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

Probing DNA damage sites reveals context-dependent and novel DNA damage response factors

Richard Cardoso da Silva*, Davide C. Recchia, Vincent Portegijs, Maria Cristina Trueba Sanchez, Kelly E. Stecker, Sander van den Heuvel, Tuncay Baubec*

bioRxiv 2024 October; doi: https://doi.org/10.1101/2024.10.23.619792

SETD2 promotes PAF1C interactions with the elongating RNA Pol II and is required for neuronal differentiation

Christina Ambrosi, Ramon Pfaendler, Stefan Butz, Davide Recchia, Xue Bao, Nina Schmolka, Tuncay Baubec*

bioRxiv 2024 October; doi: https://doi.org/10.1101/2024.10.23.619798

Chrom-seq identifies RNAs at chromatin marks

Ligang Fan, Wei Sun, Yitong Lyu, Furong Ju, Wenju Sun, Jie Chen, Haiqian Ma, Shifei Yang, Xiaomin Zhou, Nan Wu, Wenkai Yi, Erfei Chen, Rodrigo Villaseñor, Tuncay Baubec, Jian Yan*

Science Advances 2024 July

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