Publications

The following publications were published exclusively under the affiliation of the Max Planck Society. For publications by the principal investigator outside of the Max Planck Society, see the links on the lower left.

Publications by the Mayer Lab

Preprints

If preprints are available, they will be listed here.

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Published

2025
Altendorfer, E.; Mundlos, S.; Mayer, A.: A transcription coupling model for how enhancers communicate with their target genes. Nature Structural & Molecular Biology 32 (4), pp. 598 - 606 (2025)
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Müller, J. M.; Altendorfer, E.; Freier, S.; Moos, K.; Mayer, A.; Tresch, A.: Halfpipe: a tool for analyzing metabolic labeling RNA-seq data to quantify RNA half-lives. NAR: genomics and bioinformatics 7 (1), Article lqaf006 (2025)
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2024
Ulicevic, J.; Shao, Z.; Jasnovidova, O.; Bressin, A.; Gajos, M.; Ng, A. H.; Annaldasula, S.; Meierhofer, D.; Church, G. M.; Busskamp, V. et al.; Mayer, A.: Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Molecular Systems Biology 20 (7), pp. 767 - 798 (2024)
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2023
Bressin, A.; Jasnovidova, O.; Arnold, M.; Altendorfer, E.; Trajkovski , F.; Kratz, T. A.; Handzlik, J. E.; Hnisz, D.; Mayer, A.: High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription. Nature Communications 14 (1), Article 4971 (2023)
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Bressin, A. S.: A Multi-Omics Analysis of Transcription Control by BRD4. Dissertation, ix, 205 pp. (2023)
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Nabavizadeh, N.; Bressin, A.; Shboul, M.; Moreno Traspas, R.; Chia, P. H.; Bonnard, C.; Szenker-Ravi, E.; Saribas, B.; Beillard, E.; Altunoglu, U. et al.; Hojati, Z.; Drutman, S.; Freier, S.; El-Khateeb, M.; Fathallah, R.; Casanova, J.-L.; Soror, W.; Arafat, A.; Escande-Beillard, N.; Mayer, A.; Reversade, B.: A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing. Embo Molecular Medicine 15 (2), Article e16478 (2023)
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Eischer, N.; Arnold, M.; Mayer, A.: Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. Wiley interdisciplinary reviews: WIREs RNA 14 (1), e1734 (2023)
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Mochalova, Y.: Illuminating the roles of transcription elongation factors TCEA1 and TCEA2 in human cells. Dissertation (2023)
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2022
Gajos, M.: Analysis of the determinants of Pol II pausing. Dissertation, vi, 125 pp. (2022)
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Altendorfer, E.; Mochalova, Y.; Mayer, A.: BRD4: a general regulator of transcription elongation. Transcription 13 (1-3), pp. 70 - 81 (2022)
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Bressin, A.; Mayer, A.: Neue Einblicke in die Genregulation mittels funktioneller Multiomik. Biospektrum 28 (3), pp. 276 - 278 (2022)
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Arnold, M.: Functional characterization of BRD4 in transcription elongation and termination. Dissertation, xliv, 152 Seiten pp. (2022)
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2021
Arnold, M.; Bressin, A.; Jasnovidova, O.; Meierhofer, D.; Mayer, A.: A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3′-processing and termination. Molecular Cell 81 (17), pp. 3589 - 3603 (2021)
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Jasnovidova, O.; Arnold, M.; Mayer, A.: Illuminating enhancer transcription at nucleotide resolution with native elongating transcript sequencing (NET-Seq). In: Enhancers and Promoters - Methods and Protocols (Methods in Molecular Biology ; 2351), Vol. 2351, pp. 41 - 65 (Ed. Borggrefe, T.). Humana, New York, NY (2021)
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Gajos, M.; Jasnovidova, O.; van Bömmel, A.; Freier, S.; Vingron, M.; Mayer, A.: Conserved DNA sequence features underlie pervasive RNA polymerase pausing. Nucleic Acids Research (London) 49 (8), pp. 4402 - 4420 (2021)
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ZIP
Annaldasula, S.; Gajos, M.; Mayer, A.: IsoTV: processing and visualizing functional features of translated transcript isoforms. Bioinformatics 37 (18), pp. 3070 - 3072 (2021)
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2020
Real, F. M.; Haas, S. A.; Franchini, P.; Xiong, P.; Simakov, O.; Kuhl, H.; Schöpflin, R.; Heller, D.; Moeinzadeh, M. H.; Heinrich, V. et al.; Krannich , T.; Bressin, A.; Hartmann, M. F.; Wudy, S. A.; Dechmann, D. K. N.; Hurtado, A.; Barrionuevo, F. J.; Schindler, M.; Harabula, I.; Osterwalder, M.; Hiller, M.; Wittler, L.; Visel, A.; Timmermann, B.; Meyer, A.; Vingron, M.; Jiménez, R.; Mundlos, S.; Lupiáñez, D. G.: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science 370 (6513), pp. 208 - 214 (2020)
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Mayer, A.: Genome Transcription Regulation During Cell Differentiation. Scientia 133, pp. 6 - 9 (2020)
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2017
Mayer, A.; Churchman, L. S.: A detailed protocol for subcellular RNA sequencing (subRNA-seq). In: Current Protocols in Molecular Biology, Vol. Suppl. 120, pp. 4.29.1 - 4.29.18 (Ed. Ausubel, F. M.). John Wiley & Sons, Inc., Hoboken, NJ (2017)
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Winter, G. E.; Mayer, A.; Buckley, D. L.; Erb, M. A.; Roderick, J. E.; Vittori, S.; Reyes,, J. M.; di Iulio, J.; Souza, A.; Ott, C. J. et al.; Roberts, J. M.; Zeid, R.; Scott, T. G.; Paulk, J.; Lachance, K.; Olson, C. M.; Dastjerdi, S.; Bauer, S.; Lin, C. Y.; Gray, N. S.; Kelliher, M. A.; Churchman, L. S.; Bradner, J. E.: BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. Molecular Cell 67 (1), pp. 5 - 18 (2017)
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Mayer, A.; Landry, H. M.; Churchman, L. S.: Pause & go: from the discovery of RNA polymerase pausing to its functional implications. Current Opinion in Cell Biology 46, pp. 72 - 80 (2017)
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Publications by Dr. Andreas Mayer before 2017

