SFB960 - Publications - Universität Regensburg

Bruckmann, Astrid (Z1)

Maldonado, R., Schwartz, U., Silberhorn, E. and Längst, G. (2019), Nucleosomes stabilise ssRNA-dsDNA triple helices in human cells. Molecular Cell. Accepted for publication.

Schwartz,U., Németh,A., Diermeier,S., Exler,J.H., Hansch,S., Maldonado,R., Heizinger,L., Merkl,R. and Längst,G. (2018), Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin. Nucleic Acids Res, 154, 515-.

Pfab A., Bruckmann A., Nazet .J, Merkl R., Grasser KD. (2018), The Adaptor Protein ENY2 Is a Component of the Deubiquitination Module of the Arabidopsis SAGA Transcriptional Co-activator Complex but not of the TREX-2 Complex. J Mol Biol. 430(10):1479-1494.

Dimartino D., Colantoni A., Ballarino M., Martone J., Mariani D., Danner J., Bruckmann A., Meister G., Morlando M., Bozzoni I. (2018), The Long Non-coding RNA lnc-31 Interacts with Rock1 mRNA and Mediates Its YB-1-Dependent Translation. Cell Rep. 23(3):733-740.

Schöller E., Weichmann F., Treiber T., Ringle S., Treiber N., Flatley A., Feederle R., Bruckmann A., Meister G. (2018), Interactions, localization, and phosphorylation of the m(6)A generating METTL3-METTL14-WTAP complex. RNA. 24(4):499-512.

Chen J., Kalinowska K., Müller B., Mergner J., Deutzmann R., Schwechheimer C., Hammes UZ, Dresselhaus T. (2018), DiSUMO-LIKE Interacts with RNA-Binding Proteins and Affects Cell-Cycle Progression during Maize Embryogenesis. Curr Biol. pii: S0960-9822(18)30424-X

Gust A., Jakob L., Zeitler DM, Bruckmann A., Kramm K., Willkomm S., Tinnefeld P., Meister G., Grohmann D. (2018), Site-Specific Labelling of Native Mammalian Proteins for Single-Molecule FRET Measurements. Chembiochem. 19(8):780-783.

Hoffmeister H., Fuchs A., Erdel F., Pinz S., Gröbner-Ferreira R., Bruckmann A., Deutzmann R., Schwartz U., Maldonado R., Huber C., Dendorfer AS, Rippe K., Längst G. (2017), CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality. Nucleic Acids Res. 45(18):10534-10554.

Antosz W., Pfab A., Ehrnsberger HF, Holzinger P., Köllen K., Mortensen SA, Bruckmann A., Schubert T., Längst G., Griesenbeck J., Schubert V., Grasser M., Grasser KD. (2017), The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors. Plant Cell. 29(4):854-870

Quévillon Huberdeau M., Zeitler DM, Hauptmann J., Bruckmann A., Fressigné L., Danner J., Piquet S., Strieder N., Engelmann JC, Jannot G., Deutzmann R., Simard MJ, Meister G. (2017), Phosphorylation of Argonaute proteins affects mRNA binding and is essential for microRNA-guided gene silencing in vivo. EMBO J. 36(14):2088-2106

Pfab A., Antosz W., Holzinger P., Bruckmann A., Griesenbeck J., Grasser KD. (2017), Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors. Methods Mol Biol. 1629:105-122.

Sørensen BB, Ehrnsberger HF, Esposito S., Pfab A., Bruckmann A., Hauptmann J., Meister G., Merkl R., Schubert T., Längst G., Melzer M., Grasser M., Grasser KD. (2017), The Arabidopsis THO/TREX component TEX1 functionally interacts with MOS11 and modulates mRNA export and alternative splicing events. Plant Mol Biol. 93(3):283-298

Ruther J., Hagström ÅK, Brandstetter B., Hofferberth J., Bruckmann A., Semmelmann
F., Fink M., Lowack H., Laberer S., Niehuis O., Deutzmann R., Löfstedt C., Sterner R. (2016), Epimerisation of chiral hydroxylactones by short-chain dehydrogenases/reductases accounts for sex pheromone evolution in Nasonia.
Sci Rep. 6:34697. doi: 10.1038/srep34697. PubMed PMID: 27703264; PubMed Central PMCID: PMC5050451.

Bruckmann A., Linnemann J., Perez-Fernandez J. (2016), Purification of RNA Polymerase I-Associated Chromatin from Yeast Cells. Methods Mol Biol.1455:213-23. doi: 10.1007/978-1-4939-3792-9_16. PubMed PMID: 27576721.

Völler D., Linck L., Bruckmann A., Hauptmann J., Deutzmann R., Meister G., Bosserhoff AK. (2016), Argonaute Family Protein Expression in Normal Tissue and Cancer Entities. PLoS One. 11(8):e0161165. doi: 10.1371/journal.pone.0161165. PubMed PMID: 27518285; PubMed Central PMCID: PMC4982624.

Hauptmann J., Schraivogel D., Bruckmann A., Manickavel S., Jakob L., Eichner N., Pfaff J., Urban M., Sprunck S., Hafner M., Tuschl T., Deutzmann R. & Meister G (2015),
Biochemical isolation of Argonaute protein complexes by Ago-APP. Proc. Natl. Acad. Sci. USA., 112(38):11841-5.

Dürr J., Lolas IB, Sørensen BB, Schubert V., Houben A., Melzer M., Deutzmann R., Grasser M., Grasser KD. (2014), The transcript elongation factor SPT4/SPT5 is involved in auxin-related gene expression in Arabidopsis. Nucleic Acids Res. 42(7):4332-47.

Merkl P., Perez-Fernandez J., Pilsl M., Reiter A., Williams L., Gerber J., Böhm M., Deutzmann R., Griesenbeck J., Milkereit P., Tschochner H. (2014), Binding of the termination factor Nsi1 to its cognate DNA site is sufficient to terminate RNA polymerase I transcription in vitro and to induce termination in vivo. Mol Cell Biol 34(20):3817-27.

Dillinger S., Garea AV, Deutzmann R., Németh A. (2014), Analysis of histone posttranslational modifications from nucleolus-associated chromatin by mass spectrometry. Methods Mol Biol 1094: 277-93.

Hamperl S., Brown CR, Garea AV, Perez-Fernandez J., Bruckmann A., Huber K., Wittner M., Babl V., Stoeckl U., Deutzmann R., Boeger H., Tschochner H., Milkereit P., Griesenbeck J. (2013), Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic Acids Res. 42(1):e2.

Hierlmeier T., Merl J., Sauert M., Perez-Fernandez J., Schultz P., Bruckmann A., Hamperl S., Ohmayer U., Rachel R., Jacob A., Hergert K., Deutzmann R., Griesenbeck J., Hurt E., Milkereit P., Baßler J., Tschochner H. (2013), Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S.cerevisiae. Nucleic Acids Res 41(2):1191-210.

Jakob S., Ohmayer U., Neueder A., Hierlmeier T., Perez-Fernandez J., Hochmuth E., Deutzmann R., Griesenbeck J., Tschochner H., Milkereit P. (2012), Interrelationships between yeast ribosomal protein assembly events and transient ribosome biogenesis factors interactions in early pre-ribosomes. PLoS One. 7(3):e32552.

Dresselhaus, Thomas (B6, MGK)

Kulich, I., Vogler, F., Bleckmann, A., Cyprys, P., Lindemeier, M., Fuchs, I., Krassini, L., Schubert, T., Steinbrenner, J., Beynon, J., Falter-Braun, P., Längst, G., Dresselhaus, T., Sprunck, S. (2020) ARMADILLO REPEAT ONLY proteins confine Rho GTPase signalling to polar growth sites. Nat. Plants 6, 1275-1288.
Dresselhaus, T., Bleckmann, A. (2020) Tagging and application of RNA probes for sequence-specific visualization of RNAs by fluorescent in situ hybridization. Meth. Mol Biol. 2166, 3-21.
Antosz, W., Deforges, J., Begcy, K., Bruckmann, A., Poirier, Y., Dresselhaus, T., Grasser, K.D. (2020) Critical role of transcript cleavage in Arabidopsis RNA polymerase II transcriptional elongation. Plant Cell 32, 1449-1463.

Bauer, N., Skiljaica, A., Malenica, N., Razdorov, G., Klasic, M., Juranic, M., Mocibob, M., Sprunck, S., Dresselhaus, T., Leljak-Levanic, D. (2019) The MATH-BTB protein TaMAB2 accumulates in ubiquitin-containing foci and interacts with the translation initiation machinery in Arabidopsis. Front. Plant Sci. 10, 1469.

