dr. H. (Hugo) van Ingen
h.vaningen@uu.nl
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Curriculum vitae

Scientific:

  • since 2017: assistant professor NMR Spectroscopy, University Utrecht
  • 2014-2017: tenure-track assistant professor Macromolecular Biochemistry, University Leiden
  • 2011-2014: post-doc NMR Spectroscopy, University Utrecht
  • 2008-2010: post-doc NMR groep Lewis Kay, University of Toronto, Canada
  • 2006-2008: post-doc with Rolf Boelens, NMR Spectroscopy, University Utrecht
  • 2001-2005: PhD candidate with Geerten Vuister & Cees Hilbers, Biophysical Chemistry, Radboud University Nijmegen

Teaching:

  • 2003-2005: curriculum development Chemistry, Molecular Life Sciences and Natural Sciences, Radboud University Nijmegen
  • 2001-2002: high-shool teacher Chemistry and Physics

Education:

  • 2004-2006: qualification University teaching (BKO), Radboud University Nijmegen
  • 2000: qualification high-school teacher Chemistry, Radboud University Nijmegen
  • 1994-1999: BSc & MSc Chemistry, Radboud University Nijmegen
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You can find a complete list via my ORCID athor-id: http://orcid.org/0000-0002-0808-3811

All publications
  2017 - Scholarly publications
Kitevski-Leblanc, Julianne, Fradet-Turcotte, Amélie, Kukic, Predrag, Wilson, Marcus D., Portella, Guillem, Yuwen, Tairan, Panier, Stephanie, Duan, Shili, Canny, Marella D., Van Ingen, Hugo, Arrowsmith, Cheryl H., Rubinstein, John L., Vendruscolo, Michele, Durocher, Daniel & Kay, Lewis E (13.04.2017). The rnf168 paralog rnf169 defines a new class of ubiquitylated histone reader involved in the response to dna damage. eLife, 6.
le Paige, Ulric B., Smits, Bauke, t Hart, Peter, Lefeber, Fons, Martin, Nathaniel I. & van Ingen, Hugo (01.05.2017). Weak coupling between magnetically inequivalent spins - The deceptively simple, complicated spectrum of a 13C-labeled trimethylated amine. Journal of Magnetic Resonance, 278, (pp. 96-103) (8 p.).
  2014 - Scholarly publications
Van Ingen, Hugo & Bonvin, Alexandre M J J (01.01.2014). Information-driven modeling of large macromolecular assemblies using NMR data. Journal of Magnetic Resonance, 241 (1), (pp. 103-114) (12 p.).
Khan, Fariha, Daniëls, Mark A., Folkers, Gert E., Boelens, Rolf, Saqlan Naqvi, S. M. & Van Ingen, Hugo (01.01.2014). Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein - Implications for its RNA chaperone function. Nucleic Acids Research, 42 (13), (pp. 8705-8718) (14 p.).
  2013 - Scholarly publications
Yu, B., van Ingen, H. & Freedberg, D.I. (2013). Constant time INEPT CT-HSQC (CTi-CT-HSQC) – A new NMR method to measure accurate one-bond J and RDCs with strong 1H–1H couplings in natural abundance. Journal of Magnetic Resonance, 228, (pp. 159-166) (8 p.).
Spruijt, C.G., Gnerlich, F., Smits, A.H., Pfaffeneder, T., Jansen, P.W.T.C., Bauer, C., Munzel, M., Wagner, M., Müller, M., Khan, F., Eberl, H.C., Mensinga, A., Brinkman, A.B., Lephikov, K., Muller, U., Walter, J., Boelens, R., van Ingen, H., Leonhardt, H. & Carell, T. (2013). Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell, 152, (pp. 1146-1159) (14 p.).
van Nuland, R., van Schaik, F.M.A., Simonis, M.J., Cuppen, E.P.J.G., Boelens, R., Timmers, H.T.M. & van Ingen, H. (2013). Nucleosomal DNA binding drives the recognition of H3K36-methylated nucleosomes by the PSIP1-PWWP domain. Epigenetics and Chromatin, 6, (pp. 1-12) (12 p.).
  2012 - Scholarly publications
Yu, B., van Ingen, H., Vivekanandan, S., Rademacher, C., Norris, S.E. & Freedberg, D.I. (2012). More accurate 1JCH coupling measurement in the presence of 3JHH strong coupling in in natural abundance. Journal of Magnetic Resonance, 215, (pp. 10-22) (13 p.).
