IFE Publications

2024 Scientific Article in EMBO Journal, The EMBO J., DOI: 10.1038/s44318-024-00227-w (2024)

Chatzitheodoridou, D. ; Bureik, D. ; Padovani, F. ; Schmoller, K.M.

Decoupled transcript and protein concentrations ensure histone homeostasis in different nutrients.

2024 Editorial in Epigenomics Epigenomics 16, 1061-1065 (2024)

Tvardovskiy, A. ; Lukauskas, S. ; Bartke, T.

Breaking the epigenetic code with MARCS: The Modification Atlas of Regulation by Chromatin States.

2024 EMBO Reports EMBO Rep., 3202–3220 (2024)

Pepin, A.-S. ; Schneider, R.

Publisher Correction: Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins.

Methods in Molecular Biology In: Chromatin Immunoprecipitation. 2024. 1-16 (Methods Mol. Biol. ; 2846)

Nitsch, S. ; Schneider, R.

Native ChIP: Studying the genome-wide distribution of histone modifications in cells and tissue.

2024 Scientific Article in Frontiers in bioengineering and biotechnology Front. Bioeng. Biotechnol. 12:1422235 (2024)

Vitacolonna, M. ; Bruch, R. ; Agaçi, A. ; Nürnberg, E. ; ... ; Padovani, F. ; Schmoller, K.M. ; Rudolf, R.

A multiparametric analysis including single-cell and subcellular feature assessment reveals differential behavior of spheroid cultures on distinct ultra-low attachment plate types.

2024 Scientific Article in Nature Communications Nat. Commun. 15:7611 (2024)

Tschuck, J. ; Padmanabhan Nair, V. ; Galhoz, A. ; Zaratiegui, C. ; Tai, H.-M. ; Ciceri, G. ; Rothenaigner, I. ; Tchieu, J. ; Stockwell, B.R. ; ... ; Cabianca, D.S. ; Menden, M.P. ; Vincendeau, M. ; Hadian, K.

Suppression of ferroptosis by vitamin A or radical-trapping antioxidants is essential for neuronal development.

2024 Scientific Article in Nature Cell Biology Nat. Cell Biol., DOI: 10.1038/s41556-024-01512-w (2024)

Al-Refaie, N. ; Padovani, F. ; Hornung, J. ; Pudelko, L ; Binando, F. ; Del Carmen Fabregat, A. ; Zhao, Q. ; Towbin, B.D. ; ... ; Schmoller, K.M. ; Cabianca, D.S.

Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis.

2024 Scientific Article in EMBO Journal, The EMBO J., DOI: 10.1038/s44318-024-00183-5 (2024)

Roussou, R. ; Metzler, D. ; Padovani, F. ; Thoma, F. ; Schwarz, R. ; ... ; Schmoller, K.M. ; Osman, C.

Real-time assessment of mitochondrial DNA heteroplasmy dynamics at the single-cell level.

2024 Review in EMBO Reports EMBO Rep. 25, 3202-3220 (2024)

Pepin, A.-S. ; Schneider, R.

Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins.

2024 Other: Opinion in Nature Reviews - Genetics Nat. Rev. Genet., DOI: 10.1038/s41576-024-00758-2 (2024)

Tvardovskiy, A. ; Lukauskas, S.

Decoding the language of chromatin modifications with MARCS.

2024 Scientific Article in Nature Structural & Molecular Biology Nat. Struct. Mol. Biol., DOI: 10.1038/s41594-024-01341-3 (2024)

Throll, P. ; G Dolce, L. ; Rico-Lastres, P. ; Arnold, K. ; Tengo, L. ; Basu, S. ; ... ; Schneider, R. ; Kowalinski, E.

Structural basis of tRNA recognition by the m3C RNA methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase.

2024 Review in Physiological Reviews Physiol. Rev. 104, 1679-1717 (2024)

Chadha, Y. ; Khurana, A. ; Schmoller, K.M.

Eukaryotic cell size regulation and its implications for cellular function and dysfunction.

2024 Scientific Article in Developmental Cell Dev. Cell 59, 2347-2363.e9 (2024)

Hu, D. ; Solovey, M. ; Ruane, S. ; Whitehead, M. ; Zhou, F. ; ... ; Scialdone, A. ; Srinivas, S.

An integrated approach identifies the molecular underpinnings of murine anterior visceral endoderm migration.

2024 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 52, 6129-6144 (2024)

Stadler, M. ; Lukauskas, S. ; Bartke, T. ; Müller, C.L.

asteRIa enables robust interaction modeling between chromatin modifications and epigenetic readers.

2024 Scientific Article in Bioinformatics Bioinformatics 40:btae267 (2024)

Stock, M. ; Popp, N. ; Fiorentino, J. ; Scialdone, A.

Topological benchmarking of algorithms to infer Gene Regulatory Networks from Single-Cell RNA-seq Data.

2024 Nature Nature 628:E6 (2024)

Lukauskas, S. ; Tvardovskiy, A. ; Nguyen, N.V. ; Stadler, M. ; Faull, P. ; Ravnsborg, T. ; Özdemir Aygenli, B. ; Dornauer, S. ; ... ; Barth, T.K. ; Brockers, K. ; Hauck, S.M. ; Müller, C.L. ; Schneider, R. ; Bartke, T.

Publisher Correction: Decoding chromatin states by proteomic profiling of nucleosome readers.

