Methods.

[39]  Hendrik G. Stunnenberg,et al.  The interplay of epigenetic marks during stem cell differentiation and development , 2017, Nature Reviews Genetics.

[40]  H. Richly,et al.  Regulation of DNA Repair Mechanisms: How the Chromatin Environment Regulates the DNA Damage Response , 2017, International journal of molecular sciences.

[41]  William A. Flavahan,et al.  Epigenetic plasticity and the hallmarks of cancer , 2017, Science.

[42]  D. Richardson,et al.  Mortality from Circulatory Diseases and other Non-Cancer Outcomes among Nuclear Workers in France, the United Kingdom and the United States (INWORKS) , 2017, Radiation Research.

[43]  K. Aziz,et al.  Complex DNA Damage: A Route to Radiation-Induced Genomic Instability and Carcinogenesis , 2017, Cancers.

[44]  C. Simillion,et al.  Metabolomic Analysis of Mice Exposed to Gamma Radiation Reveals a Systemic Understanding of Total-Body Exposure , 2017, Radiation Research.

[45]  I. Koturbash,et al.  Effects of ionizing radiation on DNA methylation: from experimental biology to clinical applications , 2017, International journal of radiation biology.

[46]  C. Instanes,et al.  Gamma radiation at a human relevant low dose rate is genotoxic in mice , 2016, Scientific Reports.

[47]  F. Drabløs,et al.  Gene regulation in the immediate-early response process. , 2016, Advances in biological regulation.

[48]  R. Preston,et al.  The role of dose rate in radiation cancer risk: evaluating the effect of dose rate at the molecular, cellular and tissue levels using key events in critical pathways following exposure to low LET radiation , 2016, International journal of radiation biology.

[49]  A. Fortuny,et al.  Epigenome maintenance in response to DNA damage , 2016, Molecular cell.

[50]  M. Little,et al.  Dose-rate effects in radiation biology and radiation protection , 2016, Annals of the ICRP.

[51]  B. Grosche,et al.  Dose and dose-rate effects of ionizing radiation: a discussion in the light of radiological protection , 2015, Radiation and environmental biophysics.

[52]  Qing-Yu He,et al.  ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization , 2015, Bioinform..

[53]  R. Minghim,et al.  InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams , 2015, BMC Bioinformatics.

[54]  Howard Y. Chang,et al.  ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide , 2015, Current protocols in molecular biology.

[55]  M. Buck,et al.  Chromatin accessibility: a window into the genome , 2014, Epigenetics & Chromatin.

[56]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[57]  N. Friedman,et al.  Chromatin state dynamics during blood formation , 2014, Science.

[58]  N. Bansal,et al.  Effects of ionizing radiation on biological molecules--mechanisms of damage and emerging methods of detection. , 2014, Antioxidants & redox signaling.

[59]  Rory Stark,et al.  Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data , 2014, Front. Genet..

[60]  G. K. Sandve,et al.  Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines , 2014, BMC Genomics.

[61]  K. Yoshikawa,et al.  Chromatin Compaction Protects Genomic DNA from Radiation Damage , 2013, PloS one.

[62]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[63]  M. Lomax,et al.  Biological consequences of radiation-induced DNA damage: relevance to radiotherapy. , 2013, Clinical oncology (Royal College of Radiologists (Great Britain)).

[64]  O. Kovalchuk,et al.  Epigenetics in radiation biology: a new research frontier , 2013, Front. Genet..

[65]  T. Pandita,et al.  Chromatin modifications and the DNA damage response to ionizing radiation , 2013, Front. Oncol..

[66]  Edouard I Azzam,et al.  Ionizing radiation-induced metabolic oxidative stress and prolonged cell injury. , 2012, Cancer letters.

[67]  A. Friedl,et al.  Radiation-induced alterations in histone modification patterns and their potential impact on short-term radiation effects , 2012, Front. Oncol..

[68]  O. Kovalchuk,et al.  Non-targeted radiation effects-an epigenetic connection. , 2011, Mutation research.

[69]  Gayle E Woloschak,et al.  Gene Expression Profiles in Mouse Liver after Long-Term Low-Dose-Rate Irradiation with Gamma Rays , 2010, Radiation research.

[70]  H. Sugiyama,et al.  Radiation exposure and circulatory disease risk: Hiroshima and Nagasaki atomic bomb survivor data, 1950-2003 , 2010, BMJ : British Medical Journal.

[71]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[72]  Kenneth J. Longmuir,et al.  Cellular organization of normal mouse liver: a histological, quantitative immunocytochemical, and fine structural analysis , 2009, Histochemistry and Cell Biology.

[73]  K. Satoh,et al.  Dose-Rate Effectiveness for Unstable-Type Chromosome Aberrations Detected in Mice after Continuous Irradiation with Low-Dose-Rate γ Rays , 2009, Radiation research.

[74]  S. Kozubek,et al.  Chromatin structure influences the sensitivity of DNA to gamma-radiation. , 2008, Biochimica et biophysica acta.

[75]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[76]  D. L. Preston,et al.  Solid Cancer Incidence in Atomic Bomb Survivors: 1958–1998 , 2007, Radiation research.

[77]  Division on Earth Health Risks from Exposure to Low Levels of Ionizing Radiation: BEIR VII Phase 2 , 2006 .

[78]  James A. Cuff,et al.  A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells , 2006, Cell.

[79]  O. Kovalchuk,et al.  Fractionated Low-Dose Radiation Exposure Leads to Accumulation of DNA Damage and Profound Alterations in DNA and Histone Methylation in the Murine Thymus , 2005, Molecular Cancer Research.

[80]  A. Hida,et al.  Cataract in atomic bomb survivors , 2004, International journal of radiation biology.

[81]  O. Kovalchuk,et al.  Methylation changes in muscle and liver tissues of male and female mice exposed to acute and chronic low-dose X-ray-irradiation. , 2004, Mutation research.

[82]  A. Hida,et al.  Effects of radiation on fatty liver and metabolic coronary risk factors among atomic bomb survivors in Nagasaki. , 2003, Hypertension research : official journal of the Japanese Society of Hypertension.

[83]  M. O. Bradley,et al.  Influence of chromatin structure on the induction of DNA double strand breaks by ionizing radiation. , 1992, Cancer research.

[84]  D. Hallahan,et al.  Ionizing radiation regulates expression of the c-jun protooncogene. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[85]  J H FOLLEY,et al.  Incidence of leukemia in survivors of the atomic bomb in Hiroshima and Nagasaki, Japan. , 1952, The American journal of medicine.

[86]  J. Davie,et al.  Immediate early response genes and cell transformation. , 2013, Pharmacology & therapeutics.

[87]  Meeseon Jeong,et al.  Health Effects of the Chernobyl Accident , 2011 .

[88]  R Wakeford,et al.  A Systematic Review of Epidemiological Associations between Low and Moderate Doses of Ionizing Radiation and Late Cardiovascular Effects, and Their Possible Mechanisms , 2008, Radiation research.

[89]  J. Valentin The 2007 Recommendations of the International Commission on Radiological Protection. ICRP publication 103. , 2007, Annals of the ICRP.