Sektion für Molekularbiologie


Chromatin- and Epigenetics Laboratory

Associate Professor & Deputy Head

Alexandra Lusser

phone: +43/512/9003-70210
Group members

Chromatin Assembly and Remodeling

The way in which eukaryotic DNA is organized in chromatin has profound effects on all processes that direct DNA metabolism (such as transcription, replication, repair and recombination). Chromatin controls access to the DNA, and it harbors epigenetic information. We are interested to learn about the establishment, maintenance and modification of eukaryotic chromatin structure. We are approaching this question by studying the molecular mechanisms and biological context of ATP-dependent chromatin assembly and remodeling and of variant histone assembly.

Moreover, we investigate “epigenetic” mechanisms at the mRNA level. In particular, we are interested in mRNA base modifications, such a 5-methylcytosine, and their potential roles for mRNA metabolism and translation.

Lusser-1 Lusser-2 Lusser-3



  1. Schoberleitner, I., Mutti, A., Sah, A., Wille, A., Gimeno-Valiente, F., Piatti, P., Torres, L., López-Rodas, G., Liu, J.J., Singewald, N., Schwarzer, C., Lusser, A. (2019) Role for chromatin remodeling factor Chd1 in learning and memory. Front. Mol. Neurosci., in press 

  2. Trixl L., Rieder D., Amort T., Lusser A. (2019) Bisulfite Sequencing of RNA for Transcriptome-Wide Detection of 5-Methylcytosine. In: Wajapeyee N., Gupta R. (eds) Epitranscriptomics. Methods in Molecular Biology, vol 1870. Humana Press, New York, NY 

  3. Neuner, E., Frener, M., Lusser*, A., Micura*, R. (2018). Superior cellular activities of azido- over amino-functionalized ligands for engineered preQ1riboswitches in E. coliRNA Biology, DOI: 10.1080/15476286.2018.1534526. *co-corresponding authors 

  4. Ordu, O., Kremser, L., Lusser, A.,Dekker, N. (2018). Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics. J. Chem. Phys.148, 123323. 

  5. Trixl L., Lusser A. (2018). The dynamic RNA modification 5‐methylcytosine and its emerging role as an epitranscriptomic mark. WIREs RNA 2018. doi: 10.1002/wrna.1510 

  6. Riml, C§., Amort§, T., Rieder§, D., Gasser, C., Lusser*, A., and Micura*, R. (2017). Osmium-mediated 4sU-to-C transformation as key to study RNA dynamics by sequencing (TUC-seq). Angew Chem Int Ed Engl.56(43), 13479–13483. doi.10.1002/anie.201707465. *co-corresponding authors 

  7. Riml, C., Lusser, A., Ennifar, E., Micura, R. (2017). Improved synthesis, thermodynamic properties, and crystal structure of RNA oligonucleotides containing 5-hydroxymethylcytosine. J. Org. Chem.82(15), 7939–7945. 

  8. Trixl L., Rieder D., Amort T., Lusser A. (2019) Bisulfite Sequencing of RNA for Transcriptome-Wide Detection of 5-Methylcytosine. In: Wajapeyee N., Gupta R. (eds) Epitranscriptomics. Methods in Molecular Biology, vol 1870. Humana Press, New York, NY

  9. Trixl, L., Amort, T., Wille, A., Zinni, M., Ebner, S., Hechenberger, C., Eichin, F., Gabriel, H., Schoberleitner, I., Huang, A., Piatti, P., Nat, R., Troppmair, J., Lusser, A. (2017). RNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity. Cell. Mol. Life Sci.

  10. Lusser, A. (ed) (2017). RNA methylation. Methods in Molecular Biology 1562, Humana Press; doi: 10.1007/978-1-4939-6807-7

  11. Amort, T., and Lusser, A. (2017). Detection of 5-Methylcytosine in Specific Poly(A) RNAs by Bisulfite Sequencing. Methods Mol Biol 1562: 107–121. Doi: 10.1007/978-1-4939-6807-7_8

  12. Amort, T., Sun, X., Khokhlova-Cubberley, D., and Lusser, A. (2017). Transcriptome-Wide Detection of 5-Methylcytosine by Bisulfite Sequencing. Methods Mol Biol 1562: 123–142. Doi: 10.1007/978-1-4939-6807-7_9

  13. Amort, T., Rieder, D., Wille, A., Khokhlova-Cubberley, D., Riml, C., Trixl, L., Jia, X.-Y., Micura, R., and Lusser, A. (2017). Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain. Genome Biol18, 1-16.

  14. Ordu, O., Lusser, A., Dekker, N.H. Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics. Biophysical Reviews (2016), doi:10.1007/s12551-016-0212-z

  15. Boltengagen, M., Huang, A., Boltengagen, A., Trixl, L., Lindner, H., Kremser, L., Offterdinger, M., and Lusser, A. (2016). A novel role for the histone acetyltransferase Hat1 in the CENP-A/CID assembly pathway in Drosophila melanogaster. Nucleic Acids Res44, 2145–2159. http://doi: 10.1093/nar/gkv1235

  16. Wille, A., Amort, T., Singewald, N., Sartori, S. B., & Lusser, A. (2016). Dysregulation of select ATP-dependent chromatin remodeling factors in high trait anxiety. Behavioural Brain Research, 311, 141–146.

