Group Schaefer

RNA Modifications: Their Impact on Gene Expression And Innate Immunity

The SCHAEFER Lab will move to the Center for Anatomy and Cell Biology at the Medical University of Vienna in Fall 2016. 
New address: 
Medical University of Vienna, Center for Anatomy & Cell Biology
Department of Cell and Developmental Biology, Unit of Epigenetics & RNA Biology
Schwarzspanierstrasse 17-I, 1090 Vienna, Austria

RNA molecules carry post-transcriptional modifications. More than 130 distinct modifications are known to exist in RNA molecules. Although some of these influence RNA maturation and stability, the biological function of most RNA modifications remains completely unclear.

It is well established that DNA and protein modifications influence gene expression. Importantly, studies of post-synthetic modifications on DNA (i.e. cytosine-methylation and its derivatives) as well as on proteins (i.e. histone modifications) contributed greatly to the concept of epigenetic regulation of gene expression. Recent findings point towards an under-appreciated role for RNA in gene expression regulation, which set the stage for defining a new and exciting concept: RNA epigenetics.

My group applies genetic and biochemical tools in the model organisms Drosophila melanogaster to understand how 5-methylcytosine marks in RNA

  • impact on RNA stability and function
  • control stress-induced RNA processing
  • affect the interaction with RNA-binding proteins
  • contribute to the regulation of gene expression

Our long-term goal is to characterize how RNA modifications contribute to genome regulation and, importantly, how they influence the re-programming of gene expression under environmental impact such as stress conditions.

Characterization of (Cytosine-5) RNA Methylomes

Every organism encodes (cytosine-5) RNA methyltransferases with unknown substrates and biological functions. We are using the recently developed technology called RNA bisulfite sequencing (RNA-BisSeq1) 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

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 have been found to inhibit protein translation, to associate with small-interfering RNA (siRNA) processing components and to affect the efficiency of siRNA pathways2. To further define the cellular pathways that are affected by stress-induced tRNA fragments we are using genetic and biochemical tools that address a number of unresolved questions concerning the biogenesis and subcellular localization of stress-induced tRNA fragments, 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

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 Drosophila3. How Dnmt2 contributes to virus control is presently unclear4. We are using biochemical tools, imaging techniques and virus-infection paradigms to determine how exactly Dnmt2 proteins affect anti-viral responses.


  1. Schaefer, M., Pollex, T., Hanna, K. & Lyko, F. RNA cytosine methylation analysis by bisulfite sequencing. Nucleic Acids Res 37, e12 (2009).
  2. Durdevic, Z., Mobin, M. B., Hanna, K., Lyko, F. & Schaefer, M. The RNA Methyltransferase Dnmt2 Is Required for Efficient Dicer-2-Dependent siRNA Pathway Activity in Drosophila. Cell Reports 4, 931–937 (2013).
  3. Durdevic, Z. et al. Efficient RNA virus control in Drosophila requires the RNA methyltransferase Dnmt2. EMBO Rep 14, 269–275 (2013).
  4. Durdevic, Z. & Schaefer, M. Dnmt2 methyltransferases and immunity: An ancient overlooked connection between nucleotide modification and host defense? Bioessays 35, 1044–1049 (2013).


Publications since 2006

Shanmugam, Raghuvaran; Aklujkar, Muktak; Schäfer, Matthias; Reinhardt, Richard; Nickel, Olaf; Reuter, Gunter; Lovley, Derek R; Ehrenhofer-Murray, Ann; Nellen, Wolfgang; Ankri, Serge; Helm, Mark; Jurkowski, Tomasz P; Jeltsch, Albert (2014). The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu. NUCLEIC ACIDS RES;42(10):6487-96. PMID: 24711368

Gigova, Andriana; Duggimpudi, Sujitha; Pollex, Tim; Schaefer, Matthias; Ko?, Martin (2014). A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability. RNA;20(10):1632-44. PMID: 25125595

