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Items: 1 to 50 of 104

1.

DNA damage detection in nucleosomes involves DNA register shifting.

Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schübeler D, Iwai S, Sugasawa K, Kurumizaka H, Thomä NH.

Nature. 2019 May 29. doi: 10.1038/s41586-019-1259-3. [Epub ahead of print]

PMID:
31142837
2.

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors.

Barisic D, Stadler MB, Iurlaro M, Schübeler D.

Nature. 2019 May;569(7754):136-140. doi: 10.1038/s41586-019-1115-5. Epub 2019 Apr 17.

PMID:
30996347
3.

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 Res. 2019 Apr;29(4):554-563. doi: 10.1101/gr.241653.118. Epub 2019 Feb 1.

4.

Non-mendelian Inheritance in Mammals Is Highly Constrained.

Isbel L, Schübeler D.

Cell. 2018 Nov 15;175(5):1179-1181. doi: 10.1016/j.cell.2018.10.046.

PMID:
30445037
5.

Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape.

Ginno PA, Burger L, Seebacher J, Iesmantavicius V, Schübeler D.

Nat Commun. 2018 Oct 2;9(1):4048. doi: 10.1038/s41467-018-06007-5.

6.

Author Correction: H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming.

Daujat S, Weiss T, Mohn F, Lange UC, Ziegler-Birling C, Zeissler U, Lappe M, Schübeler D, Torres-Padilla ME, Schneider R.

Nat Struct Mol Biol. 2018 Aug;25(8):743. doi: 10.1038/s41594-018-0090-0.

PMID:
29995840
7.

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

Colombo DF, Burger L, Baubec T, Schübeler D.

PLoS Genet. 2017 Dec 21;13(12):e1007102. doi: 10.1371/journal.pgen.1007102. eCollection 2017 Dec.

8.

Evidence for Converging DNA Methylation Pathways in Placenta and Cancer.

Lorincz MC, Schübeler D.

Dev Cell. 2017 Nov 6;43(3):257-258. doi: 10.1016/j.devcel.2017.10.009. Review.

9.

Cis-regulatory landscapes of four cell types of the retina.

Hartl D, Krebs AR, Jüttner J, Roska B, Schübeler D.

Nucleic Acids Res. 2017 Nov 16;45(20):11607-11621. doi: 10.1093/nar/gkx923.

10.

Multidimensional pooled shRNA screens in human THP-1 cells identify candidate modulators of macrophage polarization.

Surdziel E, Clay I, Nigsch F, Thiemeyer A, Allard C, Hoffman G, Reece-Hoyes JS, Phadke T, Gambert R, Keller CG, Ludwig MG, Baumgarten B, Frederiksen M, Schübeler D, Seuwen K, Bouwmeester T, Fodor BD.

PLoS One. 2017 Aug 24;12(8):e0183679. doi: 10.1371/journal.pone.0183679. eCollection 2017.

11.

Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters.

Krebs AR, Imanci D, Hoerner L, Gaidatzis D, Burger L, Schübeler D.

Mol Cell. 2017 Aug 3;67(3):411-422.e4. doi: 10.1016/j.molcel.2017.06.027. Epub 2017 Jul 20.

12.

Impact of cytosine methylation on DNA binding specificities of human transcription factors.

Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J.

Science. 2017 May 5;356(6337). pii: eaaj2239. doi: 10.1126/science.aaj2239.

PMID:
28473536
13.

Pioneering Activity of the C-Terminal Domain of EBF1 Shapes the Chromatin Landscape for B Cell Programming.

Boller S, Ramamoorthy S, Akbas D, Nechanitzky R, Burger L, Murr R, Schübeler D, Grosschedl R.

Immunity. 2016 Mar 15;44(3):527-541. doi: 10.1016/j.immuni.2016.02.021.

14.

Competition between DNA methylation and transcription factors determines binding of NRF1.

Domcke S, Bardet AF, Adrian Ginno P, Hartl D, Burger L, Schübeler D.

Nature. 2015 Dec 24;528(7583):575-9. doi: 10.1038/nature16462. Epub 2015 Dec 16.

PMID:
26675734
15.

Loss of Ezh2 promotes a midbrain-to-forebrain identity switch by direct gene derepression and Wnt-dependent regulation.

Zemke M, Draganova K, Klug A, Schöler A, Zurkirchen L, Gay MH, Cheng P, Koseki H, Valenta T, Schübeler D, Basler K, Sommer L.

BMC Biol. 2015 Nov 30;13:103. doi: 10.1186/s12915-015-0210-9.

16.

Aging-Dependent Demethylation of Regulatory Elements Correlates with Chromatin State and Improved β Cell Function.

Avrahami D, Li C, Zhang J, Schug J, Avrahami R, Rao S, Stadler MB, Burger L, Schübeler D, Glaser B, Kaestner KH.

Cell Metab. 2015 Oct 6;22(4):619-32. doi: 10.1016/j.cmet.2015.07.025. Epub 2015 Aug 27.

17.

YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers.

