Ciapponi, M., Karlukova, E., Schkölziger, S., Benda, C. and Müller, J. (2022). Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1. Nat Struct Mol Biol


Bonnet, J., Boichenko, I., Kalb, R. Le Jeune, M., Maltseva, S., Pieropan, M., Finkl, K., Fierz, B. and Müller, J. (2022). PR-DUB preservers Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of chromatin compaction. Genes Dev 36, 1046-1061


Elizarev, P., Finkl, K. and Müller, J. (2021).  Distinct requirements for Pho, Sfmbt, and Ino80 for cell survival in Drosophila. Genetics 219, Issue 1, September 2021


Finogenova, K., Bonnet, J., Poepsel, S., Schäfer, I.B., Finkl, K., Schmid, K., Litz, C., Strauss, M., Benda, C. and Müller, J. (2020). Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3.  eLife 2020;9:e61964


Bonnet, J., Lindeboom, R.G.H., Pokrovsky, D., Stricker, G., Çelik, M.H., Rupp, R.A.W., Gagneur, J., Vermeulen, M., Imhof, A. and Müller, J. (2019). Quantification of proteins and histone marks in Drosophila embryos reveals stoichiometric relationships impacting chromatin regulation. Dev Cell 51, 632-644.

Lee, Y., Yoon, E., Cho, S., Schmähling, S. Müller, J. and Song, J.J. (2019). Structural basis of MRG15-mediated activation of the ASH1L histone methyltransferase by releasing an autoinhibitory loop. Structure 27, 846-852.


Copur, O., Gorchakov, A., Finkl, K., Kuroda, M.I. and Müller, J. (2018). Sex-specific phenotypes of histone H4 point mutants establish dosage compensation as the critical function of H4K16 acetylation in Drosophila. Proc. Natl. Acad. Sci. 115, 13336-13341.

Schmähling, S., Meiler, A., Lee, Y., Mohammed, A., Finkl, K., Tauscher, K., Israel, L., Borath, M., Philippou-Massier, J., Blum, H., Habermann, B., Imhof, A., Song, J.J. and Müller, J. (2018). Regulation and function of H3K36 di-methylation by the trithorax-group protein complex AMC. Development, doi: 10.1242/dev.163808

Copur, O. and Müller J. (2018). Histone Demethylase Activity of Utx Is Essential for Viability and Regulation of HOX Gene Expression in Drosophila. Genetics 208, 633-637.


Choi, J.Y., Bachmann, A.L., Tauscher, K., Benda, C., Fierz, B. and Müller, J. (2017). DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation. Nat Struct Mol Biol 24, 1039–1047.

Laprell, F., Finkl, K. and Müller, J. (2017). Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA. Science 356, 85-88.


Frey, F., Sheahan, T., Finkl, K., Stoehr, G., Mann, M., Benda, C. and Müller, J. (2016). Molecular basis of PRC1 targeting to Polycomb Response Elements by PhoRC. Genes Dev 30, 11161127. 


Kassis, J.A. and Müller, J. (2015). Transcription through Polycomb Response Elements does not induce a switch from repression to activation. Proc. Natl. Acad. Sci. 112, 14755-14756.

Pengelly, A.R., Kalb, R, Finkl, K. and Müller, J. (2015). Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation. Genes Dev 29, 1487-1492.

Gambetta, M.C. and Müller, J. (2015). A critical perspective of the diverse roles of O-GlcNAc transferase in chromatin.  Chromosoma 124, 429-442.


Gambetta, M.C. and Müller, J. (2014). O-GlcNAcylation prevents aggregation of the Polycomb group repressor Polyhomeotic.  Dev Cell 31, 629-639.

Müller, J. and Müller, C.W. (2014).  Structural Biology: Enzyme-chromatin complex visualized.  Nature 514, 572-573. (News & Views article)

Kalb, R., Latwiel, S., Baymaz, H.I., Jansen, P.W.T.C., Müller, C.W., Vermeulen, M. and Müller, J. (2014).  Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression.  Nat Struct Mol Biol 21, 569-571.


Alfieri, C., Gambetta, M.C., Matos, R., Glatt, S., Sehr, P., Fraterman, S., Wilm, M., *Müller, J. and *Müller, C.W. (2013).  Structural Basis for Targeting the Chromatin Repressor Sfmbt to Polycomb Response Elements. Genes Dev 27, 2367-2379.

Copur, O. and Müller J. (2013). The histone H3-K27 demethylase Utx regulates HOX gene expression in Drosophila in a temporally restricted manner. Development 140, 3478-3485.

Pengelly, A.R., Copur, O., Jäckle, H., Herzig, A. and Müller, J. (2013). A histone mutant reproduces the phenotype caused by loss of histone modifying factor Polycomb. Science 339, 698-699.


Scheuermann, J.C., Gutierrez, L. and Müller, J. (2012). Histone H2A monoubiquitination and Polycomb repression: the missing pieces of the puzzle. Fly 6, 162 - 168.

Gutierrez, L., Oktaba, K., Scheuermann, J.C., Gambetta, M.C., Ly-Hartig, N. and Müller, J. (2012). The role of the histone H2A ubiquitinase Sce/dRing in Polycomb repression. Development 139, 117-127. (Epub Nov 17, 2011).


Richter, C., Oktaba, K., Steinmann, J. Müller, J. and Knoblich, J.A. (2011). The tumor suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements. Nat Cell Biol. 13, 1029-1039.

