Fig. 1

Characterisation of a somatic L1-associated DNA rearrangement within MeCP2. a Patient #2 MeCP2 mutant allele: a 0.9 kb L1PA2 sequence antisense to MeCP2. Direction of transcription (blue arrows), transcript isoforms (purple/pink lines) and qRT-PCR primers for MeCP2 expression assays (arrowheads) are indicated. b L1 mutation magnified view: RC-seq reads detected at the L1 5′ terminus (black/white bars). The L1 sequence comprises a truncated fragment of L1 ORF2 (white box), the 3′UTR without a poly-A tail (red box) and 37 nt from an Alu (black box). A 58 nucleotide deletion was also identified (triangle). Primers used for PCR validation are indicated as grey arrows. c Mutation site PCR validation: the mutant MeCP2 allele carrying L1 (filled) was only detected in patient #2 tumour whilst the empty site was found in both tumour and adjacent brain samples. No amplification was detected when water was used as template (NTC). d qRT-PCR measurement of MeCP2 transcript isoforms: The relative levels of RNA from both isoforms were significantly reduced in tumour (blue) versus adjacent brain (green) samples. Data for each group were normalised to non-tumour values, pooled and presented as mean +/− SEM (*p < 0.008, two tailed t-test, df = 6). Text colour relates with the primer pair used as represented in (a). e qRT-PCR measurement of L1 transcript abundance measured at the L1 5′UTR and ORF2 regions: The relative levels of RNA from both regions were significantly increased in tumour (blue) versus adjacent brain (green) samples. Data for each group were normalised to adjacent brain values, pooled and presented as mean +/− SEM (*p < 0.001, two tailed t-test, df = 10). f L1 promoter methylation: CpG methylation was measured across the L1 promoter CpG-island sequence. Tumour samples (blue) showed reduced methylation when compared to adjacent brain samples (green). Data for each group were normalised to non-tumour values, pooled and presented as mean +/− SEM (*p < 0.001, paired t-test, df = 18)