Cover Page
The handle
http://hdl.handle.net/1887/74050
holds various files of this Leiden University
dissertation.
Author: Kaczmarczyk, A.
Title: Nucleosome stacking in chromatin fibers probed with single-molecule force- and
torque-spectroscopy
Propositions
accompanying the thesis
Nucleosome stacking in chromatin fibers probed with
single-molecule force- and torque-spectroscopy
1. The hierarchical folding of chromatin in vivo enables more efficient pro-cessing of the genome compared to a disordered chromatin state.
Chapter 1 of this thesis 2. Nucleosome stacking into chromatin fibers protects nucleosomal DNA from external forces up to 5 pN. However, the large degree of elasticity of chromatin fibers implies that such structures would not necessarily act as a repressor of gene expression.
Chapter 3 and 4 of this thesis 3. Chromatin fibers can largely accommodate torsional stress. This means that the transcription-generated DNA supercoiling has less potential to regulate gene expression than stated before.
Chapter 4 of this thesis and S. Corless and N. Gilbert, Briefings in Functional Genomics 16, 379 (2017). 4. Linker histones do not affect the stretching stiffness of chromatin fibers. Presumably, further measurements could reveal that the torsional stiffness of chromatin fibers with linker histones is higher than that of linker histone-free fibers.
Chapter 4 and 5 of this thesis 5. Chromatin fibers with linker histones and a Nucleosome Repeat Length of 197 base pairs do not fold into tetranucleosomal units. This supports the model of 197-NRL chromatin as a one-start, solenoidal fiber.
Chapter 5 of this thesis and W. Li et al., Molecular Cell 64, 120 (2016). 6. Stretching native chromatin, extracted from yeast, resulted in unfolding
transitions that are qualitatively similar to those obtained from stretching nucleosome arrays assembled on Widom-601 sequences. This highlights the relevance of studies that employ in vitro reconstituted chromatin.
7. The latest improvements in chromosome conformation capture methods and in microscopy techniques allow to reveal distinct structural motifs between nucleosomes in situ. This may help to reach consensus on the "30 nm fiber" dilemma.
M. Ohno et al., Cell 176, 520 (2019). S. Cai et al., Molecular Biology of Cell 29, 2450 (2018). V. Risca et al., Nature 541, 237 (2017). 8. Recent single-molecule approaches have advanced our understanding of
epigenetic regulation thanks to the application of more heterogeneous chromatin substrates.
B. Fierz, ACS Chemical Biology 11, 609 (2016). 9. Social media can play a significant role in transferring academic
achieve-ments to peers and public audiences.
10. In the most fruitful and rewarding collaborations, mutual interests span beyond the main frame of the shared project.