Chen, J., Müller, B., Wang, H. and Dresselhaus, T. (2019) Overexpression of SUMO1 located predominately to euchromatin of dividing cells affects reproductive development in maize. Plant Signal. Behav. 14, e1588664.

Sprunck, S., Urban, M., Strieder, N., Lindemeier, M., Bleckmann, A., Evers, M., Hackenberg, T., Möhle, C., Dresselhaus, T., Engelmann, J.C. (2019) Elucidating small RNA pathways in Arabidopsis thaliana egg cells. bioRxiv, doi.org/10.1101/525956.

Chen, J., Kalinowska, K., Müller, B., Mergner, J., Deutzmann, R., Schwechheimer, C., Hammes, U.Z., Dresselhaus, T. (2018), DiSUMO-LIKE interacts with RNA-binding proteins and affects cell-cycle progression during maize embryogenesis. Curr. Biol. 28, 1548-1560.

Chen, J., Strieder, N., Krohn, N.G., Cyprys, P., Sprunck, S., Engelmann, J.C., Dresselhaus, T. (2017), Zygotic genome activation occurs shortly after fertilization in maize. Plant Cell 29, 2106-2125.

Bleckmann, A., Dresselhaus, T. (2017), Whole mount RNA-FISH on ovules and developing seeds. Methods Mol. Biol. 1669, 159-171.

Zhao, P., Begcy, K., Dresselhaus, T.*, Sun, M.X.* (2017), Does early embryogenesis in eudicots and monocots involve the same mechanism and molecular players? Plant Physiol. 173, 130-142.

Ghosh Dastidar, M., Mosiolek, M., Bleckmann, A., Dresselhaus, T., Nodine, M.D. and Maizel, A. (2016), Sensitive whole mount in situ localization of small RNAs in plants. Plant J. 88, 694-702.

Bleckmann, A., Dresselhaus, T. (2016), Fluorescent whole-mount RNA in situ hybridization (F-WISH) in plant germ cells and the fertilized ovule. Methods 98, 66-73

Dresselhaus, T., Sprunck, S., Wessel, G.M. (2016), Fertilization mechanisms in flowering plants. Curr. Biol. 26, R125-R139.

Hou, Y., Guo, X., Cyprys, P., Zhang, Y., Bleckmann, A., Cai, L., Huang, Q., Luo, Y., Gu, H., Dresselhaus, T., Dong, J., Qu, L.J. (2016), Maternal ENODLs are required for pollen tube reception in Arabidopsis. Curr. Biol. 26, 2343-2350.

Müller, B., Fastner, A., Karmann, J., Mansch, V., Hoffmann, T., Schwab, W., Suter-Grotemeyer, M., Rentsch, D., Truernit, E., Ladwig, F., Bleckmann, A., Dresselhaus, T., Hammes, U. Z. (2015), Amino acid export in developing Arabidopsis seeds depends on UmamiT facilitators. Curr. Biol. 25, 3126-3131.

Bleckmann, A., Alter, S., Dresselhaus, T. (2014), The beginning of a seed: regulatory mechanisms of double fertilization. Front. Plant Sci. 5, 452.

Denninger, P., Bleckmann, A., Lausser, A., Vogler, F., Ott, T., Ehrhardt, D., Frommer, W.B., Sprunck, S., Dresselhaus, T.*, Grossmann, G.* (2014), Male-female communication triggers calcium signatures during fertilization in Arabidopsis. Nat. Comm. 5, 4645.

Schönberger, J., Hammes, U.Z., Dresselhaus, T. (2012), In vivo visualization of RNA in plants cells using the lambda N22 system and a GATEWAY-compatible vector series for candidate RNAs. Plant J. 71, 173-181.

Engel, Christoph (A8)

Kramm K., Engel C., Grohmann D. Transcription initiation factor TBP - old friend new questions. Biochemical Society Transactions. (accepted; CRC 960 cooperation)

Engel C., Neyer S., Cramer P. (2018) Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II. Annual review of biophysics, 47 S. 425-446.

Engel C., Gubbey T., Neyer S., Sainsbury S., Oberthuer C., Baejen C., Bernecky C., Cramer P. (2017) Structural basis of RNA polymerase I transcription initiation. Cell, 169(1), 120-131.

Neyer S,, Kunz M., Geiss C., Hantsche M., Hodirnau V-V., Seybert A., Engel C., Scheffer M., Cramer P., Frangakis A. (2016) Structure of RNA polymerase I transcribing rDNA genes. Nature, 540 (7634), 607-610.

Engel C., Plitzko J., Cramer P. (2016) RNA polymerase I-Rrn3 complex at 4.8 Å resolution. Nature Communications, Jul 15;7:12129.

Engel C. (2016) Purification of crystallization-grade RNA polymerase I from S. cerevisiae. Methods Mol Biol, 1455, 85-97.

Lisica A., Engel C., Jahnel M., Galburt E., Roldan E., Cramer P., Grill S. (2016) Mechanisms of backtrack recovery by RNA polymerases I and II. Proc Natl Acad Sci U S A, Mar 15;113(11):2946-51.

Kostrewa D., Kuhn C., Engel C., Cramer P. (2015) An alternative RNA polymerase I structure reveals a dimer hinge. Acta Crystallogr D, 2015, Sep;71:1850-5

Engel C., Sainsbury S., Cheung A.C., Kostrewa D., Cramer P. (2013) RNA polymerase I structure and transcription regulation, Nature, 502(7473):650-5.

Ferreira-Cerca, Sébastien (B13)

Jüttner M., Weiß M., Ostheimer N., Reglin C., Kern M., Knüppel R., Ferreira-Cerca S. (2019), A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea. Nucleic Acids Res. 2019 Dec 12. pii: gkz1156. doi: 10.1093/nar/gkz1156. [Epub ahead of print] PMID: 31828323

Mitterer V., Shayan R., Ferreira-Cerca S., Murat G., Enne T., Rinaldi D., Weigl S., Omanic H., Gleizes P.E., Kressler D., Plisson-Chastang C., Pertschy B. (2019), Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism. Nat Commun. 2019 Jun 21;10(1):2754. doi: 10.1038/s41467-019-10678-z. PMID: 31227701

Linnemann J., Pöll G., Jakob S., Ferreira-Cerca S., Griesenbeck J., Tschochner H., Milkereit P. (2019), Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors. PLoS One. 2019 Jan 17;14(1):e0203415. doi: 10.1371/journal.pone.0203415. eCollection 2019. PMID:30653518

Berto G., Ferreira-Cerca S., De Wulf P. (2019), The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability. Curr Genet. 2019 Apr;65(2):457-466. doi: 10.1007/s00294-018-0912-y. Epub 2018 Dec 4. Review. PMID: 30515528

Iacovella M.G., Bremang M., Basha O., Giacò L., Carotenuto W., Golfieri C., Szakal B., Dal Maschio M., Infantino V., Beznoussenko G.V., Joseph C.R., Visintin C., Mironov A.A., Visintin R., Branzei D., Ferreira-Cerca S., Yeger-Lotem E., De Wulf P. (2018), Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. Nucleic Acids Res. 2018 Sep 6;46(15):7586-7611. doi: 10.1093/nar/gky618. PMID: 30011030

Knüppel R., Christensen R.H., Gray F.C., Esser D., Strauß D., Medenbach J., Siebers B., MacNeill SA, LaRonde N., Ferreira-Cerca S. (2018), Insights into the evolutionary conserved regulation of Rio ATPase activity. Nucleic Acids Research. 46(3):1441-1456. PMID: 29237037.

Ferreira-Cerca S. (2017), Book Chapter. Life and Death of Ribosomes in Archaea. In RNA Metabolism and Gene Expression in Archaea, B. Clouet-d’Orval, ed. (Cham: Springer International Publishing), pp. 129–158. Print ISBN 978-3-319-65794-3

Knüppel R., Kuttenberger C., Ferreira-Cerca S. (2017), Toward Time-Resolved Analysis of RNA Metabolism in Archaea Using 4-Thiouracil. Front Microbiol. 8:286. PMID: 28286499

Grasser, Klaus (A6)

Antosz, W., Deforges, J., Begcy, K., Bruckmann, A., Poirier, Y., Dresselhaus, T., Grasser, K.D. (2020) Critical role of transcript cleavage in Arabidopsis RNA polymerase II transcriptional elongation. Plant Cell 32, 1449-1463.

Michl-Holzinger, P., Mortensen, S.A. and Grasser, K.D. (2019) The SSRP1 subunit of the histone chaperone FACT is required for seed dormancy in Arabidopsis. J. Plant Physiol. 236, 105-108.