2024 Scientific Article in Nature Communications Nat. Commun. 15:2960 (2024)

Yamaguchi, K. ; Chen, X. ; Rodgers, B. ; Miura, F. ; ... ; Özdemir Aygenli, B. ; Bartke, T. ; Defossez, P.A.

Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells.

2024 Scientific Article in Nature Nature 627, 671-679 (2024)

Lukauskas, S. ; Tvardovskiy, A. ; Nguyen, N.V. ; Stadler, M. ; Faull, P. ; Ravnsborg, T. ; Özdemir Aygenli, B. ; Dornauer, S. ; Flynn, H. ; ... ; Barth, T.K. ; Brockers, K. ; Hauck, S.M. ; Müller, C.L. ; Schneider, R. ; Bartke, T.

Decoding chromatin states by proteomic profiling of nucleosome readers.

2024 Review in Current Opinion in Genetics & Development Curr. Opin. Genet. Dev. 85:102173 (2024)

Pudelko, L ; Cabianca, D.S.

The influencers' era: How the environment shapes chromatin in 3D.

2023 Nature Structural & Molecular Biology Nat. Struct. Mol. Biol., DOI: 10.1038/s41594-023-01179-1 (2023)

Basu, S. ; Shukron, O. ; Hall, D.W. ; Parutto, P. ; ... ; Bartke, T. ; Laue, E.D.

Publisher Correction: Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD.

2023 Scientific Article in BioSpektrum BioSpektrum 29, 378-380 (2023)

Mairhörmann, B. ; Padovani, F. ; Schmoller, K.M.

Zugängliche KI-Algorithmen für bessere Zellmikroskopie.

2023 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 51, 12303-12324 (2023)

Chanou, A. ; Weiß, M. ; Holler, K. ; Sajid, A. ; Straub, T. ; Krietsch, J. ; Sanchi, A. ; Ummethum, H. ; Lee, C.S.K. ; Kruse, E. ; Trauner, M. ; Werner, M. ; Lalonde, M. ; ... ; Scialdone, A. ; Hamperl, S.

Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency.

2023 Other: Opinion in Molecular Cell Mol. Cell 83, 3946-3947 (2023)

Khurana, A. ; Chadha, Y. ; Schmoller, K.M.

Too big not to fail: Different paths lead to senescence of enlarged cells.

2023 Scientific Article in Nature Structural & Molecular Biology Nat. Struct. Mol. Biol. 30, 1628-1639 (2023)

Basu, S. ; Shukron, O. ; Hall, D. ; Parutto, P. ; ... ; Bartke, T. ; Laue, E.D.

Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD.

2023 Scientific Article in Nature Structural & Molecular Biology Nat. Struct. Mol. Biol. 30, 1549-1560 (2023)

Seel, A. ; Padovani, F. ; Mayer, M. ; Finster, A. ; Bureik, D. ; Thoma, F. ; Osman, C. ; ... ; Schmoller, K.M.

Regulation with cell size ensures mitochondrial DNA homeostasis during cell growth.

2023 Review in AoB Plants AoB Plants 15:plad032 (2023)

Auge, G. ; Hankofer, V. ; Groth, M. ; Antoniou-Kourounioti, R. ; Ratikainen, I. ; Lampei, C.

Plant environmental memory: Implications, mechanisms and opportunities for plant scientists and beyond.

2023 Scientific Article in Nature Cell Biology Nat. Cell Biol. 25, 1017-1032 (2023)

Gaggioli, V. ; Lo, C.S.Y. ; Reveron-Gomez, N. ; Jasencakova, Z. ; ... ; Tvardovskiy, A. ; Taneja, N.

Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability.

2023 Scientific Article in Nature Methods Nat. Methods 20, 1037-1047 (2023)

Beagrie, R.A. ; Thieme, C.J. ; Annunziatella, C. ; Baugher, C. ; ... ; Scialdone, A. ; Pombo, A.

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.

2023 Scientific Article in Genes and Development Genes Dev. 37, 336-350 (2023)

Guthmann, M. ; Qian, C. ; Gialdini, I. ; Nakatani, T. ; Ettinger, A. ; Schauer, T. ; Kukhtevich, I. ; Schneider, R. ; Lamb, D.C. ; Burton, A. ; Torres-Padilla, M.E.

A change in biophysical properties accompanies heterochromatin formation in mouse embryos.

2023 Scientific Article in Development / Company of Biologists Development 150:12 (2023)

Lubatti, G. ; Stock, M. ; Iturbide Martinez De Albeniz, A. ; Ruiz Tejada Segura, M.L. ; Riepl, M. ; Tyser, R.C.V. ; Danese, A. ; Colomé-Tatché, M. ; Theis, F.J. ; Srinivas, S. ; Torres-Padilla, M.E. ; Scialdone, A.

CIARA: A cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data.

2023 Scientific Article in Molecular Metabolism Mol. Metab. 74:101748 (2023)

Nieborak, A. ; Lukauskas, S. ; Capellades, J. ; Heyn, P. ; Santos, G.S. ; Motzler, K. ; Zeigerer, A. ; Bester, R. ; Protzer, U. ; Schelter, F. ; Wagner, M. ; ... ; Schneider, R.

Depletion of pyruvate kinase (PK) activity causes glycolytic intermediate imbalances and reveals a PK-TXNIP regulatory axis.

2023 Scientific Article in Physical Review E Phys. Rev. E 107:044403 (2023)

Lazzardi, S. ; Valle, F. ; Mazzolini, A. ; Scialdone, A. ; Caselle, M. ; Osella, M.

