Alternative splicing of pre-messenger RNA is a key feature of transcriptome 
expansion in eukaryotic cells, yet its regulation is poorly understood. 
Spliceosome assembly occurs co-transcriptionally, raising the possibility that 
DNA structure may directly influence alternative splicing. Supporting such an 
association, recent reports have identified distinct histone methylation 
patterns, elevated nucleosome occupancy and enriched DNA methylation at exons 
relative to introns. Moreover, the rate of transcription elongation has been 
linked to alternative splicing. Here we provide the first evidence that a 
DNA-binding protein, CCCTC-binding factor (CTCF), can promote inclusion of weak 
upstream exons by mediating local RNA polymerase II pausing both in a mammalian 
model system for alternative splicing, CD45, and genome-wide. We further show 
that CTCF binding to CD45 exon 5 is inhibited by DNA methylation, leading to 
reciprocal effects on exon 5 inclusion. These findings provide a mechanistic 
basis for developmental regulation of splicing outcome through heritable 
epigenetic marks.