Ehrnsberger, H.F., Grasser, M. and Grasser, K.D. (2019) Nucleocytosolic mRNA transport in plants: export factors and their influence in growth and development. J. Exp. Bot. 70, 3757-3763.

Ehrnsberger, H.F., Pfaff, C., Hachani, I., Flores-Tornero, M., Sørensen, B.B., Längst, G., Sprunck, S., Grasser, M. and Grasser, K.D. (2019) The UAP56-interacting export factors UIEF1 and UIEF2 function in mRNA export. Plant Physiol. 179, 1525-1536.

Wolozynska, M., Le Gall, S., Neyt, P., Boccardi, T.M., Grasser, M., Längst, G., Aesaert, S., Coussens, G., Dhondt, S., Van De Slijke, E., Buno, L., Fung-Uceda, J., Mas, P., Van Montagu, M., Inzé, D., Himanen, K., De Jaeger, G., Grasser, K.D. and Van Lijsebettens, M. (2019) Histone H2B monoubiquitination complex integrates transcript elongation with splicing at circadian clock and flowering time regulators. Proc. Natl. Acad. Sci. USA 116, 8060-8069.

Pfab A., Bruckmann A., Nazet J., Merkl R. and Grasser K.D. (2018), The adaptor protein ENY2 is a component of the deubiquitination module of the Arabidopsis SAGA transcriptional co-activator complex but not of the TREX-2 complex. J. Mol. Biol. 430, 1479-1494.

Pfaff C., Ehrnsberger H.F., Flores-Tornero M., Sørensen B.B., Schubert T., Längst G., Griesenbeck J., Sprunck S., Grasser M. and Grasser K.D. (2018), ALY RNA-binding proteins are required for nucleo-cytosolic mRNA transport and modulate plant growth and development in Arabidopsis. Plant Physiol. 177, 226-240.

Grasser M. and Grasser K.D. (2018), The plant RNA polymerase II elongation complex: A hub coordinating transcript elongation and mRNA processsing . Transciption 9, 117-122.

Antosz W., Pfab A., Ehrnsberger H.F., Holzinger P., Köllen K., Mortensen S.A., Bruckmann A., Schubert T., Längst G., Griesenbeck J., Schubert V., Grasser M. and Grasser K.D. (2017), Composition of the Arabidopsis RNA polymerase II transcript elongation complex reveals the interplay between elongation and mRNA processsing factors. Plant Cell 29, 854-870.

Sørensen B.B., Ehrnsberger H.F., Esposito S., Pfab A., Bruckmann A., Hauptmann A., Meister G., Merkl R., Schubert T., Längst G., Melzer M., Grasser M. and Grasser K.D. (2017), The Arabidopsis THO/TREX component TEX1 functionally interacts with MOS11 and modulates mRNA export and alternative splicing events. Plant Mol. Biol. 93, 283-298.

Pfab A., Antosz W., Holzinger P., Bruckmann A., Griesenbeck J. and Grasser K.D. (2017), Analysis of in vivo chromatin and protein interactions of Arabidopsis transcript elongation factors. Meth. Mol. Biol. 1629, 105-122.

Köllen K., Dietz L., Bies-Etheve N., Lagrange T., Grasser M., Grasser K.D. (2015), The zinc-finger protein SPT4 interacts with SPT5L/KTF1 and modulates transcriptional silencing in Arabidopsis. FEBS Lett. 589(21):3254-7. doi: 10.1016/j.febslet.2015.09.017.

Van Lijsebettens M., Grasser K.D. (2014), Transcript elongation factors: shaping transcriptomes after transcript initiation. Trends Plant Sci. 19(11):717-26. doi: 10.1016/j.tplants.2014.07.002.

Van Lijsebettens M., Dürr J., Woloszynska M., Grasser K.D. (2014), Elongator and SPT4/SPT5 complexes as proxy to study RNA polymerase II transcript elongation control of plant development. Proteomics. 14(19):2109-14. doi: 10.1002/pmic.201400024.

Dürr J., Lolas IB, Sørensen BB, Schubert V., Houben A., Melzer M., Deutzmann R., Grasser M., Grasser K.D. (2014), The transcript elongation factor SPT4/SPT5 is involved in auxin-related gene expression in Arabidopsis. Nucleic Acids Res. 42(7):4332-47. doi: 10.1093/nar/gku096.

Kammel C., Thomaier M., Sørensen BB, Schubert T., Längst G., Grasser M., Grasser K.D. (2013), Arabidopsis DEAD-box RNA helicase UAP56 interacts with both RNA and DNA as well as with mRNA export factors. PLoS One. 8(3):e60644. doi: 10.1371/journal.pone.0060644.

Griesenbeck, Joachim (A5, A1, B1)

Hannig K., Babl V., Hergert K., Maier A., Pilsl M., Schächner C., Stöckl U., Milkereit P., Tschochner H., Seufert W., Griesenbeck J. (2019) The C-terminal region of Net1 is an activator of RNA polymerase I transcription with conserved features from yeast to human.PLoS Genet. 2019 Feb 25;15(2):e1008006. doi: 10.1371/journal.pgen.1008006. eCollection 2019 Feb.

Linnemann J., Pöll G., Jakob S., Ferreira-Cerca S., Griesenbeck J., Tschochner H., Milkereit P. (2019) Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors.PLoS One. 2019 Jan 17;14(1):e0203415. doi: 10.1371/journal.pone.0203415. eCollection 2019.

Pfaff C., Ehrnsberger H.F., Flores-Tornero M., Sørensen B.B., Schubert T., Längst G., Griesenbeck J., Sprunck S., Grasser M. and Grasser K.D. (2018), ALY RNA-Binding Proteins Are Required for Nucleocytosolic mRNA Transport and Modulate Plant Growth and Development. Plant Physiol. 177, 226–240.

Antosz W., Pfab A., Ehrnsberger H.F., Holzinger P., Köllen K., Mortensen S.A., Bruckmann A., Schubert T., Längst G., Griesenbeck J., et al. (2017). The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay Between Elongation and mRNA Processing Factors. Plant Cell.

Griesenbeck J., Tschochner H. and Grohmann D. (2017), Structure and Function of RNA Polymerases and the Transcription Machineries. Subcell. Biochem. 83:225–270.
doi: 10.1007/978-3-319-46503-6_9.PMID:28271479

Hermans N., Huisman J.J., Brouwer T.B., Schächner C., van Heusden G.P.H., Griesenbeck J. and van Noort J. (2017), Toehold-enhanced LNA probes for selective pull down and single-molecule analysis of native chromatin. Sci Rep 7, 16721.

Pfab A., Antosz W., Holzinger P., Bruckmann A., Griesenbeck J., and Grasser K.D. (2017), Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors. Methods Mol. Biol. 1629, 105–122.

Pöll G., Müller C., Bodden M., Teubl F., Eichner N., Lehmann G., Griesenbeck J., Tschochner H. and Milkereit P. (2017), Structural transitions during large ribosomal subunit maturation analyzed by tethered nuclease structure probing in S. cerevisiae. PLoS ONE 12, e0179405.

Pilsl M., Crucifix C., Papai G., Krupp F., Steinbauer R., Griesenbeck J., Milkereit P., Tschochner H., Schultz P. (2016), Structure of the initiation-competent RNA polymerase I and its implication for transcription. Nat Commun. 7:12126. doi: 10.1038/ncomms12126. PMID: 27418187

Pilsl M., Merkl PE, Milkereit P., Griesenbeck J., Tschochner H. (2016), Analysis of S. cerevisiae RNA Polymerase I Transcription In Vitro. Methods Mol Biol. 1455:99-108. doi: 10.1007/978-1-4939-3792-9_8.PMID: 27576713

Ohmayer U., Gil-Hernández Á, Sauert M., Martín-Marcos P., Tamame M., Tschochner H., Griesenbeck J., Milkereit P. (2015), Studies on the Coordination of Ribosomal Protein Assembly Events Involved in Processing and Stabilization of Yeast Early Large Ribosomal Subunit Precursors. PLoS One. 10(12):e0143768. doi: 10.1371/journal.pone.0143768. eCollection 2015.

Babl V., Stöckl U., Tschochner H., Milkereit P., Griesenbeck J. (2015), Chromatin Endogenous Cleavage (ChEC) as a Method to Quantify Protein Interaction with Genomic DNA in Saccharomyces cerevisiae. Methods Mol Biol. 1334:219-32. doi: 10.1007/978-1-4939-2877-4_14.

Brown CR, Eskin JA, Hamperl S., Griesenbeck J., Jurica MS, Boeger H. (2015), Chromatin structure analysis of single gene molecules by psoralen cross-linking and electron microscopy. Methods Mol Biol. 1228:93-121. doi: 10.1007/978-1-4939-1680-1_9.

