Chromosome pairing, stress response, and the interwoven layers of 3D chromatin organization
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PROVIDER: PRJNA881336 | ENA |
REPOSITORIES: ENA
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Project description:Chromatin is organized into a 3D interwoven tapestry of multi-layer architectural features important for controlling gene expression. How distinct layers influence each other and quickly they quickly they respond to cellular environment is unclear. Using Hi-C in Drosophila melanogaster, we measure how 3D chromatin organization responds to cellular hyperosmotic stress. In combination with the hd-pairing method, we demonstrate that chromosome unpairing represents a fast an reversible response to hyperosmotic stress. We identify a novel function of the Z4 protein as an anti-pairer, which we demonstrate is necessary for changes to chromatin organization during hyperosmotic stress. Finally, we demonstrate how changes to pairing impacts the other interwoven layers of 3D chromatin organization.
2024-03-19 | GSE213552 | GEO
Project description:Chromatin is organized into a 3D interwoven tapestry of multi-layer architectural features important for controlling gene expression. How distinct layers influence each other and quickly they quickly they respond to cellular environment is unclear. Using Hi-C in Drosophila melanogaster, we measure how 3D chromatin organization responds to cellular hyperosmotic stress. In combination with the hd-pairing method, we demonstrate that chromosome unpairing represents a fast an reversible response to hyperosmotic stress. We identify a novel function of the Z4 protein as an anti-pairer, which we demonstrate is necessary for changes to chromatin organization during hyperosmotic stress. Finally, we demonstrate how changes to pairing impacts the other interwoven layers of 3D chromatin organization.
2024-03-19 | GSE213551 | GEO
Project description:Chromatin is organized into a 3D interwoven tapestry of multi-layer architectural features important for controlling gene expression. How distinct layers influence each other and quickly they quickly they respond to cellular environment is unclear. Using Hi-C in Drosophila melanogaster, we measure how 3D chromatin organization responds to cellular hyperosmotic stress. In combination with the hd-pairing method, we demonstrate that chromosome unpairing represents a fast an reversible response to hyperosmotic stress. We identify a novel function of the Z4 protein as an anti-pairer, which we demonstrate is necessary for changes to chromatin organization during hyperosmotic stress. Finally, we demonstrate how changes to pairing impacts the other interwoven layers of 3D chromatin organization.
2024-03-19 | GSE213550 | GEO
Project description:HiCrayon reveals distinct layers of multi-state 3D chromatin organization
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Project description:Determinants of chromosome organization: Loop extrusion or boundary:boundary pairing?
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Project description:This SuperSeries is composed of the SubSeries listed below.
2024-03-19 | GSE213553 | GEO
Project description:The co-visualization of chromatin conformation with 1D 'omics data is key to the multi-omics driven data analysis of 3D genome organization. Chromatin contact maps are often shown as 2D heatmaps and visually compared to 1D genomic data by simple juxtaposition. While common, this strategy is imprecise, placing the onus on the reader to align features with each other. To remedy this, we developed HiCrayon, an interactive tool that facilitates the integration of 3D chromatin organization maps and 1D datasets. This visualization method integrates data from genomic assays directly into the chromatin contact map by coloring interactions according to 1D signal. HiCrayon is implemented using R shiny and python to create a graphical user interface (GUI) application, available in both web or containerized format to promote accessibility. HiCrayon is implemented in R, and includes a graphical user interface (GUI), as well as a slimmed-down web-based version that lets users quickly produce publication-ready images. We demonstrate the utility of HiCrayon in visualizing the effectiveness of compartment calling and the relationship between ChIP-seq and various features of chromatin organization. We also demonstrate the improved visualization of other 3D genomic phenomena, such as differences between loops associated with CTCF/cohesin vs. those associated with H3K27ac. We then demonstrate HiCrayon's visualization of organizational changes that occur during differentiation and use HiCrayon to detect compartment patterns that cannot be assigned to either A or B compartments, revealing a distinct 3rd chromatin compartment. Overall, we demonstrate the utility of co-visualizing 2D chromatin conformation with 1D genomic signals within the same matrix to reveal fundamental aspects of genome organization.
2024-02-12 | GSE255264 | GEO
Project description:In mammals, homologous chromosomes rarely pair outside meiosis. One exception is the X chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem (ES) cells. The subtelomeric, pseudoautosomal regions (PARs) of the two sex chromosomes (X and Y) also undergo pairing in both female and male cells. PARs transcribe a class of telomeric RNA, dubbed PAR-TERRA, which accounts for a vast majority of all TERRA transcripts. PAR-TERRA binds throughout the genome, including to the PAR and Xic. During X-chromosome pairing, PAR-TERRA anchors the Xic to the PAR, creating a ‘tetrad’ of pairwise homologous interactions (Xic–Xic, PAR–PAR, and Xic–PAR). Xic pairing occurs within the tetrad. Depleting PAR-TERRA abrogates pairing and blocks initiation of XCI, whereas autosomal PAR-TERRA induces ectopic pairing. We propose a ‘constrained diffusion model’ in which PAR-TERRA creates an interaction hub to guide Xic homology searching during XCI.
2017-07-10 | GSE69887 | GEO
Project description:Two different models have been proposed to explain how the endpoints of chromatin looped domains (“TADs”) in eukaryotic chromosomes are determined. In the first a cohesin complex extrudes a loop until it encounters a boundary element roadblock, generating a stem-loop (and an unanchored loop). In this model, boundaries are functionally autonomous: they have an intrinsic ability to halt the movement of incoming cohesin complexes that is independent of the properties of neighboring boundaries. In the second, loops are generated by boundary:boundary pairing. In this model, boundaries are functionally non-autonomous, and their ability to form a loop depends upon how well they match with their neighbors. Moreover, unlike the loop-extrusion model, pairing interactions can generate both stem-loops and circle-loops. We have used a combination of Micro-C to analyze how TADs are organized and experimental manipulations of the even-skipped TAD boundary, homie, to test the predictions of the “loop-extrusion” and the “boundary-pairing” models. Our findings are incompatible with the loop-extrusion model and instead suggest that endpoints of TADs in flies are determined by a mechanism in which boundary elements physically pair with their neighbors, either head-to-head, or head-to-tail.
2024-02-25 | GSE222999 | GEO
Project description:Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focused on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first addressed the long-standing question of whether pairing extends genome-wide and, to this end, developed a haplotype-resolved Hi-C approach that uses a new strategy to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This approach revealed striking genome-wide pairing in Drosophila embryos. Moreover, we discovered pairing to be surprisingly structured, with trans-homolog domains and interaction peaks, many coinciding with the positions of analogous cis features. We also found a significant correlation between pairing and the chromatin accessibility mediated by the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered more than a century ago.
2018-10-16 | GSE121255 | GEO