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 firstname.lastname@example.org if you are interested.
- Mario Amendola Postdoctoral fellow
- Joris van Arensbergen Postdoctoral fellow
- Eva BrinkmanPhD student
- Tao ChenPhD student
- Carolyn de GraafPostdoctoral fellow
- Marcel de HaasTechnician
- Jop KindPostdoctoral fellow
- Ludo Pagie Postdoctoral fellow
- Sandra de VriesTechnician
- Laura BrücknerPhD student
- Lauren TraceyMaster student
The nuclear lamina interacts with large genomic regions indicated as lamina-associated domains (LADs) and constitutes a repressive chromatin environment. How LADs are recruited to the nuclear lamina and how this interaction contributes to the nonrandom spatial organization of chromosomes is still poorly understood. My research focus is understanding the functional role and the mechanism of action of specific nuclear envelope proteins in mediating these processes.
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 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.
Carolyn de Graaf
I received my PhD from The Walter and Eliza Hall Institute of
Medical Research in Melbourne, Australia in 2010, before starting
in the Van Steensel group in 2011. My PhD studies looked at the
genetic regulation hematopoiesis, in particular during
megakaryocyte development and platelet production.
I am currently investigating factors involved in the regulation of interactions between the genome and the nuclear lamina, using a high-througput DamID-based screen.
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 received my PhD from the EMBL Heidelberg, Germany in 2008 in partnership with the Radboud University Nijmegen, The Netherlands. During my PhD I worked in the lab of Asifa Akhtar where I studied the process of dosage compensation in flies. I joined the Van Steensel group as a postdoc in 2008. Currently I am developing novel tools to study the dynamics of genome - nuclear lamina interactions in single cells.
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.
Sandra de Vries
After working 16 years in the group of Hein te Riele on DNA mismatch repair and oligotargeting, I recently broadened my horizon by joining the group of Bas van Steensel. Here I started working on chromatin organization and specifically on its interaction with the nuclear lamina.
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 am a Masters student studying at UPMC in Paris, originally from Canada. Currently I am completing my senior internship at the NKI studying factors involved in regulating genome interactions with the nuclear lamina.
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
Single-cell dynamics of genome-nuclear lamina interactions
Cell. 2013; 153: 178-92
Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries SS, Janssen H, Amendola M, Nolen LD, Bickmore WA, van Steensel B.Link to PubMed
Genome architecture: domain organization of interphase chromosomes
Cell. 2013; 152: 1270-84
Bickmore WA, van Steensel B.Link to PubMed
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