Van Leeuwen group – Epigenetics

Switching genes on or off and keeping them in that state involves packaging of the genome by wrapping it around histone proteins. Histones carry different chemical modifications that affect the packaging of DNA by epigenetic mechanisms. The Van Leeuwen lab, located at the Netherlands Cancer Institute, studies mechanisms and principles of epigenetic regulation using innovative proteomic, genetic, and (epi)genomics approaches.

Contact: F. van Leeuwen (f.vanleeuwen@amsterdamumc.nl; fred.v.leeuwen@nki.nl), LinkedIn

Research overview

The Van Leeuwen lab is affiliated with the Department of Medical Biology and located at the Netherlands Cancer Institute (NKI) at the Division of Gene Regulation.

Switching genes on or off and keeping them in that state involves packaging of the genome by wrapping it around histone proteins. Histones carry different chemical modifications that affect the packaging of DNA by epigenetic mechanisms. The Van Leeuwen lab studies mechanisms and principles of epigenetic regulation using innovative proteomic, genetic, and (epi)genomics approaches.

The general strategy of the Van leeuwen lab is to develop new tools and technologies, most recently two DNA-barcoding approaches to discover epigenetic regulators and to decode proteomes of specific genomic loci. These innovations enable us to explore new areas of chromatin biology and to dissect specific chromatin processes in high molecular detail. We take advantage of yeast as a powerful model system. In parallel we are developing tools in mice and cultured human cells using CRISPR-Cas9 to translate our findings to mammals.

Function and regulation of histone methylation
Errors in chemical modifications of histones can lead to changes in gene expression and cancer. We previously discovered the histone methyltransferase Dot1, which methylates lysine 79 of histone H3 (H3K79; Fig. 1). This modification influences gene regulation and oncogenic transformation in mammals. A major goal of our research is to understand the regulation of H3K79 methylation and its function in gene control. We recently discovered a conserved regulatory mechanism of Dot1 in yeast and DOT1L in mouse T cells with relevance for lymphomagenesis (Fig. 2). We are currently studying DOT1L in lymphoma and in epigenetic control of normal T- and B-lymphocyte fate and differentiation.

Decoding chromatin proteomes by DNA sequencing
Gene regulation involves interactions of specific genomic loci with many different proteins. How these interactions are orchestrated at any given location is largely unknown because systematically measuring protein-DNA interactions at a specific locus in the genome is challenging. To address this problem, we developed DNA barcode-based Epigenetics technologies in yeast. By Recombination-Induced Tag exchange (RITE) we have been able to track turnover and dynamics of histones (Fig. 3). Epi-ID, which is aimed at identifying regulators of known chromatin marks or chromatin-binding proteins, recently led to the discovery that H3K79 methylation in yeast and mice is regulated by a histone deacetylase (Fig. 4). Epi-Decoder, a method orthogonal to proteomics, enables decoding of local chromatin proteomes. Using this method we uncovered hundreds of chromatin-interacting proteins at actively transcribed barcoded loci (Fig. 5).

Together, the aim of our studies is to provide a deep molecular understanding of the dynamics and inheritance of protein-based epigenetic information in dividing cells and the impact of chromatin-based information on gene regulation in normal development and disease.

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

People

Fred Van Leeuwen PhD Group leader
Thom Molenaar MSc PhD student
Eliza Mari Maliepaard MSc PhD student
Muddassir Malik MSc PhD student
Marlize van Breugel MSc PhD student
Tibor Van Welsem Technical staff
Maxime Kempers Master student

Publications

All publications of the van Leeuwen lab can also be found here:
Fred van Leeuwen at the NKI
Fred van Leeuwen on Google Scholar
Fred van Leeuwen on Publons

