Shimada Y, Carl SH, Skribbe M, Flury V, Kuzdere T, Kempf G, Bühler M. (2021). An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing. PLoS Genet. DOI: 10.1371/journal.pgen.1009645


Tuck AC, Bühler M (2020) Long Non-coding RNA Depletion Using Self-Cleaving Ribozymes. Methods in Molecular Biology. In: Scarborough R.J., Gatignol A. (eds) Ribozymes. Methods in Molecular Biology, vol 2167. Humana, New York, NY.

Carl SH, Duempelmann L, Shimada Y, Bühler M. (2020).  A fully automated deep learning pipeline for high-throughput colony segmentation and classification.  Biol Open. bio.052936 doi: 10.1242/bio.052936 Published 2 June 2020

Tuck AC*, Rankova A*, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, Castelo-Szekely V, Gatfield D and Bühler B. (2020). Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation. Mol Cell. 2020;S1097-2765(20)30007-1. doi:10.1016/j.molcel.2020.01.007

Duempelmann L*, Skribbe M*, Bühler M. (2020). Small RNAs in the Transgenerational Inheritance of Epigenetic Information. Trends in Genetics. doi: 10.1016/j.tig.2019.12.001


Kaaij LJT*, Mohn F*, van der Weide RH, de Wit E, Bühler M. (2019). The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse. Cell. doi: 10.1016/j.cell.2019.08.007.

Welte T*, Tuck AC*, Papasaikas P, Carl SH, Flemr M, Knuckles P, Rankova A, Bühler M, Großhans H. (2019). The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1. Genes & Dev. doi: 10.1101/gad.328492.119. Epub 2019 Aug 1.

Duempelmann L, Mohn F, Shimada Y, Oberti D, Andriollo A, Lochs S, Bühler M. (2019). Inheritance of a Phenotypically Neutral Epimutation Evokes Gene Silencing in Later Generations. Mol Cell. doi: 10.1016/j.molcel.2019.02.009. Epub 2019 Mar 18.


Tuck AC, Natarajan KN, Rice GM, Borawski J, Mohn F, Rankova A, Flemr M, Wenger A, Nutiu R, Teichmann S and Bühler M. (2018). Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions. Life Science Alliance. doi:10.26508/lsa.201800124

Ostapcuk V, Mohn F, Carl SH, Basters A, Hess D, Iesmantavicius V, Lampersberger L, Flemr M, Pandey A, Thomä NH, Betschinger J and Bühler M. (2018). Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes. Nature. Epub ahead of print May 23. doi:10.1038/s41586-018-0153-8.

Knuckles P and Bühler M. (2018). Adenosine methylation as a molecular imprint defining the fate of RNA. FEBS Lett. Epub ahead of print May 21. doi: 10.1002/1873-3468.13107.

Knuckles P*, Lence T*, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M and Roignant JY. (2018). Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d. Genes & Dev. Published in Advance March 13, 2018, doi: 10.1101/gad.309146.117.


Berry S, Rosa S, Howard M, Bühler M and Dean C. (2017). Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression. Genes & Dev. Published in Advance December 6, 2017, doi: 10.1101/gad.305227.117.

Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M. (2017). The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1. Mol Cell. Epub ahead of print Jun 14. doi: 10.1016/j.molcel.2017.05.026.

Knuckles P, Carl SH, Musheev M, Niehrs C, Wenger A, Bühler M. (2017). RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding. Nat Struct Mol Biol. Epub ahead of print Jun 5. doi: 10.1038/nsmb.3419.


Shimada Y, Mohn F, Bühler M. (2016). The RNA-induced transcriptional silencing complex targets chromatin exclusively via interacting with nascent transcripts. . Genes and Development. Published in Advance December 9, 2016, doi:10.1101/gad.292599.116

Brykczynska U, Pecho-Vrieseling E, Thiemeyer A, Klein J, Fruh I, Doll T, Manneville C, Fuchs S, Iazeolla M, Beibel M, Roma G, Naumann U, Kelley N, Oakeley EJ, Mueller M, Gomez-Mancilla B, Bühler M, Tabolacci E, Chiurazzi P, Neri G, Bouwmeester T, Di Giorgio FP, Fodor BD (2016). CGG Repeat-Induced FMR1 Silencing Depends on the Expansion Size in Human iPSCs and Neurons Carrying Unmethylated Full Mutations. Stem Cell Reports, pii: S2213-6711(16)30242-9.


