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All publications of SFB960

Find all the all the publication records from June 2011 until now PubMed.

SFB Publications by Principal Investigators


Bruckmann, Astrid / Deutzmann, Rainer (Z1)

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)

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.


Engelmann, Julia (Z2a)

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

Maurits Evers, Michael Huttner, Anne Dueck, Gunter Meister, Julia C Engelmann (2015), miRA: Adaptable novel miRNA identification using small RNA sequencing data. BMC Bioinformatics 16:370.

Inga Loedige, Leonhard Jakob, Thomas Treiber, Debashish Ray, Mathias Stotz, Nora Treiber, Janosch Hennig, Kate B. Cook, Quaid Morris, Tim Hughes, Julia C. Engelmann, Michael Krahn, Gunter Meister (2015), The crystal structure of the NHL domain in complex with RNA reveals the molecular basis of Drosophila Brain tumor-mediated gene regulation. Cell Reports 13 (6): 1206-1220.

de Jel MM, Engelmann JC, Kunz M., Schiffner S., Kuphal S., Bosserhoff AK (2014), Transcriptome sequencing of melanocytic nevi and melanomas from Grm1 transgenic mice to determine melanoma driver mutations. Pigment Cell & Melanoma Research 27 (4): 678-680.

Engelmann JC and Spang R. (2012), A least angle regression model for the prediction of canonical and non-canonical miRNA-mRNA interactions. PLoS One 7(7): e40634.

Publications within the broader context of the SFB960 (analyses of high-throughput datasets, including sequence analyses)

Hannus M., Beitzinger M., Engelmann JC, Weickert MT, Spang R., Hannus S., Meister G. (2014), siPools: highly complex but accurately defined siRNA pools eliminate off-target effects. Nucleic Acids Research 42 (12): 8049-8061.

Aryee MJ, Liu W., Engelmann JC, Nuhn P., Gurel M., Haffner MC, Esopi D., Irizarry RA, Getzenberg RH, Nelson WG, Luo J., Xu J., Isaacs WB, Bova GS, Yegnasubramanian S. (2013), DNA Methylation Alterations Exhibit Intraindividual Stability and Interindividual Heterogeneity in Prostate Cancer Metastases. Science Translational Medicine 5:169. 169ra10.

Dolnik A.*, Engelmann JC*, Scharfenberger-Schmeer M., Mauch J., Kelkenberg-Schade S., Haldemann B., Fries T., Kroenke J., Kuehn MWM, Paschka P., Kayser S., Wolf S., Gaidzik VI, Schlenk RF, Ruecker FG, Doehner H., Lottaz C., Doehner K., Bullinger L. (2012), Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin-remodeling and splicing. Blood 120:18. e83-92.
*contributed equally

Vogelmann K., Drechsel G., Bergler J., Subert C., Philippar K., Soll J., Engelmann JC, Engelsdorf T., Voll LM, Hoth S. (2012), Early senescence and cell death in Arabidopsis saul1 mutants involves the PAD4-dependent salicylic acid pathway. Plant Physiology 159:4.1477-87.

Lee CW, Efetova M., Engelmann JC, Kramell R., Wasternack C., Ludwig-Müller J., Hedrich R., Deeken R. (2009), Agrobacterium tumefaciens promotes tumor induction by modulating pathogen-defense in Arabidopsis thaliana. Plant Cell 21:9.2948-2962.

 


Grasser, Klaus (A6)

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)

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)

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.


Kretz, Markus (B9)

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)

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)

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 RH, 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 LH, 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.

 


Merkl, Rainer (Z2b)

Filarsky M., Zillner K., Araya I., Villar-Garea A., Merkl R., Längst G., Németh A., (2015), The extended AT-hook is a novel RNA binding motif. RNA Biol. 9:0. [Epub ahead of print] PubMed PMID: 26156556.

Woriedh M., Merkl R., Dresselhaus T. (2015), Maize EMBRYO SAC family peptides interact differentially with pollen tubes and fungal cells. J Exp Bot. pii: erv268. [Epub ahead of print] PubMed PMID: 26071527.

Diermeier S., Kolovos P., Heizinger L., Schwartz U., Georgomanolis T., Zirkel A.,
Wedemann G., Grosveld F., Knoch TA, Merkl R., Cook PR, Längst G., Papantonis A. (2014), TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biol. 15(12):536. doi:10.1186/s13059-014-0536-6. PubMed PMID: 25608606; PubMed Central PMCID: PMC4268828.

Hauptmann J., Kater L., Löffler P., Merkl R., Meister G. (2014), Generation of catalytic human Ago4 identifies structural elements important for RNA cleavage. RNA. 1532-8. doi: 10.1261/rna.045203.114. Epub 2014 Aug 11. PubMed PMID: 25114291; PubMed Central PMCID: PMC4174435.

