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versatile “one-fits-all" system to acutely deplete RNA binding proteins from condensates.

J. Cell Biol. 2024 Vol. 223 No. 2 e202304030. DOI:


Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia.

de Oliveira Freitas Machado C, Schafranek M, Brüggemann M, Hernández Cañás MC, Keller M, Di Liddo A, Brezski A, Blümel N, Arnold B, Bremm A, Wittig I, Jaé N, McNicoll F, Dimmeler S, Zarnack K, Müller-McNicoll M. Nucleic Acids Res. 2023 Jan 25;51(2):870-890. doi: 10.1093/nar/gkac1225. PMID: 36620874 


The G3BP1-UPF1-Associated Long Non-Coding RNA CALA Regulates RNA Turnover in the Cytoplasm.

Kirchhof L, Fouani Y, Knau A, Aslan GS, Heumüller AW, Wittig I, Müller-McNicoll M, Dimmeler S, Jaé N. Noncoding RNA. 2022 Jun 30;8(4):49. doi: 10.3390/ncrna8040049. PMID: 35893232

NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin.

Tants JN, Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A. Nucleic Acids Res. 2022 Mar 31:gkac212. doi: 10.1093/nar/gkac212. Online ahead of print. PMID: 35357505

Exploring the multifunctionality of SR proteins.
Slišković I, Eich H, Müller-McNicoll M. Biochem Soc Trans. 2021 Dec 23:BST20210325. doi: 10.1042/BST20210325.


SUMO: Glue or Solvent for Phase-Separated Ribonucleoprotein Complexes and Molecular Condensates?
Keiten-Schmitz J, Röder L, Hornstein E, Müller-McNicoll M, Müller S. Front Mol Biosci. 2021 May 7;8:673038. doi: 10.3389/fmolb.2021.673038.

The SRSF4-GAS5-Glucocorticoid Receptor Axis Regulates Ventricular Hypertrophy.
Larrasa-Alonso J, Villalba-Orero M, Martí-Gómez C, Ortiz-Sánchez P, López-Olañeta MM, Rey-Martín MA, Sánchez-Cabo F, McNicoll F, Müller-McNicoll M, García-Pavía P, Lara-Pezzi E. Circ Res. 2021 Sep 3;129(6):669-683. doi: 10.1161/CIRCRESAHA.120.318577.

SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels
Oliver Daniel Schwich, Nicole Blümel
, Mario Keller, Marius Wegener, Samarth Thonta Setty, Melinda Elaine Brunstein, Ina Poser , Igor Ruiz De Los Mozos, Beatrix Suess, Christian Münch, François McNicoll, Kathi Zarnack, Michaela Müller-McNicoll
Genome Biol. 2021 Mar 11;22(1):82.doi: 10.1186/s13059-021-02298-y


A paralog-specific role of COPI vesicles in the neuronal differentiation of mouse pluripotent cells
Manu Jain Goyal, Xiyan Zhao, Mariya Bozhinova, Karla Andrade-López, Cecilia de Heus, Sandra Schulze-Dramac, Michaela Müller-McNicoll, Judith Klumperman, Julien Béthune
Life Sci Alliance. 2020 Jul 14;3(9):e202000714.doi: 10.26508/lsa.202000714

SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly.
Vanessa Königs, Camila de Oliveira Freitas Machado, Benjamin Arnold, Nicole Blümel, Anfisa Solovyeva, Sinah Löbbert, Michal Schafranek, Igor Ruiz De Los Mozos, Ilka Wittig, Francois McNicoll, Marcel H. Schulz & Michaela Müller-McNicoll
Nat Struct Mol Biol. 2020 Mar;27(3):260-273. doi: 10.1038/s41594-020-0385-9


View from an mRNP: The Roles of SR Proteins in Assembly, Maturation and Turnover.
Marius Wegener & Michaela Müller-McNicoll
Adv Exp Med Biol. 2019;1203:83-112. doi: 10.1007/978-3-030-31434-7_3

A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress.
Antonella Di Liddo, Camila de Oliveira Freitas Machado, Sandra Fischer, Stefanie Ebersberger, Andreas W Heumüller, Julia E Weigand, Michaela Müller-McNicoll, Kathi Zarnack
J Mol Cell Biol. 2019 Sep 27. pii: mjz094. doi: 10.1093/jmcb/mjz094

Long and Repeat-Rich Intronic Sequences Favor Circular RNA Formation under Conditions of Reduced Spliceosome Activity.
Mantian Wang, Jingyi Hou, Michaela Müller-McNicoll, Wei Chen, Erin M.Schuman
2019 Oct 25;20:237-247. doi: 10.1016/j.isci.2019.08.058

The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development
Nicole Ritter, Tamer Ali, Nina Kopitchinski, Peggy Schuster, Arica Beisaw, David A. Hendrix, Marcel H. Schulz, Michaela Müller-McNicoll, Stefanie Dimmeler, Phillip Grote
Dev Cell. 2019 Aug 12. doi:10.1016/j.devcel.2019.07.013

