If Almost All The Genome Transcribes, What Does All The RNA Do?

The NIH-sponsored ENCODE project results once and for all put to rest the idea that most of a eukaryotic genome is just junk.  Given that most of a genome transcribes at some level, the focus of genomic activity shifts from thinking just about genes and their related proteins to thinking about how patterns of transcription orchestrate cellular activity at all levels.  This is the 12^th workshop in which the idea of Connectrons has been discussed.  A Connectron is a four-sequence relation of two RNA transcript signals that bind in the major groove of two different DNA double-strand sequences to form two triple-stranded Hoogsteen (RNA-DNA-DNA) helices.  Physical experiment have now shown that these general-sequence Hoogsteen helices form in prokaryotes.  The RNA sequence and the dominant-strand DNA sequence are identical.  The effect of Connectron formation in prokaryotes is to terminate transcription where the Connectron forms.  In eukaryotes Connectrons and the associated condensin proteins form 30nm loops that are then silenced by methylation. 

This talk focuses on the several roles of Connectrons in shaping the structure of the nucleus and in controlling gene expression within and across chromosomes.  SNPs act to change the folding patterns of the intronic RNAs where the Connectron signals are located.