Accumulating evidence over the last decade has presented us with the intriguing 
observation that the majority of eukaryotic genomes are pervasively transcribed 
to encode a complex network of small and long noncoding RNAs. Long noncoding 
RNAs are of particular interest, as they were once thought to be restricted to 
housekeeping functions and are now linked to a wide variety of biological 
functions related to physiology, embryology and development. Emerging evidence 
indicates that a subset of long noncoding RNAs mediate their biological 
functions by using chromatin as a substrate, to index the genetic information 
encoded in the genome. This chapter will discuss how noncoding RNAs and the 
processes underlying their transcription mediate transcriptional regulation, by 
epigenetically regulating the structure of chromatin in various biological 
contexts.