Stein C, Bardet AF, Roma G, Bergling S, Clay I, Ruchti A, Agarinis C, Schmelzle T, Bouwmeester T, Schübeler D, Bauer A.

PLoS Genet. 2015 Aug 21;11(8):e1005465. doi: 10.1371/journal.pgen.1005465. eCollection 2015 Aug.

18.

ESCI award lecture: regulation, function and biomarker potential of DNA methylation.

Schübeler D.

Eur J Clin Invest. 2015 Mar;45(3):288-93. doi: 10.1111/eci.12403. Epub 2015 Feb 14. Review.

PMID:
25608229
19.

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 Apr 9;520(7546):243-7. doi: 10.1038/nature14176. Epub 2015 Jan 21.

PMID:
25607372
20.

Function and information content of DNA methylation.

Schübeler D.

Nature. 2015 Jan 15;517(7534):321-6. doi: 10.1038/nature14192. Review.

PMID:
25592537
21.

Genomation: a toolkit to summarize, annotate and visualize genomic intervals.

Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D.

Bioinformatics. 2015 Apr 1;31(7):1127-9. doi: 10.1093/bioinformatics/btu775. Epub 2014 Nov 21.

PMID:
25417204
22.

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease.

Gilsbach R, Preissl S, Grüning BA, Schnick T, Burger L, Benes V, Würch A, Bönisch U, Günther S, Backofen R, Fleischmann BK, Schübeler D, Hein L.

Nat Commun. 2014 Oct 22;5:5288. doi: 10.1038/ncomms6288.

23.

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions.

Krebs AR, Dessus-Babus S, Burger L, Schübeler D.

Elife. 2014 Sep 26;3:e04094. doi: 10.7554/eLife.04094.

24.

Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation.

Jermann P, Hoerner L, Burger L, Schübeler D.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3415-21. doi: 10.1073/pnas.1400672111. Epub 2014 Aug 4.

25.

DNA methylation is required for the control of stem cell differentiation in the small intestine.

Sheaffer KL, Kim R, Aoki R, Elliott EN, Schug J, Burger L, Schübeler D, Kaestner KH.

Genes Dev. 2014 Mar 15;28(6):652-64. doi: 10.1101/gad.230318.113.

26.

Genomic patterns and context specific interpretation of DNA methylation.

Baubec T, Schübeler D.

Curr Opin Genet Dev. 2014 Apr;25:85-92. doi: 10.1016/j.gde.2013.11.015. Epub 2014 Mar 7. Review.

PMID:
24614011
27.

DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes.

Gaidatzis D, Burger L, Murr R, Lerch A, Dessus-Babus S, Schübeler D, Stadler MB.

PLoS Genet. 2014 Feb 13;10(2):e1004143. doi: 10.1371/journal.pgen.1004143. eCollection 2014 Feb.

28.

Ezh2 is required for neural crest-derived cartilage and bone formation.

Schwarz D, Varum S, Zemke M, Schöler A, Baggiolini A, Draganova K, Koseki H, Schübeler D, Sommer L.

Development. 2014 Feb;141(4):867-77. doi: 10.1242/dev.094342.

29.

Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions.

Feldmann A, Ivanek R, Murr R, Gaidatzis D, Burger L, Schübeler D.

PLoS Genet. 2013;9(12):e1003994. doi: 10.1371/journal.pgen.1003994. Epub 2013 Dec 19.

30.

Gene regulation and priming by topoisomerase IIα in embryonic stem cells.

Thakurela S, Garding A, Jung J, Schübeler D, Burger L, Tiwari VK.

Nat Commun. 2013;4:2478. doi: 10.1038/ncomms3478.

PMID:
24072229
31.

Twisting chromatin in stem cells.

Ginno P, Schübeler D.

EMBO J. 2013 Aug 28;32(17):2304-6. doi: 10.1038/emboj.2013.179. Epub 2013 Aug 6. No abstract available.

32.

Identification of active regulatory regions from DNA methylation data.

Burger L, Gaidatzis D, Schübeler D, Stadler MB.

Nucleic Acids Res. 2013 Sep;41(16):e155. doi: 10.1093/nar/gkt599. Epub 2013 Jul 4.

33.

Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa.

Erkek S, Hisano M, Liang CY, Gill M, Murr R, Dieker J, Schübeler D, van der Vlag J, Stadler MB, Peters AH.

Nat Struct Mol Biol. 2013 Jul;20(7):868-75. doi: 10.1038/nsmb.2599. Epub 2013 Jun 16. Erratum in: Nat Struct Mol Biol. 2013 Oct;20(10):1236.

PMID:
23770822
34.

Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming.

Tiwari N, Tiwari VK, Waldmeier L, Balwierz PJ, Arnold P, Pachkov M, Meyer-Schaller N, Schübeler D, van Nimwegen E, Christofori G.

Cancer Cell. 2013 Jun 10;23(6):768-83. doi: 10.1016/j.ccr.2013.04.020.

35.

Protein complex interactor analysis and differential activity of KDM3 subfamily members towards H3K9 methylation.

