Extended Data Fig. 2: Characterisation of VM-IAP methylation levels in the Mtrrgt/gt mouse model.
From: Variably methylated retrotransposons are refractory to a range of environmental perturbations
a, VM-IAP methylation levels are altered in Mtrrgt/gt brain. VM-IAP methylation levels were compared between C57BL/6J (n = 8, grey box plots) and Mtrrgt/gt (n = 8, red box plots) brains. P-values were calculated by two-tailed Welch’s t-tests (ns indicates p > 0.05). b, Global DNA methylation levels are equivalent between C57BL/6J (n = 8, grey circles) and Mtrrgt/gt (n = 8, red circles) brain (left; p-value = 0.147) and kidney (right; p-value = 0.989) samples (unpaired two-tailed Student’s t-test; ns indicates p > 0.05). Global 5-methyl-cytosine (5mC) content was determined by liquid chromatography-tandem mass spectrometry and expressed as a percentage relative to total cytosine in the genome. c, VM-IAP methylation levels are unaffected by the Mtrrgt allele in mature sperm. VM-IAP methylation levels were quantified in sperm collected from the cauda epididymides and vas deferens of C57BL/6J (n = 8, grey circles), Mtrr+/+ (n = 8, hollow red circles), Mtrr+/gt (n = 8, half-filled red circles), and Mtrrgt/gt (n = 8, red circles) adult fertile males. d, VM-IAP methylation states are not associated with phenotypic severity in whole Mtrrgt/gt embryos. VM-IAP methylation levels were compared across C57BL/6J embryos (n = 7, grey circles), phenotypically normal Mtrrgt/gt embryos (n = 7, red circles), and severely affected Mtrrgt/gt embryos (n = 6, red circles) at E10.5 by Welch’s ANOVA. Adjusted p-values were calculated by two-tailed Tamhane T2 post hoc tests (ns indicates p > 0.05). Methylation data in all panels are shown as average percentage of DNA methylation across the four most distal CpGs at VM-IAP 5′ LTRs. Box-plot elements: centre line, median; box limits, 25th and 75th percentiles; whiskers, maximum and minimum; all data points shown.
