Abstract

Coordination of Functionally Related mRNAs and Proteins in Granules, GW/P bodies, and Vesicles

Jack Keene, James B. Duke Professor, Duke University Medical Center

Gene expression is determined by transcriptional and post-transcriptional mechanisms that coordinate regulatory layers and are localized in many cellular sub-environments. Post-transcriptional regulatory layers consist of trans RNA-binding proteins and multiple copies of cis messenger RNAs (mRNAs) and noncoding RNAs (miRNAs and other ncRNAs) that together form modular RNA regulons (RBPs) that in turn, coordinate the latter state of gene expression on a global level. The multi-targeting of mRNAs in RNA regulons include cis binding sites that are: a) RBP sequence specific, b) miR binding sites, c) modified mRNAs (e.g. methylated), that together produce functionally related proteins that can be found in cellular vesicles, bodies or granules by translation. Thus, RNA regulons are found in nearly all species and coordinate RNA turnover, localization, and/or translation globally in response to biological activation or repression. RNA regulons have myriad ramifications for biological coordination. Over time, dozens of RNA regulons have been reported in many biological systems and in dozens of species. For examples from the field: 1) PUF RNA regulons coordinate fungal metabolism and pathogenesis dating back over 500 million years; 2) trypanosome RNA regulons coordinate parasite differentiation in the blood at a time when transcription is silenced. 3) dozens of mammalian RNA regulons have biological and physiological ramifications in which mRNAs encoding functionally related proteins bound to several of the ~1,500 RBPs now known RBPs. Thus, RNA regulons can efficiently utilize and locate protein building blocks and regulatory factors that function as complex traits. Moreover, these overlapping mRNA subsets are highly dynamic and responsive to intrinsic and extrinsic signals. To understand these dynamic processes our lab developed Digestion Optimized-RIP-seq that is quantitative and applicable to understanding how combinatorial mechanisms regulate dynamic coordination of RNA targets during growth and differentiation, as well as revealing novel RNA regulons in cancer, neurodegeneration and liver development/regeneration. Our goal is to teach these technologies to students and fellows in order to decipher the remodeling of RNA regulons so to reveal underlying mechanisms of disease.