Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape

Front Genet. 2012 Apr 26:3:57. doi: 10.3389/fgene.2012.00057. eCollection 2012.


Perhaps no other topic in contemporary genomics has inspired such diverse viewpoints as the 95+% of the genome, previously known as "junk DNA," that does not code for proteins. Here, we present a theory in which dark matter RNA plays a role in the generation of a landscape of spatial micro-domains coupled to the information signaling matrix of the nuclear landscape. Within and between these micro-domains, dark matter RNAs additionally function to tether RNA interacting proteins and complexes of many different types, and by doing so, allow for a higher performance of the various processes requiring them at ultra-fast rates. This improves signal to noise characteristics of RNA processing, trafficking, and epigenetic signaling, where competition and differential RNA binding among proteins drives the computational decisions inherent in regulatory events.

Keywords: RNA binding protein; RNA editing; RNA processing; biological signaling; dark matter RNA; molecular scaffold; non-coding RNA; vlinc RNA.