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Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin structures

ABSTRACT: To investigate the mechanisms underlying the rearrangement patterns,we compared the rearrangement map with local chromatin structures and the three-dimensional genome architecture via assay for transposase-accessible chromatin using sequencing (ATAC-seq) and genome-wide chromosome conformation capture (Hi-C), respectively

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE168182 | GEO | 2022/06/10

REPOSITORIES: GEO

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Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin structures

Project description:Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin structures

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Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization.

Project description:Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary processes. Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural variations. Here, we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes (synII, synIII, synV, circular synVI, synIXR and synX). Remarkably, we find that the rearrangement events exhibit a specific landscape of frequency. We further reveal that the landscape is shaped by the combined effects of chromatin accessibility and spatial contact probability. The rearrangements tend to occur in 3D spatially proximal and chromatin-accessible regions. The enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution, and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution.

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Alterations in chromosome spatial compartmentalization classify prostate cancer progression [array]

Project description:Through a systematic analysis of chromosome conformation capture in a cohort of cells that model cancer progression, San Martin et.al. find that rearrangement of the 3D genome structure in prostate cancer is a potential mechanism for disease exacerbation and that genome-wide compartment identity can classify cancer according to progression

2021-05-01 | GSE172098 | GEO

Chromatin architecture landscape in hierarchical hematopoietic cells

Project description:The spatiotemporal chromatin reorganization during hematopoietic differentiation has not been well characterized, which partly limited by the large amounts of starting cells for the current high-throughput chromatin conformation capture approaches. Here, we introduce a low-input Hi-C method, tagHi-C, to capture the chromatin structures in hundreds of cells. We proved tagHi-C was a feasible and reproducible approach.

2020-08-01 | GSE152918 | GEO

Alterations in chromosome spatial compartmentalization classify prostate cancer progression [Hi-C]

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Evolution of hierarchical porous structures in supramolecular guest-host hydrogels.

Project description:Macromolecular interactions are used to form supramolecular assemblies, including through the interaction of guest-host chemical pairs. Microstructural heterogeneity has been observed within such physical hydrogels; yet, systematic investigation of the microstructure and its determining inputs are lacking. Herein, we investigated the hierarchical self-assembly of hyaluronic acid (HA) modified by the guest-host pair adamantane (Ad-HA, guest) and β-cyclodextrin (CD-HA, host), as well as with methacrylate groups to both tether fluorescent agents and to covalently stabilize the material structure. We observed microporous materials in the hydrated state, which temporally arose from initially homogenous hydrogels composed of the two polymers. Independent fluorescent labeling of Ad-HA and CD-HA demonstrated spatiotemporal co-localization, indicative of guest-host polymer condensation on the microscale. The hydrogel void fractions and pore diameters were independently tuned through incubation time (0-7 days), polymer concentration (1.25-10 wt%), and polymer modification (25-50% Ad-HA modification). Void fractions as great as 93.3 ± 2.4% were achieved and pore diameters ranged from 2.1 ± 0.5 to 1025.4 ± 209.4 μm. The segregation of discrete solid and solute phases was measured with both atomic force microscopy and diffusive microparticle tracking analysis, where the solute phase contained only dilute polymer. The study represents a systematic investigation of hierarchical self-assembly in binary associating hydrogels, and provides insights on mechanisms that control microstructure within supramolecular hydrogels.

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Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution.

Project description:Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals. Preexisting heterogeneities in dosage sensitivity, manifesting as differences in the extent of miRNA-mediated repression, predicted either the retention of a Y homolog or the acquisition of XCI following Y gene decay. Analogous heterogeneities among avian Z-linked genes predicted either the retention of a W homolog or gene-specific dosage compensation following W gene decay. Genome-wide analyses of human copy number variation indicate that these heterogeneities consisted of sensitivity to both increases and decreases in dosage. We propose a model of XY/ZW evolution incorporating such preexisting dosage sensitivities in determining the evolutionary fates of individual genes. Our findings thus provide a more complete view of the role of dosage sensitivity in shaping the mammalian and avian sex chromosomes and reveal an important role for post-transcriptional regulatory sequences (miRNA target sites) in sex chromosome evolution.

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A Streamlined Tethered Chromosome Conformation Capture Protocol

Project description:Background: Identification of locus-locus contacts at the chromatin level provides a valuable foundation for understanding of nuclear architecture and function and a valuable tool for inferring long-range linkage relationships. As one approach to this, chromatin conformation capture-based techniques allow creation of genome spatial organization maps. While such approaches have been available for some time, methodological advances will be of considerable use in minimizing both time and input material required for successful application. Results: Here we report a modified tethered conformation capture protocol that utilizes a series of rapid and efficient molecular manipulations. We applied the method to Caenorhabditis elegans, obtaining chromatin interaction maps that provide a sequence-anchored delineation of salient aspects of Caenorhabditis elegans chromosome structure, demonstrating a high level of consistency in overall chromosome organization between biological samples collected under different conditions. In addition to the application of the method to defining nuclear architecture, we found the resulting chromatin interaction maps to be of sufficient resolution and sensitivity to enable detection of large-scale structural variants such as inversions or translocations. Conclusion: Our streamlined protocol provides an accelerated, robust, and broadly applicable means of generating chromatin spatial organization maps and detecting genome rearrangements without a need for cellular or chromatin fractionation. Application of modified version of TCC protocl using different C. elegans strains (N2 and glp-1) in L1, and adult life stages.

2016-01-20 | E-GEOD-76930 | biostudies-arrayexpress

Primary monocyte to macrophage differentiation involves significant changes in chromosome conformation different from cultured THP-1 cells

Project description:Use human native monocyte and induce to macrophae by GM-CSF, reserach the chromatin conformation of these two cell types.

2021-02-23 | E-MTAB-8262 | biostudies-arrayexpress

Structural variation-induced changes of chromatin architecture and gene expression

Project description:Copy number variants (CNVs) influence the expression of genes that map not only within the rearrangement, but also to its flanks. To assess the possible mechanism(s) underlying this “neighboring effect”, we compared intrachromosomal interactions and histone modifications in cell lines of patients affected by genomic disorders and control individuals. Using chromosome conformation capture (4C-seq), we observed that a set of genes flanking the Williams-Beuren Syndrome critical region (WBSCR) were often looping together, possibly forming an interacting cluster with each other and the WBSCR. Deletion of the WBSCR disrupts the expression of this group of flanking genes, as well as long-range interactions between them and the rearranged interval. We also pinpointed concomitant changes in histone modifications between samples.We conclude that large genomic rearrangements can lead to chromatin conformation changes that extend far away from the structural variant, thereby possibly modulating expression globally and modifying the phenotype. For example, we determined that the chromatin conformation, histone marks and relative expression levels of the flanking AUTS2 gene, mutations of which are associated with autism and intellectual disabilities, are modified in cell lines from Williams-Beuren syndrome patients. Examination of 4C-seq interaction profile of seven different genes (of which three in duplicate) in 2 different cell lines.

2013-11-20 | E-GEOD-33867 | biostudies-arrayexpress

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