EXPERIMENT_TITLE: GSM7081349: HiC_sgBPTF_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed using the Arima Hi-C Kit according to the manufacturer's protocol. Hi-C was performed using the Arima Hi-C Kit according to the manufacturer's protocol.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Efficient treatment of Acute Myeloid Leukemia (AML) patients remains a challenge despite recent advances. Here using a CRISPRi screen targeting chromatin factors, we identified BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader modules of BPTF are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML. Overall design: Cells transduced with either a non-targeting sgRNA (sgNegCtrl, 2 biological replicates) or sgRNAs inducing knockout of BPTF (2 biological replicates) or SMARCA5 (2 biological replicates)
SAMPLE_TITLE: HiC_sgBPTF_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "blood"}, {"TAG": "tissue", "VALUE": "blood"}, {"TAG": "cell line", "VALUE": "THP-1"}, {"TAG": "cell type", "VALUE": "monocyte"}, {"TAG": "genotype", "VALUE": "BPTF KO"}, {"TAG": "treatment", "VALUE": "lentiviral transduction"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: HiC_sgBPTF_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_sgBPTF_rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "BPTF-2-HiC_IGO_10579_4_S4_R1_001.fastq.gz", "size": "19736705105", "date": "2023-03-06 12:36:48", "md5": "23c1ce4ea06e8f3c945547ef408cc6ee", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "BPTF-2-HiC_IGO_10579_4_S4_R2_001.fastq.gz", "size": "20522169167", "date": "2023-03-06 12:37:57", "md5": "b8d46e099144866e79b2f02075ad8e30", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR23705178", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-run-36/SRR023/23705/SRR23705178/SRR23705178.1", "size": "24112560917", "date": "2023-03-06 12:41:16", "md5": "cad92ec0a3fd1bb8b5f5b537e9ae75ab", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]