Fig. 1

Genome-wide screens and site-specific validation of candidate variably methylated IAP elements (VM-IAPs) identify 51 loci with constitutive variable methylation and 26 loci with tissue-specific variability. a Bisulphite pyrosequencing of 103 candidate VM-IAPs in ear tissue and B cells led to classification of constitutive VM-IAPs (cVM-IAPs), tissue-specific VM-IAPs (tsVM-IAPs), or false positives – three representative examples are shown for each. The threshold for validation as a VM-IAP is a 10% methylation range amongst individuals. IAP elements with ≥10 and < 10% range in methylation are coloured red and black, respectively. Each point represents an individual and is the average methylation of four distal CpGs in the LTR. n = 8 for ear samples and 7 for B cell samples. b IAP-Cyp4a12a (top) is a representative example of tsVM-IAPs with variable methylation in multiple tissues. IAP-Mapk4 (bottom) is a representative example of tsVM-IAPs whose variable methylation is restricted to B cells. c IAP elements of the LTR1_Mm–Ez-int (fully-structured) and the LTR2_Mm (solo LTR) types are over-represented in cVM-IAPs. The frequencies of cVM-IAP and tsVM-IAP structures are compared with the relative frequency of genome-wide IAP structures. In the IAP type labels, fully-structured IAPs with flanking LTRs are indicated with “–”, and incomplete IAPs missing one or both flanking LTRs are indicated with “||”. Only IAP types with at least one cVM-IAP or tsVM-IAP are shown. d In B cells, expression of Acss2 is inversely correlated with the methylation level of the nearby tsVM-IAP, IAP-Acss2 (two-tailed Pearson). Expression was quantified by qPCR, normalised to housekeeping genes, Pgk1 and Gapdh, and analysed across multiple exon-exon junctions: 1–2, 3–7 and 4–7