Merkl P., Perez-Fernandez J., Pilsl M., Reiter A., Williams L., Gerber J., Böhm M., Deutzmann R., Griesenbeck J., Milkereit P., Tschochner H. (2014), Binding of the termination factor Nsi1 to its cognate DNA site is sufficient to terminate RNA polymerase I transcription in vitro and to induce termination in vivo. Mol Cell Biol. 34(20):3817-27. doi: 10.1128/MCB.00395-14.

Hamperl S, Brown CR, Perez-Fernandez J., Huber K., Wittner M., Babl V., Stöckl U., Boeger H., Tschochner H., Milkereit P., Griesenbeck J. (2014), Purification of specific chromatin domains from single-copy gene loci in Saccharomyces cerevisiae. Methods Mol Biol. 1094:329-41. doi: 10.1007/978-1-62703-706-8_26.

Hamperl S, Brown CR, Garea AV, Perez-Fernandez J., Bruckmann A., Huber K., Wittner M., Babl V., Stoeckl U., Deutzmann R., Boeger H., Tschochner H., Milkereit P., Griesenbeck J. (2014), Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic Acids Res. 42(1):e2. doi: 10.1093/nar/gkt891.

Tremblay M., Charton R., Wittner M., Levasseur G., Griesenbeck J., Conconi A. (2014), UV light-induced DNA lesions cause dissociation of yeast RNA polymerases-I and establishment of a specialized chromatin structure at rRNA genes. Nucleic Acids Res. 42(1):380-95. doi: 10.1093/nar/gkt871.

Ohmayer U., Gamalinda M., Sauert M., Ossowski J., Pöll G., Linnemann J., Hierlmeier T., Perez-Fernandez J., Kumcuoglu B., Leger-Silvestre I., Faubladier M., Griesenbeck J., Woolford J., Tschochner H., Milkereit P. (2013), Studies on the assembly characteristics of large subunit ribosomal proteins in S. cerevisae. PLoS One. 8(7):e68412. doi: 10.1371/journal.pone.0068412.

Hamperl S., Wittner M., Babl V., Perez-Fernandez J., Tschochner H., Griesenbeck J. (2013), Chromatin states at ribosomal DNA loci. Biochim Biophys Acta. 1829(3-4):405-17. doi: 10.1016/j.bbagrm.2012.12.007.

Hierlmeier T., Merl J., Sauert M., Perez-Fernandez J., Schultz P., Bruckmann A., Hamperl S., Ohmayer U., Rachel R., Jacob A., Hergert K., Deutzmann R., Griesenbeck J., Hurt E., Milkereit P., Baßler J., Tschochner H. (2013), Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S. cerevisiae. Nucleic Acids Res. 41(2):1191-210. doi: 10.1093/nar/gks1056.

Németh A., Perez-Fernandez J., Merkl P., Hamperl S., Gerber J., Griesenbeck J., Tschochner H. (2013), RNA polymerase I termination: Where is the end? Biochim Biophys Acta.1829(3-4):306-17. doi: 10.1016/j.bbagrm.2012.10.007.

Ohmayer U., Perez-Fernandez J., Hierlmeier T., Pöll G., Williams L., Griesenbeck J., Tschochner H., Milkereit P. (2012), Local tertiary structure probing of ribonucleoprotein particles by nuclease fusion proteins. PLoS One. 7(8):e42449. doi: 10.1371/journal.pone.0042449.

Reiter A., Hamperl S., Seitz H., Merkl P., Perez-Fernandez J., Williams L., Gerber J., Németh A., Léger I., Gadal O., Milkereit P., Griesenbeck J., Tschochner H. (2012), The Reb1-homologue Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast. EMBO J. 31(16):3480-93. doi: 10.1038/emboj.2012.185.

Jakob S., Ohmayer U., Neueder A., Hierlmeier T., Perez-Fernandez J., Hochmuth E., Deutzmann R., Griesenbeck J., Tschochner H., Milkereit P. (2012), Interrelationships between yeast ribosomal protein assembly events and transient ribosome biogenesis factors interactions in early pre-ribosomes. PLoS One. 7(3):e32552. doi: 10.1371/journal.pone.0032552.

Griesenbeck J., Wittner M., Charton R., Conconi A. (2012), Chromatin endogenous cleavage and psoralen crosslinking assays to analyze rRNA gene chromatin in vivo. Methods Mol Biol. 809:291-301. doi: 10.1007/978-1-61779-376-9_20.

Lorch Y., Griesenbeck J., Boeger H., Maier-Davis B., Kornberg RD (2011), Selective removal of promoter nucleosomes by the RSC chromatin-remodeling complex. Nat Struct Mol Biol. 18(8):881-5. doi: 10.1038/nsmb.2072.

Grohmann, Dina (A7)

Sarah Willkomm, Leonhard Jakob, Kevin Kramm, Veronika Graus, Julia Neumeier, Gunter Meister & Dina Grohmann Single-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2 Nature Communications. Article number: 3825 (2022)

Dexl S., Reichelt R., Kraatz K., Schulz S., Grohman D., Bartlett M., Thomm M., Displacement of the Transcription Factor B Reader Domain during Transcription Initiation. Nucleic Acids Research (accepted)

Molle J., Jakob L., Bohlen J., Raab M., Tinnefeld P., Grohmann D., Towards Structural Biology with Super-Resolution Microscopy. Nanoscale (accepted)

Gust A., Leonhard J., Zeitler D., Bruckmann A., Kramm K., Willkomm S., Tinnefeld P., Meister G. and Grohmann D., Site-specific fluorescent labelling of endogenous mammalian proteins for single-molecule FRET analysis. ChemBioChem. 19:780-783.

Gouge J., Guthertz N., Dergai O., Kramm K., Abascal-Palacios G., Satia K., Cousin P., Nouria Hernandez N., Grohmann D., and Vannini A. (2017). Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA Polymerase III transcription initiation. Nature Structural and Molecular Biology, Nature Communications. 8(1): 130 .doi: 10.1038/s41467-017-00126-1.

Blombach F. and Grohmann D., (2017). Same but different: the evolution of TBP in archaea and their eukaryotic offspring. Transcription. 8:162-168.

Sheppard C., Blombach F., Belsom A., Schulz S., Daviter T., Smollett K., Mahieu E., Erdmann S., Tinnefeld P., Garrett R., Grohmann D., Rappsilber J. and Werner F. (2016), Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP. Nature Communications (in press)

Nickels P.C., Wünsch B., Holzmeister P., Bae W., Kneer L.M., Grohmann D., Tinnefeld P. and Liedl T. (2016), Molecular Force Spectroscopy with a DNA Origami-Based Nanoscopic Force Clamp. Science. 354(6310):305-307.

Blombach B., Smollett K.L., Grohmann D. and Werner F. (2016), Molecular Mechanisms of Transcription Initiation – structure, function and evolution of TFE/TFIIE-like factors and open complex formation. Journal of Molecular Biology. 428(12):2592-606.

Schulz S., Gietl A., Smollett K., Tinnefeld P., Werner F. and Grohmann D. (2016), TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle. Proceedings of the National Academy of Sciences U.S.A. 112(13): E1816-25

Jakob L., Treiber T., Treiber N., Gust A., Kramm K., Hansen K., Stotz M., Wankerl L., Herzog F., Hannus S., Grohmann D. and Meister G. (2016), Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA. 22(3): 383-96.

Schulz S., Kramm K., Werner F., Grohmann D. (2015), A fluorescently labeled recombinant RNAP system to probe archaeal transcription initiation. Methods (epub, ahead of print)

Willkomm S., Zander A., Gust A., Grohmann D. (2015), A prokaryotic twist on Argonaute action. Life. 5 (1), 538-553.

Nagy J., Grohmann D., Cheung A.C.M., Schulz S., Smollett K., Werner F. & Michaelis J. (2015), Complete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS. Nature Communications, 6:6161

Gietl A., Holzmeister P., Blombach F., Schulz S., Voithenberg L.V.v., Lamb D., Werner F., Tinnefeld P., Grohmann D. (2014), Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways. Nucleic Acids Research. 42(10):6219-31.

Zander A., Holzmeister P., Klose D., Tinnefeld P. and Grohmann D. (2014), Single-molecule FRET supports the two-state model of Argonaute action. RNA Biology 11(1):45-56.

Grohmann D. and Werner F. (2011), Recent advances in the understanding of archaeal transcription. Curr Opin Microbiol.