Emergent statistical laws in single-cell transcriptomic data.

2023 Editorial in Nucleic Acids Research Nucleic Acids Res. 51, 7709-7713 (2023)

Bannister, A.J. ; Schneider, R. ; Varga-Weisz, P.

Editorial: Colyn Crane-Robinson (1935-2023).

2023 Scientific Article in Life Science Alliance Life Sci. All. 6:19 (2023)

Karl, L.A. ; Galanti, L. ; Bantele, S.C. ; Metzner, F. ; ... ; Foster, B. ; Bartke, T. ; Pfander, B.

A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler.

2023 Scientific Article in EMBO Reports EMBO Rep. 24:e56150 (2023)

Yahia, Y. ; Pigeot, A. ; El Aabidine, A.Z. ; Shah, N. ; Karasu, N. ; ... ; Eick, D. ; Andrau, J.C.

RNA polymerase II CTD is dispensable for transcription and required for termination in human cells.

2023 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 51, 4252-4265 (2023)

Sheikh, A.H. ; Nawaz, K. ; Tabassum, N. ; Almeida-Trapp, M. ; ... ; Groth, M. ; Hirt, H.

Linker histone H1 modulates defense priming and immunity in plants.

2023 Scientific Article in Cell Reports Cell Rep. 42:112045 (2023)

Weiß, M. ; Chanou, A. ; Schauer, T. ; Tvardovskiy, A. ; Meiser, S. ; König, A.-C. ; Schmidt, T. ; Kruse, E. ; Ummethum, H. ; Trauner, M. ; Werner, M. ; Lalonde, M. ; Hauck, S.M. ; Scialdone, A. ; Hamperl, S.

Single-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control.

2022 Letter to the Editor in Development / Company of Biologists Development 149:dev201404 (2022)

Scialdone, A. ; Rivron, N.

In preprints: Improving and interrogating embryo models.

2022 Scientific Article in Cell Reports Cell Rep. 41:111656 (2022)

Kukhtevich, I. ; Rivero-Romano, M. ; Rakesh, N. ; Bheda, P. ; Chadha, Y. ; Rosales-Becerra, P. ; Hamperl, S. ; Bureik, D. ; Dornauer, S. ; Dargemont, C. ; Kirmizis, A. ; Schmoller, K.M. ; Schneider, R.

Quantitative RNA imaging in single live cells reveals age-dependent asymmetric inheritance.

2022 Scientific Article in PLoS Computational Biology PLoS Comput. Biol. 18:e1010640 (2022)

Schuh, L. ; Kukhtevich, I. ; Bheda, P. ; Schulz, M. ; Bordukova, M. ; Schneider, R. ; Marr, C.

Altered expression response upon repeated gene repression in single yeast cells.

2022 Scientific Article in Biophysical Journal Biophys. J. 121, 4702-4713 (2022)

Freitag, M. ; Jaklin, S. ; Padovani, F. ; Radzichevici, E. ; Zernia, S. ; Schmoller, K.M. ; Stigler, J.

Single-molecule experiments reveal the elbow as an essential folding guide in SMC coiled coil arms.

2022 Scientific Article in BMC Biology BMC Biol. 20:174 (2022)

Padovani, F. ; Mairhörmann, B. ; Falter-Braun, P. ; Lengefeld, J. ; Schmoller, K.M.

Segmentation, tracking and cell cycle analysis of live-cell imaging data with Cell-ACDC.

2022 Scientific Article in Proceedings of the National Academy of Sciences of the United States of America Proc. Natl. Acad. Sci. U.S.A. 119:e2200512119 (2022)

Beer, S. ; Wange, L.E. ; Zhang, X. ; Kuklik-Roos, C. ; Enard, W. ; Hammerschmidt, W. ; Scialdone, A. ; Kempkes, B.

EBNA2-EBF1 complexes promote MYC expression and metabolic processes driving S-phase progression of Epstein-Barr virus-infected B cells.

2022 Scientific Article in Life Science Alliance Life Sci. All. 5:e202201572 (2022)

Wang, X. ; Rosikiewicz, W. ; Sedkov, Y. ; Mondal, B. ; ... ; Tvardovskiy, A. ; Schneider, R. ; Herz, H.M.

The MLL3/4 complexes and MiDAC co-regulate H4K20ac to control a specific gene expression program.

Methods in Molecular Biology In: Histone Methyltransferases. 2022. 327-403 (Methods Mol. Biol. ; 2529)

Tvardovskiy, A. ; Nguyen, N. ; Bartke, T.

Identifying specific protein interactors of nucleosomes carrying methylated histones using quantitative mass spectrometry.

2022 Scientific Article in Molecular Biology of the Cell Mol. Biol. Cell 33:lt1 (2022)

Schmoller, K.M. ; Lanz, M.C. ; Kim, J. ; Koivomagi, M. ; Qu, Y. ; ... ; Kukhtevich, I. ; Schneider, R. ; Skotheim, J.M.

Whi5 is diluted and protein synthesis does not dramatically increase in pre-Start G1.

2022 Scientific Article in Micromachines Micromachines 13:1146 (2022)

Yakimov, A.S. ; Denisov, I.A. ; Bukatin, A.S. ; Lukyanenko, K.A. ; Belousov, K.I. ; Kukhtevich, I. ; ... ; Belobrov, P.

