Publications

Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer KM. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nature Reviews Molecular Cell Biology. 2024 Mar 20.

Neugebauer KM. How cell biology can save the planet. Nature Cell Biology. 2024 Jan 16. PMID: 38228830

Chen K, Guo Y, How K, Acosta A, Documet D, Liang C, Arul D, Wood S, Moon K, Oliver LS, Lopez Fajardo E, Kopyto M, Shine M, Neugebauer KM. Five questions on how biochemistry can combat climate change. BBA Advances. 2023 Nov 24. PMID: 38075469

Podszywalow-Bartnicka P, Neugebauer KM. Splicing under stress: A matter of time and place. Journal of Cell Biology. 2023 Nov 21. PMID: 37988026

Bergfort A, Neugebauer KM: The promoter as a trip navigator: Guiding alternative polyadenylation site destinations. Molecular Cell. 2023 July 20. PMID: 37478824

Šimčíková D, Gelles-Watnick S, Neugebauer KM: Tudor-dimethylarginine interactions: the condensed version. Trends Biochem Sci. 2023 May 6. PMID: 37156649

Courchaine E, Gelles-Watnick S, Machyna M, Straube K, Sauyet S, Enright J, Neugebauer KM: The coilin N-terminus mediates multivalent interactions between coilin and Nopp140 to form and maintain Cajal bodies. Nat Commun. 2022 Oct 12. PMID: 36224177

Draycott AS, Schaening-Burgos C, Rojas-Duran MF, Wilson L, Schärfen L, Neugebauer KM, Nachtergaele S, Gilbert WV: Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA. PLoS Biol. 2022 May 24. PMID: 35609439

Karmakar S, Ramirez O, Paul KV, Gupta AK, Kumari V, Botti V, de Los Mozos IR, Neuenkirchen N, Ross RJ, Karanicolas J, Neugebauer KM, Pillai MM: Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2). NAR Cancer. 2022 May 2. PMID: 35528200

Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S: Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Mol Cell. 2022 Mar 17. PMID: 35303483

Schärfen L, Zigackova D, Reimer KA, Stark MR, Slat VA, Francoeur NJ, Wells ML, Zhou L, Blackshear PJ, Neugebauer KM, Rader SD: Identification of Alternative Polyadenylation in Cyanidioschyzon merolae Through Long-Read Sequencing of mRNA. Front Genet. 2022 Jan 28. PMID: 35154260

Boddu PC, Gupta AK, Kim JS, Neugebauer KM, Waldman T, Pillai MM: Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase. Commun Biol. 2021 Oct 13. PMID: 34645977

Schärfen L, Neugebauer K: Transcription Regulation Through Nascent RNA Folding. Review J Mol Biol. 2021 Jul 9. PMID: 33811916

Courchaine EM, Barentine AES, Straube K, Lee DR, Bewersdorf J, Neugebauer KM: DMA-tudor interaction modules control the specificity of in vivo condensates. Cell. 2021 Jul 8. PMID: 34115980

Rodenfels J, Neugebauer KM: Calorimetric Heat Dissipation Measurements of Developing Zebrafish Embryos. Methods Mol Biol. 2021 Jun 4. PMID: 34085232

Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CBF, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF: SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface. medRxiv. 2021 Jan 26. PMID: 33532791. Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. Med (NY) 2021 May 14. PMID: 33969332

Reimer KA, Mimoso C, Adelman K, and Neugebauer KM: Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis. Mol Cell. 2021 Jan 12. PMID: 33440169

Gordon JM, Phizicky DV and Neugebauer KM: Nuclear mechanisms of gene expression control: pre-mRNA splicing as a life or death decision. Current Opinion in Genetics & Development. 2020 Dec 5. PMID: 33291060

Alpert T, Straube K, Oesterreich FC, Herzel L, and Neugebauer KM: Widespread Transcriptional Readthrough Caused by Nab2 Depletion Leads to Chimeric Transcripts with Retained Introns. Cell Reports. 2020 Oct 27. PMID: 33113357

Reimer KA and Neugebauer KM: Preparation of Mammalian Nascent RNA for Long Read Sequencing. Current Protocols in Molecular Biology. 2020 Oct 21. PMID: 33085989

Carrocci, TJ and Neugebauer KM: Pre-mRNA Splicing in the Nuclear Landscape. Cold Spring Harb Symp Quant Biol. 2020 Jun 3. PMID: 32493763 

Fauver, JR et al:  Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell. 2020 May 28. PMID: 32386545 

Rodenfels J, Sartori P, Golfier S, Nagendra K, Neugebauer KM, and Howard J: Contributions of increasing plasma membrane to the energetic cost of early zebrafish embryogenesis. Mol Biol Cell. 2020 Feb 12. PMID: 32049586

Courchaine EM, Lu A, Neugebauer KM: Droplet organelles? EMBO J. 2016 Aug 1; 2016 Jun 29. PMID: 27357569

Oesterreich FC, Herzel L, Straube K, Hujer K, Howard J, Neugebauer KM: Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II. Cell. 2016 Apr 7; 2016 Mar 24. PMID: 27020755

