258 research outputs found
Spatially confined polymer chains: implications of chromatin fibre flexibility and peripheral anchoring on telomere-telomere interaction RID A-1843-2011 RID B-8670-2009
No full textWe simulate the extension of spatially confined chromatin fibres modelled as polymer chains and examine the effect of the flexibility of the fibre and its degree of freedom. The developed formalism was used to analyse experimental data of telomere-telomere distances in living yeast cells in the absence of confining factors as identified by the proteins Sir4 and yKu70. Our analysis indicates that intrinsic properties of the chromatin fibre, in particular its elastic properties and flexibility, can influence the juxtaposition of the telomeric ends of chromosomes. However, measurements in intact yeast cells showed that the telomeres of chromosomes 3 and 6 come even closer together than the parameters of constraint imposed on the simulations would predict. This juxtaposition was specific to telomeres on one contiguous chromosome and overrode a tendency for separation that is imposed by anchoring
NUCLEON-NUCLEON SCATTERING DATA IN LIGHT OF RECENT PHASE SHIFT ANALYSES
No full textNous discutons les données de la diffusion nucléon-nucléon jusqu'à l' énergie de 1 GeV. La comparaison des analyses en déphasages récentes permet de déterminer les énérgies où les mesures devraient être complétées.Available nucleon-nucleon elastic scattering data up to 1 GeV are discussed. Comparison of recent phase shift analyses shows what are the energy regions where measurements should be performed
Chromatin Dynamics In Homology Directed Repair
No full textThis thesis consist of six chapters and the appendices. Each chapter starts with a brief summary page. If parts or the whole of the chapter has been published, that sheet indicates the title, author list and the date of the publication as well as my personal contribution to the papers.
Chapter I is an overview of chromatin organization and dynamics in the context of DNA double-strand break (DSB) repair.
Chapter II is a specific published guideline for DNA recombination and repair studies. This chapter is an extracted section of my contribution to a published review. It describes the method I used to visualize and quantify chromosomal dynamics upon DNA double strand breaks in yeast S. cerevisiae.
Chapter III describes my main thesis research question, results, discussion and experimental procedures. This study show that DNA damage induced histone depletion enhances homology search through the induced chromatin expansion and ectopic locus mobility, independently of local DSB movement. Moreover, we show that local DSB dynamics is cell cycle dependent and is regulated by Cohesin turnover. Finally, we find that centromeres do not detach upon DNA damage.
Chapter IV in an overview of the roles of two post-translational modifications (PTMs) in the regulation of DNA repair pathway choice in budding yeast: Ubiquitination and the small ubiquitin-related modifier protein (SUMO). This chapter introduces the research context to Chapter V.
Chapter V contains a study to which I had contributed in which we reported that the presence of telomeric repeat sequences on one side of a double-strand break alters the outcome of repair. We show that the two sides of the break show uncoordinated movement and are repaired asymmetrically leading to translocation. We observed that the repair outcome is tightly controlled by SUMO targeted ubiquitin ligases.
Chapter VI summarizes the main conclusion of this thesis and discusses the results stemming from Chapter III together with relevant future directions.
Finally, the appendices contain a list of abbreviations, my curriculum vitae and acknowledgments
Coupling chromatin structure and dynamics by live super-resolution imaging
No full textChromatin conformation regulates gene expression and thus, constant remodeling of chromatin structure is essential to guarantee proper cell function. To gain insight into the spatiotemporal organization of the genome, we use high-density photoactivated localization microscopy and deep learning to obtain temporally resolved super-resolution images of chromatin in living cells. In combination with high-resolution dense motion reconstruction, we find elongated ∼45- to 90-nm-wide chromatin "blobs."A computational chromatin model suggests that these blobs are dynamically associating chromatin fragments in close physical and genomic proximity and adopt topologically associated domain-like interactions in the time-average limit. Experimentally, we found that chromatin exhibits a spatiotemporal correlation over ∼4 μm in space and tens of seconds in time, while chromatin dynamics are correlated over ∼6 μm and last 40 s. Notably, chromatin structure and dynamics are closely related, which may constitute a mechanism to grant access to regions with high local chromatin concentration.BN/Cees Dekker La
Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription
No full textIntrinsic dynamics of chromatin contribute to gene regulation. How chromatin mobility responds to genomic processes, and whether this response relies on coordinated chromatin movement is still unclear. Here, we introduce an approach called Dense Flow reConstruction and Correlation (DFCC), to quantify correlation of chromatin motion with sub-pixel sensitivity at the level of the whole nucleus. DFCC reconstructs dense global flowfields of fluorescent images acquired in real-time.We applied our approach to analyze stochastic movements of DNA and histones, based on direction and magnitude at different time lags in human cells. We observe long-range correlations extending over several μm between coherently moving regions over the entire nucleus. Spatial correlation of global chromatin dynamics was reduced by inhibiting elongation by RNA polymerase II, and abolished in quiescent cells. Furthermore, quantification of spatial smoothness over time intervals up to 30 s points to clear-cut boundaries between distinct regions, while smooth transitions in small (<1 μm) neighborhoods dominate for short time intervals. Rough transitions between regions of coherent motion indicate directed squeezing or stretching of chromatin boundaries, suggestive of changes in local concentrations of actors regulating gene expression. The DFCC approach hence allows characterizing stochastically forming domains of nuclear activity.</p
Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription
No full textThe eukaryotic genome is hierarchically structured yet highly dynamic. Regulating transcription in this environment demands a high level of coordination to permit many proteins to interact with chromatin fiber at appropriate sites in a timely manner. We describe how recent advances in quantitative imaging techniques overcome caveats of sequencing-based methods (Hi-C and related) by enabling direct visualization of transcription factors and chromatin at high resolution, from single genes to the whole nucleus. We discuss the contribution of fluorescence imaging to deciphering the principles underlying this coordination within the crowded nuclear space in living cells and discuss challenges ahead.BN/Cees Dekker La
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