Although not directly tested, alternative effects of THC-associated DMRs on gene regulation are also likely. Notably, we observed a significant enrichment of DMRs in gene bodies, which, in addition to potential roles for regulating mRNA levels, could be suggestive of effects on gene splicing and isoform-specific regulation. There is also evidence that gene body methylation, particularly in CpGi's, could highlight secondary sites of transcription initiation (Deaton and Bird, 2011; Jones, 2012); in this context, ~47% of DMR-CpGs identified here within gene bodies also resided within CpGi's. In addition, it is important to consider that observed methylation signatures could mediate molecular processes in a more complex manner, for example, only in response to certain stimuli, in conjunction with regulatory proteins, or in a time-dependent manner at specific developmental stages. For example, a recent genome-wide DNA methylation study in schizophrenia showed that disease-associated changes were preferentially located at CpGs that exhibit dynamic variation during fetal development, suggesting that disease-associated methylation disturbances may exert effects during earlier neurodevelopmental periods prior to disease onset (Pidsley et al, 2014).