Droplet microfluidic device for chemoenzymatic sensing.

2022 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 50, 8491-8511 (2022)

Stolz, P. ; Mantero, A.S. ; Tvardovskiy, A. ; Ugur, E. ; Wange, L.E. ; ... ; Schneider, R. ; Bartke, T. ; Bultmann, S.

TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation.

2022 Scientific Article in PLoS Computational Biology PLoS Comput. Biol. 18:e1009552 (2022)

Fiorentino, J. ; Scialdone, A.

The role of cell geometry and cell-cell communication in gradient sensing.

2022 Scientific Article in Cell Reports Cell Rep. 38:110547 (2022)

Ruiz Tejada Segura, M.L. ; Abou Moussa, E. ; Garabello, E. ; Nakahara, T.S. ; Makhlouf, M. ; Mathew, L.S. ; ... ; Scialdone, A. ; Saraiva, L.R.

A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell.

2022 Scientific Article in Nature Communications Nat. Commun. 13:1303 (2022)

Günsel, G.G. ; Conlon, T.M. ; Jeridi, A. ; Kim, R. ; Ertüz, Z. ; Lang, N.J. ; Ansari, M. ; Novikova, M. ; Jiang, D. ; Strunz, M. ; Gaianova, M. ; Hollauer, C. ; Gabriel, C. ; Angelidis, I. ; Doll, S. ; Pestoni, J. ; Edelmann, S.L. ; Kohlhepp, M.S. ; Guillot, A. ; Bassler, K. ; ... ; Ballester-Lopez, C. ; Genes Robles, C.M. ; Smirnova, N.F. ; Rehberg, M. ; Agarwal, C. ; Krikki, I. ; Stöger, T. ; Burgstaller, G. ; Heissmeyer, V. ; Rinkevich, Y. ; Schiller, H. B. ; Conrad, M. ; Schneider, R. ; Yildirim, A.Ö.

The arginine methyltransferase PRMT7 promotes extravasation of monocytes resulting in tissue injury in COPD.

2022 Nature Structural & Molecular Biology Nat. Struct. Mol. Biol. 29:282 (2022)

Iturbide Martinez De Albeniz, A. ; Ruiz Tejada Segura, M.L. ; Noll, C. ; Schorpp, K.K. ; Rothenaigner, I. ; Lubatti, G. ; Agami, A. ; Hadian, K. ; Scialdone, A. ; Torres-Padilla, M.E.

Author Correction: Retinoic acid signaling is critical during the totipotency window in early mammalian development.

2022 Scientific Article in Nature Genetics Nat. Genet. 54, 318–327 (2022)

Nakatani, T. ; Lin, J. ; Ji, F. ; Ettinger, A. ; Pontabry, J. ; Tokoro, M. ; Altamirano-Pacheco, L. ; Fiorentino, J. ; Mahammadov, E. ; Hatano, Y. ; ... ; Ruiz-Morales, E.R. ; Scialdone, A. ; Torres-Padilla, M.E.

DNA replication fork speed underlies cell fate changes and promotes reprogramming.

2022 Review in Nature Reviews - Genetics Nat. Rev. Genet. 23, 563-580 (2022)

Millán-Zambrano, G. ; Burton, A. ; Bannister, A.J. ; Schneider, R.

Histone post-translational modifications - cause and consequence of genome function.

In: Epigenetics and Metabolomics. 2021. 75-95

Bheda, P.

Aging-associated changes in metabolic regulation of epigenetic modifications and gene expression.

2021 Scientific Article in Molecular Cell Mol. Cell 81, 4861-4875.e7 (2021)

Swaffer, M.P. ; Kim, J. ; Chandler-Brown, D. ; Langhinrichs, M. ; ... ; Schmoller, K.M. ; Skotheim, J.M.

Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size.

2021 Scientific Article in Nature Communications Nat. Commun. 12:4202 (2021)

Claude, K.-L. ; Bureik, D. ; Chatzitheodoridou, D. ; Adarska, P. ; Singh, A. ; Schmoller, K.M.

Transcription coordinates histone amounts and genome content.

2021 Scientific Article in Molecular Cell Mol. Cell 81, 2944-2959.e10 (2021)

Skalska, L. ; Begley, V. ; Beltran, M. ; Lukauskas, S. ; Khandelwal, G. ; ... ; Tvardovskiy, A. ; Foster, B. ; Bartke, T. ; Jenner, R.G.

Nascent RNA antagonizes the interaction of a set of regulatory proteins with chromatin.

2021 Scientific Article in Review of Scientific Instruments Rev. Sci. Instruments 92:065001 (2021)

De Pastina, A. ; Padovani, F. ; Brunetti, G. ; Rotella, C. ; Niosi, F. ; ... ; Hegner, M.

Multimodal real-time frequency tracking of cantilever arrays in liquid environment for biodetection: Comprehensive setup and performance analysis.

2021 Review in EMBO Reports EMBO Rep. 22:e52774 (2021)

Nitsch, S. ; Zorro Shahidian, L. ; Schneider, R.

Histone acylations and chromatin dynamics: Concepts, challenges, and links to metabolism.

2021 Scientific Article in Nature Structural & Molecular Biology Nat. Struct. Mol. Biol. 28, 521-532 (2021)

Iturbide Martinez De Albeniz, A. ; Ruiz Tejada Segura, M.L. ; Noll, C. ; Schorpp, K.K. ; Rothenaigner, I. ; Ruiz-Morales, E.R. ; Lubatti, G. ; Agami, A. ; Hadian, K. ; Scialdone, A. ; Torres-Padilla, M.E.