Auto-regulatory feedback by RNA-binding proteins.
Müller-McNicoll M
, Rossbach O, Hui J, Medenbach J.
J Mol Cell Biol. 2019 Jun 1. pii: mjz043. doi: 10.1093/jmcb/mjz043

Loss of SRSF3 in Cardiomyocytes Leads to Decapping of Contraction Related mRNAs and Severe Systolic Dysfunction.
Ortiz-Sánchez P, Villalba-Orero M, López-Olañeta MM, Larrasa-Alonso J, Sanchez-Cabo F, Martí-Gómez C, Camafeita E, Gomez-Salinero JM, Ramos-Hernández L, Nielsen PJ, Vazquez J, Müller-McNicoll M, Garcia-Pavia P, Lara-Pezzi E.
Circ Res. 2019 May 30. doi: 10.1161/CIRCRESAHA.118.314515

Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5′ splice-site sequences due to weak interactions with SR proteins
Krchnáková Z, Thakur PK, Krausová M, Bieberstein N, Haberman N, Müller-McNicoll M, Stanek D.
Nucleic Acids Research, Volume 47, Issue 2, 25 January 2019, Pages 911–928,


Characterization of cis-acting elements that control oscillating alternative splicing
Gesine Goldammer, Alexander Neumann, Miriam Strauch, Michaela Müller-Mcnicoll, Florian Heyd & Marco Preußner
RNA Biol. 2018 Sep 10:1-12. doi: 10.1080/15476286.2018.1502587. [Epub ahead of print]

A Quantitative Heterokaryon Assay to Measure the Nucleocytoplasmic Shuttling of Proteins
François McNicoll, Michaela Müller-McNicoll  
2018 Sep 05. doi: DOI:10.21769/BioProtoc.2472

High-Throughput Screens for cis-Acting RNA Sequence Elements That Promote Nuclear Retention.
Zarnack K, Müller-McNicoll M. 
Biochemistry. 2018 May 24. doi: 10.1021/acs.biochem.8b00479.
[Epub ahead of print] No abstract available


Nuclear retention of mRNAs - quality control, gene regulation and disease 
Wegener M, Müller-McNicoll M 
Semin Cell Dev Biol. 2017 Nov 1. pii: S1084-9521(17)30442-1. doi: 10.1016/j.semcdb.2017.11.001

Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm 
Brugiolo M, Botti V, Liu N, Müller-McNicoll M, Neugebauer KM
Nucleic Acids Research, PMID: 28977534 DOI: 10.1093/nar/gkx671

TGFβ/SMAD signalling modulates MLL and MLL-AF4 mediated 5-lipoxygenase promoter activation
Saul MJ, Groher F, Hegewald AB, Müller-McNicoll M, Marschalek R, Suess B, Steinhilber
Prostaglandins & Other Lipid Mediators, 2017, PMID: 28803964 doi: 10.1016/j.prostaglandins.2017.07.006

RNA secondary structure and nucleotide composition of the conserved hallmark sequence of Leishmania SIDER2 retroposons are essential for endonucleolytic cleavage and mRNA degradation
Hiva Azizi, Tatiany P. Romão, Karen Santos Charret, Prasad K. Padmanabhan, Osvaldo P. de Melo Neto, Michaela Müller-McNicoll, Barbara Papadopoulou
PLOS One, July 13, 2017, doi:

Body Temperature Cycles Control Rhythmic Alternative Splicing in Mammals
Marco Preußner, Gesine Goldammer, Alexander Neumann,&nbspTom Haltenhof, Pia Rautenstrauch, Michaela Müller-McNicoll,Florian Heyd
Molecular Cell , Volume 67 , Issue 3 , 433 - 446.e4, doi:

Cellular differentiation state modulates the mRNA export activity of SR proteins
Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M
J Cell Biol. 2017 Jun 7. pii: jcb.201610051. doi: 10.1083/jcb.201610051

SIDER2 retroposon-mediated mRNA decay in Leishmania is coupled to translation
Azizi H, Müller-McNicoll M, Papadopoulou B
J. MBio. 2017 Jan 31;8(1). pii: e02288-16. doi: 10.1128/mBio.02288-16.

Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes
Dixit S, Müller-McNicoll M, David V, Zarnack K, Ule J, Hashimi H, Lukeš
J. MBio. 2017 Jan 31;8(1). pii: e02288-16. doi: 10.1128/mBio.02288-16.


SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export
Michaela Müller-McNicoll, Valentina Botti, Antonio M. de Jesus Domingues, Holger Brandl, Oliver D. Schwich, Michaela C. Steiner, Tomaz Curk, Ina Poser, Kathi Zarnack, and Karla M. Neugebauer
Genes & Dev. 2016. 30: 553-566, doi:10.1101/gad.276477.115


Approaches for Studying mRNA Decay Mediated by SIDER2 Retroposons in Leishmania 
Barbara Papadopoulou, Michela Müller-McNicoll, Prasad K. Padmanabhan 
DOI: 10.1007/978-1-4939-1438-8_7
In book: Methods in Molecular Biology, Vol. 1201 Parasites Genomic Protocols, Chapter: Approaches for Studying mRNA Decay Mediated by SIDER2 Retroposons in Leishmania, Publisher: Springer, Editors: Christopher Peacock


Good cap/bad cap: how the cap-binding complex determines RNA fate.
Müller-McNicoll M, Neugebauer KM
Nat Struct Mol Biol. 2014 Jan;21(1):9-12. doi: 10.1038/nsmb.2751.