  2011 - Scholarly publications
Kato, Hidenori, Van Ingen, Hugo, Zhou, Bing-Rui, Feng, Hanqiao, Bustin, Michael, Kay, Lewis E & Bai, Yawen (26.07.2011). Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR. Proceedings of the National Academy of Sciences of the United States of America, 108 (30), (pp. 12283-12288) (6 p.).
  2010 - Scholarly publications
Brondijk, T.H.C., de Ruiter, T., Ballering, J., Wienk, H., Lebbink, R.J., van Ingen, H., Boelens, R., Farndale, R.W., Meyaard, L. & Huizinga, E.G. (2010). Crystal structure and collagen-binding site of immune inhibitory receptor LAIR-1: unexpected implications for collagen binding by platelet receptor GPVI. Blood, 115 (7), (pp. 1364-1373) (10 p.).
  2009 - Scholarly publications
van Ingen, Hugo, Korzhnev, Dmitry M & Kay, Lewis E (2009). An analysis of the effects of 1HN-(1)HN dipolar couplings on the measurement of amide bond vector orientations in invisible protein states by relaxation dispersion NMR. Journal of Physical Chemistry B, 113 (29), (pp. 9968-9977) (10 p.).
van Ingen, H., van Schaik, F.M.A., Wienk, H., Rehmann, H., Kruijtzer, J.A.W., Liskamp, R.M.J., Timmers, H.T.M. & Boelens, R. (2009). Recognition of trimethylated K4 of histone H3 by the TFIID subunit TAF3. Journal of Biomolecular Structure and Dynamics, 26, (pp. 909) (1 p.).
  2008 - Scholarly publications
van Ingen, H., van Schaik, F.M.A., Wienk, H., Ballering, J., Rehmann, H., Dechesne, A.C., Kruijzer, J.A.W., Liskamp, R.M.J., Timmers, H.T.M. & Boelens, R. (2008). Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3. Structure with Folding & design, 16 (8), (pp. 1245-1256) (12 p.).
Codutti, L., van Ingen, H., Vascotto, C., Fogolari, F., Corazza, A., Tell, G., Quadrifoglio, F., Viglino, P., Boelens, R. & Esposito, G. (28.11.2008). The solution structure of DNA-free Pax-8 paired box domain accounts for redox regulation of transcriptional activity in the Pax protein family. Journal of Biological Chemistry, 283 (48), (pp. 33321-33328) (8 p.).
  2006 - Scholarly publications
Van Ingen, Hugo, Vuister, Geerten W., Wijmenga, Sybren & Tessari, Marco (29.03.2006). CEESY: Characterizing the conformation of unobservable protein states. Journal of the American Chemical Society, 128 (12), (pp. 3856-3857) (2 p.).
van Ingen, Hugo, Baltussen, Maria A.H., Aelen, Jan & Vuister, Geerten W. (28.04.2006). Role of Structural and Dynamical Plasticity in Sin3: The Free PAH2 Domain is a Folded Module in mSin3B. Journal of Molecular Biology, 358 (2), (pp. 485-497) (13 p.).
  2004 - Scholarly publications
Van Ingen, Hugo, Lasonder, Edwin, Jansen, Jacobus F. A., Kaan, Anita M., Spronk, Christian A.E.M., Stunnenberg, Henk G & Vuister, Geerten W. (13.01.2004). Extension of the Binding Motif of the Sin3 Interacting Domain of the Mad Family Proteins. Biochemistry, 43 (1), (pp. 46-54) (9 p.).
  2003 - Scholarly publications
Wingens, Miriam, Walma, Tine, Van Ingen, Hugo, Stortelers, Catelijne, Van Leeuwen, Jeroen E. M., Van Zoelen, Everardus J. J. & Vuister, Geerten W. (03.10.2003). Structural analysis of an epidermal growth factor/transforming growth factor-α chimera with unique ErbB binding specificity. Journal of Biological Chemistry, 278 (40), (pp. 39114-39123) (10 p.).
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Molecular basis of chromatin function

Chromatin stores and regulates access to our DNA. My group studies the processes operating on the smallest units of chromatin, called nucleosomes. Using a combination of state-of-the-art NMR , biochemical and computational methods, the molecular basis of chromatin function we aim to decipher at atomic detail.