Schmitges, F.W., Prusty, A.B., Faty, M., Stützer, A., Lingaraju, G.M., Aiwazian, J., Sack, R., Hess, D., Li, L., Zhou, S., Wirth, U., Bouwmeester, T., Bauer, A., Ly-Hartig, N., Zhao, K., Chan, H., Gu, J., Gut, H., Fischle, W., *Müller, J. and *Thomä, N.H. (2011). Histone methylation by PRC2 is inhibited by active chromatin marks. Mol Cell 42, 330-341.


Friberg, A., Oddone, A., Klymenko, T. Müller, J. and Sattler, M. (2010) Structure of an atypical Tudor domain in the Drosophila Polycomblike protein. Protein Science 19, 1906-1916.

Scheuermann, J.C., Gaytán de Ayala Alonso, A., Oktaba, K., Ly-Hartig, N, McGinty, R.K., Fraterman, S., Wilm, M., Muir, T.W. and Müller, J. (2010). Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 465, 243-247.


Grimm, C., Matos, R., Ly-Hartig, N., Steuerwald, U., Rybin, V., *Müller, J. and *Müller, C.W. (2009). Molecular recognition of histone lysine methylation by the Polycomb repressor dSfmbt. EMBO J 28, 1965-1977.

Gambetta, M.C., Oktaba, K. and Müller, J. (2009). Essential role of the glycosyltransferase Sxc/Ogt in Polycomb repression. Science 325, 93-96.

Müller, J. and Verrijzer, C.P. (2009). Biochemical Mechanisms of Gene Regulation by Polycomb Group Protein Complexes. Curr Opin Gene Dev 19, 150-158.


Oktaba, K, Gutierrez, L., Gagneur, J., Girardot, C., Sengupta, A.K., Furlong, E.E.M. and Müller, J. (2008). Dynamic regulation by Polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila. Dev Cell 15, 877-889.

Fiedler, M., Sánchez-Barrena, M.J., Nekrasov, M., Mieszczanek, J., Rybin, V., Müller, J., Evans, P. and Bienz, M. (2008). Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex. Mol Cell 30, 507-518.


Grimm, C., Gaytan de Ayala Alonso, A., Rybin, V., Steuerwald, U., Ly-Hartig, N., Fischle, W., *Müller, J. and *Müller, C.W. (2007). Structural and functional analyses of methyllysine binding by the malignant brain tumour repeat protein Sex comb on midleg. EMBO Rep. 8, 1031-1037.

Nekrasov, M., Klymenko, T., Fraterman, S., Papp, B., Oktaba, K., Köcher, T., Cohen, A., Stunnenberg, H., Wilm, M. and Müller, J. (2007). Pcl-PRC2 is needed to generate high levels of H3-K27 tri-methylation at Polycomb target genes. EMBO J. 26, 4078–4088.

Gaytan de Ayala Alonso, A., Gutierrez, L., Fritsch, C., Papp, B., Beuchle, D. and Müller, J. (2007). A genetic screen identifies novel Polycomb group genes in Drosophila. Genetics 176, 2099-2108.


Müller, J. and Kassis, J.A. (2006). Polycomb response elements and targeting of Polycomb group proteins in Drosophila. Curr Opin Gene Dev 16, 476-484.

Papp, B. and Müller, J. (2006). Histone tri-methylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes Dev 20, 2041-2054.

Klymenko, T., Papp, B., Fischle, W., Köcher, T., Schelder, M., Fritsch, C., Wild, B., Wilm, M. and Müller, J. (2006). A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine binding activities. Genes Dev 20, 1110-1122.

Mendjan, S., Taipale, M., Kind, J., Holz, H., Gebhardt, P., Schelder, M., Vermeulen, M., Buscaino, A., Duncan, K., Müller, J., Wilm, M., Stunnenberg, H.G. Saumweber, H., Akhtar, A. (2006) Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila. Mol Cell 21, 811-823.


King, I.F., Emmons, R.B., Francis, N.J., Wild, B., Müller, J., Kingston, R.E. & Wu, C.T. (2005). Analysis of a Polycomb group protein defines regions that link repressive activity on nucleosomal templates to in vivo function. Mol Cell Biol 25, 6578-6591.

Nekrasov, M., Wild, B. and Müller, J. (2005). Nucleosome binding and histone methyltransferase activity of Drosophila PRC2. EMBO Rep. 6, 348-353.


Klymenko, T. and Müller, J. (2004). The histone methyltransferases Trithorax and Ash-1 prevent transcriptional silencing by Polycomb group proteins. EMBO Rep. 5, 373-375.

Sengupta, A.K., Kuhrs, A. and Müller, J. (2004). General transcriptional silencing by a Polycomb response element in Drosophila. Development 131, 1959-1965.


Fritsch, C., Beuchle, D. and Müller, J. (2003). Molecular and genetic analysis of the Polycomb group gene Sex combs extra/Ring in Drosophila. Mech. Dev. 120, 949-954.

Brown, J.L., Fritsch, C., Müller, J. and Kassis, J.A. (2003). The Drosophila pho-like gene encodes a YY1-related DNA binding protein that is redundant with pleiohomeotic in homeotic gene silencing. Development 130, 285-294.


Müller, J., Hart, C.M., Francis, N.J., Vargas, M.L., Sengupta, A., Wild, B., Miller, E.L., O’Connor, M.B., Kingston, R.E. and Simon, J.A. (2002). Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111, 197-208.


Birve, A., Sengupta, A., Beuchle, D., Larsson, J., Kennison, J.A., Rasmusson-Lestander, A. and Müller, J. (2001). Su(z)12, a novel Drosophila Polycomb group gene that is conserved in vertebrates and plants. Development 128, 3371-3379.

Beuchle, D., Struhl, G., Müller, J. (2001). Polycomb group gene function and heritable silencing of HOX genes in Drosophila. Development 128, 993-1004.

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