Stunnenberg R, Kulasegaran-Shylini R, Keller C, Kirschmann MA, Gelman L, Bühler M. (2015). H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein. EMBO J. 2015 Nov 12;34(22):2789-803. doi: 10.15252/embj.201591320. Epub 2015 Oct 5.

Flemr M, Bühler M.(2015). Single-Step Generation of Conditional Knockout Mouse Embryonic Stem Cells. Cell Rep. Jul 28;12(4):709-16. doi: 10.1016/j.celrep.2015.06.051. Epub 2015 Jul 16.

Kowalik KM, Shimada Y, Flury V, Stadler MB, Batki J, Bühler M. (2015). The Paf1 complex represses small-RNA-mediated epigenetic gene silencing. Nature. 520(7546):248-52.
Highlighted in: Zaratiegui, Nature, 2015, 520:162-164

Villasenor R, Miraglia L, Romero A, Tu B, Punga T, Knuckles P, Duss S, Orth T, Bühler M (2015). Genome-engineering tools to establish accurate reporter cell lines that enable identification of therapeutic strategies to treat Friedreich’s Ataxia. J Biomol Screen. 2015 Jul;20(6):760-7. doi: 10.1177/1087057114568071. Epub 2015 Jan 23.

Oberti D, Biasini A, Kirschmann MA, Genoud C, Stunnenberg R, Shimada Y, Bühler M. (2015). Dicer and Hsp104 function in a negative feedback loop to confer robustness to environmental stress. Cell Rep, 10(1):47-61.


Lalevée S, Lapaire O, Bühler M (2014). miR455 is linked to hypoxia signalling and is deregulated in preeclampsia. Cell Death Dis., 5:e1408


Keller C, Kulasegaran-Shylini R, Shimada, Y, Hotz HR, Bühler M (2013). Non-coding RNAs prevent spreading of a repressive histone mark. Nature Structural and Molecular Biology, 20(8):994-1000.

Tropberger P, Pott S, Keller C, Kamieniarz K, Caron M, Richter F, Li G, Mittler G, Liu ET, Bühler M, Margueron R, Schneider R (2013). Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell, 152(4):859-872.

Keller C and Bühler M (2013). Chromatin-associated ncRNA activities. Chromosome Research, 21(6-7):627-41.

Woolcock KJ and Bühler M (2013). Nuclear organization and RNAi in fission yeast. Current Opinion in Cell Biology, 25(3):372-7.


Shimada Y and Bühler M (2012). Schizosaccharomyces pombe reporter strains for relative quantitative assessment of heterochromatin silencing. Yeast, 29(8):335-341.

Keller C, Adaixo R, Stunnenberg R, Woolcock KJ, Hiller S, Bühler M (2012). HP1Swi6 mediates the recognition and destruction of heterochromatic RNA transcripts. Molecular Cell, 47(2): 215-227.
Highlighted in: Ren and Martienssen, EMBO Journal, 2012; 31(15): 3237-3238.  Schuldt, Nature Reviews Molecular Cell Biology, 2012; 13, 478-479. Creamer and Partridge, Molecular Cell, 2012; 47(2): 153-155. Barbash D, Faculty of 1000, 2012;

Woolcock KJ, Stunnenberg R, Gaidatzis D, Hotz HR, Emmerth S, Barraud P, Bühler M (2012). RNAi keeps Atf1-bound stress response genes in check at nuclear pores. Genes and Development, 26(7):683-92.
Highlighted in: Holoch and Moazed, Genes Dev. 2012; 26(8): 741-5.

Bühler M and Hiller S (2012). Dynamic nature of heterochromatin highlighted by a HP1Swi6- dependent gene silencing mechanism. Cell Cycle, 11(21): 3907-3908.

Stunnenberg R and Bühler M (2012). A detour to mature. Molecular Cell, 46(6): 719-7212011

Barraud P, Emmerth E, Shimada Y, Hotz HR, Allain F and Bühler M (2011). An extended dsRBD with a novel zinc-binding motif mediates nuclear retention of fission yeast dicer. EMBO J, 30: 4223-4235.


Woolcock KJ, Gaidatzis D, Punga T and Bühler M (2011). Dicer associates with chromatin to repress genome activity. Nature Structural and Molecular Biology 18(1):94-9.
Highlighted in: Collins K: 2011.


