Publications
2022
Scholarly publications
Veggiani, G., Villaseñor, R., Martyn, G. D., Tang, J. Q., Krone, W. M., Gu, J., Chen, C., Waters, M. L., Pearce, K. H., Baubec, T., & Sidhu, S. S. (2022). High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression. Nature Communications, 13(1), Article 6975. https://doi.org/10.1038/s41467-022-34269-7
Yang, B., Borgeaud, A. C., Buřičová, M., Aeschbach, L., Rodríguez-Lima, O., Ruiz Buendía, G. A., Cinesi, C., Taylor, A. S., Baubec, T., & Dion, V. (2022). Expanded CAG/CTG repeats resist gene silencing mediated by targeted epigenome editing. Human Molecular Genetics, 31(3), 386-398. https://doi.org/10.1093/hmg/ddab255
Butz, S., Schmolka, N., Karemaker, I., Villaseñor, R., Schwarz, I., Domcke, S., Uijttewaal, E. C. H., Jude, J., Lienert, F., Krebs, A., Wagenaar, N. P. D., Bao, X., Zuber, J., Elling, U., Schübeler, D., & Baubec, T. (2022). DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions. Nature Genetics, 54(11), 1702-1710. Advance online publication. https://doi.org/10.1038/s41588-022-01210-z
Molenaar, T. M., Malik, M., Silva, J., Liu, N. Q., Haarhuis, J. H. I., Ambrosi, C., Kwesi-Maliepaard, E. M., Welsem, T. V., Baubec, T., Faller, W. J., & Leeuwen, F. V. (2022). The histone methyltransferase SETD2 negatively regulates cell size. Journal of Cell Science, 135(19), 1-15. Article jcs259856. https://doi.org/10.1242/jcs.259856
2021
Scholarly publications
Mallona, I., Ilie, I. M., Karemaker, I. D., Butz, S., Manzo, M., Caflisch, A., & Baubec, T. (2021). Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Research, 49(1), 145-157. https://doi.org/10.1093/nar/gkaa1168
Villaseñor, R., & Baubec, T. (2021). Regulatory mechanisms governing chromatin organization and function. Current Opinion in Cell Biology, 70, 10-17. https://doi.org/10.1016/j.ceb.2020.10.015
2020
Scholarly publications
Dalcher, D., Tan, J. Y., Bersaglieri, C., Peña-Hernández, R., Vollenweider, E., Zeyen, S., Schmid, M. W., Bianchi, V., Butz, S., Roganowicz, M., Kuzyakiv, R., Baubec, T., Marques, A. C., & Santoro, R. (2020). BAZ2A safeguards genome architecture of ground-state pluripotent stem cells. EMBO Journal, 39(23), e105606. https://doi.org/10.15252/embj.2020105606
Karemaker, I. D., & Baubec, T. (2020). DNA methyltransferases hitchhiking on chromatin. Schweizerische Medizinische Wochenschrift, 150, w20329. https://doi.org/10.4414/smw.2020.20329
Ruiz Buendía, G. A., Leleu, M., Marzetta, F., Vanzan, L., Tan, J. Y., Ythier, V., Randall, E. L., Marques, A. C., Baubec, T., Murr, R., Xenarios, I., & Dion, V. (2020). Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion. Science advances, 6(27), eaaz4012. https://doi.org/10.1126/sciadv.aaz4012
Ringel, T., Frey, N., Ringnalda, F., Janjuha, S., Cherkaoui, S., Butz, S., Srivatsa, S., Pirkl, M., Russo, G., Villiger, L., Rogler, G., Clevers, H., Beerenwinkel, N., Zamboni, N., Baubec, T., & Schwank, G. (2020). Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance. Cell Stem Cell, 26(3), 431-440.e8. https://doi.org/10.1016/j.stem.2020.02.007
Villaseñor, R., Pfaendler, R., Ambrosi, C., Butz, S., Giuliani, S., Bryan, E., Sheahan, T. W., Gable, A. L., Schmolka, N., Manzo, M., Wirz, J., Feller, C., von Mering, C., Aebersold, R., Voigt, P., & Baubec, T. (2020). Publisher Correction: ChromID identifies the protein interactome at chromatin marks. Nature Biotechnology, 38(6), 757. https://doi.org/10.1038/s41587-020-0484-5
