EXPERIMENT_TITLE: Illumina NovaSeq 6000 paired end sequencing
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Structural variants (SVs) are known to be influenced by the local chromatin state and the 3D chromatin architecture. Studies relating SVs to chromatin organization in cancer have primarily been conducted retrospectively, years to decades after SV occurrence, complicating their analysis. Here, we apply Hi-C to study chromatin organization before and after catastrophic SV induction in human cultured cells. We assemble derivative chromosomes following massive complex rearrangements, which we used to study the sources of SV formation and their consequences on gene regulation. We observe an action-reaction interplay whereby the 3D chromatin architecture directly impacts on the location and formation of SVs. In turn, the SVs reshape the chromatin organization to alter the local topologies, replication timing and gene regulation in cis. We show that genomic compartments and replication timing are important determinants for juxtaposing distant loci to form SVs across 30 different cancer types with a pronounced abundance of SVs between early replicating regions in uterine cancer. We find that SVs frequently occur at 3D loop-anchors, cause compartment switching and changes in replication timing, and that this is a major source of SV-mediated effects on nearby gene expression changes.
SAMPLE_TITLE: RPE-1 BM175 TP53-deficient doxorubicin-treated (TP53-/-DOX+) cells
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "ENA first public", "VALUE": "2022-01-30"}, {"TAG": "ENA last update", "VALUE": "2022-01-30"}, {"TAG": "External Id", "VALUE": "SAMEA8772065"}, {"TAG": "INSDC center alias", "VALUE": "Biotech Research and Innovation Centre (BRIC), University of Copenhagen"}, {"TAG": "INSDC center name", "VALUE": "Biotech Research and Innovation Centre (BRIC), University of Copenhagen"}, {"TAG": "INSDC first public", "VALUE": "2022-01-30T08:17:16Z"}, {"TAG": "INSDC last update", "VALUE": "2022-01-30T08:17:16Z"}, {"TAG": "INSDC status", "VALUE": "public"}, {"TAG": "Submitter Id", "VALUE": "BM175"}, {"TAG": "cell line", "VALUE": "hTERT RPE-1"}, {"TAG": "common name", "VALUE": "human"}, {"TAG": "sample name", "VALUE": "BM175"}]
Pool_Member_@attributes_sample_title: RPE-1 BM175 TP53-deficient doxorubicin-treated (TP53-/-DOX+) cells
RUN_SET_RUN_Pool_Member_@attributes_sample_title: RPE-1 BM175 TP53-deficient doxorubicin-treated (TP53-/-DOX+) cells
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