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Highlighted publications

Mimoso, C. A.*, Vlaming, H.*#, De Wagenaar, N.P., Siegenfeld, A.P. & Adelman, K.# (2025). Restrictor slows early transcription elongation to render RNA polymerase II susceptible to termination at non-coding RNA loci. Genes & Development.  
*Authors marked with * are co-first authors, authors marked with # are corresponding authors.

In this paper, we use both INSERT-seq and nascent RNA sequencing methods to learn about the target specificity and function of Restrictor. We find that it promiscuously makes early elongating RNAPII susceptible to termination, but the presence of a 5' splice site protects most mRNAs from this activity.

Vlaming, H., Mimoso, C. A., Field, A. R., Martin, B. J. E. & Adelman, K. (2022). Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential. Nature Structural and Molecular Biology, 29(6). 
This paper can be freely accessed .

The work described in this paper has been foundational to our lab: the development of the INSERT-seq methodology and the observation that the transcribed sequence is a key contributor to RNAPII elongation potential.

Full publication list

2025

Mimoso, C. A.*, Vlaming, H.*#, De Wagenaar, N.P. Siegenfeld, A.P. & Adelman, K.# (2025). Restrictor slows early transcription elongation to render RNA polymerase II susceptible to termination at non-coding RNA loci. Genes & Development.  
*Authors marked with * are co-first authors, authors marked with # are corresponding authors.

2022

Kwesi-Maliepaard, E. M., Malik, M., Welsem, T. V., Doorn, R. V., Vermeer, M. H., Vlaming, H., Jacobs, H., & van Leeuwen, F. (2022). DOT1L inhibition does not modify the sensitivity of cutaneous T cell lymphoma to pan-HDAC inhibitors in vitro. Frontiers in Genetics, 13. 

Vlaming, H., Mimoso, C. A., Field, A. R., Martin, B. J. E., & Adelman, K. (2022). Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential. Nature Structural and Molecular Biology, 29(6). 

2021

Kollenstart, L., van der Horst, S. C., Vreeken, K., Janssen, G. M. C., Martino, F., Vlaming, H., van Veelen, P. A., van Leeuwen, F., & van Attikum, H. (2021). Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies. Scientific Reports, 11(1). 

Cucinotta, C. E.*, Martin, B. J. E.*, González, M. N.*, Raman, P.*, Teif, V. B.*, & Vlaming, H.* (2021). Strength is in engagement: The rise of an online scientific community during the COVID‐19 pandemic. EMBO Reports, 22(5). 

2020

Kwesi-Maliepaard, E. M., Aslam, M. A., Alemdehy, M. F., Brand, T. V. D., McLean, C., Vlaming, H., Welsem, T. V., Korthout, T., Lancini, C., Hendriks, S., Ahrends, T., Dinther, D. V., Haan, J. M. M. D., Borst, J., Wit, E. D., van Leeuwen, F., & Jacobs, H. (2020). The histone methyltransferase DOT1L prevents antigen-independent differentiation and safeguards epigenetic identity of CD8 + T cells. Proceedings of the National Academy of Sciences, 117(34). 

2019

Vlaming, H.*, McLean, C. M.*, Korthout, T., Alemdehy, M. F., Hendriks, S., Lancini, C., Palit, S., Klarenbeek, S., Kwesi‐Maliepaard, E. M., Molenaar, T. M., Hoekman, L., Schmidlin, T. T., Altelaar, M., Welsem, T., Dannenberg, JH., Jacobs, H., & van Leeuwen, F. (2019). Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L‐dose dependency in HDAC1‐deficient thymic lymphoma. EMBO Journal, 38(14). 

2018

van Welsem, T., Korthout, T., Ekkebus, R., Morais, D., Molenaar, T. M., Van Harten, K., Poramba-Liyanage, D., Sun, S. M., Lenstra, T. L., Srivas, R., Ideker, T., Holstege, F. C. P., van Attikum, H., El Oualid, F., Ovaa, H., Stulemeijer, I. J. E., Vlaming, H., & van Leeuwen, F. (2018). Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism. Nucleic Acids Research, 46(21). 

2017

De Vos, D., Vlaming, H., Bakker, B. M., & van Leeuwen, F. (2017). Modeling Distributive Histone Modification by Dot1 Methyltransferases: From Mechanism to Biological Insights. In Epigenetics and Systems Biology Elsevier. 

2016

Vlaming, H., & van Leeuwen, F. (2016). The upstreams and downstreams of H3K79 methylation by DOT1L. Chromosoma, 125(4).

Vlaming, H., Molenaar, T., van Welsem, T., Poramba-Liyanage, D., Smith, D., Velds, A., Hoekman, L., Korthout, T., Hendriks, S., Altelaar, A. F. M., & van Leeuwen, F. (2016). Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1. eLife, 5(e18919), 1-22. 

2015

Zimberlin, CD., Lancini, C., Sno, R., Rosekrans, SL., McLean, CM., Vlaming, H., van, D. B. GR., Bots, M., Medema, JP., Medema, J. P., & Dannenberg, JH. (2015). HDAC1 and HDAC2 collectively regulate intestinal stem cell homeostasis. FASEB Journal, 29(5). 

Hustedt, N., Seeber, A., Sack, R., Tsai-Pflugfelder, M., Bhullar, B., Vlaming, H., van Leeuwen, F., Guénolé, A., van Attikum, H., Srivas, R., Ideker, T., Shimada, K., & Gasser, S. M. (2015). Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. Molecular Cell, 57(2). 

Stulemeijer, I. J. E., De Vos, D., Van Harten, K., Joshi, O. K., Blomberg, O., Van Welsem, T., Terweij, M., Vlaming, H., De Graaf, E. L., Altelaar, A. F. M., Bakker, B. M., & Van Leeuwen, F. (2015). Dot1 histone methyltransferases share a distributive mechanism but have highly diverged catalytic properties. Scientific Reports, 5, [9824]. 

2014

Vlaming, H., van Welsem, T., de Graaf, E. L., Ontoso, D., Altelaar, A. F. M., San-Segundo, P. A., Heck, A. J. R., & van Leeuwen, F. (2014). Flexibility in crosstalk between H2B ubiquitination and H3 methylation in vivo. EMBO Reports, 15(10), 1077-84. 

2012

Vlaming, H., & van Leeuwen, F. (2012). Crosstalk between aging and the epigenome. Epigenomics, 4(1).