EXPERIMENT_TITLE: GSM8635230: IAA-2-3; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Briefly, five million CTCF-AID knock-in HEL cells without or with IAA treatment for 24 hours were crosslinked with 1% formaldehyde for 10 min at room temperature, digested with 125 units of MboI, labeled with biotinylated nucleotides and ligated for proximity ligation. After de-crosslinking, the ligated DNA was purified and sheared to 300–500 bps. Ligation junctions were pulled down with streptavidin beads and prepared as a standard Illumina library. Each library underwent 75 cycles of paired-end sequencing on the Illumina HiSeq 4000 system.Each sample had two replicates, and we merged the replicates after confirming reproducibility. Each sample contained > 250 million paired-end fragments, > 60% ligation motif present, and > 200 million contacts.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Backgrounds:The three-dimensional chromatin niche provides a precise gene expression control of cell identity, differentiation, and disease development. CTCF is considered as the most essential transcription factor regulating chromatin architecture and gene expression. However, the genome-wide impact of CTCF on erythropoiesis has not yet been extensively investigated. Results:Here, using a state-of-the-art human erythroid progenitor cell model (HUDEP-2 and HEL cell lines), we systematically investigated the effects of acute CTCF loss by an auxin-inducible degron system on transcriptional programs, chromatin accessibility, CTCF genome occupancy, and the 3D genome architecture. By integrating multi-omics datasets, we revealed that acute CTCF loss notably disrupted genome-wide chromatin accessibility and transcription network. Importantly, we identified that over thousands of chromatin accessibility regions were decreased while only a few hundred increased regions after depletion of CTCF in both HUDEP-2 and HEL lines, suggesting the role of CTCF in maintaining the proper chromatin openness in erythroid lineage. Moreover, CTCF depletion in the erythroid context significantly disrupted TAD boundary integrity and chromatin loops while not affecting the nuclear compartmentalization. Our study also reported that hundreds of erythroid lineage-specific genes were suppressed in both immature and mature stages, including metabolism-related target genes such as GOT2 and FXN. Notably, we identified a subset of genes increased their transcriptional level after the CTCF depletion, accompanied by the decreased chromatin accessibility regions that were enriched with the GATA motif. Specifically, we identified that CTCF repressed the master transcription factor GATA2 with distal decreased chromatin regions via multiple functional studies, including CTCF occupancy profiling and CRISPR/Cas9 editing of the CTCF binding site. These results suggest a suppressive role of CTCF in gene expression in erythroid lineage specification. Conclusions:In summary, our results revealed a novel role of CTCF in regulating erythroid differentiation by maintaining its proper chromatin openness, which will undoubtedly extend our understanding of CTCF biology. Overall design: The HEL cells used in the experiment were knock in cell lines of GFP-miniAID-CTCF constructed by ourselves. We treated the cell lines with drugs for 24 hours, The drugs used included DMSO and IAA. IAA wa used for quick depletion CTCF  protein.
SAMPLE_TITLE: IAA-2-3
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Human bone marrow"}, {"TAG": "tissue", "VALUE": "Human bone marrow"}, {"TAG": "cell line", "VALUE": "HEL, Human erythroleukemia cell"}, {"TAG": "cell type", "VALUE": "Erythroblast"}, {"TAG": "genotype", "VALUE": "mClover3_miniAID_CTCF_homozygous"}, {"TAG": "treatment", "VALUE": "500uM IAA (indole-3-acetic acid)"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: IAA-2-3
RUN_SET_RUN_Pool_Member_@attributes_sample_title: IAA-2-3
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