  17. Sebald, J., Willi, M., Schoberleitner, I., Krogsdam, A., Orth-Höller, D., Trajanoski, Z., & Lusser, A. (2016). Impact of the Chromatin Remodeling Factor CHD1 on Gut Microbiome Composition of Drosophila melanogaster. PLoS ONE, 11(4), e0153476.

  18. Schafferer, S., Khurana, R., Refolo, V., Venezia, S., Sturm, E., Piatti, P., Hechenberger, C., Hackl, H., Kessler, R., Willi, M., Gstir, R., Krogsdam, A., Lusser, A., Poewe, W., Wenning, G.K., Hüttenhofer, A., Stefanova, N. (2016). Changes in the miRNA-mRNA regulatory network precede motor symptoms in a mouse model of multiple system atrophy: clinical implications. PLoS ONE, 11(3), e0150705. doi: 10.1371/journal.pone.0150705

  19. Wille, A., Maurer, V., Piatti, P., Whittle, N., Rieder, D., Singewald, N., & Lusser, A. (2015). Impaired Contextual Fear Extinction Learning is Associated with Aberrant Regulation of CHD-Type Chromatin Remodeling Factors. Frontiers in Behavioral Neuroscience, 9, 4071.

  20. Rieder, D., Amort, T., Kugler, E., Lusser, A., & Trajanoski, Z. (2015). meRanTK: methylated RNA analysis ToolKit. Bioinformatics (Oxford, England).

  21. Vlijm, R., Lee, M., Ordu, O., Boltengagen, A., Lusser, A., Dekker, N. H., & Dekker, C. (2015). Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes. PLoS ONE, 10(10), e0141267.

  22. Vlijm, R., Lee, M., Lipfert, J., Lusser, A., Dekker, C., Dekker, N.H. (2015). Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes. Cell Reports, 10(2): 216-225. doi: 10.1016/j.celrep.2014.12.022

  23. Katan, A. J., Vlijm, R., Lusser, A., Dekker, C. (2015) Dynamics of nucleosomal structures measured by high-speed Atomic Force Microscopy. Small, 11(8): 976-984. doi: 10.1002/smll.201401318

  24. Piatti, P., Lim, C.Y., Nat, R., Villunger, A., Geley, S., Shue, Y.T., Soratroi, C., Moser, M., and Lusser, A. (2015). Embryonic stem cell differentiation requires full length Chd1. Sci Rep5, 8007. doi: 10.1038/srep08007

  25. Etemad, S., Obermair, G.J., Bindreither, D., Benedetti, A., Stanika, R., Di Biase, V., Burtscher, V., Koschak, A., Kofler, R., Geley, S., Wille, A., Lusser, A., Flockerzi, V., Flucher B.E. (2014) Differential neuronal targeting of a new and two known calcium channel beta4 subunit splice variants correlates with their regulation of gene expression. J Neurosci 34(4): 1446-1461. doi: 10.1523/JNEUROSCI.3935-13.2014.

  26. Amort, T, Soulière, M. F., Wille, A., Jia, X.-Y., Fiegl, H., Wörle, H., Micura, R.,  and Lusser, A. (2013) Long non-coding RNAs as targets for cytosine methylation. RNA Biol. 10(6). doi: 10.4161/rna.24454;

  27. Vlijm R, Smitshuijzen JSJ, Lusser A, Dekker C (2012) NAP1-Assisted Nucleosome Assembly on DNA Measured in Real Time by Single-Molecule Magnetic Tweezers. PLoS ONE 7(9): e46306.  doi: 10.1371/journal.pone.0046306;

  28. Sebald, J., Morettini, S., Podhraski, V., Lass-Flörl, C., Lusser, A. (2012) CHD1 contributes to intestinal resistance against infection by P. aeruginosa in Drosophila melanogaster. PLoS ONE, 7(8): e43144. doi:10.1371/journal.pone.0043144;

  29. Fischnaller, S., Dowell, F., Lusser, A., Schlick-Steiner, B., Steiner, F.M. (2012) Non-destructive species identification of Drosophila obscura and D. subobscura (Diptera) using near-infrared spectroscopy. Fly (Austin) 6(4): 1-6; doi:10.4161/fly.21535;

  30. Zeilner, A., Piatti, P., Lusser, A. (2012) Chromatin Dynamics and Higher Order Chromatin Organization. In: Meyers, R. A. (ed) Epigenetic Regulation and Epigenomics. Wiley-Blackwell. ISBN 978-3-527-32682-2

  31. Morettini, S., Tribus, M., Zeilner, A., Sebald, J., Campo-Fernandez, B., Scheran, G., Wörle, H., Podhraski, V., Fyodorov, D.F., Lusser, A. (2011) The chromodomains of CHD1 are critical for enzymatic activity but less important for chromatin localization. Nucleic Acids Res. 39(8): 103-115. doi:10.1093/nar/gkq1298;