  1. van Kruijsbergen I, Mulder MPC, Uckelmann M, van Welsem T, de Widt J, Spanjaard A, Jacobs H, El Oualid F, Ovaa H, and Van Leeuwen F (2020). Strategy for development of site-specific ubiquitin antibodies. Frontiers in Chemistry 8: 111.
  2. Ahrends T, Busselaar J, Severson TM, Babala N, de Vries E, Bovens A, Wessels L, van Leeuwen F, and Borst J (2019). CD4(+) T cell help creates memory CD8(+) T cells with innate and help-independent recall capacities. Nat Commun 10: 5531.
  3. Poramba-Liyanage DW, Korthout T, and Van Leeuwen F (2019). Epi-ID: systematic and direct screening for chromatin regulators in yeast by Barcode-ChIP-Seq. Methods Mol Biol 2049: 87-103.
  4. Salgado C, Kwesi-Maliepaard EM, Jochemsen AG, Visser M, Harland M, van Leeuwen F, van Doorn R, and Gruis N (2019). A novel germline variant in the DOT1L gene co-segregating in a Dutch family with a history of melanoma. Melanoma Res 29: 582-589.
  5. Vlaming H, McLean C, Korthout T, Alemdehy MF, Hendriks S, Lancini C, Palit S, Klarenbeek S, Kwesi-Maliepaard EM, Molenaar TM, Hoekman L, Schmidlin TT, Altelaar M, van Welsem T, Dannenberg J-H, Jacobs H, and van Leeuwen F (2019). Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L-dose dependency in HDAC1-deficient thymic lymphoma. EMBO J 38: e101564.
  6. Huseinovic A, van Dijk M, Vermeulen NP, Van Leeuwen F, Kooter JM, and Vos JC (2018). Drug toxicity profiling of a Saccharomyces cerevisiae deubiquitinase deletion panel shows that acetaminophen mimics tyrosine. Toxicology in Vitro 47: 259-268.
  7. Korthout T, Poramba-Liyanage DW, van Kruijsbergen I, Verzijlbergen KF, van Gemert FPA, van Welsem T, and van Leeuwen F (2018). Decoding the chromatin proteome of a single genomic locus by DNA sequencing. PLoS Biol 16: e2005542.
  8. van Welsem T, Korthout T, Ekkebus R, Morais D, Molenaar TM, van Harten K, Poramba-Liyanage DW, Sun SM, Lenstra TL, Srivas R, Ideker T, Holstege FCP, van Attikum H, El Oualid F, Ovaa H, Stulemeijer IJE, Vlaming H, and van Leeuwen F (2018). Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism. Nucl Acids Res 46: 11251-11261.
  9. De Vos D, Vlaming H, Bakker BM, and van Leeuwen F (2017). Chapter 6 – Modeling distributive histone modification by Dot1 methyltransferases: from mechanism to biological insights. In Epigenetics and Systems Biology, L. Ringrose, ed. (Elsevier S&T Books), pp. 117-141.
  10. Huseinovic A, van Leeuwen JS, van Welsem T, Stulemeijer IJ, van Leeuwen F, vermeulen NP, Kooter JM, and Vos JC (2017). The effect of acetaminophen on ubiquitin homeostasis in Saccharomyces cerevisiae PLoS One 12: e0173573.
  11. Vlaming H, Molenaar TM, van Welsem T, Poramba-Liyanage DW, Smith DE, Velds A, Hoekman L, Korthout T, Hendriks S, Altelaar AM, and van Leeuwen F (2016). Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1. eLife 5: 10.7554/eLife.18919.
  12. Vlaming H, and van Leeuwen F (2016). The upstreams and downstreams of H3K79 methylation by DOT1L. Chromosoma 125: 593-605.
  13. Stulemeijer IJE, De Vos D, van Harten K, Joshi OK, Blomberg O, van Welsem T, Terweij M, Vlaming H, de Graaf EL, Altelaar AFM, Bakker BM, and van Leeuwen F (2015). Dot1 histone methyltransferases share a distributive mechanism but have highly diverged catalytic properties. Sci Rep 5: 9824.
  14. van Deventer S, Menendez-Benito V, van Leeuwen F, and Neefjes J (2015). N-terminal acetylation and replicative age affect proteasome localization and cell fitness during aging. J Cell Sci 128: 109-117.
  15. Zimberlin CD, Lancini C, Sno R, Rosekrans SL, McLean CM, Vlaming H, van den Brink GR, Bots M, Medema JP, and Dannenberg J-H (2015). HDAC1 and HDAC2 collectively regulate intestinal stem cell homeostasis. FASEB J 29: 2070-2080.