Emmerth S, Schober H, Gaidatzis D, Roloff T, Jacobeit K, Bühler M (2010). Nuclear retention of fission yeast Dicer is a prerequisite for RNAi-mediated heterochromatin assembly. Developmental Cell, 18, 1:102-113.
Highlighted in: Kaaij and Ketting. Dev Cell. 2010 Jan 19; 18(1):6-7.

Punga T, Bühler M (2010). Long intronic GAA repeats causing Friedreich Ataxia do not affect transcription initiation but provoke abortive transcription. EMBO Molecular Medicine, 2: 120-129.

Keller C, Woolcock KJ, Hess D and Bühler M (2010). Proteomic and functional analysis of the non-canonical poly(A) polymerase Cid14. RNA, 16(6):1124-9


Bühler M and Gasser S (2009). Silent chromatin at the middle and ends: lessons learned from yeasts. EMBO Journal, 28(15): 2149-2161

Bühler M (2009). RNA turnover and chromatin-dependent gene silencing. Chromosoma, Vol. 118(2): 141-151


Bühler M, Spies N, Bartel D and Moazed D (2008). TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nature Structural and Molecular Biology, Vol. 15, 10:999-1226.
Highlighted in: Thon G. Nat Struct Mol Biol., 2008; 15(10):1001-2.


Colmenares SU, Buker SM, Bühler M, Dlakić M, and Moazed D (2007). Coupling of double- stranded RNA synthesis and siRNA generation in fission yeast RNAi. Molecular Cell, Vol. 27, 3:449-461.
Highlighted in: Shiekhattar R. Mol Cell. 2007 Aug 17; 27(4):519-20.

Bühler M, Haas W, Gygi SP and Moazed D (2007). RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell, Vol. 129, 4:707-721.
Highlighted in: Bayne, White and Allshire, Cell. 2007; 129(4): 651-653. Asher Mullard, Nature Reviews Molecular Cell Biology. 2007; 8: 513

Buker SM, Iida T, Bühler M, Villén J, Gygi SP, Nakayama JI, and Moazed D (2007). Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast. Nature Structural and Molecular Biology, Vol. 14, 200-207.
Highlighted in: Ekwall K. Nat Struct Mol Biol. 2007 Mar; 14(3):178-9

Bühler M and Moazed D (2007). Transcription and RNAi in heterochromatic gene silencing. Nature Structural and Molecular Biology, 5;14(11):1041-1048.


Bühler M, Verdel A and Moazed D (2006). Tethering RITS to a Nascent Transcript Initiates RNAi- and Heterochromatin-Dependent Gene Silencing. Cell, Vol. 125, 5: 873-886
Highlighted in: Nature Structural & Molecular Biology. 2006; 13: 575

Moazed D, Bühler M, Buker SM, Colmenares SU, Gerace EL, Gerber SA, Hong EJ, Motamedi MR, Verdel A, Villen J, Gygi SP (2006). Studies on the Mechanism of RNAi-dependent Heterochromatin Assembly. Cold Spring Harb Symp Quant Biol., 71:461-471.

Bühler M, Steiner S, Mohn F, Paillusson A and Mühlemann O (2006). EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3′ UTR length. Nature Structural and Molecular Biology, Vol. 13, 462-464


Bühler M, Mohn F, Stalder L and Mühlemann O (2005). Transcriptional Silencing of Nonsense Codon-Containing Ig Minigenes. Molecular Cell, Vol. 18, 307-317.
Highlighted in: Science. 2005; 308: 759 Luehrmann R: 2005.

Mohn F*, Bühler M* and Mühlemann O (2005). Nonsense-associated alternative splicing of T- cell receptor beta genes: No evidence for frame dependence. RNA, Vol. 11, 2: 147-156

Bühler M and Mühlemann O (2005). Alternative Splicing induced by nonsense mutations in the immunoglobulin beta VDJ exon is independent of truncation of the open reading frame. RNA, Vol. 11, 2: 139-146


Bühler M, Paillusson A, and Mühlemann O (2004). Efficient down-regulation of immunoglobulin beta mRNA with premature translation-termination codons requires the 5’- half of the VDJ exon. Nucleic Acids Research, Vol. 32, 11:3304-3315


Bühler M, Wilkinson MF, and Mühlemann O (2002). Intranuclear degradation of nonsense codon – containing mRNA. EMBO Reports, 3:646 – 651

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