Regulation of protein multi-functionality by 3 UTRs

Regulation of protein multi-functionality by 3′UTRs SUMMARY Many protein functions are mediated by protein complexes whose formation is often regulated by abundance as higher levels increase the chance to encounter an interaction partner. mRNAs contain a coding region that is translated into protein, but they also contain a 3′ untranslated region (3′UTR). In addition to regulation by

abundance, my lab discovered that protein function can be regulated by 3′UTRs as during protein synthesis 3′UTRs mediate protein-protein interactions. 3′UTR-dependent protein complex assembly is mediated by the local translation environment. Each mRNA generates its own translation environment that consists of the

proteins bound by the mRNA together with the recruited proteins. As a result, mRNA isoforms with alternative 3′UTRs – that often differ substantially in length – provide drastically different translation environments, and thus encode different protein functions. Currently, thousands of 3′UTR-dependent functions are unknown

because they cannot be inferred from canonical protein functions. We have developed a method to systematically identify protein functions mediated by long 3′UTR isoforms of multi-UTR genes using a CRISPR-based approach. We will identify 3′UTRs that mediate so far unknown protein functions involved in

the evasion of cell death, in the regulation of migration, and differentiation. We currently know of two ways to achieve 3′UTR-dependent functions. As described above, an mRNA that contains a long 3′UTR can generate its own translation environment. Moreover, mRNAs can use elements in their 3′UTRs to localize to pre-existing translation environments that are formed by phase-separated cytosolic

compartments. Within these large cytosolic membraneless organelles the environment is generated by many mRNAs together with their recruited proteins. We discovered such a compartment called TIS granule network. We determined hundreds of enriched mRNAs and observed that usually only half of transcripts with the same

3′UTR localize to TIS granules. This implies that proteins can have alternative functions depending on whether they are translated in the cytosol or in TIS granules. Our goal is to investigate how proteins change their function when translated within TIS granules. To study TIS granule-dependent protein functions, we have

engineered cells that are unable to assemble TIS granules. For candidates whose mRNAs are strongly enriched in TIS granules, we are investigating if translation in TIS granules controls the addition of post- translational modifications, the establishment of specific protein complexes, or if it suppresses protein

aggregation. If successful, our research will reveal a widespread role of mRNA in the compartmentalization and physical scaffolding during translation. It will show how elements in 3′UTRs contribute to the diversification of protein function. In the long-term, it will facilitate the development of mRNA therapeutics where inclusion of specific

3′UTR elements allows mRNAs to encode proteins with more robust or alternative functions.