Chromatin accessibility: methods, mechanisms, and biological insights

Mansisidor, Andrés; Risca, Viviana I.

doi:10.1080/19491034.2022.2143106

Cited by 54 publications

(32 citation statements)

References 395 publications

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“…5E, F); this may reflect the fact that paternal cross-over events are biased towards the tip of the chromosomes (Broman et al 1998) and, similarly, Subramanian (2019) observed an increase in DSB formation in telomere-proximal regions in yeast. Chromatin accessibility ranked highly in the models of ssDNA and recombination hotspots, consistent with the observation that PRDM9 creates nucleosome-depleted regions (Mansisidor and Risca 2022); however, previous studies have lacked accessibility data from meiotic human cells. Local GC content and meiotic replication timing also ranked highly across models, and both features are known to correlate with levels of recombination (Eyre-Walker 1993; Pratto et al 2021).…”

Section: Resultssupporting

confidence: 78%

CTCF-anchored chromatin loop dynamics during human meiosis

Kaiser,

Semple

2024

Preprint

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During meiosis, the mammalian genome is organised within chromatin loops, which facilitate synapsis, crossing over and chromosome segregation, setting the stage for recombination events and the generation of genetic diversity. Chromatin looping is thought to play a major role in the establishment of cross overs during prophase I of meiosis, in diploid early primary spermatocytes. However, chromatin conformation dynamics during human meiosis are difficult to study experimentally, due to the transience of each cell division and the difficulty of obtaining stage-resolved cell populations. Here, we employed a machine learning framework trained on single cell ATAC-seq and RNA-seq data to predict chromatin looping during spermatogenesis, including cell types at different stages of meiosis. We find dramatic changes in genome-wide looping patterns throughout meiosis: compared to pre-and-post meiotic germline cell types, loops in meiotic early primary spermatocytes are more abundant, more variable between individual cells, and more evenly spread throughout the genome. In preparation for the first meiotic division, loops also include longer stretches of DNA, encompassing more than half of the total genome. These loop structures then influence the rate of recombination initiation and resolution as cross overs. In contrast, in later mature sperm stages, we find evidence of genome compaction, with loops being confined to the telomeric ends of the chromosomes. Overall, we find that chromatin loops do not orchestrate the gene expression dynamics seen during spermatogenesis, but loops do play important roles in recombination, influencing the positions of DNA breakage and cross over events.

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Section: Resultssupporting

confidence: 78%

CTCF-anchored chromatin loop dynamics during human meiosis

Kaiser,

Semple

2024

Preprint

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“…Fig 2A presents an overview on a recent study on true-to-scale DNA-density maps of chromatin where absolute chromatin compaction differences in the range between <5 Mb/μm3 up to >300 Mb/μm3 were described using single molecule localization microscopy (SMLM) 29 . Such massive differences, if confirmed by future studies, have a strong impact on the accessibility of individual macromolecular complexes to their DNA target sites such as the replisome assembly 30 . According to Maeshima and colleagues 31,32 , nucleosome arrangements at a density <40 Mb/µm 3 provide sufficient space to allow a high degree of accessibility for macromolecular protein complexes that have been typically assigned with a size >20nm diameter 32,33 .…”

Section: Introductionmentioning

confidence: 72%

Space-time dynamics of genome replication studied with super-resolved microscopy

Gelléri,

Sterr,

Strickfaden

et al. 2024

Preprint

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Genome replication requires duplication of the complete set of DNA sequences together with nucleosomes and epigenetic signatures. Notwithstanding profound knowledge on mechanistic details of DNA replication, major problems of genome replication have remained unresolved. In this perspective article, we consider the accessibility of replication machines to all DNA sequences in due course, the maintenance of functionally important positional and structural features of chromatid domains during replication, and the rapid transition of CTs into prophase chromosomes with two chromatids. We illustrate this problem with EdU pulse-labeling (10 min) and chase experiments (80 min) performed with mouse myeloblast cells. Following light optical serial sectioning of nuclei with 3D structured illumination microscopy (SIM), seven DNA intensity classes were distinguished as proxies for increasing DNA compaction. In nuclei of cells fixed immediately after the pulse-label, we observed a relative under-representation of EdU-labeled DNA in low DNA density classes, representing the active nuclear compartment (ANC), and an over-representation in high density classes representing the inactive nuclear compartment (INC). Cells fixed after the chase revealed an even more pronounced shift to high DNA intensity classes. This finding contrasts with previous studies of the transcriptional topography demonstrating an under-representation of epigenetic signatures for active chromatin and RNAPII in high DNA intensity classes and their over-representation in low density classes. We discuss these findings in the light of current models viewing CDs either as structural chromatin frameworks or as phase-separated droplets, as well as methodological limitations that currently prevent an integration of this contrasting evidence for the spatial nuclear topography of replication and transcription into a common framework of the dynamic nuclear architecture.

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“…High chromatin accessibility for multiple CD5 ZF-Rs can be the consequence of low nucleosome occupancy, or high nucleosome occupancy with low stability and/or an increase in inter-nucleosomal spacing. 42–44…”

Section: Discussionmentioning

confidence: 99%

Epigenetic control of multiple genes with a single lentiviral vector encoding transcriptional repressors fused to compact zinc finger arrays

Monteferrario,

David,

Tadi

et al. 2024

Preprint

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Gene silencing without gene editing holds great potential for the development of safe therapeutic applications. Here, we describe a novel strategy to concomitantly repress multiple genes using zinc finger proteins fused to Kruppel-Associated Box repression domains (ZF-Rs). This was achieved via the optimization of a lentiviral system tailored for the delivery of ZF-Rs in hematopoietic cells. We showed that an optimal design of the lentiviral backbone is crucial to multiplex up to three ZF-Rs or two ZF-Rs and a chimeric antigen receptor. ZF-R expression had no impact on the integrity and functionality of transduced cells. Furthermore, gene repression in ZF-R-expressing T cells was highly efficient in vitro and in vivo during the entire monitoring period (up to ten weeks), and it was accompanied by epigenetic remodeling events. Finally, we described an approach to improve ZF-R specificity to illustrate the path towards the generation of ZF-Rs with a safe clinical profile. In conclusion, we successfully developed an epigenetic-based cell engineering approach for concomitant modulation of multiple gene expressions that bypass the risks associated with DNA editing.

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Chromatin accessibility: methods, mechanisms, and biological insights

Cited by 54 publications

References 395 publications

CTCF-anchored chromatin loop dynamics during human meiosis

CTCF-anchored chromatin loop dynamics during human meiosis

Space-time dynamics of genome replication studied with super-resolved microscopy

Epigenetic control of multiple genes with a single lentiviral vector encoding transcriptional repressors fused to compact zinc finger arrays

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