Gene Regulation: Bas van Steensel
Bas van Steensel, Ph.D professorGroup leaderAbout Bas van Steensel
Chromatin is probably the most complex molecular ensemble in the cell. It consists of genomic DNA bound by hundreds of protein and RNA molecules. All of these components work in concert, and cannot be fully understood unless they are studied in their complete context. In addition, the spatial organization of interphase chromosomes is thought to be of key importance for genome expression and maintenance. Yet, this three-dimensional chromosome organization and its impact on gene regulation and other functions are still poorly understood.
In order to gain insight into these fundamental processes, we
take a broad integrative genomics approach, using both fruit fly
and mammalian cells as model systems. We conduct our studies in the
living cell, in the context of the entire genome. We develop and
apply new genomics techniques to reveal the interplay among many
chromatin proteins, to visualize the architecture of chromosomes
inside the nucleus, and to detect the genome-wide effects of these
factors on gene expression. We analyze the large datasets that we
generate using a range of bioinformatics approaches.
From time to time we have positions available for PhD students, postdocs, bioinformaticians or technicians. Please send your application and CV to email@example.com if you are interested.
- Joris van Arensbergen Postdoctoral fellow
- Eva BrinkmanPhD student
- Laura BrücknerPhD student
- Tao ChenPhD student
- Marcel de HaasTechnician
- Ludo Pagie Postdoctoral fellow
- Tom van SchaikPhD student
- J Omar Yáñez CunaPostdoctoral fellow
- Christ LeemansPhD student
- Daan Peric HupkesTechnician
- Schep, RubenPhD student
- Marloes van der ZwalmTechnician
Joris van Arensbergen
I'm interested in how chromatin domains are established and the role that discrete genomic elements play in this, particularly in repressed chromatin. Therefore I'm setting up a novel screen to functionally identify sequences that play a role in repressive chromatin formation.
I started my study Life Science & Technology at the Delft University of Technology and Leiden University. As a student I participated in the international synthetic biology competition, iGEM, where our team finished as one of the six finalists. After completing my studies, I co-founded a company that is engaged in education and communication of life sciences. Although running a company is a great experience, I still was eager to extend my scientific knowledge and skills in fundamental research. At the NKI, I am working at the regulation of DNA repair in relation to the location and status of chromatin.
I graduated from the University of Vienna, Austria with a master's degree in Molecular Biology but originally hail from Germany. My research interests lie in gene regulation and epigenetics and I joined the NKI in November 2013. For my PhD I am working on the protein-mediated regulation of chromatin states in drosophila cells.
I have been doing my PhD in van Steensel lab since 2012, working on the connections between chromatin and mRNA. I am focusing on chromatin control of mRNA stability and transcription termination. I have been having a good time here, particularly because the lab has such a strong interdisciplinary atmosphere where I have chance to address important questions both experimentally and computationally. I wish to be able to contribute some important insights to biology by the end of my PhD.
Marcel de Haas
I entered the NKI in 1991 for an internship at the division of Cellular Biochemistry. After graduating I applied for a job as research technician in the Multi Drug Resistance group of Piet Borst at the division of Molecular Biology. I started to learn the ways of molecular biology and I learned how to survive and love doing research at the NKI. After being lab manager for 7 years I decided after 20 years to change groups and applied for a position in the group of Bas van Steensel, where I develop a 96-well version of DamID.
I am a bioinformatician collaborating on several projects in the
group. My expertise is in analysis of genome wide data, primarily
DamID and expression data, and the analysis of sequence data in the
context of barcoded reporter assays.
For the institute I organize bioinformatics courses. Personally I teach an introductory R and statistics course. In addition I also organize several in-house seminar series.
Tom van Schaik
During my studies at Radboud University Nijmegen, I became very intrigued by the (epi)genome and the regulatory mechanisms involved to establish and maintain cell identity. Consequently, I shifted my focus to bioinformatics to be able to grasp these complex networks, including an 8-month internship in the bioinformatics group of Erik Bongcam at the SLU, Sweden. In December 2015, I joined the van Steensel group at the NKI to continue on this path. Here, I will combine experimental and computational work to create genome-wide maps of genome compartmentalization.
J Omar Yáñez Cuna
I did my bachelor in Biomedical Sciences at Maastricht university and my master in Bioinformatics in Wageningen. To keep some connection to the human health topics, I did my masters thesis on the evolution of transcription factors in modern humans and Neanderthals. After this I started my internship at Columbia University where I did computational modeling of transcription factor binding. After my master I did lab-work in a study on fish phylogeny at the museum of natural history in Paris. My internship at Columbia brought me into contact with Bas van Steensel's group, where I will study Lamina Associated Domains.
Daan Peric Hupkes
I'm a graduate of the University of Utrecht, and completed my PhD work at the NKI in 2011. After several years of working outside science, I have now (2016) returned to the most fun job in the world. I'm currently working on the dynamics of genome organization in single cells.
I graduated for my masters in genetics and development in D. Duboule's lab in Geneva in 2015. Gene regulation and chromatin architecture have been my main topics of interest since then. After a short period in a neurogenetics lab in 2016, I joined Bas van Steensel's group as a PhD student to study the effects of chromatin state and location on DNA repair mechanisms.
Marloes van der Zwalm
After I finished my bachelor's degree in Breda, I moved to Amsterdam for doing master's in Biomolecular Sciences. During my studies I joined several scientific institutes for internships and I got familiar with various molecular biology techniques. In September 2016 I became part of the van Steensel group to participate in different research projects.
Key publications View All Publications
Systematic protein location mapping reveals five principal chromatin types in Drosophila cells
Cell. 2010; 143: 212-24
Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel et al.Link to Pubmed
Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation
Mol Cell. 2010; 38: 603-13
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels et al.Link to PubMed
Recent publications View All Publications
Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells
Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny...Link to PubMed
Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells.
EMBO Rep. 2015;16:610-617
Amendola M, van Steensel B.Link to PubMed
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