Brauchle M, Yao Z, Arora R, Thigale S, Clay I, Inverardi B, Fletcher J, Taslimi P, Acker MG, Gerrits B, Voshol J, Bauer A, Schübeler D, Bouwmeester T, Ruffner H.

PLoS One. 2013 Apr 11;8(4):e60549. doi: 10.1371/journal.pone.0060549. Print 2013.

36.

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

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

Cell. 2013 Apr 11;153(2):480-92. doi: 10.1016/j.cell.2013.03.011.

37.

Molecular biology. Epigenetic islands in a genetic ocean.

Schübeler D.

Science. 2012 Nov 9;338(6108):756-7. doi: 10.1126/science.1227243. No abstract available.

PMID:
23139324
38.

Tracking the evolution of cancer methylomes.

Krebs AR, Schübeler D.

Nat Genet. 2012 Nov;44(11):1173-4. doi: 10.1038/ng.2451.

PMID:
23104061
39.

Identification of Dlk1-Dio3 imprinted gene cluster noncoding RNAs as novel candidate biomarkers for liver tumor promotion.

Lempiäinen H, Couttet P, Bolognani F, Müller A, Dubost V, Luisier R, Del Rio Espinola A, Vitry V, Unterberger EB, Thomson JP, Treindl F, Metzger U, Wrzodek C, Hahne F, Zollinger T, Brasa S, Kalteis M, Marcellin M, Giudicelli F, Braeuning A, Morawiec L, Zamurovic N, Längle U, Scheer N, Schübeler D, Goodman J, Chibout SD, Marlowe J, Theil D, Heard DJ, Grenet O, Zell A, Templin MF, Meehan RR, Wolf RC, Elcombe CR, Schwarz M, Moulin P, Terranova R, Moggs JG.

Toxicol Sci. 2013 Feb;131(2):375-86. doi: 10.1093/toxsci/kfs303. Epub 2012 Oct 22.

PMID:
23091169
40.

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome.

Thomson JP, Lempiäinen H, Hackett JA, Nestor CE, Müller A, Bolognani F, Oakeley EJ, Schübeler D, Terranova R, Reinhardt D, Moggs JG, Meehan RR.

Genome Biol. 2012 Oct 3;13(10):R93. doi: 10.1186/gb-2012-13-10-r93.

41.

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting.

Arnold P, Schöler A, Pachkov M, Balwierz PJ, Jørgensen H, Stadler MB, van Nimwegen E, Schübeler D.

Genome Res. 2013 Jan;23(1):60-73. doi: 10.1101/gr.142661.112. Epub 2012 Sep 10.

42.

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels.

Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D.

Mol Syst Biol. 2012 Jul 17;8:593. doi: 10.1038/msb.2012.23.

43.

Target genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin state.

Tiwari VK, Burger L, Nikoletopoulou V, Deogracias R, Thakurela S, Wirbelauer C, Kaut J, Terranova R, Hoerner L, Mielke C, Boege F, Murr R, Peters AH, Barde YA, Schübeler D.

Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E934-43. doi: 10.1073/pnas.1119798109. Epub 2012 Apr 2.

44.

BLUEPRINT to decode the epigenetic signature written in blood.

Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, Lernmark Å, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S.

Nat Biotechnol. 2012 Mar 7;30(3):224-6. doi: 10.1038/nbt.2153. No abstract available.

PMID:
22398613
45.

A chromatin-modifying function of JNK during stem cell differentiation.

Tiwari VK, Stadler MB, Wirbelauer C, Paro R, Schübeler D, Beisel C.

Nat Genet. 2011 Dec 18;44(1):94-100. doi: 10.1038/ng.1036.

PMID:
22179133
46.

DNA-binding factors shape the mouse methylome at distal regulatory regions.

Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D.

Nature. 2011 Dec 14;480(7378):490-5. doi: 10.1038/nature10716. Erratum in: Nature. 2012 Apr 26;484(7395):550. van Nimwegen, Erik [added].

PMID:
22170606
47.

Identification of genetic elements that autonomously determine DNA methylation states.

Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schübeler D.

Nat Genet. 2011 Oct 2;43(11):1091-7. doi: 10.1038/ng.946.

PMID:
21964573
48.

Determinants and dynamics of genome accessibility.

Bell O, Tiwari VK, Thomä NH, Schübeler D.

Nat Rev Genet. 2011 Jul 12;12(8):554-64. doi: 10.1038/nrg3017. Review.

PMID:
21747402
49.

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 Genet. 2011 Jun;7(6):e1002090. doi: 10.1371/journal.pgen.1002090. Epub 2011 Jun 2.

50.

Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice.

Lempiäinen H, Müller A, Brasa S, Teo SS, Roloff TC, Morawiec L, Zamurovic N, Vicart A, Funhoff E, Couttet P, Schübeler D, Grenet O, Marlowe J, Moggs J, Terranova R.

PLoS One. 2011 Mar 24;6(3):e18216. doi: 10.1371/journal.pone.0018216.

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