Publications



Highlighted Publications

DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions

Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T*

Nature Genetics 2022 November


ChromID identifies the protein interactome at chromatin marks

Villaseñor R, Pfändler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, Baubec T*

Nature Biotechnology 2020 March


Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

Baubec T*, Colombo DF, Wirbelauer C, Schmidt J, Burger L, Krebs AR, Akalin A, Schübeler D*

Nature 2015 April



2024

Targeted CRISPR-Cas9 screening identifies transcription factor network controlling murine haemato-endothelial fate commitment

Teske M, Wertheimer T, Butz S, Zwicky P, Mallona I, Elling U, Lancrin C, Becher B, Grosso AR, Baubec T, Schmolka N*

biorXiv 2024 January


2023

Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex function during cellular differentiation

Schmolka N, Karemaker ID, Cardoso da Silva R, Recchia DC, Spegg V, Bhaskaran J, Teske M, de Wagenaar NP, Altmeyer M, Baubec T*

Nature Communications 2023 June


2022

DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions

Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T*

Nature Genetics 2022 November


The histone methyltransferase SETD2 negatively regulates cell size

Molenaar TM, Malik M, Silva J, Liu NQ, Haarhuis JHI, Ambrosi C, Kwesi-Maliepaard EM, van Welsem T, Baubec T,  Faller WJ, van Leeuwen F*

Journal of Cell Science 2022 October


Expanded CAG/CTG repeats resist gene silencing mediated by targeted epigenome editing

Yang B, Borgeaud AC, Buricova M, Aeschbach F, Rodriguez-Lima O, Ruiz Buendia GA, Cinezi C, Taylor AS, Baubec T, Dion V*

Human Molecular Genetics 2022 February


2021

Flanking sequence preference modulates de novo DNA methylation in the mouse genome

Mallona I, Ilie IM, Karemaker ID, Butz S, Manzo M, Caflisch A, Baubec T*

Nucleic Acids Research 2021 Jan. 11


Regulatory mechanisms governing chromatin organization and function

Villaseñor R*, Baubec T*

Current Opinion in Cell Biology 2021 June


Dissecting the roles of MBD2 isoforms in regulating NuRD complex function during cellular differentiation

Schmolka N, Bhaskaran J, Karemaker ID, Baubec T*

bioRxiv 2021 March


Nucleosomal Asymmetry Shapes Histone Mark Binding and Promotes Poising at Bivalent Domains

Bryan E, Warburton M, Webb KM, McLaughlin KA, Spanos C, Ambrosi C, Major V, Baubec T, Rappsilber J, Voigt P*

bioRxiv 2021 February


2020

BAZ2A safeguards genome architecture of ground‐state pluripotent stem cells

Dalcher D, Yihong Tan J, Bersaglieri C, Peña‐Hernández R, Vollenweider E, Zeyen S, Schmid MW, Bianchi V, Butz S, Roganowicz M, Kuzyakiv R, Baubec T, Marques AC, Santoro R*

EMBO Journal 2020 October


DNA methyltransferases hitchhiking on chromatin

Karemaker ID*, Baubec T*
Swiss Medical Weekly 2020 August

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

Ruiz Buendía GA, Leleu M, Marzetta F, Vanzan L, Tan JY, Ythier V, Randall EL, Marques AC, Baubec T, Murr R, Xenarios I, Dion V*

Science Advances 2020 Juli


Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance

Ringel T, Frey N, Ringnalda F, Janjuha S, Cherkaoui S, Butz S, Srivatsa S, Pirkl M, Russo G, Villiger L, Rogler G, Clevers H, Beerenwinkel N, Zamboni N, Baubec T, Schwank G*

Cell Stem Cell 2020 March


ChromID identifies the protein interactome at chromatin marks

Villaseñor R, Pfändler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, Baubec T*

Nature Biotechnology 2020 March


Reading DNA modifications

Baubec T* and Defossez PA*

Journal of Molecular Biology 2020 February


2019

Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection.

