Recent advances in both mass spectroscopy and next generation sequencing methodology have revealed a new class of 5’ end RNA modification, which resembles the canonical eukaryotic 7-methyl-guanosine cap. These alternative “cap” structures are made up of metabolites such as Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) or Nicotinamide Adenosine Dinucleotide (NAD). The universality of these cap structures suggests that metabolite capping is a fundamental new facet of basic biology and are a novel mechanism for how a cell can fine tune gene expression levels based on metabolic state. To date, all of the work to determine the biological function of these caps has focused on NAD cap structures. However, recent experiments to quantify metabolite RNA caps showed that UDP-GlcNAc capped transcripts are present at higher levels than NAD capped transcripts in metazoans, fungi, bacteria and viruses. Considering the abundance of UDP-sugar capped transcripts, and the important role that these cap species play in cellular processes, it is imperative study the role these “glyco”-RNA caps play both on the function of RNA. To do this, we must first identify the specific transcripts which carry these caps and second, identify proteins that preferentially interact with these UDP-sugar capped transcripts by: 1. Developing and utilizing a novel method ClickNAz-tag seq, which takes advantage of orthogonally labeling UDP-GlcNAc and UDP MurNAc in E. coli with click-chemistry capable chemical groups, which will be used to pull-down UDP-sugar capped transcripts for identification by RNA-seq. 2. Develop and utilize a method UDP-Sugar capped RNA affinity pulldown (UcRAP), which will utilize a 5’UDP-sugar capped RNA as a probe to pulldown cap interacting proteins from E. coli for identification by tandem mass spectroscopy. Developing these tools, knowing which transcripts are UDP-sugar capped, and which proteins interact with these caps, will be instrumental in dissecting the function of UDP-sugar caps on specific transcripts. These studies will inform our follow up studies, which will address: 1. The mechanism of capping, 2. The functional consequence of capping of specific transcripts and 3. When during the cell cycle and why this capping occurs.