Müller-McNicoll M, Botti V, de Jesus Domingues AM, Brandl H, Schwich OD, Steiner MC, Curk T, Poser I, Zarnack K, Neugebauer KM: SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export. Genes Dev. 2016 Mar 1. PMID: 26944680

Herzel L, Neugebauer KM: Quantification of co-transcriptional splicing from RNA-Seq data. Methods. 2015 Sep 1; 2015 Apr 27. PMID: 25929182

Courchaine E, Neugebauer KM: Paraspeckles: paragons of functional aggregation. J Cell Biol. 2015 Aug 17. PMID: 26283795

Neugebauer KM: RNA: master or servant? RNA. 2015 Apr. PMID: 25780198

Heyn P, Kalinka AT, Tomancak P, Neugebauer KM: Introns and gene expression: cellular constraints, transcriptional regulation, and evolutionary consequences. Bioessays. 2015 Feb; 2014 Nov 14. PMID: 25400101

Machyna M, Neugebauer KM, Staněk D: Coilin: The first 25 years. RNA Biol. 2015. PMID: 25970135

Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM: The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies. Mol Cell. 2014 Nov 6; 2014 Nov 6. PMID: 25514182

Heyn P, Kircher M, Dahl A, Kelso J, Tomancak P, Kalinka AT, Neugebauer KM: The earliest transcribed zygotic genes are short, newly evolved, and different across species. Cell Rep. 2014 Jan 30; 2014 Jan 16. PMID: 24440719

Bieberstein NI, Straube K, Neugebauer KM: Chromatin immunoprecipitation approaches to determine co-transcriptional nature of splicing. Methods Mol Biol. 2014. PMID: 24549674

Müller-McNicoll M, Neugebauer KM: Good cap/bad cap: how the cap-binding complex determines RNA fate. Nat Struct Mol Biol. 2014 Jan. PMID: 24389545

Pabis M, Neufeld N, Steiner MC, Bojic T, Shav-Tal Y, Neugebauer KM: The nuclear cap-binding complex interacts with the U4/U6·U5 tri-snRNP and promotes spliceosome assembly in mammalian cells. RNA. 2013 Aug; 2013 Jun 21. PMID: 23793891

Brugiolo M, Herzel L, Neugebauer KM: Counting on co-transcriptional splicing. F1000Prime Rep. 2013; 2013 Apr 2. PMID: 23638305

Müller-McNicoll M, Neugebauer KM: How cells get the message: dynamic assembly and function of mRNA-protein complexes. Nat Rev Genet. 2013 Apr; 2013 Mar 12. PMID: 23478349

Machyna M, Heyn P, Neugebauer KM: Cajal bodies: where form meets function. Wiley Interdiscip Rev RNA. 2013 Jan-Feb; 2012 Oct 5. PMID: 23042601

Bieberstein NI, Carrillo Oesterreich F, Straube K, Neugebauer KM: First exon length controls active chromatin signatures and transcription. Cell Rep. 2012 Jul 26; 2012 Jul 20. PMID: 22840397

Ankö ML, Neugebauer KM: RNA-protein interactions in vivo: global gets specific. Trends Biochem Sci. 2012 Jul; 2012 Mar 15. PMID: 22425269

Änkö ML, Müller-McNicoll M, Brandl H, Curk T, Gorup C, Henry I, Ule J, Neugebauer KM: The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biol. 2012. PMID: 22436691

Görnemann J, Barrandon C, Hujer K, Rutz B, Rigaut G, Kotovic KM, Faux C, Neugebauer KM, Séraphin B: Cotranscriptional spliceosome assembly and splicing are independent of the Prp40p WW domain. RNA. 2011 Dec; 2011 Oct 21. PMID: 2202097

Tripsianes K, Madl T, Machyna M, Fessas D, Englbrecht C, Fischer U, Neugebauer KM, Sattler M: Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nat Struct Mol Biol. 2011 Nov 20; 2011 Nov 20. PMID: 22101937

Krastev DB, Slabicki M, Paszkowski-Rogacz M, Hubner NC, Junqueira M, Shevchenko A, Mann M, Neugebauer KM, Buchholz F: A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly. Nat Cell Biol. 2011 Jun 5; 2011 Jun 5. PMID: 21642980

Carrillo Oesterreich F, Bieberstein N, Neugebauer KM: Pause locally, splice globally. Trends Cell Biol. 2011 Jun; 2011 Apr 27. PMID: 21530266

Domingues AM, Neugebauer KM, Fern R: Identification of four functional NR3B isoforms in developing white matter reveals unexpected diversity among glutamate receptors. J Neurochem. 2011 May; 2011 Mar 14. PMID: 21320125

Brody Y, Neufeld N, Bieberstein N, Causse SZ, Böhnlein EM, Neugebauer KM, Darzacq X, Shav-Tal Y: The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLoS Biol. 2011 Jan 11; 2011 Jan 11. PMID: 21264352

