2019

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors
D Barisic*, MB Stadler*, M Iurlaro*, D Schübeler
Nature, 2019

CG dinucleotides enhance promoter activity independent of DNA methylation
D Hartl, AR Krebs, RS Grand, T Baubec, L Isbel, C Wirbelauer, L Burger and D Schubeler
Genome Research 29, 554–563

2018

Non-mendelian Inheritance in Mammals Is Highly Constrained
L Isbel, D Schübeler
Cell 175 (5), 1179-1181

Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape
PA Ginno, L Burger, J Seebacher, V Iesmantavicius, D Schübeler
Nature Communications 9 (1), 4048

2017

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content
DF Colombo*, L Burger*, T Baubec, D Schübeler
PLoS Genetics 13 (12), e1007102

Evidence for Converging DNA Methylation Pathways in Placenta and Cancer
MC Lorincz, D Schübeler
Developmental Cell 43 (3), 257-258

Cis-regulatory landscapes of four cell types of the retina
D Hartl*, AR Krebs*, J Jüttner*, B Roska, D Schübeler
Nucleic Acids Research 45 (20), 11607-11621

Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters
AR Krebs, D Imanci, L Hoerner, D Gaidatzis, L Burger, D Schübeler
Molecular Cell 67 (3), 411-422. e4

Multidimensional pooled shRNA screens in human THP-1 cells identify candidate modulators of macrophage polarization
E Surdziel, I Clay, F Nigsch, A Thiemeyer, C Allard, G Hoffman, JS Reece-Hoyes, T Phadke, R Gambert, CG Keller, M-G Ludwig, B Baumgarten, M Frederiksen, D Schübeler, K Seuwen, T Bouwmeester, BD Fodor
PloS One 12 (8), e0183679

Impact of cytosine methylation on DNA binding specificities of human transcription factors
Y Yin, E Morgunova, A Jolma, E Kaasinen, B Sahu, S Khund-Sayeed, Pratyush K Das, T Kivioja, K Dave, F Zhong, KR Nitta, M Taipale, A Popov, PA Ginno, S Domcke, J Yan, D Schübeler, C Vinson, J Taipale
Science 356 (6337), eaaj2239

2016

The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery
HG Stunnenberg and The International Human Epigenome Consortium
Cell 167 (5), 1145-1149

Pioneering activity of the C-terminal domain of EBF1 shapes the chromatin landscape for B cell programming
S Boller, S Ramamoorthy, D Akbas, R Nechanitzky, L Burger, R Murr, D Schübeler, R Grosschedl
Immunity 44 (3), 527-541

2015

Competition between DNA methylation and transcription factors determines binding of NRF1
S Domcke*, AF Bardet*, PA Ginno, D Hartl, L Burger, D Schübeler
Nature 528 (7583), 575

Loss of Ezh2 promotes a midbrain-to-forebrain identity switch by direct gene derepression and Wnt-dependent regulation
M Zemke, K Draganova, A Klug, A Schöler, L Zurkirchen, MHP Gay, P Cheng, H Koseki, T Valenta, D Schübeler, K Basler, L Sommer
BMC biology 13 (1), 103

Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved β cell function
D Avrahami, C Li, J Zhang, J Schug, R Avrahami, S Rao, MB Stadler, L Burger, D Schübeler, B Glaser, KH Kaestner
Cell Metabolism 22 (4), 619-632

YAP1 exerts its transcriptional control via TEAD-mediated activation of enhancers
C Stein*, AF Bardet*, G Roma, S Bergling, I Clay, A Ruchti, C Agarinis, T Schmelzle, T Bouwmeester, D Schuebeler*, A Bauer*
PLoS Genetics 11 (8), e1005465

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation
T Baubec, DF Colombo, C Wirbelauer, J Schmidt, L Burger, AR Krebs, A Akalin, D Schübeler
Nature 520 (7546), 243

ESCI award lecture: regulation, function and biomarker potential of DNA methylation
D Schübeler
European journal of clinical investigation 45 (3), 288-293

Function and information content of DNA methylation
D Schübeler
Nature 517 (7534), 321

2014

Genomation: a toolkit to summarize, annotate and visualize genomic intervals
A Akalin*, V Franke, K Vlahoviček, CE Mason*, D Schübeler*
Bioinformatics 31 (7), 1127-1129

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease
R Gilsbach, S Preissl, BA Grüning, T Schnick, L Burger, V Benes, A Würch, U Bönisch, S Günther, R Backofen, BK Fleischmann, D Schübeler, L Hein
Nature Communications 5, 5288

