EXPERIMENT_TITLE: GSM5366692: Hub_22_7_knockout_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C sample preparation was performed according to Arima-HiC kit (Arima Genomics Inc) as described by the manufacturer.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Most non-coding regions of the human genome do not harbour any annotated element and are even not marked with any epigenomic or protein binding signal. However, an overlooked aspect of their possible role in stabilizing 3D chromatin organization has not been extensively studied. To illuminate their structural importance, we started with the non-coding regions forming many 3D contacts (referred to as hubs) and performed a CRISPR library screening to identify dozens of hubs essential for cell viability. Hi-C and single cell transcriptomic analyses showed that their deletion could significantly alter chromatin organization and impact the distal genes expression. This study revealed the 3D structural importance of non-coding loci that are not associated with any functional element, providing a new mechanistic understanding of disease-associated genetic variations (GVs), and we focused on single nucleotide variations. Furthermore, our analyses also suggest a powerful approach to develop "one-drug-multiple-targets" therapeutics targeting disease-specific non-coding regions. Overall design: Our above analysis suggested that hubs can be critical for maintaining the chromatin structure. Deletion of a hub may have a global impact that can propagate through the 3D genome to alter chromatin organization and thus gene expression in the distal genomic regions. One hub loci in K-562 cell line was deleted with CRISPR/Cas9. And their overall chromatin organization in distal genomic regions were compared with non-modified parental cells.
SAMPLE_TITLE: Hub_22_7_knockout_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "genomic modified cell line"}, {"TAG": "cell line", "VALUE": "K-562"}, {"TAG": "cell type", "VALUE": "Lymphoblast"}, {"TAG": "genomic locus deleted", "VALUE": "chr22: 17325000-17329999"}, {"TAG": "restriction enzyme", "VALUE": "Arima (multi-enzyme)"}]
Pool_Member_@attributes_sample_title: Hub_22_7_knockout_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hub_22_7_knockout_HiC
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