  16. Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guenole A, van Attikum H, Srivas R, Ideker T, Shimada K, and Gasser R (2014). Yeast PP4 interacts with ATR homologue Ddc2-Mec1 and regulates checkpoint signaling. Mol Cell 57: 273-289.
  17. McLean CM, Karemaker ID, and van Leeuwen F (2014). The emerging roles of DOT1L in leukemia and normal development. Leukemia 28: 2131-2138.
  18. Vlaming H, van Welsem T, de Graaf EL, Ontoso D, Altelaar AM, San-Segundo PA, Heck AJ, and van Leeuwen F (2014). Flexibility in crosstalk between H2B ubiquitination and H3 methylation in vivo. EMBO Rep 15: 1077-1084.
  19. Menendez-Benito V, van Deventer SJ, Jimenez-Garcia V, Roy-Luzarraga M, van Leeuwen F, and Neefjes J (2013). Spatiotemporal analysis of organelle and macromolecular complex inheritance. Proc Natl Acad Sci USA 110: 175-180.
  20. Ontoso D, Acosta I, van Leeuwen F, Freire R, and San-Segundo PA (2013). Dot1-dependent histone H3K79 methylation promotes activation of the Mek1 meiotic checkpoint effector kinase by regulating the Hop1 adaptor. PLoS Genet 9: e1003262.
  21. Srivas R, Costelloe T, Sarkar S, Malta E, Sun SM, Pool M, Licon K, Van Welsem T, Van Leeuwen F, McHugh PJ, Van Attikum H, and Ideker T (2013). A UV-Induced Genetic Network Links the RSC Complex to Nucleotide Excision Repair and Shows Dose-Dependent Rewiring. Cell Rep 5: 1714-1724.
  22. Terweij M, van Welsem T, van Deventer S, Verzijlbergen KF, Menendez-Benito V, Ontoso D, San-Segundo P, Neefjes J, and van Leeuwen F (2013). Recombination-induced tag exchange (RITE) cassette series to monitor protein dynamics in Saccharomyces cerevisiae. “G3: Genes, Genomes, Genetics” 3: 1261-1272.
  23. van Bemmel JG, Filion GJ, Rosado A, Talhout W, de Haas M, van Welsem T, van Leeuwen F, and van Steensel B (2013). A network model of the molecular organization of chromatin in Drosophila. Mol Cell 49: 759-771.
  24. Hegnauer AM, Hustedt N, Shimada K, Pike BL, Vogel M, Amsler P, Rubin SM, Van Leeuwen F, Guenole A, van Attikum H, Thoma NH, and Gasser SM (2012). An N-terminal acidic region of Sgs1 interacts with Rpa70 and recruits Rad53 kinase to stalled forks. EMBO J 12: 3768-3783.
  25. Radman-livaja M, Quan TK, Valenzuela L, Armstrong JA, van Welsem T, Kim T, Lee LJ, Buratowski S, van Leeuwen F, Rando OJ, and Hartzog GA (2012). A Key Role for Chd1 in Histone H3 Dynamics at the 3′ Ends of Long Genes in Yeast. PLoS Genet 8: e1002811-e1002811.
  26. van Leeuwen F, Frederiks F, Terweij M, De Vos D, and Bakker BM (2012). News about old histones – A role for histone age in controlling the epigenome. Cell Cycle 11: 11-12.
  27. Vlaming H, and van Leeuwen F (2012). Cross-talk between aging and the epigenome. Epigenomics 4: 5-7.
  28. De Vos D, Frederiks F, Terweij M, van Welsem T, Verzijlbergen KF, Iachina E, de Graaf EL, Altelaar AFM, Oudgenoeg G, Heck AJ, Krijgsveld J, Bakker BM, and van Leeuwen F (2011). Progressive methylation of ageing histones by Dot1 functions as a timer. EMBO Rep 12: 956-962.
  29. Frederiks F, Stulemeijer IJ, Ovaa H, and van Leeuwen F (2011). A modified epigenetics toolbox to study histone modifications on the nucleosome core. ChemBioChem 12: 308-313.
  30. Radman-Livaja M, Verzijlbergen KF, Weiner A, van Welsem T, Friedman N, Rando OJ, and van Leeuwen F (2011). Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biol 9: e1001075.
  31. Stulemeijer IJE, Pike BL, Faber AW, Verzijlbergen KF, van Welsem T, Frederiks F, Lenstra TL, Holstege FC, Gasser SM, and van Leeuwen F (2011). Dot1 binding induces chromatin rearrangements by histone methylation-dependent and -independent mechanisms. Epigen Chrom 4: 2.
