| Literature DB >> 27036964 |
Soren Impey1,2,3, Carl Pelz4, Amanuel Tafessu4, Tessa Marzulla5, Mitchell S Turker6, Jacob Raber7,8,9.
Abstract
BACKGROUND: Proton irradiation poses a potential hazard to astronauts during and following a mission, with post-mitotic cells at most risk because they cannot dilute resultant epigenetic changes via cell division. Persistent epigenetic changes that result from environmental exposures include gains or losses of DNA methylation of cytosine, which can impact gene expression. In the present study, we compared the long-term epigenetic effects of whole body proton irradiation in the mouse hippocampus and left ventricle. We used an unbiased genome-wide DNA methylation study, involving ChIP-seq with antibodies to 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) to identify DNA regions in which methylation levels have changed 22 weeks after a single exposure to proton irradiation. We used DIP-Seq to profile changes in genome-wide DNA methylation and hydroxymethylation following proton irradiation. In addition, we used published RNAseq data to assess whether differentially methylated regions were linked to changes in gene expression.Entities:
Keywords: DNA methylation; Epigenetic; Hippocampus; Left ventricle; Proton irradiation; RNAseq; Ventricle
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Year: 2016 PMID: 27036964 PMCID: PMC4815246 DOI: 10.1186/s12864-016-2581-x
Source DB: PubMed Journal: BMC Genomics ISSN: 1471-2164 Impact factor: 3.969
Fig. 15hmC is enriched in the gene bodies of active genes while 5mC is depleted at the 5’ regions of active genes. (a and b). Pie chart depicts accumulation of 5hmC or 5mC DIP-Seq signal in the indicated genomic regions. Data that matched multiple categories was matched to the closest annotation. (c and d). Heatmaps depict DIP-Seq sequence density (500 bp bins) at RefSeq genes rank-ordered by levels of gene expression (RNA-Seq data from other studies). The color ramp shows min-max DIP/ChIP signal density normalized to the 80th quantile. The black bar illustrates the transcribed region with the 5’ end on the left
Fig. 2a-d Pie chart depicts accumulation of 5hmC (a, b) and 5mC (c, d) DIP-Seq signal in the indicated genomic repetitive sequence annotation (DIP-Seq counts per million repeat sequences). Data that matched multiple categories were matched exclusively to the closest annotation
Fig. 3a-d Strip plots indicate the accumulation of normalized 5hmC and 5mC DiP-Seq sequences (counts per million repeat sequences). The decreased accumulation of 5mC in ventricle tRNA and rRNA repeats, as well as the increased accumulation of 5hmC in ventricle tRNA repeats, was significant (p < 0.05, n = 4)
Fig. 4a and b Venn diagrams depict directional overlap between differentially hydroxymethylated and methylated regions (FDR-adjusted p < 0.01) in a 25 kb window. The three Venn diagrams with the highest level of significance for the overlap are highlighted by the black boxes they are placed in
Fig. 5a Bar graph depicts gene ontology categories significantly enriched in the indicated radiation-regulated differentially methylated regions (FDR-adjusted p < 0.01) identified from left ventricle and hippocampus. Note the gene categories-associated with cardiovascular function (red) and neuronal function (green) are restricted to the indicated tissues. (b and c). Diagrams depict selected genes that regulate vascular development or neurogenesis that were significantly associated with decreased methylation in the indicated tissue. (d and e). UCSC genome browser diagrams depict mC-DIP-Seq signal upstream the Activin receptor 1c gene in ventricle and upstream the Synaptopodin gene in hippocampus that showed significant differences following radiation exposure. The wiggle tracks depict median-scaled tag count density above background at an FDR of 5 %. The highlighted region was statistically significant (FDR-adjusted p < 0.001)