Michiel Vermeulen
Radboud University Nijmegen
Molecular biologyGeneticsChromatinBiologyCell biology
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Publications 149
#1Velin Marita Sequeira (Radboud University Nijmegen)H-Index: 1
#2Michiel Vermeulen (Radboud University Nijmegen)H-Index: 38
Abstract DNA methylation is an epigenetic modification, which regulates gene expression during cellular differentiation. This important function is thought to be carried out by transcriptional regulators, which are ‘readers’ and effectors of this mark. In recent years, quantitative mass spectrometry-based interaction proteomics technology has emerged as a powerful tool to identify readers for methylated and unmethylated DNA in different cellular contexts. Furthermore, recent technology enables p...
1 CitationsSource
#1Mathilde Gauchier (University of Montpellier)H-Index: 1
#2Guido van Mierlo (Radboud University Nijmegen)H-Index: 5
Last. Jérôme Déjardin (University of Montpellier)H-Index: 15
view all 4 authors...
Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then describe the published strategies and discuss their advantages and limitations. We conclude by discussing why significant technology developments are required to unambiguously desc...
#1Alessia Soldano (University of Trento)
#1A. Soldano (UNIL: University of Lausanne)
view all 21 authors...
N6-methyladenosine (m6A) regulates a variety of physiological processes through modulation of RNA metabolism. The modification is particularly enriched in the nervous system of several species, and its dysregulation has been associated with neurodevelopmental defects and neural dysfunctions. In Drosophila, loss of m6A alters fly behavior albeit the underlying mechanism and the role of m6A during nervous system development have remained elusive. Here we find that impairment of the m6A pathway lea...
#1Ramy Ragheb (University of Cambridge)
#2Sarah GharbiH-Index: 3
Last. Brian Hendrich (University of Cambridge)H-Index: 20
view all 9 authors...
Differentiation of mammalian pluripotent cells involves large-scale changes in transcription and, among the molecules that orchestrate these changes, chromatin remodellers are essential to initiate, establish and maintain a new gene regulatory network. The NuRD complex is a highly conserved chromatin remodeller which fine-tunes gene expression in embryonic stem cells. While the function of NuRD in mouse pluripotent cells has been well defined, no study yet has defined NuRD function in human plur...
#1Michiel Vermeulen (Radboud University Nijmegen)H-Index: 38
#2Jérôme Déjardin (University of Montpellier)H-Index: 15
#1Michiel Vermeulen (Radboud University Nijmegen)H-Index: 38
#2Jérôme Déjardin (University of Montpellier)H-Index: 15
Identifying factors bound to specific genomic loci in an unbiased manner is the holy grail of chromatin research, because it would provide an ultimate description of locus function. In this Comment, we explain why purifying a single locus represents a major technical challenge and provide recommendations for achieving this goal. Michiel Vermeulen and Jerome Dejardin recommend how best to characterize the proteins that bind any specific genomic locus.
#1Rita Pinto (University of Oslo)H-Index: 6
#2Cathrine Broberg Vågbø (NTNU: Norwegian University of Science and Technology)H-Index: 18
Last. Pål Ø. Falnes (University of Oslo)H-Index: 28
view all 16 authors...
RNA methylations are essential both for RNA structure and function, and are introduced by a number of distinct methyltransferases (MTases). In recent years, N6-methyladenosine (m6A) modification of eukaryotic mRNA has been subject to intense studies, and it has been demonstrated that m6A is a reversible modification that regulates several aspects of mRNA function. However, m6A is also found in other RNAs, such as mammalian 18S and 28S ribosomal RNAs (rRNAs), but the responsible MTases have remai...
1 CitationsSource
#1Diana van den Heuvel (LUMC: Leiden University Medical Center)H-Index: 8
#2Cornelia G. Spruijt (Radboud University Nijmegen)
Last. Martijn S. Luijsterburg (LUMC: Leiden University Medical Center)H-Index: 26
view all 17 authors...
The coordinated transcription of genes involves the regulated release of RNA polymerase II (RNAPII) from promoter-proximal sites into active elongation. DNA lesions in transcribed strands block elongation and induce a strong transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but this is not sufficient to resume transcription. Through proteomics screens, we find that the TCR-specific CSB protein loads the evolutionary con...
#1Cathrin Gräwe (Radboud University Nijmegen)H-Index: 1
#2Matthew Makowski (Radboud University Nijmegen)H-Index: 9
Last. Michiel Vermeulen (Radboud University Nijmegen)H-Index: 38
view all 3 authors...
Abstract In recent years, various mass spectrometry-based approaches have been developed to determine global protein-DNA binding specificities using DNA affinity purifications from crude nuclear extracts. However, these assays are semi-quantitative and do not provide information about interaction affinities. We recently developed a technology that we call Protein-nucleic acid Affinity Quantification by MAss spectrometry in Nuclear extracts or PAQMAN, that can be used to determine apparent affini...
#1Matthijs Baars (UU: Utrecht University)H-Index: 1
#2Thera Douma (UU: Utrecht University)
Last. Yvonne Vercoulen (UU: Utrecht University)H-Index: 3
view all 14 authors...
RasGRP1 is a Ras guanine nucleotide exchange factor (GEF), and an essential regulator of lymphocyte receptor signaling. In mice, deletion of Rasgrp1 results in defective T lymphocyte development. RASGRP1-deficient patients suffer from immune deficiency, and the RASGRP1 gene has been linked to autoimmunity. However, how RasGRP1 levels are regulated, and if RasGRP1 dosage alterations contribute to autoimmunity remains unknown. Here we analyzed the efficiency of selection of developing T lymphocyte...