  32. Verzijlbergen KF, van Welsem T, Sie D, Lenstra TL, Turner DJ, Holstege FCP, Kerkhoven RM, and van Leeuwen F (2011). A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover. PLoS Genet 7: e1002284.
  33. Frederiks F, van Welsem T, Oudgenoeg G, Heck AJ, Janzen CJ, and van Leeuwen F (2010). Heterologous expression reveals distinct enzymatic activities of two DOT1 histone methyltransferases of Trypanosoma brucei. J Cell Sci 123: 4019-4023.
  34. Verzijlbergen KF, Menendez-Benito V, van Welsem T, van Deventer SJ, Lindstrom DL, Ovaa H, Neefjes J, Gottschling DE, and van Leeuwen F (2010). Recombination-induced tag exchange to track old and new proteins. Proc Natl Acad Sci USA 107: 64-68.
  35. Frederiks F, Heynen GJ, van Deventer SJ, Janssen H, and van Leeuwen F (2009). Two Dot1 isoforms in Saccharomyces cerevisiae as a result of leaky scanning by the ribosome. Nucl Acids Res 37: 7047-7058.
  36. Martino F, Kueng S, Robinson P, Tsai-Pflugfelder M, van Leeuwen F, Ziegler M, Cubizolles F, Cockell MM, Rhodes D, and Gasser SM (2009). Reconstitution of Yeast Silent Chromatin: Multiple Contact Sites and O-AADPR Binding Load SIR Complexes onto Nucleosomes In Vitro. Mol Cell 33: 323-334.
  37. Sampath V, Yuan P, Wang IX, Prugar E, van Leeuwen F, and Sternglanz R (2009). Mutational analysis of the Sir3 BAH domain reveals multiple points of interaction with nucleosomes. Mol Cell Biol 29: 2532-2545.
  38. Verzijlbergen KF, Faber AW, Stulemeijer IJ, and van Leeuwen F (2009). Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae. BMC Mol Biol 10: 76.
  39. Backer R, van Leeuwen F, Kraal G, and den Haan JM (2008). CD8- dendritic cells preferentially cross-present Saccharomyces cerevisiae antigens. Eur J Immunol 38: 370-380.
  40. Frederiks F, Tzouros M, Oudgenoeg G, van Welsem T, Fornerod M, Krijgsveld J, and van Leeuwen F (2008). Nonprocessive methylation by Dot1 leads to functional redundancy of histone H3K79 methylation states. Nat Struct Mol Biol 15: 550-557.
  41. Ovaa H, and van Leeuwen F (2008). Chemical biology approaches to probe the proteome. ChemBioChem 9: 2913-2919.
  42. van Welsem T, Frederiks F, Verzijlbergen KF, Faber AW, Nelson ZW, Egan DA, Gottschling DE, and van Leeuwen F (2008). Synthetic lethal screens identify gene silencing processes in yeast and implicate the acetylated amino terminus of Sir3 in recognition of the nucleosome core. Mol Cell Biol 28: 3861-3872.
  43. Bell O, Wirbelauer C, Hild M, Scharf AN, Schwaiger M, MacAlpine DM, Zilbermann F, van Leeuwen F, Bell SP, Imhof A, Garza D, Peters AH, and Schubeler D (2007). Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila. EMBO J 26: 4974-4984.
  44. van Leeuwen F, and van Steensel B (2005). Histone modifications: from genome-wide maps to functional insights. Genome Biol 6: 113.
  45. Schubeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling DE, O’Neill LP, Turner BM, Delrow J, Bell SP, and Groudine M (2004). The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev 18: 1263-1271.
  46. van Leeuwen F, and Gottschling DE (2003). The histone minority report: the variant shall not be silenced. Cell 112: 591-593.
  47. van Leeuwen F, Gafken PR, and Gottschling DE (2002). Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109: 745-756.
  48. van Leeuwen F, and Gottschling DE (2002a). Genome-wide histone modifications: gaining specificity by preventing promiscuity. Curr Opin Cell Biol 14: 756-762.
  49. van Leeuwen F, and Gottschling DE (2002b). Assays for gene silencing in yeast. Methods Enzymol 350: 165-186.
  50. van Leeuwen F, Kieft R, Cross M, and Borst P (2000). Tandemly repeated DNA is a target for the partial replacement of thymine by beta-D-glucosyl-hydroxymethyluracil in Trypanosoma brucei. Mol Biochem Parasitol 109: 133-145.
