Decoding the mRNA capping code

Proteins are the building blocks of life. The instructions for building these proteins reside in molecules known as messenger RNAs (mRNAs) that specify both which protein and how much of that protein should be made. This regulation is, to a large extent, determined by the various features of the mRNA. One of the most ubiquitous of these features is the 5' cap, a structure that is attached to the start of a newly-synthesized mRNA. Several decades of research have revealed that the cap is an interface for many features of mRNAs such as stability, splicing, polyadenylation, mRNA export, and translation. A less appreciated fact is that the mRNA cap can be modified in several ways resulting in many different types of caps. The combination of these different modifications can be considered a cap code that can destine the mRNA for different fates. The aim of this project is to develop a method that can determine caps and decipher the meaning of the cap code.

Proteins are the building blocks of life. The instructions for building these proteins reside in molecules known as messenger RNAs (mRNAs) that specify both which protein and how much of that protein should be made. This regulation is, to a large extent, determined by the various features of the mRNA. One of the most ubiquitous of these features is the 5' cap, a structure that is attached to the start of a newly-synthesized mRNA. Several decades of research have revealed that the cap is an interface for many features of mRNAs such as stability, splicing, polyadenylation, mRNA export, and translation. A less appreciated fact is that the mRNA cap can be modified in several ways resulting in many different types of caps. The combination of these different modifications can be considered a cap code that can destine the mRNA for different fates. Currently, the complete cap structure can only be identified through bulk methods that rely on cleaving the cap from the transcripts, thereby losing the connection between mRNAs and their specific caps. This limitation is a significant obstacle in understanding the cap code and the function of its more enigmatic members. We thus still do not know how a given cap leads to a given fate. This lack of understanding of such a ubiquitous and central component of all eukaryotes represents a major knowledge gap. The objective of this project is to develop a novel method that can identify cap types on individual mRNAs, and use this to decode and understand the cap code. This is made possible by the recent convergence of several novel technologies. These technologies have been used and developed in our lab over several years and present us with an unprecedented chance to unravel the cap code.