  32. Piatti P, Zeilner A, Lusser A. (2011). ATP-dependent chromatin remodeling factors and their roles in affecting nucleosome fiber composition. Int. J. Mol. Sci. 12(10): 6544-65. doi: 10.3390/ijms12106544;

  33. Podhraski, V., Campo-Fernandez, B., Wörle, H., Piatti, P., Niederegger, H., Böck, G., Fyodorov, D.F., Lusser, A. (2010) CenH3/CID incorporation is not dependent on the chromatin assembly factor CHD1 in Drosophila. PLoS ONE 5: e10120. doi: 10.1371/journal.pone.0010120;

  34. Morettini, S., Podhraski, V., Lusser, A. (2008) ATP-dependent chromatin remodeling enzymes and their various roles in cell cycle control. Front. Biosci., 13: 5522-32. doi: 10.2741/3096.

  35. Konev, A.Y, Tribus, M., Podhraski, V., Park, S.Y., Lim, C.Y., Emelyanov, A.V., Vershilova, E., Pirrotta, V., Kadonaga, J.T., Lusser*, A., Fyodorov*, D.V. (2007)  The CHD1 motor protein is required for deposition of histone H3.3 into chromatin in vivo. Science 317: 1087-1090. doi:10.1126/science.1145339 *co-corresponding authors

  36. Lusser, A., Urwin, D.L., Kadonaga, J.T. (2005) Distinct Activities of CHD1 and ACF in ATP-dependent Chromatin Assembly. Nat. Struct. Mol. Biol. 12(2):160-16

  37. Alexiadis, V., Lusser, A., Kadonaga, J.T. (2004) A conserved N-terminal motif in Rad54 is important for chromatin remodeling and homologous strand pairing. J. Biol. Chem. 279:27824-27829

  38. Lusser, A., Kadonaga, J.T. (2004) Strategies for the reconstitution of chromatin. Nat. Methods 1:19-26

  39. Lusser, A., Kadonaga, J.T. (2003) Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25:1192-11200

  40. Pipal, A., Goralik-Schramel, M., Lusser, A., Sarg, B., Lindner, H., Lanzanova, C., Rossi, V., Loidl, P. (2003) Regulation and processing of maize histone deacetylase Hda1 by limited proteolysis. Plant Cell 15:1904-1917

  41. Rossi, V., Locatelli, S., Lanzanova, C., Boniotti, M.B., Varotto, S., Pipal, A., Goralik-Schramel, M., Lusser, A., Gatz, C., Gutierrez, C., Motto, M. (2003) A maize histone deacetylase and retinoblastoma-related protein physically interact and cooperate in repressing gene transcription. Plant Mol. Biol. 51:401-413

  42. Brandtner, E.M., Lechner, T., Loidl, P., Lusser, A. (2002) Molecular identification of PpHDAC1, the first histone deacetylase from the slime mold Physarum polycephalum. Cell Biol. Int. 26:783-789

  43. Lusser, A. (2002) Acetylated, methylated, remodeled: chromatin states for gene regulation. Curr. Opin. Plant Biol. 5:437-443

  44. Dangl, M., Brosch, G., Haas, H., Loidl, P., Lusser, A. (2001) Comparative analysis of HD2 type histone deacetylases in higher plants. Planta 213:280-285

  45. Lusser, A., Kölle, D., Loidl, P. (2001) Histone acetylation: lessons from the plant kingdom. Trends Plant Sci. 6:59-65

  46. Lechner§, T., Lusser§, A., Pipal, A., Brosch, G., Loidl, A., Goralik-Schramel, M., Sendra, R., Wegener, S., Walton, J.D., Loidl, P. (2000) RPD3-type histone deacetylases in maize embryos. Biochemistry 39: 1683-1692   §  co-first authors

  47. Lusser, A., Eberharter, A., Loidl, A., Goralik-Schramel, M., Horngacher, M., Haas, H., Loidl, P. (1999) Analysis of the histone acetyltransferase B complex of maize embryos. Nucleic. Acids Res. 27:4427-4435

  48. Kölle, D., Brosch, G., Lechner, T., Lusser, A., Loidl, P. (1998) Biochemical methods for analysis of histone deacetylases. Methods 15:323-331

  49. Lusser, A., Brosch, G., Lopez-Rodas, G., Loidl, P. (1997) Histone acetyltransferases during the cell cycle and differentiation of Physarum polycephalum. Eur. J. Cell Biol. 74:102-110

  50. Lusser, A., Brosch, G., Loidl, A., Haas, H., Loidl, P. (1997) Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277:88-91

  51. Brosch, G., Lusser, A., Goralik-Schramel, M., Loidl, P. (1996) Purification and characterization of a high molecular weight histone deacetylase complex (HD2) of maize embryos. Biochemistry 35:15907-15914

  52. Lechner, T., Lusser, A., Brosch, G., Eberharter, A., Goralik-Schramel, M., Loidl, P. (1996) A comparative study of histone deacetylases of plant, fungal and vertebrate cells. Biochm. Biophys. Acta, 1296:181-188

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