1.  *Ulicevic J, *Shao Z, *Jasnovidova O, Bressin A, Gajos M, Ng AHM, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A (2024). Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol,

  2. *Bressin A, *Jasnovidova O, *Arnold M, Altendorfer E, Trajkovski F, Kratz TA, Handzlik JE, Hnisz D, Mayer A (2023). High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription. Nat Commun,

  3. *Nabavizadeh N, *Bressin A, Shboul M, Traspas RM, Chia PH, Bonnard C, Szenker-Ravi E, Sarıbaş B, Beillard E, Altunoglu U, Hojati Z, Drutman S, Freier S, El‑Khateeb M, Fathallah R, Casanova JL, Soror W, Arafat A, Escande-Beillard N, **Mayer A, **Reversade B (2023). A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing. EMBO Mol Med,

  4. *Altendorfer E, *Mochalova Y, Mayer A (2022). BRD4: a general regulator of transcription elongation. Transcription,

  5. Eischer N, Arnold M, Mayer A (2022). Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. WIREs RNA,

  6. *Arnold M, *Bressin A, Jasnovidova O, Meierhofer D, Mayer A (2021). A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3’-processing and termination. Mol Cell,

  7. Gajos M, Jasnovidova O, van Bömmel A, Freier S, Vingron M, Mayer A (2021). Conserved DNA sequence features underlie pervasive RNA polymerase pausing. Nucleic Acids Res,
  8. *Jasnovidova O, *Arnold M, Mayer A (2021). Illuminating enhancer transcription at nucleotide resolution with native elongating transcript sequencing (NET-Seq). Methods Mol Biol 2351: 41-65. 
  9. Annaldasula S, Gajos M, Mayer A (2021). IsoTV: processing and visualizing functional features of translated transcript isoforms. Bioinformatics ,
  10. **Mayer A & **Churchman LS (2017). A detailed protocol for subcellular RNA sequencing (subRNA-seq). Curr Protoc Mol Biol 120: 4.29.1-4.29.18.
  11. *Winter GE, *Mayer A, *Buckley DL, Erb MA, Roderick JE, Vittori S, Reyes JM, di Iulio J, Souza A, Ott CJ, Roberts JM, Zeid R, Scott TG, Paulk J, Lachance K, Olson CM, Dastjerdi S, Bauer S, Lin CY, Gray NS, Kelliher MA, Churchman LS, Bradner JE (2017). BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. Mol Cell 67: 5-18.
  12. *Mayer A , *Landry HM, Churchman LS (2017). Pause & go: from the discovery of RNA polymerase pausing to its functional implications. Curr Opin Cell Biol 46: 72-80.
  13. **Mayer A & **Churchman LS (2016). Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing. Nat Protocols 11: 813-833.  
  14. *Mayer A, *di Iulio J, Maleri S, Eser U, Reynolds A, Vierstra J, Sandstrom R, Stamatoyannopoulos JA, Churchman LS (2015). Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell 161: 541-554.
  15. Padovan-Merhar O, Nair GP, Biaesch A, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A (2015). Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Mol Cell 58: 339-352.
  16. Muehlbacher W, Mayer A, Sun M, Remmert M, Cheung AC, Niesser J, Soeding J, Cramer P (2015). Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold. Proteins 83: 1849-1858.
  17. *Hirschmann WD, *Westendorf H, Mayer A, Cannarozzi G, Cramer P, Jansen RP (2014). Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast. Nucleic Acids Res 42: 4043-4055.
  18. Heo DH, Yoo I, Kong J, Lidschreiber M, Mayer A, Choi BY, Hahn Y, Cramer P, Buratowski S, Kim M (2013). 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. J Biol Chem 288: 36676-36690.
  19. Meinel DM, Burkert-Kautzsch C, Kieser A, O’Duibhir E, Siebert M, Mayer A, Cramer P, Soeding J, Holstege FC, Straesser K (2013). Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II. PLoS Genet 11: e1003914.
  20. *Mayer A, *Heidemann M, Lidschreiber M, Schreieck A, Sun M, Hintermair C, Kremmer E, Eick D, Cramer P (2012). Tyrosine phosphorylation impairs termination factor recruitment to transcribing RNA polymerase II. Science 336: 1723-1725.
  21. *Mayer A, *Schreieck A, Lidschreiber M, Leike K, Martin DE, Cramer P (2012) The Spt5 C-terminal region recruits yeast 3’-RNA cleavage factor I. Mol Cell Biol 32: 1321-1331.
  22. Blattner C, Jennebach S, Herzog F, Mayer A, Cheung ACM, Witte G, Lorenzen K, Hopfner KP, Heck AJR, Aebersold U, Cramer P (2011). Architecture of the RNA polymerase I-Rrn3 initiation complex and implications for cell growth regulation. Genes Dev 25: 2093-2105.
  23. *Müller M, *Heym RG, Mayer A, Kramer K, Schmid M, Cramer P, Urlaub H, Jansen RP, Niessing D (2011). A cytoplasmic complex mediates specific mRNA recognition and localization in yeast. PLoS Biology 9: e1000611
  24. *Miller C, *Schwalb B, *Maier K, Schulz D, Dümcke S, Zacher B, Mayer A, Sydow J, Marcinowski L, Dölken L, Martin DE, Tresch A, Cramer P (2011). Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7, article number 458.
  25. Clausing E, Mayer A, Chanarat S, Muller, B, Germann SM, Cramer P, Lisby M, Strasser K (2010). The transcription elongation factor Bur1-Bur2 interacts with replication protein A and maintains genome stability during replication stress. J Biol Chem 285: 41665-41674.
  26. Sun M, Lariviere L, Dengl S, Mayer A, Cramer P (2010). A tandem SH2 domain in transcription elongation factor Spt6 binds the phosphorylated RNA polymerase II CTD. J Biol Chem 285: 41597-41603.
  27. *Mayer A, *Lidschreiber M, *Siebert M, Leike K, Söding J, Cramer P (2010). Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol 17: 1272-1278.
  28. *Röther S, *Burkert C, *Brünger KM, *Mayer A, Kieser A, Strässer K (2010). Nucleocytoplasmic shuttling of the La motif-containing protein Sro9 might link its nuclear and cytoplasmic functions. RNA 16: 1393-1401.
  29. Dengl S, Mayer A, Sun M, Cramer P (2009). Structure and in vivo requirement of the yeast Spt6 SH2 domain. J Mol Biol 389: 211-225.
  30. Hepperger C, Mayer A, Merz J, Vanderwall DK, Dietzel S (2009). Parental genomes mix in mule and human cell nuclei. Chromosoma 118: 335-347.

 ** co-corresponding authorship
 *   equal authorship

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