Durdevic, Zeljko; Schaefer, Matthias (2013). Dnmt2 methyltransferases and immunity: an ancient overlooked connection between nucleotide modification and host defense? BIOESSAYS;35(12):1044-9. PMID: 24019003

Durdevic, Zeljko; Mobin, Mehrpouya Balaghy; Hanna, Katharina; Lyko, Frank; Schaefer, Matthias (2013). The RNA methyltransferase Dnmt2 is required for efficient Dicer-2-dependent siRNA pathway activity in Drosophila. Cell Rep;4(5):931-7. PMID: 24012760

Raddatz, Günter; Guzzardo, Paloma M; Olova, Nelly; Fantappié, Marcelo Rosado; Rampp, Markus; Schaefer, Matthias; Reik, Wolf; Hannon, Gregory J; Lyko, Frank (2013). Dnmt2-dependent methylomes lack defined DNA methylation patterns. P NATL ACAD SCI USA;110(21):8627-31. PMID: 23641003

Durdevic, Zeljko; Schaefer, Matthias (2013). tRNA modifications: necessary for correct tRNA-derived fragments during the recovery from stress? BIOESSAYS;35(4):323-7. PMID: 23315679

Durdevic, Zeljko; Hanna, Katharina; Gold, Beth; Pollex, Tim; Cherry, Sara; Lyko, Frank; Schaefer, Matthias (2013). Efficient RNA virus control in Drosophila requires the RNA methyltransferase Dnmt2. EMBO REP;14(3):269-75. PMID: 23370384

Tuorto, Francesca; Liebers, Reinhard; Musch, Tanja; Schaefer, Matthias; Hofmann, Sarah; Kellner, Stefanie; Frye, Michaela; Helm, Mark; Stoecklin, Georg; Lyko, Frank (2012). RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nat Struct Mol Biol;19(9):900-5. PMID: 22885326

Schaefer, Matthias; Lyko, Frank (2010). Lack of evidence for DNA methylation of Invader4 retroelements in Drosophila and implications for Dnmt2-mediated epigenetic regulation. NAT GENET;42(11):920-1; autho. PMID: 20980983

Pollex, Tim; Hanna, Katharina; Schaefer, Matthias (2010). Detection of cytosine methylation in RNA using bisulfite sequencing. Cold Spring Harbor protocols.;2010(10):pdb.prot5505. PMID: 20889702

Schaefer, Matthias; Pollex, Tim; Hanna, Katharina; Tuorto, Francesca; Meusburger, Madeleine; Helm, Mark; Lyko, Frank (2010). RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. GENE DEV;24(15):1590-5. PMID: 20679393

Schaefer, Matthias; Lyko, Frank (2010). Solving the Dnmt2 enigma. CHROMOSOMA;119(1):35-40. PMID: 19730874

Schaefer, Matthias; Hagemann, Sabine; Hanna, Katharina; Lyko, Frank (2009). Azacytidine inhibits RNA methylation at DNMT2 target sites in human cancer cell lines. CANCER RES;69(20):8127-32. PMID: 19808971

Yi, Xia; de Vries, Hilda I; Siudeja, Katarzyna; Rana, Anil; Lemstra, Willy; Brunsting, Jeanette F; Kok, Rob M; Smulders, Yvo M; Schaefer, Matthias; Dijk, Freark; Shang, Yongfeng; Eggen, Bart J L; Kampinga, Harm H; Sibon, Ody C M (2009). Stwl modifies chromatin compaction and is required to maintain DNA integrity in the presence of perturbed DNA replication. MOL BIOL CELL;20(3):983-94. PMID: 19056684

Schaefer, Matthias; Pollex, Tim; Hanna, Katharina; Lyko, Frank (2009). RNA cytosine methylation analysis by bisulfite sequencing. NUCLEIC ACIDS RES;37(2):e12. PMID: 19059995