Retinoic acid signaling is critical during the totipotency window in early mammalian development.

2021 Scientific Article in Molecular Cell Mol. Cell 81, 2793-2807.e8 (2021)

Santos-Rosa, H. ; Millán-Zambrano, G. ; Han, N. ; Leonardi, T. ; ... ; Nasiscionyte, S. ; Bartke, T. ; Kouzarides, T.

Methylation of histone H3 at lysine 37 by Set1 and Set2 prevents spurious DNA replication.

2021Vortrag: Cell Bio Virtual 2020, 2-16 December 2020, Virtual. (2021)

Schmoller, K.M.

Coordination of mitochondrial homeostasis with cell size.

2021 Scientific Article in Scientific Reports Sci. Rep. 11:8797 (2021)

Belousov, K.I. ; Filatov, N.A. ; Kukhtevich, I. ; Kantsler, V. ; Evstrapov, A.A. ; Bukatin, A.S.

An asymmetric flow-focusing droplet generator promotes rapid mixing of reagents.

2021 Scientific Article in Nanoscale Nanoscale 13, 2338-2349 (2021)

Brunetti, G. ; Padovani, F. ; De Pastina, A. ; Rotella, C. ; Monahan, A. ; ... ; Daubenberger, C. ; Hegner, M.

Nanotechnological immunoassay for rapid label-free analysis of candidate malaria vaccines.

2021 Scientific Article in EMBO Reports EMBO Rep. 22:e51009 (2021)

Zorro Shahidian, L. ; Haas, M. ; Le Gras, S. ; Nitsch, S. ; Mourao, A. ; Geerlof, A. ; Margueron, R. ; ... ; Schneider, R.

Succinylation of H3K122 destabilizes nucleosomes and enhances transcription.

2021 Review in Nucleic Acids Research Nucleic Acids Res. 49, 3020–3032 (2021)

Petryk, N. ; Bultmann, S. ; Bartke, T. ; Defossez, P.-A.

Staying true to yourself: Mechanisms of DNA methylation maintenance in mammals

2020 Scientific Article in STAR Protocols STAR Protoc. 1:100228 (2020)

Bheda, P. ; Aguilar-Gómez, D. ; Kukhtevich, I. ; Becker, J. ; Charvin, G. ; ... ; Schneider, R.

Microfluidics for single-cell lineage tracking over time to characterize transmission of phenotypes in Saccharomyces cerevisiae.

2020 Review in Annual Review of Genetics Annu. Rev. Genet. 54, 167-187 (2020)

Fiorentino, J. ; Torres-Padilla, M.E. ; Scialdone, A.

Measuring and modeling single-cell heterogeneity and fate decision in mouse embryos.

2020 Scientific Article in Science Advances Sci. Adv. 6:eaaz4551 (2020)

Ignatova, V.V. ; Kaiser, S. ; Ho, J.S.Y. ; Bing, X. ; ... ; Lastres, P.R. ; Gerlini, R. ; Rathkolb, B. ; Aguilar-Pimentel, J.A. ; Sanz-Moreno, A. ; Klein-Rodewald, T. ; Calzada-Wack, J. ; Ibragimov, E. ; Valenta, M. ; Lukauskas, S. ; Marschall, S. ; Leuchtenberger, S. ; Fuchs, H. ; Gailus-Durner, V. ; Hrabě de Angelis, M. ; Schneider, R.

METTL6 is a tRNA m3C methyltransferase that regulates pluripotency and tumor cell growth.

2020 Review in Current Genetics Curr. Genet. 66, 1029–1035 (2020)

Bheda, P. ; Kirmizis, A. ; Schneider, R.

The past determines the future: Sugar source history and transcriptional memory.

2020 Scientific Article in Nature Communications Nat. Commun. 11:3559 (2020)

Strunz, M. ; Simon, L. ; Ansari, M. ; Kathiriya, J.J. ; Angelidis, I. ; Mayr, C. ; Tsidiridis, G. ; Lange, M. ; Mattner, L. ; Yee, M. ; Ogar, P. ; Sengupta, A. ; Kukhtevich, I. ; Schneider, R. ; Zhao, Z. ; Voss, C. ; Stöger, T. ; ... ; Hilgendorff, A. ; Behr, J. ; Lehmann, M. ; Burgstaller, G. ; Königshoff, M. ; Theis, F.J. ; Schiller, H. B.

Alveolar regeneration through a Krt8+transitional stem cell state that persists in human lung fibrosis.

2020 Scientific Article in Molecular Metabolism Mol. Metab. 40:101038 (2020)

Huang, S.S.Y. ; Makhlouf, M. ; AbouMoussa, E.H. ; Ruiz Tejada Segura, M.L. ; Mathew, L.S. ; ... ; Scialdone, A. ; Saraiva, L.R.

Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting.

2020 Scientific Article in Nature Communications Nat. Commun. 11:2952 (2020)

Kukhtevich, I. ; Lohrberg, N. ; Padovani, F. ; Schneider, R. ; Schmoller, K.M.

Cell size sets the diameter of the budding yeast contractile ring.

2020 Scientific Article in Molecular Cell Mol. Cell 78, 915-925 (2020)

Bheda, P. ; Aguilar-Gomez, D. ; Becker, N.B. ; Becker, J. ; Stavrou, E. ; Kukhtevich, I. ; ... ; Marr, C. ; Schneider, R.