Villaseñor, R., Pfaendler, R., Ambrosi, C., Butz, S., Giuliani, S., Bryan, E., Sheahan, T. W., Gable, A. L., Schmolka, N., Manzo, M., Wirz, J., Feller, C., von Mering, C., Aebersold, R., Voigt, P., & Baubec, T. (2020). ChromID identifies the protein interactome at chromatin marks. Nature Biotechnology, 38(6), 728-736. https://doi.org/10.1038/s41587-020-0434-2
Baubec, T., & Defossez, P-A. (2020). Reading DNA Modifications. Journal of Molecular Biology. Advance online publication. https://doi.org/10.1016/j.jmb.2020.02.001
2019
Scholarly publications
Caiado, F., Maia-Silva, D., Jardim, C., Schmolka, N., Carvalho, T., Reforço, C., Faria, R., Kolundzija, B., Simões, A. E., Baubec, T., Vakoc, C. R., da Silva, M. G., Manz, M. G., Schumacher, T. N., Norell, H., & Silva-Santos, B. (2019). Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection. Nature Communications, 10(1), 4986. https://doi.org/10.1038/s41467-019-12983-z
Caiado, F., Maia-Silva, D., Jardim, C., Schmolka, N., Carvalho, T., Reforço, C., Faria, R., Kolundzija, B., Simões, A. E., Baubec, T., Vakoc, C. R., da Silva, M. G., Manz, M. G., Schumacher, T. N., Norell, H., & Silva-Santos, B. (2019). Author Correction: Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection. Nature Communications, 10(1), 5451. https://doi.org/10.1038/s41467-019-13453-2
Teloni, F., Michelena, J., Lezaja, A., Kilic, S., Ambrosi, C., Menon, S., Dobrovolna, J., Imhof, R., Janscak, P., Baubec, T., & Altmeyer, M. (2019). Efficient Pre-mRNA Cleavage Prevents Replication-Stress-Associated Genome Instability. Molecular Cell, 73(4), 670-683.e12. https://doi.org/10.1016/j.molcel.2018.11.036
Hartl, D., Krebs, A. R., Grand, R. S., Baubec, T., Isbel, L., Wirbelauer, C., Burger, L., & Schübeler, D. (2019). CG dinucleotides enhance promoter activity independent of DNA methylation. Genome Research, 29(4), 554-563. https://doi.org/10.1101/gr.241653.118
2018
Scholarly publications
Manzo, M., Ambrosi, C., & Baubec, T. (2018). Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells. Methods in Molecular Biology, 1766, 157-174. https://doi.org/10.1007/978-1-4939-7768-0_9
2017
Scholarly publications
Colombo, D. F., Burger, L., Baubec, T., & Schübeler, D. (2017). Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content. PLoS Genetics, 13(12). https://doi.org/10.1371/journal.pgen.1007102
Manzo, M., Wirz, J., Ambrosi, C., Villaseñor, R., Roschitzki, B., & Baubec, T. (2017). Isoform-specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands. EMBO Journal, 36(23), 3421-3434. https://doi.org/10.15252/embj.201797038
Ambrosi, C., Manzo, M., & Baubec, T. (2017). Dynamics and Context-Dependent Roles of DNA Methylation. Journal of Molecular Biology, 429(10), 1459-1475. https://doi.org/10.1016/j.jmb.2017.02.008
2016
Scholarly publications
Baubec, T., & Akalin, A. (2016). Genome-Wide Analysis of DNA Methylation Patterns by High-Throughput Sequencing. In A. M. Aransay, & J. L. Lavín Trueba (Eds.), Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing (pp. 197-221). Article Chapter 9 Springer. https://doi.org/10.1007/978-3-319-31350-4_9
Hiragami-Hamada, K., Soeroes, S., Nikolov, M., Wilkins, B., Kreuz, S., Chen, C., De La Rosa-Velázquez, I. A., Zenn, H. M., Kost, N., Pohl, W., Chernev, A., Schwarzer, D., Jenuwein, T., Lorincz, M., Zimmermann, B., Walla, P. J., Neumann, H., Baubec, T., Urlaub, H., & Fischle, W. (2016). Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin. Nature Communications, 7, Article 11310. https://doi.org/10.1038/ncomms11310
