Long non-coding RNAs (lncRNAs) are increasingly being recognized as epigenetic 
regulators of gene transcription. The diversity and complexity of lncRNA genes 
means that they exert their regulatory effects by a variety of mechanisms. 
Although there is still much to be learned about the mechanism of lncRNA 
function, general principles are starting to emerge. In particular, the 
application of high throughput (deep) sequencing methodologies has greatly 
advanced our understanding of lncRNA gene function. lncRNAs function as adaptors 
that link specific chromatin loci with chromatin-remodeling complexes and 
transcription factors. lncRNAs can act in cis or trans to guide 
epigenetic-modifier complexes to distinct genomic sites, or act as scaffolds 
which recruit multiple proteins simultaneously, thereby coordinating their 
activities. In this review we discuss the genomic organization of lncRNAs, the 
importance of RNA secondary structure to lncRNA functionality, the multitude of 
ways in which they interact with the genome, and what evolutionary conservation 
tells us about their function.