We seek to understand how the nuclear RNA silencing as well as RNA surveillance machinery work together with the chromatin modifying machinery to organize the genome. Recent genomic analyses show that the genomes of higher eukaryotes are widely transcribed. For example, even though only 2% of the human genome codes for mRNA almost 85% of it is transcribed. Much of this RNA is destroyed, the job of the RNA surveillance machinery. The question is whether this is just a wasteful side effect of the transcriptional machinery, or is it functional? We would argue that it is functional and that the transcripts across the genome provide a platform for organizing the genome, and are working to provide evidence for this hypothesis using the model system of Drosophila. Our data suggest that transcripts across the genome shape the chromatin primarily through post transcriptional modification of histones.