Grohmann D., Nagy J., Chakraborty A., Klose D., Fielden D., Ebright R.H., Michaelis J., Werner F.* (2011), The Initiation Factor TFE and the Elongation Factor Spt4/5 Compete for the RNAP Clamp during Transcription Initiation and Elongation. Molecular Cell, 43:263-74.

Werner F. and Grohmann D. (2011), Evolution of multisubunit RNA polymerases in the three domains of life. Nature Rev Microbiol.9:85-98.

Wörle E., Jakob L., Schmidbauer A., Zinner G., Grohmann D. (2021). Decoupling the bridge helix of Cas12a results in a reduced trimming activity, increased mismatch sensitivity and impaired conformational transitions. Nucleic Acids Research, https://doi.org/10.1093/nar/gkab286

Weixlbaumer A., Grünberger F., Werner F. and Grohmann D. (2021). Coupling of transcription and translation in archaea: cues from the bacterial world. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2021.661827

Heise, Tilmann (B14)

Sommer G, Sendlmeier C, Heise T. Salt-Dependent Modulation of the RNA Chaperone Activity of RNA-Binding Protein La. Methods Mol Biol (2020) 2106:121-136. PMID:31889254

Kretz, Markus (B9)

Reichelt-Wurm S., Wirtz T., Chittka D., Lindenmeyer M., Reichelt R.M., Beck S., Politis P., Charonis A., Kretz M., Huber T., Liu S., Banas B., Banas M.C. (2019). Glomerular expression pattern of long no-coding RNAs in the type 2 diabetes mellitus BTBR mouse model. Sci Rep, 9, 9765.

Ziegler C.*, Graf J.*, Faderl S., Schedlbauer J., Strieder N., Förstl B., Spang R., Bruckmann A., Merkl R., Hombach S., Kretz M. (2019). The long non-coding RNA LINC00941 and SPRR5 are novel regulators of human epidermal homeostasis. EMBO Rep, 20(2):e46612.

Tanis S.E.J., Jansen P.W.T.C., Zhou H., van Heeringen S.J., Vermeulen M., Kretz M., Mulder K.W. (2018). Splicing and chromatin factors jointly regulate epidermal differentiation. Cell Rep, 25, 1292–1303.e5.

Lee C.S., Mah A., Aros C.J., Lopez-Pajares V., Bhaduri A., Webster D.E., Kretz M., Khavari P.A. (2018), Cancer-Associated Long Noncoding RNA SMRT-2 Controls Epidermal Differentiation. J Invest Dermatol. [Epub].

Ziegler C., Kretz M. (2017), The more the merrier – complexity in long non-coding RNA loci. Front Endocrinol (Lausanne), 8(90) [Epub].

Lopez-Pajares V., Qu, K., Zhang, J., Webster, D.E., Barajas, B.C., Siprashvili, Z., Zarnegar, B.J., Boxer, L.D., Rios, E.J., Tao, S., Kretz, M., Khavari, P.A. (2015), A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Dev Cell, 32(6): 693-706.

Kretz M. (2013), TINCR, staufen1, and cellular differentiation. RNA Biol, 10(10): 1597-601.

Hombach S., Kretz M. (2013), The non-coding skin: Exploring the roles of long non-coding RNAs in epidermal homeostasis and disease. Bioessays, 35(12): 1093-100.

Kretz M., Siprashvili Z.*, Chu C.*, Webster D.E.*, Zehnder A., Lee C.S., Flockhart R.J., Chow J., Johnston D., Groff A.F., Kim G.E., Raj A., Rinn J.L., Chang H.Y., Khavari P.A. (2013), Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature, 493(7431):231-5.

Flockhart R.J., Webster D.E., Qu K., Mascarenhas N., Kovalski J., Kretz M., Khavari P.A. (2012), BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Genome Res, 2012 Jun;22(6):1006-14.

Kretz M.*, Webster D.E.*, Flockhart R.J., Lee C.S., Zehnder A., Lopez-Pajares V., Qu K., Zheng G. X. Y., Chow J., Kim G. E., Rinn J.L., Chang H.Y., Siprashvili Z., Khavari P.A. (2012), Suppression of progenitor differentiation requires the long non-coding RNA ANCR. Genes Dev, 26(4):338-43.

Siprashvili Z., Webster D.E., Kretz M., Johnston D., Rinn J.L., Chang H.Y., Khavari P.A. (2012), Identification of proteins binding coding and non-coding human RNAs using protein microarrays. BMC Genomics, 13(1):633.

Längst, Gernot (A4/B2, Z2)

Maldonado, R., Schwartz, U., Silberhorn, E. and Längst, G. (2019), Nucleosomes stabilise ssRNA-dsDNA triple helices in human cells. Molecular Cell. Accepted for publication.

Schwartz,U., Németh,A., Diermeier,S., Exler,J.H., Hansch,S., Maldonado,R., Heizinger,L., Merkl,R. and Längst,G. (2018), Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin. Nucleic Acids Res, 154, 515-.

Pfab A., Grønlund J.T., Holzinger P., Längst G. and Grasser K.D. (2018), The Arabidopsis Histone Chaperone FACT: Role of the HMG-Box Domain of SSRP1. J Mol Biol, 430, 2747–2759.

Kovač K., Sauer A., Mačinković I., Awe S., Finkernagel F., Hoffmeister H., Fuchs A., Müller R., Rathke C., Längst G., et al. (2018), Tumour-associated missense mutations in the dMi-2 ATPase alters nucleosome remodelling properties in a mutation-specific manner. Nat Commun, 9, 2112.

Pfaff C., Ehrnsberger H.F., Flores-Tornero M., Soerensen B.B., Schubert T., Längst G., Griesenbeck J., Sprunck S., Grasser M. and Grasser K.D. (2018), ALY RNA-binding proteins are required for nucleo-cytosolic mRNA transport and modulate plant growth and development. Plant Physiol, 177, pp.00173.2018–240.

Maldonado R., Filarski M., Grummt I. and Längst G. (2018), Purine- and pyrimidine-triple-helix-forming oligonucleotides recognize qualitatively different target sites at the ribosomal DNA locus. RNA, 24, 371–380.

Beck A., Trippel F., Wagner A., Joppien S., Felle M., Vokuhl C., Schwarzmayr T., Strom T.M., Schweinitz von D., Längst G., et al. (2018), Overexpression of UHRF1 promotes silencing of tumor suppressor genes and predicts outcome in hepatoblastoma. Clin Epigenetics, 10, 1503.

Hoffmeister H., Fuchs A., Erdel F., Pinz S., Gröbner-Ferreira R., Bruckmann A., Deutzmann R., Schwartz U., Maldonado R., Huber C., Dendorfer AS, Rippe K., Längst G. (2017), CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality. Nucleic Acids Res, 45, 10534–10554.

Antosz W., Pfab A., Ehrnsberger H.F., Holzinger P., Köllen K., Mortensen S.A., Bruckmann A., Schubert T., Längst G., Griesenbeck J., Schubert V., Grasser M., Grasser KD. (2017), The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors. Plant Cell, 29, 854–870.

Sørensen B.B., Ehrnsberger H.F., Esposito S., Pfab A., Bruckmann A., Hauptmann J., Meister G., Merkl R., Schubert T., Längst G., Melzer M., Grasser M., Grasser K.D. (2017), The Arabidopsis THO/TREX component TEX1 functionally interacts with MOS11 and modulates mRNA export and alternative splicing events. Plant Mol. Biol., 93, 283–298.

Mueller A.M., Breitsprecher D., Duhr S., Baaske P., Schubert T. and Längst G. (2017), MicroScale Thermophoresis: A Rapid and Precise Method to Quantify Protein-Nucleic Acid Interactions in Solution. Methods Mol Biol, 1654, 151–164.

König F., Schubert T. and Längst G. (2017), The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences. PLoS ONE, 12, e0178875.

Silberhorn E., Schwartz U., Löffler P., Schmitz S., Symelka A., de Koning-Ward T., Merkl R. and Längst G. (2016), Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning. PLoS Pathog, 12, e1006080.

Nardocci G., Simonet N.G., Navarro C., Längst G. and Alvarez M. (2016), Differential enrichment of TTF-I and Tip5 in the T-like promoter structures of the rDNA contribute to the epigenetic response of Cyprinus carpio during environmental adaptation. Biochem. Cell Biol., 94, 315–321.

Schwartz U. and Längst G. (2016), Bioinformatic Analysis of ChIP-seq Data on the Repetitive Ribosomal RNA Gene. Methods Mol Biol, 1455, 225–230.

Längst G. (2016), Preparation of Chromatin Templates to Study RNA Polymerase I Transcription In Vitro. Methods Mol Biol, 1455, 109–119.

