Professional Education


  • PhD, Utrecht University, Chromatin, Epigenetics, Transcription (2013)
  • Master of Science, Vrije Universiteit Amsterdam (2008)
  • Bachelor of Science, Vrije Universiteit Amsterdam (2006)

Stanford Advisors


Lab Affiliations


All Publications


  • Histone H4 Lysine 20 (H4K20) Methylation, Expanding the Signaling Potential of the Proteome One Methyl Moiety at a Time MOLECULAR & CELLULAR PROTEOMICS van Nuland, R., Gozani, O. 2016; 15 (3): 755-764

    Abstract

    Covalent post-translational modifications (PTMs) of proteins can regulate the structural and functional state of a protein in the absence of primary changes in the underlying sequence. Common PTMs include phosphorylation, acetylation, and methylation. Histone proteins are critical regulators of the genome and are subject to a highly abundant and diverse array of PTMs. To highlight the functional complexity added to the proteome by lysine methylation signaling, here we will focus on lysine methylation of histone proteins, an important modification in the regulation of chromatin and epigenetic processes. We review the signaling pathways and functions associated with a single residue, H4K20, as a model chromatin and clinically important mark that regulates biological processes ranging from the DNA damage response and DNA replication to gene expression and silencing.

    View details for DOI 10.1074/mcp.R115.054742

    View details for Web of Science ID 000371894700002

    View details for PubMedID 26598646

  • Multivalent Engagement of TFIID to Nucleosomes PLOS ONE van Nuland, R., Schram, A. W., van Schaik, F. M., Jansen, P. W., Vermeulen, M., Timmers, H. T. 2013; 8 (9)

    Abstract

    The process of eukaryotic transcription initiation involves the assembly of basal transcription factor complexes on the gene promoter. The recruitment of TFIID is an early and important step in this process. Gene promoters contain distinct DNA sequence elements and are marked by the presence of post-translationally modified nucleosomes. The contributions of these individual features for TFIID recruitment remain to be elucidated. Here, we use immobilized reconstituted promoter nucleosomes, conventional biochemistry and quantitative mass spectrometry to investigate the influence of distinct histone modifications and functional DNA-elements on the binding of TFIID. Our data reveal synergistic effects of H3K4me3, H3K14ac and a TATA box sequence on TFIID binding in vitro. Stoichiometry analyses of affinity purified human TFIID identified the presence of a stable dimeric core. Several peripheral TAFs, including those interacting with distinct promoter features, are substoichiometric yet present in substantial amounts. Finally, we find that the TAF3 subunit of TFIID binds to poised promoters in an H3K4me3-dependent manner. Moreover, the PHD-finger of TAF3 is important for rapid induction of target genes. Thus, fine-tuning of TFIID engagement on promoters is driven by synergistic contacts with both DNA-elements and histone modifications, eventually resulting in a high affinity interaction and activation of transcription.

    View details for DOI 10.1371/journal.pone.0073495

    View details for Web of Science ID 000326734500037

    View details for PubMedID 24039962

  • Nucleosomal DNA binding drives the recognition of H3K36-methylated nucleosomes by the PSIP1-PWWP domain EPIGENETICS & CHROMATIN van Nuland, R., van Schaik, F. M., Simonis, M., van Heesch, S., Cuppen, E., Boelens, R., Timmers, H. T., van Ingen, H. 2013; 6

    Abstract

    Recognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription. The structural basis of these interactions is usually studied using histone peptide models, neglecting the nucleosomal context. Here, we provide the structural and thermodynamic basis for the recognition of H3K36-methylated (H3K36me) nucleosomes by the PSIP1-PWWP domain, based on extensive mutational analysis, advanced nuclear magnetic resonance (NMR), and computational approaches.The PSIP1-PWWP domain binds H3K36me3 peptide and DNA with low affinity, through distinct, adjacent binding surfaces. PWWP binding to H3K36me nucleosomes is enhanced approximately 10,000-fold compared to a methylated peptide. Based on mutational analyses and NMR data, we derive a structure of the complex showing that the PWWP domain is bound to H3K36me nucleosomes through simultaneous interactions with both methylated histone tail and nucleosomal DNA.Concerted binding to the methylated histone tail and nucleosomal DNA underlies the high- affinity, specific recognition of H3K36me nucleosomes by the PSIP1-PWWP domain. We propose that this bipartite binding mechanism is a distinctive and general property in the recognition of histone modifications close to the nucleosome core.