  51. Cross M, Kieft R, Sabatini R, Wilm M, de Kort M, van der Marel GA, van Boom JH, van Leeuwen F, and Borst P (1999). The modified base J is the target for a novel DNA-binding protein in kinetoplastid protozoans. EMBO J 18: 6573-6581.
  52. Blundell PA, van Leeuwen F, Brun R, and Borst P (1998). Changes in expression site control and DNA modification in Trypanosoma brucei during differentiation of the bloodstream form to the procyclic form. Mol Biochem Parasitol 93353: 115-130.
  53. Borst P, Bitter W, Blundell PA, Chaves I, Cross M, Gerrits H, van Leeuwen F, McCulloch R, Taylor M, and Rudenko G (1998). Control of VSG gene expression sites in Trypanosoma brucei. Mol Biochem Parasitol 91413: 67-76.
  54. van Leeuwen F, de Kort M, van der Marel G, van Boom JH, and Borst P (1998a). The modified DNA base b-D-glucosyl-hydroxymethyluracil confers resistance to micrococcal nuclease and is incompletely recovered by 32P-postlabeling. Anal Biochem 258372: 223-229.
  55. van Leeuwen F, Dirks Mulder A, Dirks RW, Borst P, and Gibson W (1998b). The modified DNA base b-D-glucosyl-hydroxymethyluracil is not found in the tsetse fly stages of Trypanosoma brucei. Mol Biochem Parasitol 94373: 127-130.
  56. van Leeuwen F, Kieft R, Cross M, and Borst P (1998c). Biosynthesis and function of the modified DNA base b-D-glucosyl-hydroxymethyluracil in Trypanosoma brucei. Mol Cell Biol 18374: 5643-5651.
  57. van Leeuwen F, Taylor MC, Mondragon A, Moreau H, Gibson W, Kieft R, and Borst P (1998d). b-D-glucosyl-hydroxymethyluracil is a conserved DNA modification in kinetoplastid protozoans and is abundant in their telomeres. Proc Natl Acad Sci USA 95191: 2366-2371.
  58. Borst P, Bitter W, Blundell PA, Cross MA, McCulloch R, Rudenko G, Taylor MC, and van Leeuwen F (1997a). The expression sites for variant surface glycoproteins of Trypanosoma brucei. In Trypanosomiasis and Leishmaniasis: biology and control, G. Hide, J.C. Mottram, G.H. Coombs, and P.H. Holmes, eds. (Oxford: BSP / CAB International), pp. 109-131.
  59. Borst P, Rudenko G, Blundell PA, van Leeuwen F, Cross MA, McCulloch R, Gerrits H, and Chaves IMF (1997b). Mechanisms of antigenic variation in African trypanosomes. Behring Inst Mitt 99396: 1-15.
  60. Borst P, and van Leeuwen F (1997). b-D-glucosyl-hydroxymethyluracil, a novel base in African trypanosomes and other Kinetoplastida. Mol Biochem Parasitol 90340: 1-8.
  61. van Leeuwen F, Wijsman ER, Kieft R, van der Marel GA, van Boom JH, and Borst P (1997). Localization of the modified base J in telomeric VSG gene expression sites of Trypanosoma brucei. Genes Dev 11190: 3232-3241.
  62. Borst P, Rudenko G, Taylor MC, Blundell PA, van Leeuwen F, Bitter W, Cross M, and McCulloch R (1996). Antigenic variation in trypanosomes. Arch Med Res 27: 379-388.
  63. van Leeuwen F, Wijsman ER, Kuyl-Yeheskiely E, van der Marel G, van Boom JH, and Borst P (1996). The telomeric GGGTTA repeats of Trypanosoma brucei contain the modified base J in both strands. Nucl Acids Res 2475: 2476-2482.
  64. Borst P, Bitter W, McCulloch R, van Leeuwen F, and Rudenko G (1995). Antigenic variation in malaria. Cell 82: 1-4.
  65. Borst P, Gommers-Ampt JH, Ligtenberg MJ, Rudenko G, Kieft R, Taylor MC, Blundell PA, and van Leeuwen F (1993). Control of antigenic variation in African trypanosomes. Cold Spring Harb Symp Quant Biol 587: 105-114.
  66. Gommers-Ampt JH, van Leeuwen F, de Beer AL, Vliegenthart JF, Dizdaroglu M, Kowalak JA, Crain PF, and Borst P (1993). b-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei. Cell 7512: 1129-1136.
  67. Tugal HB, van Leeuwen F, Apps DK, Haywood J, and Phillips JH (1991). Glycosylation and transmembrane topography of bovine chromaffin granule p65. Biochem J 279: 699-703.