Friedrich U., Datta S., Schubert T., Plössl K., Schneider M., Grassmann F., Fuchshofer R., Tiefenbach K.J., Längst G. and Weber B.H. (2015), Synonymous variants in HTRA1 implicated in AMD susceptibility impair its capacity to regulate TGF-β signaling. Hum Mol Genet, 24, 6361–6373.

Längst G. and Manelyte L. (2015), Chromatin Remodelers: From Function to Dysfunction. Genes 2015, Vol. 6, Pages 299-324, 6, 299–324.

Josling G.A., Petter M., Oehring S.C., Gupta A.P., Dietz O., Wilson D.W., Schubert T., Längst G., Gilson P.R., Crabb B.S., et al. (2015), A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression. Cell Host Microbe, 17, 741–751.

Kelly S., Georgomanolis T., Zirkel A., Diermeier S., O'Reilly D., Murphy S., Längst G., Cook P.R. and Papantonis A. (2015), Splicing of many human genes involves sites embedded within introns. Nucleic Acids Res, 43, 4721–4732.

Schrader A., Gross T., Thalhammer V. and Längst G. (2015), Characterization of Dnmt1 Binding and DNA Methylation on Nucleosomes and Nucleosomal Arrays. PLoS ONE, 10, e0140076.

Filarski M., Zillner K., Araya I., Villar-Garea A., Merkl R., Längst G. and Németh A. (2015), The extended AT-hook is a novel RNA binding motif. RNA Biol, 12, 864–876.

Diermeier S., Kolovos P., Heizinger L., Schwartz U., Georgomanolis T., Zirkel A., Wedemann G., Grosveld F., Knoch T.A., Merkl R., Cook P.R., Längst G., Papantonis A. (2014), TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biol, 15, 536.

Loedige I., Stotz M., Qamar S., Kramer K., Hennig J., Schubert T., Löffler P., Längst G., Merkl R., Urlaub H., Meister G. (2014), The NHL domain of BRAT is an RNA-binding domain that directly contacts the hunchback mRNA for regulation. Genes Dev, 28, 749–764.

Krinner S, Heitzer AP, Diermeier SD, Obermeier I, Längst G.*, Wagner* R. (2014), CpG domains downstream of TSSs promote high levels of gene expression. Nucleic Acids Res. 2014 Apr;42(6):3551-64.

Diermeier SD, Längst G. (2014), Deep sequencing of small chromatin-associated RNA: bioinformatic analysis. Methods Mol Biol. 2014;1094:355-9.

Diermeier SD, Schubert T., Längst G. (2014), Deep sequencing of small chromatin-associated RNA: isolation and library preparation. Methods Mol Biol. 2014;1094:343-53.

Manelyte L., Strohner R., Gross T., Längst G. (2014), Chromatin targeting signals, nucleosome positioning mechanism and non-coding RNA-mediated regulation of the chromatin remodeling complex NoRC. PLoS Genet. 2014 Mar 20;10(3):e1004157.

Diermeier SD, Németh A., Rehli M., Grummt I., Längst G. (2013), Chromatin-specific regulation of mammalian rDNA transcription by clustered TTF-I binding sites. PLoS Genet. 2013;9(9):e1003786.

Zillner K., Filarsky M., Rachow K., Weinberger M., Längst G.*, Németh A.* (2013), Large-scale organization of ribosomal DNA chromatin is regulated by Tip5. Nucleic Acids Res. 2013 May 1;41(10):5251-62.

Pham TH, Minderjahn J., Schmidl C., Hoffmeister H., Schmidhofer S., Chen W., Längst G., Benner C., Rehli M. (2013), Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res. 2013 Jul;41(13):6391-402.

Schubert T. and Längst G., (2013), Changes in higher order structures of chromatin by RNP complexes. RNA Biol. 10(2)

Schubert T., Pusch M., Diermeier S., Benes V., Kremmer E., Imhof A. and Längst G. (2012), Df31 protein and snoRNAs maintain accessible higher order structures of chromatin. Mol Cell. Nov 9;48(3):434-44

Zillner K., Jerabek-Willemsen M., Duhr S., Braun D., Längst G., and Baaske P. (2012), Microscale thermophoresis as a sensitive method to quantify protein: nucleic Acid interactions in solution. Methods Mol Biol. 815:241-52.

Hochstatter J., Hölzel M., Rohrmoser M., Schermelleh L., Leonhardt H., Keough R., Gonda T., Imhof A., Eick D., Längst G.* and Németh A.* (2012), Myb-binding Protein 1a (Mybbp1a) Regulates Levels and Processing of Pre-ribosomal RNA. J Biol Chem. Jul 13;287(29):24365-77

Németh A., Längst G. (2011), Genome organization in and around the nucleolus. Trends Genet. 27(4), 149-156

Felle M., Hoffmeister H., Rothammer J., Fuchs A., Exler JH, Längst G. (2011), Nucleosomes protect DNA from DNA methylation in vivo and in vitro. Nucleic Acids Res. 39(16):6956-69.

Medenbach, Jan (B11)

Nguyen C., Malchow S., Reich S., Loroch S., Sickmann A., Tews B., Medenbach J., and Ahrends R. (2019), PRM-deep: The absolute quantification of transcription factors and membrane proteins central to the unfolded protein response using multiplexed high-resolution targeted proteomics – Scientific Reports 20;9(1):8836

Müller-McNicoll M., Rossbach O., Hui J., and Medenbach J. (2019), Auto-regulatory feedback by RNA-binding proteins –Journal of Molecular Cell Biology 11(10):930

Urdaneta E.C., Vieira C. , Hick T., Wessels H.H., Moschall R., Medenbach J., Ohler U., Granneman S., Selbach M., and Beckmann B.M. (2019), Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction – Nature Communications 10(1):990

Moschall R., Rass M., Rossbach O., Lehmann G., Kullmann L., Eichner N., Strauss D., Meister G., Schneuwly S., Krahn M., and Medenbach J. (2019), Sister of Sex-lethal antagonizes Sxl-dependent alternative splicing to maintain a male-specific gene expression pattern in Drosophila – Nucleic Acids Research 18;47(5):2276

Moschall R., Strauss D., Garcia-Beyaert M., Gebauer F., and Medenbach J. (2018), Sister-of-Sex-lethal represses translation of Drosophila msl-2 mRNA. RNA, 24:149-58

Knüppel R., Christensen R.H., Gray FC, Esser D., Strauß D., Medenbach J., Siebers B., MacNeill SA, LaRonde N., Ferreira-Cerca S. (2018), Insights into the evolutionary conserved regulation of Rio ATPase activity. Nucleic Acids Res. 46(3):1441-56

Moschall R., Gaik M. and Medenbach J. (2017), Promiscuity in post-transcriptional control of gene expression: Drosophila Sex-lethal and its regulatory partnerships. FEBS Lett., 591(11):1471-88

Schneider T., Hung L.H., Schreiner S., Starke S., Eckhof H., Rossbach O., Reich S., Medenbach J., Bindereif A. (2016), CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs. Sci Rep., 11,6:31313

Beckmann BM, Castello A., Medenbach J. (2016), The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions. Pflugers Arch. 468(6):1029-40. doi:
10.1007/s00424-016-1819-4. Epub 2016 May 10. Review. PubMed PMID: 27165283;

Medenbach, J., Seiler, M., and Hentze, MW. (2011), Translational control via protein-regulated upstream open reading frames. Cell, 145(6):902-13.

Meister, Gunter (B3/B4)

Gust A., Jakob L., Zeitler DM, Bruckmann A., Kramm K., Willkomm S., Tinnefeld P., Meister G., Grohmann D. (2018), Site-specific labelling of native mammalian proteins for single-molecule FRET measurements. Chembiochem. 2018 Apr 16;19(8):780-783.

Quévillon Huberdeau M., Zeitler DM, Hauptmann J., Bruckmann A., Fressigné L., Danner J., Piquet S., Strieder N., Engelmann J.C., Jannot G., Deutzmann R., Simard M.J. and Meister G. (2017), Phosphorylation of Argonaute proteins affects mRNA binding and is essential for microRNA-guided gene silencing in vivo. EMBO J.; Jul 14;36(14):2088-2106.

Hauptmann J. and Meister G. (2017), Peptide-Based Isolation of Argonaute Protein Complexes Using Ago-APP. Methods Mol Biol.;1580:107-116.

Sørensen B.B., Ehrnsberger H.F., Esposito S., Pfab A., Bruckmann A., Hauptmann J., Meister G., Merkl R., Schubert T., Längst G., Melzer M., Grasser M. and Grasser K.D. (2017), The Arabidopsis THO/TREX component TEX1 functionally interacts with MOS11 and modulates mRNA export and alternative splicing events. Plant Mol Biol. 2017 Feb;93(3):283-298.

