Project Details
Projekt
Dynamics of methylated nucleosides and their derivatives in RNAs
Subject Area
Biological and Biomimetic Chemistry
Term
from 2015 to 2024
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 277312423
Modifications in cellular RNAs, collectively termed the “epitranscriptome”, have recently been shown to be more widespread in cellular RNAs than previously anticipated and they have emerged as critical regulators of most aspects of RNA metabolism. Thereby, they play important roles in modulating fundamental cellular processes such as gene expression, the cell cycle, development and differentiation. Recent advances in next-generation sequencing-based methods for transcriptome-wide mapping of RNA modifications have revealed the presence of pseudouridine, N6-methyladenosine (m6A), N6-2’-O-dimethyladenosine (m6Am), 5-methylcytosine (m5C), 1-methyladenosine (m1A) and 2’-O-methylations (Nm) in messenger RNAs (mRNAs) and many other RNA species. While knowledge of the enzymes responsible for installing specific RNA modifications (“writers”) continues to expand, interestingly, recent work has uncovered the presence of demethylases that can act as modifications “erasers” as well as “reader” proteins that specifically bind modified RNAs thereby regulating their biogenesis, functions and stability. Together with the discovery that many RNA modifications are present at substoichiometric levels, this has highlighted the dynamic nature of the epitranscriptome and emphasised the importance of RNA modifications as key regulators of gene expression. During the first funding period THE project, we have explored the roles of m6A and m5C modifications in RNAs, including the characterisation of various writer and reader proteins as well as the dissection of the interactions these factors establish with their substrates on the molecular and atomic levels. Building on these findings, in this project we will further address the functions, substrate specificity and mode of action of different modification enzymes that contribute to the dynamics of RNA modifications. The cellular RNA-interactomes of such enzymes will be determined using UV crosslinking and analysis of cDNA (CRAC) and other in vivo analyses, and the spectrum of nucleotides targeted by these enzymes will be identified. The development of transcriptome-wide mapping approaches for selected RNA modifications and the analysis of the effects of loss of specific modifications in normal growth conditions and also upon exposure to stresses will provide insight into the functions of RNA modifications in modulating gene expression. Structural and biochemical analyses will be employed to elucidate the fundamental principles of substrate recognition and catalysis by these enzymes.
DFG Programme
Priority Programmes
