Publications

  1. Perino, M, van Mierlo, G, Loh, C, Wardle, SMT, Zijlmans, DW, Marks, H et al.. Two Functional Axes of Feedback-Enforced PRC2 Recruitment in Mouse Embryonic Stem Cells. Stem Cell Reports. 2020; :. doi: 10.1016/j.stemcr.2020.07.007. PubMed PMID:32763159 .
  2. Smits, JPH, Dirks, RAM, Qu, J, Oortveld, MAW, Brinkman, AB, Zeeuwen, PLJM et al.. Terminal keratinocyte differentiation in vitro is associated with a stable DNA methylome. Exp. Dermatol. 2020; :. doi: 10.1111/exd.14153. PubMed PMID:32681572 .
  3. Neagu, A, van Genderen, E, Escudero, I, Verwegen, L, Kurek, D, Lehmann, J et al.. In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states. Nat. Cell Biol. 2020;22 (5):534-545. doi: 10.1038/s41556-020-0508-x. PubMed PMID:32367046 .
  4. Bell, E, Curry, EW, Megchelenbrink, W, Jouneau, L, Brochard, V, Tomaz, RA et al.. Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency. Nat Commun. 2020;11 (1):1112. doi: 10.1038/s41467-020-14916-7. PubMed PMID:32111830 PubMed Central PMC7048827.
  5. Ter Huurne, M, Peng, T, Yi, G, van Mierlo, G, Marks, H, Stunnenberg, HG et al.. Critical Role for P53 in Regulating the Cell Cycle of Ground State Embryonic Stem Cells. Stem Cell Reports. 2020;14 (2):175-183. doi: 10.1016/j.stemcr.2020.01.001. PubMed PMID:32004494 PubMed Central PMC7013234.
  6. De Clerck, L, Taelman, J, Popovic, M, Willems, S, Van der Jeught, M, Heindryckx, B et al.. Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human. Sci Rep. 2019;9 (1):17240. doi: 10.1038/s41598-019-53681-6. PubMed PMID:31754138 PubMed Central PMC6872658.
  7. van Mierlo, G, Wester, RA, Marks, H. A Mass Spectrometry Survey of Chromatin-Associated Proteins in Pluripotency and Early Lineage Commitment. Proteomics. 2019;19 (14):e1900047. doi: 10.1002/pmic.201900047. PubMed PMID:31219242 .
  8. van Mierlo, G, Veenstra, GJC, Vermeulen, M, Marks, H. The Complexity of PRC2 Subcomplexes. Trends Cell Biol. 2019;29 (8):660-671. doi: 10.1016/j.tcb.2019.05.004. PubMed PMID:31178244 .
  9. Atlasi, Y, Megchelenbrink, W, Peng, T, Habibi, E, Joshi, O, Wang, SY et al.. Publisher Correction: Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. Nat. Cell Biol. 2019;21 (7):911-912. doi: 10.1038/s41556-019-0341-2. PubMed PMID:31097792 .
  10. Atlasi, Y, Megchelenbrink, W, Peng, T, Habibi, E, Joshi, O, Wang, SY et al.. Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. Nat. Cell Biol. 2019;21 (5):568-578. doi: 10.1038/s41556-019-0310-9. PubMed PMID:31036938 .
  11. Furlan, C, Dirks, RAM, Thomas, PC, Jones, RC, Wang, J, Lynch, M et al.. Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements. Nat Commun. 2019;10 (1):1525. doi: 10.1038/s41467-019-09533-y. PubMed PMID:30948724 PubMed Central PMC6449397.
  12. Dirks, RAM, van Mierlo, G, Kerstens, HHD, Bernardo, AS, Kobolák, J, Bock, I et al.. Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states. Epigenetics Chromatin. 2019;12 (1):14. doi: 10.1186/s13072-019-0259-8. PubMed PMID:30767785 PubMed Central PMC6376749.
  13. van Mierlo, G, Dirks, RAM, De Clerck, L, Brinkman, AB, Huth, M, Kloet, SL et al.. Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency. Cell Stem Cell. 2019;24 (1):123-137.e8. doi: 10.1016/j.stem.2018.10.017. PubMed PMID:30472157 .
  14. van Mierlo, G, Wester, RA, Marks, H. Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state. Stem Cell Res. 2018;33 :135-145. doi: 10.1016/j.scr.2018.09.017. PubMed PMID:30352361 .
  15. Bernardo, AS, Jouneau, A, Marks, H, Kensche, P, Kobolak, J, Freude, K et al.. Mammalian embryo comparison identifies novel pluripotency genes associated with the naïve or primed state. Biol Open. 2018;7 (8):. doi: 10.1242/bio.033282. PubMed PMID:30026265 PubMed Central PMC6124576.
  16. Perino, M, van Mierlo, G, Karemaker, ID, van Genesen, S, Vermeulen, M, Marks, H et al.. MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding. Nat. Genet. 2018;50 (7):1002-1010. doi: 10.1038/s41588-018-0134-8. PubMed PMID:29808031 .
  17. Fisher, CL, Marks, H, Cho, LT, Andrews, R, Wormald, S, Carroll, T et al.. An efficient method for generation of bi-allelic null mutant mouse embryonic stem cells and its application for investigating epigenetic modifiers. Nucleic Acids Res. 2017;45 (21):e174. doi: 10.1093/nar/gkx811. PubMed PMID:28981838 PubMed Central PMC5716182.
  18. Kalkan, T, Olova, N, Roode, M, Mulas, C, Lee, HJ, Nett, I et al.. Tracking the embryonic stem cell transition from ground state pluripotency. Development. 2017;144 (7):1221-1234. doi: 10.1242/dev.142711. PubMed PMID:28174249 PubMed Central PMC5399622.
  19. Dirks, RA, Stunnenberg, HG, Marks, H. Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics. 2016;8 :122. doi: 10.1186/s13148-016-0284-4. PubMed PMID:27895806 PubMed Central PMC5117701.
  20. Marks, H, Kerstens, HH, Barakat, TS, Splinter, E, Dirks, RA, van Mierlo, G et al.. Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq. Genome Biol. 2016;17 :22. doi: 10.1186/s13059-016-0885-4. PubMed PMID:26850229 PubMed Central PMC4743200.
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