Illuminating the nucleosome using methyl group based NMR

 The repeating unit of chromatin, the nucleosome, is a 200,000 Da supramolecular assembly of roughly one part DNA and one part protein. The massive size of the nucleosome calls for state-of-the-art NMR techniques that are tailored for such high-molecular weight systems. These techniques use the ultra-sensitive observation of methyl-groups in the proteins to produce beautiful high-quality spectra. This in turn allows us to use these methyl groups as probes to monitor the structure, dynamics and interactions of the nucleosome.

Structural basis of epigenetic recognition

The post-translational modification of histone proteins is a key mechanism in epigenetics. The majority of these chemical marks on chromatin serve as binding platforms for so-called reader proteins that in turn coordinate the functional state of chromatin. These protein-nucleosome interactions have in recent years become targets for the development of so-called ‘epigenetic drugs’.

The structural basis of reader-nucleosome interactions is an important focus of our research. Using tricks from chemical biology, we produce of nucleosomes that are decorated with specific epigenetic modifications. These tailor-made nucleosome can then be interrogated to reveal the molecular mechanism of epigenetic read-out.

Using this approach, we uncovered an unexpected role for the nucleosomal DNA in driving the recognition of an epigenetic mark. We determined the complex structure between a reader protein and a complete nucleosomes carrying an epigenetic mark at lysine 36 in histone H3. Importantly, this structure showed how the binding affinity of the reader protein for the trimethylated lysine is strongly enhanced by additional binding to the nucleosomal DNA, underscoring the potential of our studies to discover new concepts in chromatin biology.

Other interests

Integrative modeling of biomolecular assemblies. For many interesting systems, including nucleosome complexes, only sparse or low-resolution data may be available.  Using integrative computational tools we can combine the data to generate meaningful atomic models of these systems.

Protein dynamics. Motions in proteins can be crucial for their function. Because of its sensitivity to motions on a very wide range of time scales, NMR is very well suited to not only study structure-function relationships, but also the role of dynamics herein.

NMR theory and methodology.As the saying goes, in theory there is no difference between theory and practice. In practice, this is only true for NMR. Well, at least practically true. NMR is essentially an applied form of quantum mechanics, allowing one to accurately design and simulate experiments.

Completed projects

Project:
ManiFold 01.09.2012 to 31.08.2016
General project description

ManiFold is an Innovative Doctoral Programme organised by members of the Bijvoet Center for Biomolecular Research and its Graduate Research School, at Utrecht University in the Netherlands. The European Union selected the most innovative doctoral programmes in Europe for funding in the prestigious Marie-Curie Initial Training Networks scheme. ManiFold was the only Innovative Doctoral Programme in the Life Sciences funded in 2012.

 
Role Researcher Funding
EU grant
Project members UU
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Additional functions and activities

secretary of the Dutch Society for the Advancement of Biochemistry and Molecular Biology (NVBMB)

see: www.nvbmb.kncv.nl

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Full name
dr. H. van Ingen Contact details
Postal address
Padualaan 8
3584 CH    UTRECHT
The Netherlands
Availability
Mo Tue Wed Thu Fr
Morning
Afternoon

Visiting address: 
Nicolaas Bloembergengebouw, room 1.04
Padualaan 8, 3584 CH Utrecht
Accessible via Kruyt Building -> first floor -> bridge to Sjoerd Groenman Building
See
https://www.uu.nl/en/research/nmr/contact/route

Postal address:
Universiteit Utrecht, NMR
Padualaan 8, 3584 CH Utrecht


Phone
 (direct)
: +31 30 253 9934

Phone (secr): +31 30 253 2652

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Last updated 23.11.2017