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. 2014 Apr 1;28(7):749-64. doi: 10.1101/gad.236513.113. PubMed PMID: 24696456; PubMed Central PMCID: PMC4015489.

Hauptmann J., Dueck A., Harlander S., Pfaff J., Merkl R., Meister G. (2013), Turning
catalytically inactive human Argonaute proteins into active slicer enzymes.
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Milkereit, Philipp (B1, A1, A5)

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

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.

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.

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. Epub 2012 Aug 2.

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)

Panvert M., Dubiez E., Arnold L., Perez J., Mechulam Y., Seufert W., Schmitt E.Structure. (2015), Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features. pii: S0969-2126(15)00267-1. doi: 10.1016/j.str.2015.06.014. [Epub ahead of print]

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

 


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)

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;

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

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.

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.

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. Epub 2013 Jan 3. Review.

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.

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.

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. Epub 2012 Aug 2.

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.

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.


Publications of Associated Projects


Ferreira-Cerca, Sébastien (AP1)

Iacovella MG, Bremang M., Basha O., Giacò L., Carotenuto W., Golfieri C., Szakal B., Dal Maschio M., Infantino V., Beznoussenko GV, Joseph CR, Visintin C., Mironov AA, 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 Research. [Epub ahead of print] PMID: 30011030.

Knüppel R., Christensen RH, 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 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

Iacovella MG, Golfieri C., Massari LF, Busnelli S., Pagliuca C., Dal Maschio M., Infantino V., Visintin R., Mechtler K., Ferreira-Cerca S., De Wulf P. (2015), Rio1 promotes rDNA stability and downregulates RNA polymerase I to ensure rDNA segregation. Nat Commun. 6:6643. PMID: 25851096.

Ferreira-Cerca S#*, Kiburu, I#, Thomson E, LaRonde Nicole*, Hurt E*. (2014), Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes. Nucleic Acids Research. 
# joint first authors. * joint corresponding authors

Thomson E#*, Ferreira-Cerca S#*, Hurt E. (2013), Eukaryotic ribosome biogenesis at a glance. J. Cell Sci.126(Pt 21):4815-21. 
# joint first authors. * joint corresponding authors

Ferreira-Cerca S#, Sagar V#, Schäfer T, Diop M, Wesseling AM, Lu H, Chai E, Hurt E, Laronde-Leblanc N. (2012), ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit. Nat. Struct. Mol. Biol. 19(12):1316-23.
# joint first authors.

 


Hausner, Winfried (AP3)


Németh, Attila (AP4)

Caudron-Herger M.#, Pankert T., Seiler J., Németh A., Voit R., Grummt I., Rippe K.# (2015), Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 34, 2758-74.

Filarsky M.*, Zillner K.*, Araya I.*, Villar-Garea A., Merkl R., Längst G.#, Németh A.# (2015), The extended AT-hook is a novel RNA binding motif. RNA Biol 12, 864-76.

Zillner K., Komatsu J., Filarsky K., Kalepu R., Bensimon A., Németh A. (2015), Active human nucleolar organizer regions are interspersed with inactive rDNA repeats in normal and tumor cells. Epigenomics 7, 363-78.

Hamdane N., Stefanovsky V., Tremblay M.G., Németh A., Paquet E., Lessard F., Sanij E., Hannan R.D. and Moss T. (2014), Conditional inactivation of Upstream Binding Factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body. PLoS Genet 10, e1004505

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

Németh A. (2014), Methyl-combing—single molecule analysis of DNA modifications on stretched DNA fibers. Methods Mol Biol 1094, 233-41.

Diermeier S., Németh A., Rehli M., Grummt I., Längst G. (2013), Chromatin-specific regulation of mammalian rDNA transcription by clustered TTF-I binding sites. PLoS Genet 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 41, 5251-62.

Németh A.#, Perez-Fernandez J., Merkl P., Hamperl S., Gerber J., Griesenbeck J., Tschochner H.# (2013), RNA polymerase I termination: where is the end?. BBA - Gene Regulatory Mechanisms 1829, 306-17. Review.

Hochstatter J., Hölzel M., Rohrmoser M., Schermelleh L., Leonhardt H., Keough R., Gonda T.J., Imhof A., Eick D., Längst G.#, Németh A.# (2012), Myb-binding protein 1a (Mybbp1a) regulates levels and processing of pre-ribosomal RNA. J Biol Chem 287, 24365-77.

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-homolog Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast. EMBO J 31, 3480-93.

Zillner K., Németh A. (2012), Single molecule, genome-scale analyses of DNA modifications: exposing the epigenome with next generation technologies. Epigenomics 4, 403-14. Review.


Perez-Fernandez, Jorge (AP2)


Ziegler, Christine (AP5)

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