According to Choi et al. Genome Biology 2009, 10:R89, DNA methylation at both coding boundaries may regulate transcription elongation and stabilize splicing by reducing the occurrences of exon skipping.
From the abstract:
Here we report a genome-wide observation of distinct peaks of
nucleosomes and methylation at both ends of a protein coding unit.
Elongating polymerases tend to pause near both coding ends immediately
upstream of the epigenetic peaks, causing a significant reduction in
elongation efficiency. Conserved features in underlying protein coding
sequences seem to dictate their evolutionary conservation across
multiple species. The nucleosomal and methylation marks are commonly
associated with high sequence-encoded DNA-bending propensity but
differentially with CpG density. As the gene grows longer, the
epigenetic codes seem to be shifted from variable inner sequences
toward boundary regions, rendering the peaks more prominent in higher
Their data (figures 1 and S2), however, do not support a generalized increase in the 3' UTR regions in either human T cells, mouse liver, yeast or flies.