How cells get the message: dynamic assembly and function of mRNA-protein complexes.
Müller-McNicoll M, Neugebauer KM.
Nat Rev Genet. 2013 Apr;14(4):275-87. doi: 10.1038/nrg3434. Epub 2013 Mar 12.


The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes.
Änkö ML, Müller-McNicoll M, Brandl H, Curk T, Gorup C, Henry I, Ule J, Neugebauer KM.
Genome Biol. 2012;13(3):R17. doi: 10.1186/gb-2012-13-3-r17.


mRNA: a complex(ed) life.
Müller M, Neugebauer KM, Eckmann C.
Genome Biol. 2010;11(5):304. doi: 10.1186/gb-2010-11-5-304.
Epub 2010 May 25.

Rapid decay of unstable Leishmania mRNAs bearing a conserved retroposon signature 3'-UTR motif is initiated by a site-specific endonucleolytic cleavage without prior deadenylation.
Müller M, Padmanabhan PK, Rochette A, Mukherjee D, Smith M, Dumas C, Papadopoulou B.
Nucleic Acids Res. 2010 Sep;38(17):5867-83. doi: 10.1093/nar/gkq349. Epub 2010 May 7.

Selective inactivation of SIDER2 retroposon-mediated mRNA decay contributes to stage- and species-specific gene expression in Leishmania.
Müller M, Padmanabhan PK, Papadopoulou B.
Mol Microbiol
. 2010 Jul;77(2):471-91. doi: 10.1111/j.1365-2958.2010.07226.x. Epub 2010 May 24.

Stage-specific expression of the glycine cleavage complex subunits in Leishmania infantum.
Müller M, Papadopoulou B.
Mol Biochem Parasitol. 2010 Mar;170(1):17-27. doi: 10.1016/j.molbiopara.2009.11.009. Epub 2009 Dec 2.


Identification of geographically distributed sub-populations of Leishmania (Leishmania) major by microsatellite analysis.
Al-Jawabreh A, Diezmann S, Müller M, Wirth T, Schnur LF, Strelkova MV, Kovalenko DA, Razakov SA, Schwenkenbecher J, Kuhls K, Schönian G.
BMC Evol Biol. 2008 Jun 24;8:183. doi: 10.1186/1471-2148-8-183.

Regulation of Gene Expression in Leishmania Throughout a Complex Digenetic Life Cycle 
Barbara Papadopoulou, Michaela Müller, Annie Rochette, Francois McNicoll,Carole Dumas, Conan Chow 
In book: Leishmania: After the Genome, Chapter: Regulation of Gene Expression in Leishmania Throughout a Complex Digenetic Life Cycle, Publisher: Horizon Scientific Press, Editors: Peter J Myler & Nicolas Fasel, pp.29-54 


Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania.
Bringaud F, Müller M, Cerqueira GC, Smith M, Rochette A, El-Sayed NM, Papadopoulou B, Ghedin E.
PLoS Pathog. 2007 Sep 7;3(9):1291-307.


A novel class of developmentally regulated noncoding RNAs in Leishmania.
Dumas C, Chow C, Müller M, Papadopoulou B.
Eukaryot Cell. 2006 Dec;5(12):2033-46. Epub 2006 Oct 27.

A combined proteomic and transcriptomic approach to the study of stage differentiation in Leishmania infantum.
McNicoll F, Drummelsmith J, Müller M, Madore E, Boilard N, Ouellette M, Papadopoulou B.
2006 Jun;6(12):3567-81.


Distinct 3'-untranslated region elements regulate stage-specific mRNA accumulation and translation in Leishmania.
McNicoll FMüller M, Cloutier S, Boilard N, Rochette A, Dubé M, Papadopoulou B.
J Biol Chem. 2005 Oct 21;280(42):35238-46. Epub 2005 Aug 22.


A coding mutation within the first exon of the human MD-2 gene results in decreased lipopolysaccharide-induced signaling.
Hamann L, Kumpf O, Müller M, Visintin A, Eckert J, Schlag PM, Schumann RR.
Genes Immun. 2004 Jun;5(4):283-8.

Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia.

de Oliveira Freitas Machado C, Schafranek M, Brüggemann M, Hernández Cañás MC, Keller M, Di Liddo A, Brezski A, Blümel N, Arnold B, Bremm A, Wittig I, Jaé N, McNicoll F, Dimmeler S, Zarnack K, Müller-McNicoll M. Nucleic Acids Res. 2023 Jan 25;51(2):870-890. doi: 10.1093/nar/gkac1225. PMID: 36620874