Leiden University Scholarly Publications

Persistent URL of this record https://hdl.handle.net/1887/138082

In Collections

This item can be found in the following collections:

Brouwer, T.B. (2020)

The role of linker DNA in chromatin fibers

Doctoral Thesis
The genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes are transcriptionally silent. Despite decades of research into this mechanism, there is no consensus on how cells realize the various degrees of DNA compaction in vivo. Eukaryotes, such as humans, compact their DNA into higher-order structures called compact chromatin fibers. We characterize these fibers through a combination of single-molecule force spectroscopy techniques like magnetic tweezers, and rigid base pair Monte Carlo simulations. We show that, for instance, the length and sequence of the linker DNA, the DNA between adjacent nucleosomes, control the mechanical properties of chromatin fibers.  Our measurements suggest the formation of more than one higher-order fiber structure. A deeper understanding of the chromatin fiber and its compaction mechanism is...Show moreThe genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes are transcriptionally silent. Despite decades of research into this mechanism, there is no consensus on how cells realize the various degrees of DNA compaction in vivo. Eukaryotes, such as humans, compact their DNA into higher-order structures called compact chromatin fibers. We characterize these fibers through a combination of single-molecule force spectroscopy techniques like magnetic tweezers, and rigid base pair Monte Carlo simulations. We show that, for instance, the length and sequence of the linker DNA, the DNA between adjacent nucleosomes, control the mechanical properties of chromatin fibers.  Our measurements suggest the formation of more than one higher-order fiber structure. A deeper understanding of the chromatin fiber and its compaction mechanism is important because the dysfunction of such regulation results in various medical conditions such as the epigenetic disorder type 1 diabetes, fragile X syndrome, or various cancers.Show less
Eukaryotic chromatin
Archaeal chromatin
DNA
Nucleosome
Magnetic tweezers
Monte Carlo rigid base pair simulations
Bead tracking
Nucleosome repeat length
All authors
Brouwer, T.B.
Supervisor
Noort S.J.T. van, Schmidt T.
Committee
Müller-Planitz, F.; Wuite, G.J.L.; Dekker, N.H.; Ingen, H. van; Schiessel, H.; Eliel, E.R.
Qualification
Doctor (dr.)
Awarding Institution
Leiden Institute of Physics (LION), Faculty of Science, Leiden University
Date
2020-11-04
Title of host publication
Casimir PhD Series
ISBN (print)
9789085934523

Publication Series

Name
2020-26