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
AR Krebs, S Dessus-Babus, L Burger, D Schübeler
eLife 3, e04094

Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation
P Jermann, L Hoerner, L Burger, D Schübeler
Proceedings of the National Academy of Sciences 111 (33), E3415-E3421

Genomic patterns and context specific interpretation of DNA methylation
T Baubec, D Schübeler
Current opinion in genetics & development 25, 85-92

Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription
V Di Cerbo, F Mohn, DP Ryan, E Montellier, S Kacem, P Tropberger, E Kallis, M Holzner, L Hoerner, A Feldmann, FM Richter, AJ Bannister, G Mittler, J Michaelis, S Khochbin, R Feil, D Schuebeler, T Owen-Hughes, S Daujat, R Schneider
eLife 3, e01632

DNA methylation is required for the control of stem cell differentiation in the small intestine
KL Sheaffer, R Kim, R Aoki, EN Elliott, J Schug, L Burger, D Schübeler, KH Kaestner
Genes & Development 28 (6), 652-664

Ezh2 is required for neural crest-derived cartilage and bone formation
D Schwarz, S Varum, M Zemke, A Schöler, A Baggiolini, K Draganova, H Koseki, D Schübeler, L Sommer
Development 141 (4), 867-877

DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes
D Gaidatzis, L Burger, R Murr, A Lerch, S Dessus-Babus, D Schübeler, MB Stadler
PLoS Genetics 10 (2), e1004143

2013

Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions
A Feldmann, R Ivanek, R Murr, D Gaidatzis, L Burger, D Schübeler
PLoS Genetics 9 (12), e1003994

Gene regulation and priming by topoisomerase IIα in embryonic stem cells
S Thakurela, A Garding, J Jung, D Schübeler, L Burger, VK Tiwari
Nature Communications 4, ncomms3478

Twisting chromatin in stem cells
P Ginno, D Schübeler
The EMBO Journal 32 (17), 2304-2306

Identification of active regulatory regions from DNA methylation data
L Burger, D Gaidatzis, D Schübeler, MB Stadler
Nucleic Acids Research 41 (16), e155-e155

Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa
S Erkek, M Hisano, CY Liang, M Gill, R Murr, J Dieker, D Schübeler, J Van Der Vlag, MB Stadler, AHFM Peters
Nature Structural & Molecular Biology 20 (7), 8681842013

Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming
N Tiwari, VK Tiwari, L Waldmeier, PJ Balwierz, P Arnold, M Pachkov, N Meyer-Schaller, D Schübeler, E van Nimwegen, G Christofori
Cancer Cell 23 (6), 768-783

A systematic comparison of enzymatic activity and protein interaction analysis of the KDM3 histone demethylase subfamily
M Brauchle, Z Yao, R Arora, I Clay, B Inverardi, B Gerrits, J Voshol, A Bauer, D Schuebeler, A Bouwmeester, H Ruffner, S Thigale
PLoS One 8 (4), e60549

Methylation-dependent and-independent genomic targeting principles of the MBD protein family
T Baubec, R Ivánek, F Lienert, D Schübeler
Cell 153 (2), 480-492

Protein complex interactor analysis and differential activity of KDM3 subfamily members towards H3K9 methylation
M Brauchle, Z Yao, R Arora, S Thigale, I Clay, B Inverardi, J Fletcher, P Taslimi, MG Acker, B Gerrits, J Voshol, A Bauer, D Schübeler, T Bouwmeester, H Ruffner
PLoS One 8 (4), e60549

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting
P Arnold*, A Schöler*, M Pachkov, PJ Balwierz, H Jørgensen, MB Stadler, E van Nimwegen*, D Schübeler*
Genome Research 23 (1), 60-73

2012

Epigenetic islands in a genetic ocean
D Schübeler
Science 338 (6108), 756-757

Tracking the evolution of cancer methylomes
AR Krebs, D Schübeler
Nature Genetics 44 (11), 1173

Identification of Dlk1-Dio3 Imprinted Gene Cluster Noncoding RNAs as Novel Candidate Biomarkers for Liver Tumor Promotion
H Lempiäinen, P Couttet, F Bolognani, A Müller, V Dubost, R Luisier, A del Rio-Espinola, V Vitry, EB Unterberger, JP Thomson, F Treindl, U Metzger, C Wrzodek, F Hahne, T Zollinger, S Brasa, M Kalteis, M Marcellin, F Giudicelli, A Braeuning, L Morawiec, N Zamurovic, U Längle, N Scheer, D Schübeler, J Goodman, S-D Chibout, J Marlowe, D Theil, DJ Heard, O Grenet, A Zell, MF Templin, RR Meehan, RC Wolf, CR Elcombe, M Schwarz, P Moulin, R Terranova, JG Moggs
Toxicological Sciences 131 (2), 375-386