Single-cell tracing dissects regulation of maintenance and inheritance of transcriptional reinduction memory.

2020 Review in Molecular Metabolism Mol. Metab. 38:100955 (2020)

Bheda, P.

Metabolic transcriptional memory.

2020 Review in Molecular Metabolism Mol. Metab. 38:100987 (2020)

Bartke, T. ; Schneider, R.

You are what you eat-How nutrition and metabolism shape the genome through epigenetics.

2020 Meeting abstract in Wound repair and regeneration Wound Repair Regen. 28, A7-A7 (2020)

Strunz, M. ; Simon, L. ; Ansari, M. ; Mattner, L. ; Angelidis, I. ; Mayr, C. ; Kathiriya, J. ; Yee, M. ; Ogar, P. ; Voss, C. ; Stöger, T. ; Kukhtevich, I. ; Schneider, R. ; Lehmann, M. ; ... ; Burgstaller, G. ; Theis, F.J. ; Schiller, H. B.

Fate trajectory modeling reveals convergence of airway derived progenitors and AT2 cells on transient KRT8+alveolar cell state during lung regeneration.

2020 Scientific Article in Genes and Development Genes Dev. 34, 715-729 (2020)

Ignatova, V.V. ; Stolz, P. ; Kaiser, S. ; Gustafsson, T.H. ; ... ; Sanz-Moreno, A. ; Cho, Y.-L. ; Aguilar-Pimentel, J.A. ; Klein-Rodewald, T. ; Calzada-Wack, J. ; Becker, L. ; Marschall, S. ; Kraiger, M. ; Garrett, L. ; Seisenberger, C. ; Hölter, S.M. ; Valenta, M. ; Wurst, W. ; Gailus-Durner, V. ; Fuchs, H. ; Hrabě de Angelis, M. ; Schneider, R.

The rRNA m6A methyltransferase METTL5 is involved in pluripotency and developmental programs.

2019 Scientific Article in OncoTarget Oncotarget 10, 6934-6943 (2019)

Decker, T.-M. ; Forné, I. ; Straub, T. ; Elsaman, H. ; Ma, G. ; Shah, N. ; Imhof, A. ; Eick, D.

Analog-sensitive cell line identifies cellular substrates of CDK9.

2019 Nature Structural & Molecular Biology Nat. Struct. Mol. Biol., DOI: 10.1038/s41594-019-0341-8 (2019)

Beltran, M. ; Tavares, M. ; Justin, N. ; Khandelwal, G. ; ... ; Foster, B. ; Tvardovskiy, A. ; Bartke, T. ; Jenner, R.G.

Author Correction: G-tract RNA removes Polycomb repressive complex 2 from genes (Nature Structural & Molecular Biology, (2019), 26, 10, (899-909), 10.1038/s41594-019-0293-z).

2019 Scientific Article in Nature Structural & Molecular Biology Nat. Struct. Mol. Biol. 26, 899-909 (2019)

Beltran, M. ; Tavares, M. ; Justin, N. ; Khandelwal, G. ; ... ; Foster, B. ; Bartke, T. ; Jenner, R.G.

G-tract RNA removes Polycomb repressive complex 2 from genes.

2019 Scientific Article in Proceedings of the National Academy of Sciences of the United States of America Proc. Natl. Acad. Sci. U.S.A. 116, 16046-16055 (2019)

Mrozek-Gorska, P. ; Buschle, A. ; Pich, D. ; Schwarzmayr, T. ; Fechtner, R. ; Scialdone, A. ; Hammerschmidt, W.

Epstein-Barr virus reprograms human B lymphocytes immediately in the prelatent phase of infection.

2019 Scientific Article in Biology letters Biol. Lett. 15:20190068 (2019)

Shah, N. ; Decker, T.-M. ; Eick, D.

Extension of the minimal functional unit of the RNA polymerase II CTD from yeast to mammalian cells.

2019Poster: CSH meeting: mechanisms of metabolic signaling, 14 May 2019, Cold Spring Harbour, NY, USA. (2019)

Pellegrino, J. ; Shahjahanpour, A. ; Lukauskas, S. ; Olayo Alarcon, R. ; Ramakrishnan, A. ; Colomé-Tatché, M. ; Schneider, R.

Glucose starvation in Huh7 cells triggers a transcriptional memory.

2019 Scientific Article in Scientific Reports Sci. Rep. 9:6584 (2019)

Ignatova, V.V. ; Jansen, P.W.T.C. ; Baltissen, M.P. ; Vermeulen, M. ; Schneider, R.

The interactome of a family of potential methyltransferases in HeLa cells.

2019 Other: Opinion in Molecular & Cellular Oncology Mol. Cell. Oncol. 6:1605820 (2019)

Bartke, T. ; Groth, A.

A chromatin-based signalling mechanism directs the switch from mutagenic to error-free repair of DNA double strand breaks.

2019 Scientific Article in Nature Cell Biology Nat. Cell Biol. 21, 311-318 (2019)

Nakamura, K. ; Saredi, G. ; Becker, J.R. ; Foster, B. ; Nguyen, N.V. ; ... ; Lukauskas, S. ; Bartke, T. ; Groth, A.

H4K20meO recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids.

