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Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

ABSTRACT: Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.

ORGANISM(S): Felis catus Bos taurus Mus musculus Rattus norvegicus Danio rerio Sus scrofa Canis lupus familiaris Homo sapiens Oryctolagus cuniculus Ovis aries Gallus gallus Macaca mulatta

PROVIDER: GSE167580 | GEO | 2022/04/12

REPOSITORIES: GEO

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Comparative 3D Genome Architecture in Vertebrates (Hi-C)

Project description:Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.

2022-04-12 | GSE167579 | GEO

Comparative 3D Genome Architecture in Vertebrates

Project description:Comparative 3D Genome Architecture in Vertebrates

| PRJNA704983 | ENA

Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

Project description:Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

| PRJNA704985 | ENA

Comparative 3D Genome Architecture in Vertebrates (Hi-C)

Project description:Comparative 3D Genome Architecture in Vertebrates (Hi-C)

| PRJNA704984 | ENA

Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates

Project description:A growing body of evidence supports the notion that variation in gene regulation plays a crucial role in speciation and adaptation. However, a comprehensive functional understanding of the mechanisms underlying regulatory evolution remains elusive. In primates, one of the crucial missing pieces of information towards a better understanding of regulatory evolution is a comparative annotation of interactions between distal regulatory elements and promoters. We used Hi-C to characterize 3D regulatory interactions in induced pluripotent stem cells (iPSCs) from humans and chimpanzees (Pan troglodytes). We overlaid these data with previously-collected RNA-seq data from the same cell lines. Generally, we observe that fine-scale distal 3D genomic interactions are conserved in humans and chimpanzees, but higher order genomic organization of contacts, such as TADs, are not as conserved. Inter-species differences in fine-scale 3D locus-locus interactions are often associated with gene expression differences between the species. To provide additional functional context to our observations, we also considered previously published chromatin data from human iPSCs. We found strong enrichment for both active and repressive marks in distal 3D genomic interactions that are both divergent between species and that are associated with inter-species differences in gene expression. Overall, our data demonstrates that, as expected, an understanding of 3D genome reorganization is key to explaining regulatory evolution.

2019-07-03 | GSE122520 | GEO

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Project description:We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

2021-04-23 | GSE169088 | GEO

Conserved Transcriptomic Profiles Underpin Monogamy across Vertebrates

Project description:We compare fore- and mid-brain transcriptomes of reproductive males in monogamous and non-monogamous species pairs of Peromyscus mice, Microtus voles, parid songbirds, dendrobatid frogs, and Xenotilapia species of cichlid fishes. Our study provides evidence of a universal transcriptomic mechanism underlying the evolution of monogamy in vertebrates.

2018-12-18 | GSE123301 | GEO

Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

Project description:Transposable elements (TEs) are major contributors of genetic material in mammalian genomes. These often include binding sites for architectural proteins, including the multifarious master protein, CTCF, which shapes the 3D genome by creating loops, domains, compartment borders and RNA-DNA interactions, all of which play a role in the compact packaging of DNA and have the potential to facilitate regulatory function. In this study, we explore the widespread contribution of TEs to mammalian 3D genomes by quantifying the extent to which they give rise to loops and domain border differences across various cell types and species using several 3D genome mapping technologies. We show that specific (sub-)families of TEs have contributed to lineage-specific 3D chromatin structures across mammalian species. In many cases, these loops may facilitate interaction between distant cis-regulatory elements and target genes, and domains may segregate chromatin state to impact gene expression in a lineage-specific manner. An experimental validation of our analytical findings using CRISPR-Cas9 to delete a candidate TE resulted in disruption of species-specific 3D chromatin structure. Taken together, we comprehensively quantify and selectively validate our finding that TEs contribute to 3D genome organization and may, in some cases, impact gene regulation during the course of mammalian evolution.

2023-01-16 | GSE222526 | GEO

Clonal evolution of the 3D chromatin landscape of relapsed ALL [H3K27ac HiChIP]

Project description:Relapsed pediatric B-cell acute lymphoblastic leukemia (B-ALL) remains one of the leading causes of cancer mortality in children. Up to 20% of children will suffer relapse and face a poor prognosis. Our recent work on the evolution of the epigenetic landscape from diagnosis to relapse demonstrates both substantial diversity in the chromatin landscape as well as shared relapse-specific superenhancer activation, highlighting the importance of chromatin changes in disease progression. However, there is a gap in our understanding of B-ALL progression through the lens of three-dimensional (3D) chromosome topology. To uncover 3D chromatin architecture-related mechanisms underlying drug resistance in B-ALL, we performed Hi-C, ATAC-seq, and RNA-seq on 12 matched primary pediatric leukemia specimens at diagnosis and relapse. Mapping of structural variations (SVs) using Hi-C data revealed previously unidentified stable, diagnosis-specific, and relapse-specific SVs providing further evidence for clonal evolution as a mechanism for drug resistance. Moreover, Hi-C analysis revealed genome wide chromatin remodeling specifically in terms of A/B compartments, TAD interactivity, and chromatin loops. Integration with ATAC-seq and RNA-seq datasets revealed strong correlation with both gene expression and chromatin accessibility. Additionally, we identified recurrent A/B compartments and TAD interactivity changes across the patient cohort for which we were able to demonstrate a crucial role in the clonal evolution of B-ALL. Shared changes in 3D genome organization drive the expression of genes/pathways previously implicated in drug resistance as well. Lastly, enrichment analysis revealed key upstream regulators of 3D genome architecture in B-ALL disease progression. These results extend the landscape of genetic alterations in relapsed B-ALL through the addition of the 3D genomic landscape and identify a breadth of novel therapeutic targets.

2024-05-01 | GSE222686 | GEO

Clonal evolution of the 3D chromatin landscape of relapsed ALL [RNA-seq]

2024-05-01 | GSE222685 | GEO

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