Coming to terms with chromatin structure

Even-Faitelson, Liron; Hassan‐Zadeh, Vahideh; Baghestani, Zahra; Bazett-Jones, David P.

doi:10.1007/s00412-015-0534-9

Cited by 23 publications

(17 citation statements)

References 135 publications

(139 reference statements)

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“…This prediction can be tested, for instance, by employing the recently developed oligonucleotide based FISH probes which seem to provide the necessary fine resolution [36,37]. An important conclusion of our work is that, although our model uses parameter values that can be associated to the traditional "10nm/30nm" chromatin fiber paradigm [9,10], our results reflect a generic physical effect [35] which ought to be observable in more general systems of crumpled polymers constituted of fibers with different thickness and/or stiffness (see section "Polymer physics aspects" and figure 9).…”

Section: Discussionmentioning

confidence: 98%

Large scale chromosome folding is stable against local changes in chromatin structure

Florescu

Therizols

Rosa

2016

Preprint

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Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple biophysical model where interphase chromosomes are described in terms of the folding of chromatin sequences composed of alternating blocks of fibers with different thicknesses and flexibilities, and we use it to study the influence of sequence disorder on chromosome behaviors in space and time. By employing extensive computer simulations,we thus demonstrate that chromosomes undergo noticeable conformational changes only on length-scales smaller than 10 5 basepairs and time-scales shorter than a few seconds, and we suggest there might exist effective upper bounds to the detection of chromosome reorganization in eukaryotes. We prove the relevance of our framework by modeling recent experimental FISH data on murine chromosomes. Author SummaryA key determining factor in many important cellular processes as DNA transcription, for instance, the specific composition of the chromatin fiber sequence has a major influence on chromosome folding during interphase. Yet, how this is achieved in detail remains largely elusive. In this work, we explore this link by means of a novel quantitative computational polymer model for interphase chromosomes where the associated chromatin filaments are composed of mixtures of fibers with heterogeneous physical properties. Our work suggests a scenario where chromosomes undergo only limited reorganization, namely on length-scales below 10 5 basepairs and time-scales shorter than a few seconds. Our conclusions are supported by recent FISH data on murine chromosomes.

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Section: Discussionmentioning

confidence: 98%

Large scale chromosome folding is stable against local changes in chromatin structure

Florescu

Therizols

Rosa

2016

Preprint

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“…On the other hand, the spread of DNA supercoiling throughout the chromosome is not hindered by wrapping DNA around a nucleosome, and in vivo data suggest that supercoiling can be transmitted over several kilobases over large DNA supercoil domains (80,81). Transcription activation leads to chromatin opening characterised by two features: spatial decompaction induced by changes in nucleosome-nucleosome interactions and linear decompaction due to changes in nucleosome density (82). In summary, DNA supercoiling induced by transcription or other factors can drive decompaction of large-scale chromatin domains prior to productive gene expression observed in the enhancer-mediated distant transcriptional regulation.…”

Section: Roles Of Parp1 and Dna Supercoiling In The Chromatin Organismentioning

confidence: 99%

Mechanistic insight into the role of Poly(ADP-ribosyl)ation in DNA topology modulation and response to DNA damage

2019

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Genotoxic stress generates single- and double-strand DNA breaks either through direct damage by reactive oxygen species or as intermediates of DNA repair. Failure to detect and repair DNA strand breaks leads to deleterious consequences such as chromosomal aberrations, genomic instability and cell death. DNA strand breaks disrupt the superhelical state of cellular DNA, which further disturbs the chromatin architecture and gene activity regulation. Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyse the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are regarded as DNA damage sensors that, upon activation by strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. Noteworthy, the regularly branched structure of poly(ADP-ribose) polymer suggests that the mechanism of its synthesis may involve circular movement of PARP1 around the DNA helix, with a branching point in PAR corresponding to one complete 360° turn. We propose that PARP1 stays bound to a DNA strand break end, but rotates around the helix displaced by the growing poly(ADP-ribose) chain, and that this rotation could introduce positive supercoils into damaged chromosomal DNA. This topology modulation would enable nucleosome displacement and chromatin decondensation around the lesion site, facilitating the access of DNA repair proteins or transcription factors. PARP1-mediated DNA supercoiling can be transmitted over long distances, resulting in changes in the high-order chromatin structures. The available structures of PARP1 are consistent with the strand break-induced PAR synthesis as a driving force for PARP1 rotation around the DNA axis.

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“…To demonstrate the applicability of our approach to these types of biological measurements, we imaged fluorescently-tagged DNA loci of live yeast cells to investigate a proposed mechanism for gene regulation: regions of the chromosome containing suppressed genes are spatially compacted (Even-Faitelson et al, 2016;Gilbert et al, 2004;Wolffe and Pruss, 1996). In brief, two arrays of operator sites were integrated into the chromosome flanking the Gal locus (Dultz et al, 2018), a region encoding several genes for the galactose-metabolism machinery (Hopper et al, 1978).…”

Section: Measuring Chromosomal Compaction States In Saccharomyces Cermentioning

confidence: 99%

High-throughput multicolor 3D localization in live cells by depth-encoding imaging flow cytometry

Weiss

Ezra

Goldberg

et al. 2019

Preprint

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Imaging flow cytometry replaces the canonical point-source detector of flow cytometry with a camera, unveiling subsample details in 2D images while maintaining high-throughput. Here we show that the technique is inherently compatible with 3D localization microscopy by point-spread-function engineering, namely the encoding of emitter depth in the emission pattern captured by a camera. By exploiting the laminar-flow profile in microfluidics, 3D positions can be extracted from cells or other objects of interest by calibrating the depth-dependent response of the imaging system using fluorescent microspheres mixed with the sample buffer. We demonstrate this approach for measuring fluorescently-labeled DNA in vitro and the chromosomal compaction state in large populations of live cells, collecting thousands of samples each minute. Furthermore, our approach is fully compatible with existing commercial apparatus, and can extend the imaging volume of the device, enabling faster flowrates thereby increasing throughput. RESULTS Device and functionalityAn illustration of the device is shown in Figure 1 A. Samples are loaded into the instrument and then directed through a multilaser-illuminated imaging volume. Emission light from the sample is captured by a 60X objective, relayed through a series of lenses, divided into separate spectral channels, and directed onto a camera, whose readout rate is synchronized with the flow speed. As a first demonstration, we show how an astigmatism can be incorporated into the system. By inserting a cylindrical lens between two of the aforementioned relay lenses (see Methods), the axial and lateral focal planes of the instrument are bifurcated, thus an object closer to the objective will appear focused laterally, but defocused axially and vice versa (Figures 1 B, C). The extent of the astigmatism contains information about the depth of the emitter, but is not a direct measurement of the z position. The typical 3D calibration used in microscopy (Huang et al., 2008) is therefore inapplicable and the incorporation of PSF engineering into flow imaging necessitates a novel 3D calibration procedure, which we describe below.

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Coming to terms with chromatin structure

Cited by 23 publications

References 135 publications

Large scale chromosome folding is stable against local changes in chromatin structure

Large scale chromosome folding is stable against local changes in chromatin structure

Mechanistic insight into the role of Poly(ADP-ribosyl)ation in DNA topology modulation and response to DNA damage

High-throughput multicolor 3D localization in live cells by depth-encoding imaging flow cytometry

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