Andreas Mayer, L Stirling Churchman
Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing
Nature Protocols volume 11, pages 813–833 (2016)
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Mühlbacher W, Mayer A, Sun M, Remmert M, Cheung AC, Niesser J, Soeding J, Cramer P
Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold
Proteins, 83(10):1849-1858, 24 Aug 2015
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Padovan-Merhar O, Nair GP, Biaesch AG, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A
Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms
Mol Cell, 58(2):339-352, 09 Apr 2015
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Mayer A, di Iulio J, Maleri S, Eser U, Vierstra J, Reynolds A, Sandstrom R, Stamatoyannopoulos JA, Churchman LS
Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution.
Cell, 161(3):541-554, 01 Apr 2015
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Hirschmann WD, Westendorf H, Mayer A, Cannarozzi G, Cramer P, Jansen RP
Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast
Nucleic Acids Res, 42(6):4043-4055, 20 Jan 2014
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Meinel DM, Burkert-Kautzsch C, Kieser A, O'Duibhir E, Siebert M, Mayer A, Cramer P, Söding J, Holstege FC, Sträßer K
Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II
PLoS Genet, 9(11):e1003914, 14 Nov 2013
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Heo DH, Yoo I, Kong J, Lidschreiber M, Mayer A, Choi BY, Hahn Y, Cramer P, Buratowski S, Kim M
The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome
Journal of Biological Chemistry, 288(51):36676-36690, 06 Nov 2013
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Mayer A, Heidemann M, Lidschreiber M, Schreieck A, Sun M, Hintermair C, Kremmer E, Eick D, Cramer P
CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II
Science, 336(6089):1723-1725, 01 Jun 2012
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Mayer A, Schreieck A, Lidschreiber M, Leike K, Martin DE, Cramer P
The spt5 C-terminal region recruits yeast 3' RNA cleavage factor I
Molecular and Cellular Biology, 32(7):1321-1331, 30 Jan 2012
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Blattner C, Jennebach S, Herzog F, Mayer A, Cheung AC, Witte G, Lorenzen K, Hopfner KP, Heck AJ, Aebersold R, Cramer P
Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth
Genes & Development, 25(19):2093-2105, 22 Sep 2011
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