EXPERIMENT_TITLE: GSM4869583: HIC_Reenter_TOP2A2B_control_rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Arima HIC KIT
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Mammalian chromosomes are three-dimensional entities shaped by converging and opposing forces acting on chromatin. Mitotic cell division induces drastic chromatin condensation, but following reentry into the G1 cell cycle phase, condensed chromosomes unwind to re-establish interphase organization. Here, we use a cell line allowing auxin-mediated degradation of RNA polymerase II to test its role in this transition. In situ Hi-C and super-resolution imaging showed that RNAPII is required for compartment and loop formation following mitosis. RNAPs also often counteract loop extrusion and, in their absence, longer and more prominent loops arise. Evidence from chromatin fractionation and in silico modeling attribute these effects to RNAPII-mediated cohesin loading at active promoters upon G1 reentry. Our findings reconcile the role of RNAPII in gene expression with that in chromatin architecture. Overall design: HiC sequencing in DLD1 cells
SAMPLE_TITLE: HIC_Reenter_TOP2A2B_control_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "colorectal adenocarcinoma cell lines"}, {"TAG": "cell line", "VALUE": "TOP2Bknockout_2A-mAID_HCT116"}, {"TAG": "cell type", "VALUE": "colorectal adenocarcinoma"}, {"TAG": "cell cycle", "VALUE": "synchronous G1 reenter sorted"}, {"TAG": "treatment", "VALUE": "untreated"}]
Pool_Member_@attributes_sample_title: HIC_Reenter_TOP2A2B_control_rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HIC_Reenter_TOP2A2B_control_rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR12914640.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR012/12914/SRR12914640/SRR12914640.lite.1", "size": "13613379384", "date": "2022-08-09 18:33:03", "md5": "02cf0e33ba59b739d28238138367d60a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR12914640", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12914640/SRR12914640", "size": "16034483844", "date": "2020-10-27 18:07:05", "md5": "057bba64b8dfbcd4717a7b2d30428f7a", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A006850084_128288_S12_L001_R2_001.fastq.gz", "size": "14037346741", "date": "2020-10-27 17:56:00", "md5": "5005355db6ad8f25780ef2fc64142ffe", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A006850084_128288_S12_L001_R1_001.fastq.gz", "size": "13494301534", "date": "2020-10-27 17:49:56", "md5": "fad45016432d3eb6e4dcadc73c2cf92d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]