2019 Scientific Article in Nature Communications Nat. Commun. 10:348 (2019)

Campagne, A. ; Lee, M.K. ; Zielinski, D. ; Michaud, A. ; ... ; Shahidian, L.Z. ; Margueron, R.

BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation.

2019 Editorial in Epigenomics Epigenomics 11, 363-366 (2019)

Brockers, K. ; Schneider, R.

Histone H1, the forgotten histone.

2019 Scientific Article in Nature Chemical Biology Nat. Chem. Biol. 15, 123–131 (2019)

Nemec, C.M. ; Singh, A.K. ; Ali, A. ; Tseng, S.C. ; ... ; Hintermair, C. ; Eick, D. ; Ansari, A.Z.

Noncanonical CTD kinases regulate RNA polymerase II in a gene-class-specific manner.

2019 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 47, 700-715 (2019)

Rohrmoser, M. ; Kluge, M. ; Yahia, Y. ; Gruber-Eber, A. ; Maqbool, M.A. ; ... ; Eick, D.

MIR sequences recruit zinc finger protein ZNF768 to expressed genes.

2018 Scientific Article in Molecular Cell Mol. Cell 73, 84-96 (2018)

Sharma, P. ; Lioutas, A. ; Fernandez-Fuentes, N. ; Quilez, J. ; ... ; Schüller, R. ; Eick, D. ; Beato, M.

Arginine citrullination at the C-terminal domain controls RNA polymerase II transcription.

2018 Scientific Article in Molecular Cell Mol. Cell 72, 739-752 (2018)

Foster, B. ; Stolz, P. ; Mulholland, C.B. ; Montoya, A. ; ... ; Bartke, T.

Critical role of the UBL domain in stimulating the E3 ubiquitin ligase activity of UHRF1 toward chromatin.

2018Poster: 40 years Myc, 50 years Polymerase II, and 65 years Dirk Eick!, 9 November 2018, Planegg-Martinsried. (2018)

Andrau, J.-C. ; Geyer, M. ; Hermeking, H. ; Hölzel, M. ; ... ; Schneider, R.

Regulation of transcription: RNA Pol II and Myc.

2018 Scientific Article in Journal of Pharmacology and Experimental Therapeutics J. Pharmacol. Exp. Ther. 367, 461-472 (2018)

Zorzan, E. ; Da Ros, S. ; Giantin, M. ; Zorro Shahidian, L. ; Guerra, G. ; ... ; Dacasto, M.

Targeting canine KIT promoter by candidate DNA G-quadruplex ligands.

2018 Scientific Article in Nature Communications Nat. Commun. 9:1653 (2018)

Makowski, M.M. ; Grawe, C. ; Foster, B. ; Nguyen, N.V. ; Bartke, T. ; Vermeulen, M.

Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry.

2018 Review in Molecular Metabolism Mol. Metab., DOI: 10.1016/j.molmet.2018.01.007 (2018)

Nieborak, A. ; Schneider, R.

Metabolic intermediates - Cellular messengers talking to chromatin modifiers.

2018 Editorial in eLife eLife 7:e32010 (2018)

Eick, D.

Getting to grips with c-Myc.

2018 Review in Cancer Genomics & Proteomics Cancer Genomics Proteomics 15, 17-39 (2018)

Weidle, U.H. ; Dickopf, S. ; Hintermair, C. ; Kollmorgen, G. ; Birzele, F. ; Brinkmann, U.

The role of micro RNAs in breast cancer metastasis: Preclinical Validation and potential therapeutic targets.

2018 Scientific Article in Molecular Cell Mol. Cell 69, 48-61.e6 (2018)

Shah, N. ; Maqbool, M.A. ; Yahia, Y. ; El Aabidine, A.Z. ; ... ; Decker, T.-M. ; Schüller, R. ; Eick, D. ; Andrau, J.C.

Tyrosine-1 of RNA polymerase II CTD controls global termination of gene transcription in mammals.

2017 Review in Current Opinion in Cell Biology Curr. Opin. Cell Biol. 49, 53-58 (2017)

Schmoller, K.M.

The phenomenology of cell size control.

2017 Scientific Article in Nature Structural & Molecular Biology Nat. Struct. Mol. Biol. 24, 1048–1056 (2017)

Kebede, A.F. ; Nieborak, A. ; Shahidian, L.Z. ; Le Gras, S. ; Richter, F.M. ; Gomez, D.A. ; Baltissen, M.P. ; ... ; Taudt, A. ; Colomé-Tatché, M. ; Schneider, R.

Histone propionylation is a mark of active chromatin.

2017 Scientific Article in eLife eLife 6:e29736 (2017)

Gressel, S. ; Schwalb, B. ; Decker, T.-M. ; Qin, W. ; Leonhardt, H. ; Eick, D. ; Cramer, P.

CDK9-dependent RNA polymerase II pausing controls transcription initiation.

2017 Scientific Article in Journal of Cell Biology, The J. Cell Biol. 216, 3017-3028 (2017)

Izzo, A. ; Ziegler-Birling, C. ; Hill, P.W.S. ; Brondani, L. ; ... ; Torres-Padilla, M.E. ; Schneider, R.

Dynamic changes in H1 subtype composition during epigenetic reprogramming.

2017 Scientific Article in PLoS Genetics PLoS Genet. 13:e1006959 (2017)

Scahill, C.M. ; Digby, Z. ; Sealy, I.M. ; Wojciechowska, S. ; ... ; Bartke, T. ; Busch-Nentwich, E.M.