Bartolomei, G., Leutert, M., Manzo, M., Baubec, T., & Hottiger, M. O. (2016). Analysis of Chromatin ADP-Ribosylation at the Genome-wide Level and at Specific Loci by ADPr-ChAP. Molecular Cell, 61(3), 474-485. https://doi.org/10.1016/j.molcel.2015.12.025
2015
Scholarly publications
Liu, C-H., Finke, A., Díaz, M., Rozhon, W., Poppenberger, B., Baubec, T., & Pecinka, A. (2015). Repair of DNA Damage Induced by the Cytidine Analog Zebularine Requires ATR and ATM in Arabidopsis. The Plant Cell, 27(6), 1788-800. https://doi.org/10.1105/tpc.114.135467
Baubec, T., Colombo, D. F., Wirbelauer, C., Schmidt, J., Burger, L., Krebs, A. R., Akalin, A., & Schübeler, D. (2015). Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature, 520(7546), 243-7. https://doi.org/10.1038/nature14176
2014
Scholarly publications
Baubec, T., & Schübeler, D. (2014). Genomic patterns and context specific interpretation of DNA methylation. Current Opinion in Genetics & Development, 25, 85-92. https://doi.org/10.1016/j.gde.2013.11.015
Baubec, T., Finke, A., Mittelsten Scheid, O., & Pecinka, A. (2014). Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis. EMBO Reports, 15(4), 446-52. https://doi.org/10.1002/embr.201337915
2013
Scholarly publications
Baubec, T., Ivánek, R., Lienert, F., & Schübeler, D. (2013). Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell, 153(2), 480-92. https://doi.org/10.1016/j.cell.2013.03.011
2011
Scholarly publications
Lienert, F., Mohn, F., Tiwari, V. K., Baubec, T., Roloff, T. C., Gaidatzis, D., Stadler, M. B., & Schübeler, D. (2011). Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells. PLoS Genetics, 7(6). https://doi.org/10.1371/journal.pgen.1002090
2010
Scholarly publications
Pecinka, A., Dinh, H. Q., Baubec, T., Rosa, M., Lettner, N., & Mittelsten Scheid, O. (2010). Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. The Plant Cell, 22(9), 3118-29. https://doi.org/10.1105/tpc.110.078493
Baubec, T., Dinh, H. Q., Pecinka, A., Rakic, B., Rozhon, W., Wohlrab, B., von Haeseler, A., & Mittelsten Scheid, O. (2010). Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic States in Arabidopsis. The Plant Cell, 22(1), 34-47. https://doi.org/10.1105/tpc.109.072819
2009
Scholarly publications
Baubec, T., Pecinka, A., Rozhon, W., & Mittelsten Scheid, O. (2009). Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine. Plant Journal, 57(3), 542-54. https://doi.org/10.1111/j.1365-313X.2008.03699.x
2008
Scholarly publications
Rozhon, W., Baubec, T., Mayerhofer, J., Mittelsten Scheid, O., & Jonak, C. (2008). Rapid quantification of global DNA methylation by isocratic cation exchange high-performance liquid chromatography. Analytical Biochemistry, 375(2), 354-60. https://doi.org/10.1016/j.ab.2008.01.001
2006
Scholarly publications
Baubec, T., & Mittelsten Scheid, O. (2006). Medea in full self-control. Trends in Plant Science, 11(10), 469-71. https://doi.org/10.1016/j.tplants.2006.08.002
2004
Scholarly publications
Braidotti, G., Baubec, T., Pauler, F., Seidl, C., Smrzka, O., Stricker, S., Yotova, I., & Barlow, D. P. (2004). The Air noncoding RNA: an imprinted cis-silencing transcript. Cold Spring Harbor Symposia on Quantitative Biology, 69, 55-66. https://doi.org/10.1101/sqb.2004.69.55