DNA methylation is known to regulate transcription and was recently found to be 
involved in exon recognition via cotranscriptional splicing. We recently 
observed that exon-intron architectures can be grouped into two classes: one 
with higher GC content in exons compared to the flanking introns, and the other 
with similar GC content in exons and introns. The first group has higher 
nucleosome occupancy on exons than introns, whereas the second group exhibits 
weak nucleosome marking of exons, suggesting another type of epigenetic marker 
distinguishes exons from introns when GC content is similar. We find different 
and specific patterns of DNA methylation in each of the GC architectures; yet in 
both groups, DNA methylation clearly marks the exons. Exons of the leveled GC 
architecture exhibit a significantly stronger DNA methylation signal in relation 
to their flanking introns compared to exons of the differential GC architecture. 
This is accentuated by a reduction of the DNA methylation level in the intronic 
sequences in proximity to the splice sites and shows that different epigenetic 
modifications mark the location of exons already at the DNA level. Also, lower 
levels of methylated CpGs on alternative exons can successfully distinguish 
alternative exons from constitutive ones. Three positions at the splice sites 
show high CpG abundance and accompany elevated nucleosome occupancy in a leveled 
GC architecture. Overall, these results suggest that DNA methylation affects 
exon recognition and is influenced by the GC architecture of the exon and 
flanking introns.