Danner J., Pai B., Wankerl L. and Meister G. (2017), Peptide-Based Inhibition of miRNA-Guided Gene Silencing. Methods Mol. Biol., 1517: 199-210.

Anne Dueck, Maurits Evers, Stefan R. Henz, Katharina Unger, Norbert Eichner, Rainer Merkl, Eugene Berezikov, Julia C. Engelmann, Detlef Weigel, Stephan Wenzl and Gunter Meister (2016), Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants. BMC Genomics 17:853

Hauptmann J., Schraivogel D., Bruckmann A., Manickavel S., Jakob L., Eichner N., Pfaff J., Urban M., Sprunck S., Hafner M., Tuschl T., Deutzmann R. and Meister G. (2015), Biochemical isolation of Argonaute protein complexes by Ago-APP. Proc. Natl. Acad. Sci. USA., 112(38):11841-5.

Schraivogel D., Schindler S.G., Danner J., Kremmer E., Pfaff J., Hannus S., Depping R. and Meister G. (2015), Importin-β facillitates nuclear import of human GW proteins and balances cytoplasmic gene silencing protein levels. Nucleic Acids Res. Sep 3,43(15):7447-61.

Tan G.C., Chan E., Molnar A., Sarkar R., Alexieva D., Isa I.M., Robinson S., Zhang S., Ellis P., Langford C.F., Guillot P.V., Chandrashekran A., Fisk N.M., Castellano L., Meister G., Winston R.M., Cui W., Baulcombe D. and Dibb N.J. (2014),  5´ isomiR variation is of functional and evolutionary importance. Nucleic Acids Res., 42(14): 9424-9435.

Schraivogel D. and Meister G. (2014), Import routes and nuclear functions of Argonaute and other small RNA-silencing proteins. Trends Biochem Sci. 39(9):420-31.

Hauptmann J., Kater L., Löffler P., Merkl R. and Meister G. (2014), Generation of catalytic human Ago4 identifies structural elements important for RNA cleavage. RNA, 20(10):1532-8.

Völler D., Reinders J., Meister G. and Bosserhoff A.K. (2013), Strong reduction of AGO2 expression in melanoma and cellular consequences. Br. J. Cancer, 109(12): 3116-3124.

Pfaff J., Hennig J., Herzog F., Aebersold R., Sattler M., Niessing D. and Meister G. (2013), Structural features of GW – Argonaute protein interactions. Proc. Natl. Acad. Sci. USA., 110(40):E3770-9.

Hauptmann J., Dueck A., Harlander S., Pfaff J., Merkl R. and Meister G. (2013), Turning catalytically inactive human Argonaute proteins into active slicer enzymes. Nat. Struct. Mol. Biol., 20(7):814-817.

Frohn A., Eberl H.C., Stöhr J., Glasmacher E., Rüdel S., Heismeyer V., Mann M. and Meister G. (2012), Dicer-dependent and -independent Argonaute2 protein interaction networks in mammalian cells. Molecular and Cellular Proteomics, 11(11):1442-56.

Dueck A., Ziegler C., Eichner A., Berezikov E. and Meister G. (2012), microRNAs associated with the different human Argonaute proteins. Nucleic Acids Res., 40(19):9850-62.

Li Z., Ender C., Meister G., Moore P.S., Chang Y. and John B. (2012), Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res., 40(14):6787-99.

Valen E., Preker P., Andersen P.R., Zhao X., Chen Y., Ender C., Dueck A., Meister G., Sandelin A. and Jensen T.H. (2011), Biogenic mechanisms and utilization of small RNAs from human protein-coding genes. Nat. Struct. Mol. Biol., 18(9):1075-82.

Rüdel S., Wang Y., Lenobel R., Körner R., Hsiao H., Urlaub H., Patel D. and Meister G. (2011), Phosphorylation of human Argonaute proteins affects small RNA binding. Nucleic Acids Research, 39(6):2330-2343.

Milkereit, Philipp (B1, A1, A5)

Linnemann J., Pöll G., Jakob S., Ferreira-Cerca S., Griesenbeck J., Tschochner H., Milkereit P. Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors. PLoS One. 2019 Jan 17;14(1):e0203415. doi: 10.1371/journal.pone.0203415eCollection 2019. PubMed PMID: 30653518; PubMed Central PMCID: PMC6336269.

Hannig K., Babl V., Hergert K., Maier A., Pilsl M., Schächner C., Stöckl U., Milkereit P., Tschochner H., Seufert W., Griesenbeck J. The C-terminal region ofNet1 is an activator of RNA polymerase I transcription with conserved featuresfrom yeast to human. PLoS Genet. 2019 Feb 25;15(2):e1008006. doi:10.1371/ journal.pgen. 1008006

Zisser G., Ohmayer U., Mauerhofer C., Mitterer V., Klein I., Rechberger GN, Wolinski H., Prattes M., Pertschy B., Milkereit P., Bergler H. (2018), Viewing pre-60Smaturation at a minute's timescale. Nucleic Acids Res. 46(6):3140-3151. doi: 10.1093/nar/gkx1293. PubMed PMID: 29294095; PubMedCentral PMCID: PMC5888160.

Pöll G., Müller C., Bodden M., Teubl F., Eichner N., Lehmann G., Griesenbeck J., Tschochner H., Milkereit P. (2017), Structural transitions during large ribosomal subunit maturation analyzed by tethered nuclease structure probing in S. cerevisiae. PLoSOne. 12(7):e0179405. doi: 10.1371/journal.pone.0179405. eCollection2017. PubMed PMID: 28686620; PubMed Central PMCID: PMC5501410.

Pilsl M., Crucifix C., Papai G., Krupp F., Steinbauer R., Griesenbeck J., Milkereit P., Tschochner H., Schultz P. (2016) , Structure of the initiation-competent RNA polymerase I and its implication for transcription. Nat Commun. 7:12126. doi: 10.1038/ncomms12126. PMID: 27418187

Ohmayer U., Gil-Hernández Á., Sauert M., Martín-Marcos P., Tamame M., Tschochner H., Griesenbeck J., Milkereit P. (2015), Studies on the Coordination of Ribosomal Protein Assembly Events Involved in Processing and Stabilization of Yeast Early Large Ribosomal Subunit Precursors. PLoS One. 10(12):e0143768. doi: 10.1371/journal.pone.0143768. eCollection 2015.

Pöll G., Li S, Ohmayer U., Hierlmeier T., Milkereit P., Perez-Fernandez J. (2014), In vitro reconstitution of yeast tUTP/UTP A and UTP B subcomplexes provides new insights into their modular architecture. PLoS One. 9(12):e114898. doi: 10.1371/journal.pone.0114898. eCollection 2014.

Merkl P., Perez-Fernandez J., Pilsl M., Reiter A., Williams L., Gerber J., Böhm M., Deutzmann R., Griesenbeck J., Milkereit P., Tschochner H. (2014), Binding of the termination factor Nsi1 to its cognate DNA site is sufficient to terminate RNA polymerase I transcription in vitro and to induce termination in vivo. Mol Cell Biol. 34(20):3817-27. doi: 10.1128/MCB.00395-14. Epub 2014 Aug 4.

Hamperl S., Brown CR, Perez-Fernandez J., Huber K., Wittner M., Babl V., Stöckl U., Boeger H., Tschochner H., Milkereit P., Griesenbeck J. (2014), Purification of specific chromatin domains from single-copy gene loci in Saccharomyces cerevisiae. Methods Mol Biol. 1094:329-41. doi: 10.1007/978-1-62703-706-8_26.

Hamperl S., Brown CR, Garea AV, Perez-Fernandez J., Bruckmann A., Huber K., Wittner M., Babl V., Stoeckl U., Deutzmann R., Boeger H., Tschochner H., Milkereit P., Griesenbeck J. (2014), Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic Acids Res. 42(1):e2. doi: 10.1093/nar/gkt891. Epub 2013 Oct 7.

Ohmayer U., Gamalinda M., Sauert M., Ossowski J., Pöll G., Linnemann J., Hierlmeier T., Perez-Fernandez J., Kumcuoglu B., Leger-Silvestre I., Faubladier M., Griesenbeck J., Woolford J, Tschochner H., Milkereit P. (2013), Studies on the assembly characteristics of large subunit ribosomal proteins in S. cerevisae. PLoS One. 8(7):e68412. doi: 10.1371/journal.pone.0068412. Print 2013.