Caiado F, Maia-Silva D, Jardim C, Schmolka N, Carvalho T, Reforço C, Faria R, Kolundzija B, Simões AE, Baubec T, Vakoc CR, da Silva MG, Manz MG, Schumacher TN, Norell H, Silva-Santos B*

Nature Communications 2019 November


Efficient Pre-mRNA Cleavage Prevents Replication-Stress-Associated Genome Instabilitys

Teloni F, Michelena J, Lezaja A, Kilic S, Christina Ambrosi C, Menon S, Dobrovolna J, Imhof R, Janscak P, Baubec T, Altmeyer M*

Molecular Cell 2019 February


CG dinucleotides enhance promoter activity independent of DNA methylation

Hartl D, Krebs AR, Grand RS, Baubec T, Isbel L, Wirbelauer C, Burger L, Schübeler D*

Genome Research 2019 February


2018

Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells

Manzo M, Ambrosi C, Baubec T*

Springer. CpG Islands – Methods and Protocols, 157-174. 2018 April


2017

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content

Colombo D, Burger L, Baubec T, Schübeler D*

PLoS Genetics 2017 December


Isoform-specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands

Manzo M, Wirz J, Ambrosi C, Villaseñor R, Roschitzki B, Baubec T*

The EMBO Journal 2017 December

News and Views by Richard Meehan and Sari Pennings


Dynamics and Context-Dependent Roles of DNA Methylation.

Ambrosi C, Manzo M, Baubec T*

Journal of Molecular Biology 2017 May


2016

Genome-Wide Analysis of DNA Methylation Patterns by High-Throughput Sequencing

Baubec T*, Akalin A*

Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing

Springer (pages 197-221)  2016 June


Dynamic and flexible H3K9me3 bridging via HP1B dimerization establishes a plastic state of condensed chromatin

Hiragami-Hamada K, Soeroes S, Nikolov M, Wilkins B, Kreuz S, Chen C, De La Rosa-Velazquez A, Zenn H, Kost N, Pohl W, Chernev A, Schwarzer D, Jenuwein T, Lorincz M, Zimmermann B, Walla PJ, Neumann H, Baubec T, Urlaub H, Fischle W*

Nature Communications 2016 April


Analysis of Chromatin ADP-Ribosylation at the Genome-wide Level and at Specific Loci by ADPr-ChAP

Bartolomei G, Leutert M, Manzo M, Baubec T, Hottiger MO*

Molecular Cell 2016 February


2015

Repair of DNA Damage Induced by the Cytidine Analog Zebularine Requires ATR and ATM in Arabidopsis

Liu CH,  Finke A,  Díaz M,  Rozhon W, Poppenberger B, Baubec T,  Pecinka A*

Plant Cell 2015 May


Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

Baubec T*, Colombo DF, Wirbelauer C, Schmidt J, Burger L, Krebs AR, Akalin A, Schübeler D*

Nature 2015 April


2014

Genomic patterns and context specific interpretation of DNA methylation

Baubec T*, Schübeler D*

Current Opinion in Genetics and Development 2014 Apr


Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis

Baubec T, Finke A, Mittelsten Scheid O, Pecinka A*

EMBO Reports 2014 April


2013

Methylation-dependent and -independent genomic targeting principles of the MBD protein family

Baubec T, Ivánek R, Lienert F, Schübeler D*

Cell 2013 April


2004-2011

Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells

Lienert F, Mohn F, Tiwari VK, Baubec T, Roloff TC, Gaidatzis D, Stadler MB, Schübeler D*

PLoS Genetics. 2011 Jun; 7(6):e1002090.


Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis

Pecinka A, Dinh HQ, Baubec T, Rosa M, Lettner N, Mittelsten Scheid O*

Plant Cell. 2010 Sep; 22(9):3118-29.


Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic States in Arabidopsis

Baubec T, Dinh HQ, Pecinka A, Rakic B, Rozhon W, Wohlrab B, von Haeseler A, Mittelsten Scheid O*

Plant Cell. 2010 Jan; 22(1):34-47.


Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine

Baubec T, Pecinka A, Rozhon W, Mittelsten Scheid O*

Plant Journal 2009 February


Rapid quantification of global DNA methylation by isocratic cation exchange high-performance liquid chromatography

Rozhon W, Baubec T, Mayerhofer J, Mittelsten Scheid O, Jonak C*

Analytical Biochemistry 2008 April


Medea in full self-control

Baubec T, Mittelsten Scheid O*.

Trends in Plant Sciences 2006 October


The Air noncoding RNA: an imprinted cis-silencing transcript

Braidotti G, Baubec T, Pauler F, Seidl C, Smrzka O, Stricker S, Yotova I, Barlow DP*

Cold Spring Harbor Symposia on Quantitative Biology 2004