A high-confidence experiment reveals the absence of telomeric DNA methylation. The complete 100-bp sequences of all the 50TRs from SRR578938 (Zemach et al. 2013) containing one or more cytosines are displayed, together with the complete sequences of some of the 50TRs lacking cytosines. The number of cytosines within 50TRs and the genomic origin estimated for all the reads are indicated in blue. Among the 222 50TRs identified in SRR578938, 199 did not contain cytosines (see Supplemental Fig. S1), 19 contained one or two cytosines, and four contained five cytosines or more. The parts of the reads that follow a continuous perfect telomeric (YYYTAAA)n pattern are shown in black with the exception of cytosines that are labeled red. The remaining bases are shown in green and have been used for mapping purposes. All the reads could be mapped to the TAIR10 database except one, which mapped to the left telomere-subtelomere junction of Chromosome I (Kuo et al. 2006). Note that all the 50TRs lacking cytosines (Supplemental Fig. S1) and those containing one or two cytosines follow a quasi-perfect telomeric (YYYTAAA)n pattern along their entire 100-bp length. Most of these reads (218 of 222) should originate from telomeres. The 50TR containing 19 cytosines also follows the perfect telomeric pattern along its entire 100-bp length and should be telomeric and originate from experimental limitations of the bisulfite technique or originate from the 300-bp ITS. The 50TRs that contain more than five cytosines originate from ITSs or from the left telomere–subtelomere junction of Chromosome I (IL). Since the frequency of these 50TRs (3 of 222; 1.4%) is expected according to the distribution of ITSs and telomere–subtelomere junctions in the Arabidopsis genome, their cytosines might reflect real methylation events.