    View details for DOI 10.1186/1756-8935-6-12

    View details for Web of Science ID 000319436800001

    View details for PubMedID 23656834

  • Quantitative Dissection and Stoichiometry Determination of the Human SET1/MLL Histone Methyltransferase Complexes MOLECULAR AND CELLULAR BIOLOGY van Nuland, R., Smits, A. H., Pallaki, P., Jansen, P. W., Vermeulen, M., Timmers, H. T. 2013; 33 (10): 2067-2077

    Abstract

    Methylation of lysine 4 on histone H3 (H3K4) at promoters is tightly linked to transcriptional regulation in human cells. At least six different COMPASS-like multisubunit (SET1/MLL) complexes that contain methyltransferase activity for H3K4 have been described, but a comprehensive and quantitative analysis of these SET1/MLL complexes is lacking. We applied label-free quantitative mass spectrometry to determine the subunit composition and stoichiometry of the human SET1/MLL complexes. We identified both known and novel, unique and shared interactors and determined their distribution and stoichiometry over the different SET1/MLL complexes. In addition to being a core COMPASS subunit, the Dpy30 protein is a genuine subunit of the NURF chromatin remodeling complex. Furthermore, we identified the Bod1 protein as a discriminator between the SET1B and SET1A complexes, and we show that the H3K36me-interactor Psip1 preferentially binds to the MLL2 complex. Finally, absolute protein quantification in crude lysates mirrors many of the observed SET1/MLL complex stoichiometries. Our findings provide a molecular framework for understanding the diversity and abundance of the different SET1/MLL complexes, which together establish the H3K4 methylation landscape in human cells.

    View details for DOI 10.1128/MCB.01742-12

    View details for Web of Science ID 000317959900016

    View details for PubMedID 23508102

  • A domino effect in drug action: from metabolic assault towards parasite differentiation MOLECULAR MICROBIOLOGY Haanstra, J. R., Kerkhoven, E. J., van Tuijl, A., Blits, M., Wurst, M., van Nuland, R., Albert, M., Michels, P. A., Bouwman, J., Clayton, C., Westerhoff, H. V., Bakker, B. M. 2011; 79 (1): 94-108

    Abstract

    Awareness is growing that drug target validation should involve systems analysis of cellular networks. There is less appreciation, though, that the composition of networks may change in response to drugs. If the response is homeostatic (e.g. through upregulation of the target protein), this may neutralize the inhibitory effect. In this scenario the effect on cell growth and survival would be less than anticipated based on affinity of the drug for its target. Glycolysis is the sole free-energy source for the deadly parasite Trypanosoma brucei and is therefore a possible target pathway for anti-trypanosomal drugs. Plasma-membrane glucose transport exerts high control over trypanosome glycolysis and hence the transporter is a promising drug target. Here we show that at high inhibitor concentrations, inhibition of trypanosome glucose transport causes cell death. Most interestingly, sublethal concentrations initiate a domino effect in which network adaptations enhance inhibition. This happens via (i) metabolic control exerted by the target protein, (ii) decreases in mRNAs encoding the target protein and other proteins in the same pathway, and (iii) partial differentiation of the cells leading to (low) expression of immunogenic insect-stage coat proteins. We discuss how these 'anti-homeostatic' responses together may facilitate killing of parasites at an acceptable drug dosage.

    View details for DOI 10.1111/j.1365-2958.2010.07435.x

    View details for Web of Science ID 000285762100009

    View details for PubMedID 21166896

  • Regulation of vitamin D receptor function in MEN1-related parathyroid adenomas MOLECULAR AND CELLULAR ENDOCRINOLOGY Dreijerink, K. M., Varier, R. A., van Nuland, R., Broekhuizen, R., Valk, G. D., van der Wal, J. E., Lips, C. J., Kummer, J. A., Timmers, H. T. 2009; 313 (1-2): 1-8

    Abstract

    Multiple endocrine neoplasia type 1 (MEN1) is a heriditary syndrome characterised by the occurrence of parathyroid, gastroenteropancreatic and pituitary tumours. The MEN1 gene product, menin, co-activates gene transcription by recruiting histone methyltransferases for lysine 4 of histone H3 (H3K4). We investigated whether in MEN1 tumours global changes in H3K4 trimethylation (H3K4me3) occur or whether alterations in gene expression can be observed. By immunohistochemistry we found that global levels of H3K4me3 are not affected in MEN1-related parathyroid adenomas. Menin can interact directly with the vitamin D receptor (VDR) and enhance the transcriptional activity of VDR. Messenger RNA levels of VDR target genes CYP24 and KLK6 were significantly lower in MEN1 parathyroid adenomas compared to normal tissue. Thus, aberrant gene expression in MEN1 tumours is not caused by lower global H3K4me3, but rather by specific effects on genes that are regulated by menin-interacting proteins, such as VDR.

    View details for DOI 10.1016/j.mce.2009.08.020

    View details for Web of Science ID 000271488700001

    View details for PubMedID 19729047