The underlying mechanisms linking antisense RNA, chromatin architecture and gene expression have not been fully elucidated. Here we show that long transcripts encoded from the Kcnq1ot1 antisense promoter silence the flanking genes more efficiently than short antisense transcripts. Interestingly, the antisense RNA-mediated deposition of inactive chromatin-specific histone modifications was higher with the longer antisense transcripts than with the shorter antisense transcripts. The kinetic studies of expression and chromatin remodeling of overlapping and nonoverlapping genes in response to antisense transcription revealed that the overlapping gene was rapidly silenced due to decrease in the occupancy of basal transcription machinery and simultaneous enrichment of its promoter with inactive chromatin modifications. The nonoverlapping gene, initially enriched with histone modifications specific to active chromatin, was subsequently silenced. Surprisingly, the flanking sequences were initially enriched with H3K9 monomethylation, as compared to di- and trimethylation, with a subsequent shift to trimethylated H3K9 enrichment. Our data provide a new perspective into antisense RNA-mediated gene silencing, and, more importantly, provide an explanation for why the antisense transcripts encoded from imprinting control regions are of significant length.