EXPERIMENT_TITLE: GSM4367041: Hi-C_HL60_KO_DKO_1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C experiments were performed using WT-, SKO-, RKO-, or DKO-cells. Briefly, two million cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Cells were permeabilized and chromatin was digested with MboI restriction enzyme, and the ends of restriction fragments were labeled with biotinylated nucleotides and ligated.  After crosslink reversal, DNA was purified and sheared with Covaris M220 (Covaris).  Then point ligation junctions were pulled down with streptavidin beads.  Then libraries were constructed with Nextera Mate Pair Sample Preparation Kit (Illumina) according to the manufacturer's protocol, and subject to sequencing using NovaSeq (Illumina).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: STAG2 encodes a cohesin component and is frequently mutated in myeloid neoplasms, showing highly significant co-mutation patterns with other drivers, including RUNX1. However, the molecular basis of cohesin-mutated leukemogenesis remains poorly understood. Here we show a critical role of an interplay between Stag2 and Runx1 in the regulation of enhancer-promoter looping and transcription in hematopoiesis. Combined loss of Stag2 and Runx1, which co-localize at enhancer-rich, Ctcf-deficient sites, synergistically attenuates enhancer-promoter loops, particularly at sites enriched for RNA polymerase II and Mediator, and deregulates gene expression, leading to myeloid-skewed expansion of hematopoietic stem/progenitor cells (HSPCs) and myelodysplastic syndromes (MDS). Attenuated enhancer-promoter loops in Stag2/Runx1-deficient cells are associated with downregulation of genes with high basal transcriptional pausing, which are important for the regulation of HSPCs. Down-regulation of high-pausing genes is also confirmed in STAG2/cohesin-mutated primary AML/MDS samples. Our results highlight a unique STAG2/RUNX1 interplay in gene regulation and provide insights into cohesin-mutated leukemogenesis. Overall design: Comprehensive epigenome sequencing (RNA-seq, ATAC-seq, ChIP-seq and Hi-C) in WT, Stag2 knockout, Runx1 knockout, and double knockout cells.
SAMPLE_TITLE: Hi-C_HL60_KO_DKO_1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HL-60"}, {"TAG": "cell line", "VALUE": "HL-60"}, {"TAG": "genotype", "VALUE": "STAG2/RUNX1 KO"}]
Pool_Member_@attributes_sample_title: Hi-C_HL60_KO_DKO_1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_HL60_KO_DKO_1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR11207826.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR011/11207/SRR11207826/SRR11207826.lite.1", "size": "55770586605", "date": "2022-06-12 13:19:22", "md5": "4c0b557c93138b9eac4791bcbba18eba", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR11207826", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11207826/SRR11207826", "size": "68081073245", "date": "2020-03-23 05:56:58", "md5": "4afe76c25744c786a8f3151ea57c4855", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_HL_D34_S7_R2_001.fastq", "size": "400493394588", "date": "2020-03-23 02:36:36", "md5": "5b322aa08db35a75d0c6cf867e8ae6ff", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_HL_D34_S7_R1_001.fastq", "size": "193045921792", "date": "2020-03-23 04:38:42", "md5": "b10943654e058141621a41f0f3b17d85", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]