Hierlmeier T., Merl J., Sauert M., Perez-Fernandez J., Schultz P., Bruckmann A., Hamperl S., Ohmayer U., Rachel R., Jacob A., Hergert K., Deutzmann R., Griesenbeck J., Hurt E., Milkereit P., Baßler J., Tschochner H. (2013), Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S. cerevisiae.Nucleic Acids Res. 41(2):1191-210. doi: 10.1093/nar/gks1056. Epub 2012 Dec 2.

Jakovljevic J., Ohmayer U., Gamalinda M., Talkish J., Alexander L., Linnemann J., Milkereit P., Woolford JL Jr. (2012), Ribosomal proteins L7 and L8 function in concert with six A₃ assembly factors to propagate assembly of domains I and II of 25S rRNA in yeast 60S ribosomal subunits. RNA. 18(10):1805-22. doi: 10.1261/rna.032540.112. Epub 2012 Aug 14.

Reiter A., Hamperl S., Seitz H., Merkl P., Perez-Fernandez J., Williams L., Gerber J., Németh A., Léger I., Gadal O., Milkereit P., Griesenbeck J., Tschochner H. (2012), The Reb1-homologue Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast. EMBO J. 31(16):3480-93. doi: 10.1038/emboj.2012.185. Epub 2012 Jul 17.

Kouba T., Dányi I., Gunišová S., Munzarová V., Vlčková V., Cuchalová L., Neueder A., Milkereit P., Valášek LS (2012), Small ribosomal protein RPS0 stimulates translation initiation by mediating 40S-binding of eIF3 via its direct contact with the eIF3a/TIF32 subunit. PLoS One.7(7):e40464. doi: 10.1371/journal.pone.0040464. Epub 2012 Jul 5.

Jakob S., Ohmayer U., Neueder A., Hierlmeier T., Perez-Fernandez J., Hochmuth E., Deutzmann R., Griesenbeck J., Tschochner H., Milkereit P. (2012), Interrelationships between yeast ribosomal protein assembly events and transient ribosome biogenesis factors interactions in early pre-ribosomes. PLoS One. 7(3):e32552. doi: 10.1371/journal.pone.0032552. Epub 2012 Mar 14.

Seufert, Wolfgang (B10)

Hannig K., Babl V., Hergert K., Maier A., Pilsl M., Schächner C., Stöckl U., Milkereit P., Tschochner H., Seufert W., Griesenbeck J. (2019), An activator of RNA polymerase I transcription with conserved features from yeast to human. PLoS Genet. 15(2):e1008006. doi: 10.1371/journal.pgen.1008006. eCollection 2019 Feb.

Girke P., Seufert W. (2019), Compositional reorganization of the nucleolus in budding yeast mitosis. Mol Biol Cell. 30(3):591-606. doi: 10.1091/mbc.E18-08-0524. Epub 2019 Jan 9.

Höckner S., Neumann-Arnold L., Seufert W. (2016), Dual control by Cdk1 phosphorylation of the budding yeast APC/C ubiquitin ligase activator Cdh1. Mol Biol Cell. 27(14):2198-2212. doi: 10.1091/mbc.E15-11-0787. Epub 2016 May 25.

Panvert M., Dubiez E., Arnold L., Perez J., Mechulam Y., Seufert W., Schmitt E. (2015), Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features. Structure. 23(9):1596-1608. doi: 10.1016/j.str.2015.06.014. Epub 2015 Jul 23.

Arnold L., Höckner S., Seufert W. (2015), Insights into the cellular mechanism of the yeast ubiquitin ligase APC/C-Cdh1 from the analysis of in vivo degrons. Mol Biol Cell. 26(5):843-858. doi: 10.1091/mbc.E14-09-1342. Epub 2014 Dec 24.

Perzlmaier AF, Richter F., Seufert W. (2013), Translation initiation requires cell division cycle 123 (Cdc123) to facilitate biogenesis of the eukaryotic initiation factor 2 (eIF2). Biol Chem. 288(30):21537-46. doi: 10.1074/jbc.M113.472290. Epub 2013 Jun 17.

Sommer, Gunhild (B14)

Sommer G, Sendlmeier C, Heise T. Salt-Dependent Modulation of the RNA Chaperone Activity of RNA-Binding Protein La. Methods Mol Biol (2020) 2106:121-136. PMID:31889254

Sprangers, Remco (B12)

Sprunck, Stefanie (B5)

Englhart M., Soljic L., Sprunck S. (2017), Manual isolation of living cells from the Arabidopsis thaliana female gametophyte by micromanipulation.Methods Mol Biol. 1669:221-234. doi: 10.1007/978-1-4939-7286-9_18.

Hauptmann J., Schraivogel D., Bruckmann A., Manickavel S., Jakob L., Eichner N., Pfaff J., Urban M., Sprunck S., Hafner M., Tuschl T., Deutzmann R., Meister G. (2015), Biochemical isolation of Argonaute protein complexes by Ago-APP. Proc Natl Acad Sci U S A 112(38):11841-5.

Völz, R., von Lyncker, L., Baumann, N., Dresselhaus, T., Sprunck, S. and Groß-Hardt, R. (2012), LACHESIS-dependent egg-cell signaling regulates the development of female gametophytic cells. Development 139, 498-502.

Sprunck, S., Rademacher, S., Vogler, S., Gheyselinck, J., Grossniklaus, U. and Dresselhaus, T. (2012), Egg cell–secreted EC1 triggers sperm cell activation during double fertilization. Science 338, 1093-1097.

Tschochner, Herbert (A1, A5, B1)

Darrière T, Pilsl M, Sarthou MK, Chauvier A, Genty T, Audibert S, Dez C, Léger-Silvestre I, Normand C, Henras AK, Kwapisz M, Calvo O, Fernández-Tornero C, Tschochner H, Gadal O. (2019) Genetic analyses led to the discovery of a super-active mutant of the RNA polymerase I. PLoS Genet. 2019 May 28;15(5):e1008157. doi: 10.1371/journal.pgen.1008157. eCollection 2019 May.

Linnemann J., Pöll G., Jakob S., Ferreira-Cerca S., Griesenbeck J., Tschochner H., Milkereit P. (2019) Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors.PLoS One. 2019 Jan 17;14(1):e0203415. doi: 10.1371/journal.pone.0203415. eCollection 2019.

Lauinger L., Li J., Shostak A., Cemel IA, Ha N., Zhang Y., Merkl PE, Obermeyer S., Stankovic-Valentin N., Schafmeier T., Wever WJ, Bowers AA, Carter KP, Palmer AE, Tschochner H., Melchior F., Deshaies RJ, Brunner M., Diernfellner A. (2017), Thiolutin is a zinc chelator that inhibits the Rpn11 and other JAMM metalloproteases. Nat Chem Biol. 2017 Jul;13(7):709-714. doi: 10.1038/nchembio.2370. Epub 2017 May 1. PMID:28459440

Griesenbeck J., Tschochner H., Grohmann D. (2017), Structure and Function of RNA Polymerases and the Transcription Machineries. Subcell Biochem. 2017;83:225-270. doi: 10.1007/978-3-319-46503-6_9.PMID:28271479

Ohmayer U., Gil-Hernández Á., Sauert M., Martín-Marcos P., Tamame M., Tschochner H., Griesenbeck J., Milkereit P. (2015), Studies on the Coordination of Ribosomal Protein Assembly Events Involved in Processing and Stabilization of Yeast Early Large Ribosomal Subunit Precursors. PLoS One.10(12):e0143768. doi: 10.1371/journal.pone.0143768. eCollection 2015.

Hamperl S., Brown CR, Garea AV, Perez-Fernandez J., Bruckmann A., Huber K., Wittner M., Babl V., Stoeckl U., Deutzmann R., Boeger H., Tschochner H., Milkereit P., Griesenbeck J. (2014), Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic Acids Res.42(1):e2. doi: 10.1093/nar/gkt891. Epub 2013 Oct 7.

Ohmayer U., Gamalinda M., Sauert M., Ossowski J., Pöll G., Linnemann J., Hierlmeier T., Perez-Fernandez J., Kumcuoglu B., Leger-Silvestre I., Faubladier M., Griesenbeck J., Woolford J., Tschochner H., Milkereit P. (2013), Studies on the assembly characteristics of large subunit ribosomal proteins in S. cerevisae. PLoS One.8(7):e68412. doi: 10.1371/journal.pone.0068412. Print 2013.

Németh A., Perez-Fernandez J., Merkl P., Hamperl S., Gerber J., Griesenbeck J., Tschochner H. (2013), RNA polymerase I termination: Where is the end? Biochim Biophys Acta.1829(3-4):306-17. doi: 10.1016/j.bbagrm.2012.10.007. Epub 2012 Oct 23. Review.

SFB 960

SFB960 - Publications

SFB Publications by Principal Investigators