The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs.

A major surprise arising from genome-wide analyses has been the observation that the majority of the genome is transcribed, generating noncoding RNAs (ncRNAs). It is still an open question whether some or all of these ncRNAs constitute functional networks regulating gene transcriptional programs. However, in light of recent discoveries and given the diversity and flexibility of long ncRNAs and their abilities to nucleate molecular complexes and to form spatially compact arrays of complexes, it becomes likely that many or most ncRNAs act as sensors and integrators of a wide variety of regulated transcriptional responses and probably epigenetic events. Because many RNA-binding proteins, on binding RNAs, show distinct allosteric conformational alterations, we suggest that a ncRNA/RNA-binding protein-based strategy, perhaps in concert with several other mechanistic strategies, serves to integrate transcriptional, as well as RNA processing, regulatory programs.