Projects

Characterization of Specific (Cytosine-5) RNA Methylomes

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Every organism encodes (cytosine-5) RNA methyltransferases with unknown substrates and biological functions. We are using recently developed technologies such as miCLiP and RNA bisulfite sequencing (RNA-BisSeq) to map 5-methylcytosine marks systematically and transcriptome-wide in different tissues and during various stress conditions. In addition, we use CRISPR-mediated genome editing to tag and manipulate the function of various (cytosine-5) RNA methyltransferases in an attempt to understand the dynamic nature of (cytosine-5) RNA methylation systems during development and environmental insults.

Biological Function of Stress-Induced Small RNAs

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Loss-of-function mutations of known (cytosine-5) RNA methyltransferases (Dnmt2 and Nsun2) cause the de-stabilization of various non-coding RNAs, including tRNAs, during embryonic development and under specific stress conditions. The resulting tRNA fragments (tRFs) have been found to inhibit protein translation, to associate with small-interfering RNA (siRNA) processing components and to affect the efficiency of siRNA pathways. To further define the cellular pathways that are affected by stress-induced tRFs we are using genetic and biochemical tools that address a number of unresolved questions concerning the biogenesis and subcellular localization of stress-induced tRFs, their stability and movement between different tissues as well as the possibility of their inheritance into the next generation.

Impact of (Cytosine-5) RNA Methylation on the Immune Response

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The innate immune system uses pattern recognition receptors to sense RNA. Post-transcriptional RNA modifications have been implicated in the discrimination between self and foreign RNA. Recently, mutations in Dnmt2, a highly conserved (cytosine-5) RNA methyltransferase, implicated (cytosine-5) methylation in the defense against specific RNA viruses in Drosophila. How (cytosine-5) methylation by Dnmt2 contributes to virus control is presently unclear. We are using biochemical tools, imaging techniques and virus-infection paradigms to determine how exactly Dnmt2 proteins affect anti-viral responses by using human cell culture and the Drosophila system.