Carrillo Oesterreich F, Preibisch S, Neugebauer KM: Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell. 2010 Nov 24. PMID: 21095587

Huranová M, Ivani I, Benda A, Poser I, Brody Y, Hof M, Shav-Tal Y, Neugebauer KM, Stanek D: The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells. J Cell Biol. 2010 Oct 4. PMID: 20921136

Ankö ML, Neugebauer KM: Long noncoding RNAs add another layer to pre-mRNA splicing regulation. Mol Cell. 2010 Sep 24. PMID: 20864030

Pabis M, Neufeld N, Shav-Tal Y, Neugebauer KM: Binding properties and dynamic localization of an alternative isoform of the cap-binding complex subunit CBP20. Nucleus. 2010 Sep-Oct. PMID: 21326824

Ankö ML, Morales L, Henry I, Beyer A, Neugebauer KM: Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells. Nat Struct Mol Biol. 2010 Aug; 2010 Jul 18. PMID: 20639886

Strzelecka M, Trowitzsch S, Weber G, Lührmann R, Oates AC, Neugebauer KM: Coilin-dependent snRNP assembly is essential for zebrafish embryogenesis. Nat Struct Mol Biol. 2010 Apr; 2010 Mar 28. PMID: 20357773

Müller M, Neugebauer KM, Eckmann C: mRNA: a complex(ed) life. Genome Biol. 2010; 2010 May 25. PMID: 20500909

Strzelecka M, Oates AC, Neugebauer KM: Dynamic control of Cajal body number during zebrafish embryogenesis. Nucleus. 2010 Jan-Feb. PMID: 21327108

Sapra AK, Ankö ML, Grishina I, Lorenz M, Pabis M, Poser I, Rollins J, Weiland EM, Neugebauer KM: SR protein family members display diverse activities in the formation of nascent and mature mRNPs in vivo. Mol Cell. 2009 Apr 24. PMID: 19394295

Martinez J, Neugebauer KM: El Sur también existe: processing RNA in the Argentine Patagonia. Meetings on ‘Cell Biology, Signaling and Alternative Splicing’ and ‘Gene Expression and RNA Processing’. EMBO Rep. 2008 Jun; 2008 May 9. PMID: 18464796

Stanek D, Pridalová-Hnilicová J, Novotný I, Huranová M, Blazíková M, Wen X, Sapra AK, Neugebauer KM: Spliceosomal small nuclear ribonucleoprotein particles repeatedly cycle through Cajal bodies. Mol Biol Cell. 2008 Jun; 2008 Mar 26. PMID: 18367544

Listerman I, Bledau AS, Grishina I, Neugebauer KM: Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PLoS Genet. 2007 Nov. PMID: 18039033

Klingauf M, Stanek D, Neugebauer KM: Enhancement of U4/U6 small nuclear ribonucleoprotein particle association in Cajal bodies predicted by mathematical modeling. Mol Biol Cell. 2006 Dec; 2006 Sep 20. PMID: 16987958

Stanek D, Neugebauer KM: The Cajal body: a meeting place for spliceosomal snRNPs in the nuclear maze. Chromosoma. 2006 Oct; 2006 Mar 31. PMID: 16575476

Listerman I, Sapra AK, Neugebauer KM: Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat Struct Mol Biol. 2006 Sep; 2006 Aug 20. PMID: 16921380

Neugebauer KM: Please hold–the next available exon will be right with you. Nat Struct Mol Biol. 2006 May. PMID: 16738604

Neugebauer KM: Keeping tabs on the women: life scientists in Europe. PLoS Biol. 2006 Apr; 2006 Apr 11. PMID: 16602822

Görnemann J, Kotovic KM, Hujer K, Neugebauer KM: Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol Cell. 2005 Jul 1. PMID: 15989964

Stanĕk D, Neugebauer KM: Detection of snRNP assembly intermediates in Cajal bodies by fluorescence resonance energy transfer. J Cell Biol. 2004 Sep 27. PMID: 15452143

Dundr M, Hebert MD, Karpova TS, Stanek D, Xu H, Shpargel KB, Meier UT, Neugebauer KM, Matera AG, Misteli T: In vivo kinetics of Cajal body components. J Cell Biol. 2004 Mar 15. PMID: 15024031

Kotovic KM, Lockshon D, Boric L, Neugebauer KM: Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast. Mol Cell Biol. 2003 Aug. PMID: 12897147

Schaft D, Roguev A, Kotovic KM, Shevchenko A, Sarov M, Shevchenko A, Neugebauer KM, Stewart AF: The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res. 2003 May 15. PMID: 12736296

Stanĕk D, Rader SD, Klingauf M, Neugebauer KM: Targeting of U4/U6 small nuclear RNP assembly factor SART3/p110 to Cajal bodies. J Cell Biol. 2003 Feb 17; 2003 Feb 10. PMID: 12578909

Neugebauer KM: On the importance of being co-transcriptional. J Cell Sci. 2002 Oct 15. PMID: 12244124