Loss of the chromatin modifier Kdm2aa causes BrafV-600E -independent spontaneous melanoma in zebrafish.

2017 Scientific Article in Scientific Reports Sci. Rep. 7:5418 (2017)

Col, E. ; Hoghoughi, N. ; Dufour, S. ; Penin, J. ; ... ; Schneider, R. ; Vourc'h, C.

Bromodomain factors of BET family are new essential actors of pericentric heterochromatin transcriptional activation in response to heat shock.

2017 Meeting abstract in Haematologica - The Hematology Journal Haematologica 102, 333-333 (2017)

Altamura, S. ; Vegi, N. ; Hueltner, L. ; Schneider, M. ; Höppe, P. ; ... ; Aichler, M. ; Walch, A.K. ; Neff, F. ; Janik, D. ; Kuklik-Roos, C. ; Ladinig, C. ; Mysliwietz, J. ; Rathkolb, B. ; Conrad, M. ; Bornkamm, G.W.

Lack of the ferroptosis inhibitor GPX4 in erythroid cells causes a block in reticulocyte maturation and a hypoxic signature with impaired hepcidin regulation.

2017 Scientific Article in Proceedings of the National Academy of Sciences of the United States of America Proc. Natl. Acad. Sci. U.S.A. 114, E3944-E3953 (2017)

Nemec, C.M. ; Yang, F. ; Gilmore, J.M. ; Hintermair, C. ; Ho, Y.H. ; ... ; Heidemann, M. ; Eick, D. ; Ansari, A.Z.

Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner.

2017 Scientific Article in OncoTarget Oncotarget 8, 38239-38250 (2017)

Chendeb, M. ; Schneider, R. ; Davidson, I. ; Fadloun, A.

Selective elimination of long INterspersed element-1 expressing tumour cells by targeted expression of the HSV-TK suicide gene.

2017 Scientific Article in Scientific Reports Sci. Rep. 7:1684 (2017)

Decker, T.-M. ; Kluge, M. ; Krebs, S. ; Shah, N. ; Blum, H. ; ... ; Eick, D.

Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1.

2016 Scientific Article in Methods in Molecular Biology Methods Mol. Biol. 1455, 121-131 (2016)

Burger, K. ; Eick, D.

A nonradioactive assay to measure production and processing of ribosomal RNA by 4sU-tagging.

2016 Scientific Article in Nature Genetics Nat. Genet. 48, 681-686 (2016)

Pradeepa, M.M. ; Grimes, G.R. ; Kumar, Y. ; Olley, G. ; ... ; Schneider, R. ; Bickmore, W.A.

Histone H3 globular domain acetylation identifies a new class of enhancers.

2016 Scientific Article in Trends in Biochemical Sciences : TIBS Trends Biochem. Sci. 41, 894-897 (2016)

Schüller, R. ; Eick, D.

Getting access to low-complexity domain modifications.

2016 Scientific Article in Scientific Reports Sci. Rep. 6:27401 (2016)

Hintermair, C. ; Voß, K. ; Forne, I. ; Heidemann, M. ; Flatley, A. ; Kremmer, E. ; Imhof, A. ; Eick, D.

Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression.

2016 Scientific Article in Nature Communications Nat. Commun. 7:11491 (2016)

Boldt, K. ; van Reeuwijk, J. ; Lu, Q. ; Koutroumpas, K. ; Nguyen, T.M. ; Texier, Y. ; van Beersum, S.E. ; Horn, N. ; ... ; van Wijk, E. ; Ueffing, M. ; Russell, R.B. ; Roepman, R.

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

2016 Scientific Article in Genes, Chromosomes and Cancer Genes Chromosomes Cancer 55, 553-567 (2016)

Vosberg, S. ; Herold, T. ; Hartmann, L. ; Neumann, M. ; Opatz, S. ; ... ; Hiddemann, W. ; Greif, P.A.

Close correlation of copy number aberrations detected by next-generation sequencing with results from routine cytogenetics in acute myeloid leukemia.

2016 Review in Annual Review of Biochemistry Annu. Rev. Biochem. 85, 405-429 (2016)

Bheda, P. ; Jing, H. ; Wolberger, C. ; Lin, H.

The substrate specificity of sirtuins.

2016 Review in Trends in Genetics Trends Genet. 32, 42-56 (2016)

Lawrence, M. ; Daujat, S. ; Schneider, R.

Lateral thinking: How histone modifications regulate gene expression.

2016 Scientific Article in Biochimica et Biophysica Acta - Gene Regulatory Mechanisms Biochim. Biophys. Acta-Gene Regul. Mech. 1859, 486-495 (2016)

Izzo, A. ; Schneider, R.

The role of linker histone H1 modifications in the regulation of gene expression and chromatin dynamics.

2016 Scientific Article in Nature Communications Nat. Commun. 7:10782 (2016)

Kabra, D.G. ; Pfuhlmann, K. ; García-Cáceres, C. ; Schriever, S.C. ; Casquero García, V. ; Kebede, A.F. ; Fuente-Martin, E. ; Trivedi, C. ; Heppner, K. ; Uhlenhaut, N.H. ; Legutko, B. ; Kabra, U.D. ; Gao, Y. ; Yi, C.-X. ; Quarta, C. ; Clemmensen, C. ; Finan, B. ; Müller, T.D. ; Meyer, C.W. ; ... ; Stemmer, K. ; Tschöp, M.H. ; Pfluger, P.T.