TY - JOUR AU - St. Laurent, Georges AU - Savva, Yiannis AU - Kapranov, Philipp PY - 2012 M3 - Hypothesis and Theory TI - Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape JO - Frontiers in Genetics UR - https://www.frontiersin.org/articles/10.3389/fgene.2012.00057 VL - 3 SN - 1664-8021 N2 - 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. ER -