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome
JP Thomson, H Lempiäinen, JA Hackett, CE Nestor, A Müller, F Bolognani, EJ Oakeley, D Schübeler, R Terranova, D Reinhardt, JG Moggs, RR Meehan
Genome Biology 13 (10), R93

Target genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin state
VK Tiwari, L Burger, V Nikoletopoulou, R Deogracias, S Thakurela, C Wirbelauer, J Kaut, R Terranova, L Hoerner, C Mielke, F Boege, R Murr, AHFM Peters, Y-A Barde, D Schübeler
Proceedings of the National Academy of Sciences, 201119798

BLUEPRINT to decode the epigenetic signature written in blood
D Adams et al.
Nature Biotechnology 30 (3), 224

Chromatin measurements reveal contributions of synthesis and decay to steady‐state mRNA levels
SC Tippmann, R Ivanek, D Gaidatzis, A Schöler, L Hoerner, E Van Nimwegen, PF Stadler, MB Stadler, D Schübeler
Molecular Systems Biology 8 (1), 593

A chromatin-modifying function of JNK during stem cell differentiation
VK Tiwari, MB Stadler, C Wirbelauer, R Paro, D Schübeler, C Beisel
Nature Genetics 44 (1), 94

2011

DNA-binding factors shape the mouse methylome at distal regulatory regions
MB Stadler*, R Murr*, L Burger*, R Ivanek, F Lienert, A Schöler, E van Nimwegen, C Wirbelauer, EJ Oakeley, D Gaidatzis, VK Tiwari, D Schübeler
Nature 480, 490–495 (2011)

Identification of genetic elements that autonomously determine DNA methylation states
F Lienert, C Wirbelauer, I Som, A Dean, F Mohn, D Schübeler
Nature Genetics 43 (11), 1091

Determinants and dynamics of genome accessibility
O Bell, VK Tiwari, NH Thomä, D Schübeler
Nature Reviews Genetics 12 (8), 554

Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells
F Lienert, F Mohn, VK Tiwari, T Baubec, TC Roloff, D Gaidatzis, MB Stadler, D Schübeler
PLoS Genetics 7 (6), e1002090

Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice
H Lempiäinen, A Müller, S Brasa, SS Teo, TC Roloff, L Morawiec, N Zamurovic, A Vicart, E Funhoff, P Couttet, D Schübeler, O Grenet, J Marlowe, J Moggs, R Terranova
PLoS One 6 (3), e18216

2010

Targets and dynamics of promoter DNA methylation during early mouse development
J Borgel, S Guibert, Y Li, H Chiba, D Schübeler, H Sasaki, T Forné, M Weber
Nature Genetics 42 (12), 1093

Chromatin in multicolor
D Schübeler
Cell 143 (2), 183-184

Tackling the epigenome: challenges and opportunities for collaboration
JS Satterlee, D Schübeler, HH Ng
Nature Biotechnology 28 (10), 1039

Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing
O Bell, M Schwaiger, EJ Oakeley, F Lienert, C Beisel, MB Stadler, D Schübeler
Nature Structural & Molecular Biology 17 (7), 894

Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa
U Brykczynska, M Hisano, S Erkek, L Ramos, EJ Oakeley, TC Roloff, C Beisel, D Schübeler, MB Stadler, AHFM Peters
Nature Structural & Molecular Biology 17 (6), 679

Characterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAs
J Krol, V Busskamp, I Markiewicz, MB Stadler, S Ribi, J Richter, J Duebel, S Bicker, HJ Fehling, D Schübeler, TG Oertner, G Schratt, M Bibel, B Roska, W Filipowicz
Cell 141 (4), 618-631

Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome
M Schwaiger, H Kohler, EJ Oakeley, MB Stadler, D Schübeler
Genome Research 20, 771–780

2009

Epigenomics: methylation matters
D Schübeler
Nature 462 (7271), 296

Chromatin: sub out the replacement
O Bell, D Schübeler
Current Biology 19 (14), R545-R547

H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming
S Daujat, T Weiss, F Mohn, UC Lange, C Ziegler-Birling, U Zeissler, M Lappe, D Schübeler, M-E Torres-Padilla, R Schneider
Nature Structural & Molecular Biology 16 (7), 777

Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa
ZA Lewis, S Honda, TK Khlafallah, JK Jeffress, M Freitag, F Mohn, D Schübeler, EU Selker
Genome Research 19 (3), 427-437

Chromatin state marks cell-type-and gender-specific replication of the Drosophila genome
M Schwaiger, MB Stadler, O Bell, H Kohler, EJ Oakeley, D Schübeler
Genes & Development 23 (5), 589-601

Genetics and epigenetics: stability and plasticity during cellular differentiation
F Mohn, D Schübeler
Trends in Genetics 25 (3), 129-136

2008

PcG proteins, DNA methylation, and gene repression by chromatin looping
VK Tiwari, KM McGarvey, JDF Licchesi, JE Ohm, JG Herman, D Schübeler, SB Baylin
PLoS Biology 6 (12), e306

DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity
KB Dong, IA Maksakova, F Mohn, D Leung, R Appanah, S Lee, HW Yang, LL Lam, DL Mager, D Schübeler, M Tachibana, Y Shinkai, MC Lorincz
The EMBO Journal 27 (20), 2691-2701

Global reorganization of replication domains during embryonic stem cell differentiation
I Hiratani, T Ryba, M Itoh, T Yokochi, M Schwaiger, CW Chang, Y Lyou, TM Townes, D Schübeler, DM Gilbert
PLoS Biology 6 (10), e245

Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors
F Mohn, M Weber, M Rebhan, TC Roloff, J Richter, MB Stadler, M Bibel, D Schübeler
Molecular Cell 30 (6), 755-766

Transcription-coupled methylation of histone H3 at lysine 36 regulates dosage compensation by enhancing recruitment of the MSL complex in Drosophila melanogaster
O Bell, T Conrad, J Kind, C Wirbelauer, A Akhtar, D Schübeler
Molecular and Cellular Biology 28 (10), 3401-3409

2007

Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila
O Bell, C Wirbelauer, M Hild, AND Scharf, M Schwaiger, DM MacAlpine, F Zilbermann, F Van Leeuwen, SP Bell, A Imhof, D Garza, AHFM Peters, D Schübeler
The EMBO Journal 26 (24), 4974-4984

RNA polymerase II: just stopping by
MC Lorincz, D Schübeler
Cell 130 (1), 16-18

Genomic patterns of DNA methylation: targets and function of an epigenetic mark
M Weber, D Schübeler
Current opinion in cell biology 19 (3), 273-280

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
M Weber, I Hellmann, MB Stadler, L Ramos, S Pääbo, M Rebhan, D Schübeler
Nature Genetics 39 (4), 457

Enhancing genome annotation with chromatin
D Schübeler
Nature Genetics 39 (3), 284

2006

Dosage compensation in high resolution: global up-regulation through local recruitment
D Schübeler
Genes & Development 20 (7), 749-753

A question of timing: emerging links between transcription and replication
M Schwaiger, D Schübeler
Current opinion in genetics & development 16 (2), 177-183

Epigenomics: Mapping the methylome
IM Wilson, JJ Davies, M Weber, CJ Brown, CE Alvarez, C MacAulay, D Schübeler,WL Lam
Cell Cycle 5 (2), 155-158

2005

Defining epigenetic states through chromatin and RNA
D Schübeler, SCR Elgin
Nature Genetics 37 (9), 917

A new map for navigating the yeast epigenome
D Schübeler, BM Turner
Cell 122 (4), 489-492

Variant histone H3. 3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias
C Wirbelauer, O Bell, D Schübeler
Genes & Development 19 (15), 1761-1766

Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
M Weber, JJ Davies, D Wittig, EJ Oakeley, M Haase, WL Lam, D Schübeler
Nature Genetics 37 (8), 853

Foreword: From genetic diversity to chromosomal biology: an array of tasks beyond expression
D Schübeler
Chromosome Research 13 (3), 223-224

Methylation of histones: playing memory with DNA
AHFM Peters, D Schübeler
Current opinion in cell biology 17 (2), 230-238

2004

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states
EJ White, O Emanuelsson, D Scalzo, T Royce, S Kosak, EJ Oakeley, S Weissman, M Gerstein, M Groudine, M Snyder, D Schübeler
Proceedings of the National Academy of Sciences 101 (51), 17771-17776

The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote
D Schübeler, DM MacAlpine, D Scalzo, C Wirbelauer, C Kooperberg, F Van Leeuwen, DE Gottschling, LP O'Neill, BM Turner, J Delrow, SP Bell, M Groudine
Genes & Development 18 (11), 1263-1271

* = equal contribution