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Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals

ABSTRACT: Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals

PROVIDER: PRJNA849168 | ENA |

REPOSITORIES: ENA

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Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals

Project description:Here we describe the principles of 3D genome folding dynamics in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (i) identified different patterns of chromosome folding across vertebrate species, (ii) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of 10 species representative of the major therian phylogroups, (iii) detected lineage-specific chromosome rearrangements and (iv) identified the dynamics of the structural properties of genome reshuffling through therian evolution.

2022-12-08 | GSE206075 | GEO

Replication dynamics identifies the folding principles of the inactive X chromosome

Project description:Replication dynamics identifies the folding principles of the inactive X chromosome

| PRJNA870918 | ENA

in situ HiPore-C reveals higher-order 3D genome folding principles

Project description:in situ HiPore-C reveals higher-order 3D genome folding principles

| PRJNA836538 | ENA

Replication dynamics identifies the folding principles of the inactive X chromosome [4C]

Project description:Replication dynamics identifies the folding principles of the inactive X chromosome [4C]

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Replication dynamics identifies the folding principles of the inactive X chromosome [RNA-seq]

Project description:Replication dynamics identifies the folding principles of the inactive X chromosome [RNA-seq]

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Replication dynamics identifies the folding principles of the inactive X chromosome [scRepli-seq]

Project description:Replication dynamics identifies the folding principles of the inactive X chromosome [scRepli-seq]

| PRJNA870926 | ENA

Evolutionary Principles Predict 3D Chromatin Organization

Project description:TADs, CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C. elegans and A. thaliana. Architectural proteins insulate compartmental domains by reducing interaction frequencies between neighboring regions in Drosophila, but CTCF loops do not play a distinct role in this organism. In mammals, compartmental domains exist alongside CTCF loop domains to form topological domains. The results suggest that compartmental domains are responsible for domain structure in all eukaryotes, with CTCF playing an important role in domain formation in mammals.

2017-08-14 | GSE89244 | GEO

Evolutionary principles of modular gene regulation in Yeasts

Project description:Evolutionary principles of modular gene regulation in Yeasts

| PRJNA153069 | ENA

Evolutionary principles of modular gene regulation in Yeasts

Project description:Evolutionary principles of modular gene regulation in Yeasts

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Mapping nucleosome resolution chromosome folding in yeast by Micro-C

Project description:We describe a Hi-C based method, Micro-C, in which micrococcal nuclease is used instead of restriction enzymes to fragment chromatin, enabling nucleosome resolution chromosome folding maps. Analysis of Micro-C maps for budding yeast reveals abundant self-associating domains similar to those reported in other species, but not previously observed in yeast. These structures, far shorted than topologically-associating domains in mammals, typically encompass one to five genes in yeast. Strong boundaries between self-associating domains occur at promoters of highly transcribed genes, and regions of rapid histone turnover that are typically bound by the RSC chromatin-remodeling complex. Investigation of chromosome folding in mutants confirms roles for RSC, “gene looping” factor Ssu72, Mediator, H3K56 acetyltransferase Rtt109, and N-terminal tail of H4 in folding of the yeast genome. This approach provides detailed structural maps of a eukaryotic genome and our findings provide insights into the machinery underlying chromosome compaction. Chromatin is fragmented by Mnase, subsequenct nucleosomal end repair, and a modified two-step method for purfiying ligation products. Using Illumina paired-end sequencing maps Micro-C library and generates nucleosome resolution contact maps. The readme.txt file contains additional description of how each processed data file was generated.

2015-06-25 | E-GEOD-68016 | biostudies-arrayexpress

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