EXPERIMENT_TITLE: GSM6599366: HIC_K562_0360min_biorep4_techrep2_seqrep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were crosslinked with 1% formaldehyde for 10 min, quenched with 2.0M glycine for 5 min, washed in PBS, and split into 3x106 cell pellet aliquots in situ Hi-C
STUDY_DESCRIPTOR_STUDY_ABSTRACT: 3D chromatin structure is thought to play a critical role in regulating gene transcription during cellular transitions. While our understanding of loop formation and maintenance is rapidly improving, much less is known about the mechanisms driving changes in looping and the impact of differential looping on gene transcription. One limitation has been a lack of well powered differential looping data sets. To address this, we conducted a deeply sequenced Hi-C time course of megakaryocyte development comprising 4 biological replicates and 6 billion reads per time point. Statistical analysis revealed 1,503 differential loops. Gained loops were enriched for AP-1 occupancy and correlated with increased expression of genes at their anchors. Lost loops were characterized by increases in expression of genes within the loop boundaries. Linear modeling revealed that changes in histone H3K27 acetylation, chromatin accessibility, and JUN binding in between the loop anchors were often just as predictive of changes in loop strength as changes to CTCF and/or cohesin occupancy at loop anchors. Finally, we built linear models and found that incorporating the dynamics of enhancer acetylation and loop strength increased accuracy of gene expression predictions. Together, our well-powered study has added to our understanding of the mechanisms that regulate looping, and the relationship of looping with gene expression. Overall design: Hi-C of K562 cells treated with PMA to differenitate into a megakaryocyte-like state after 0, 6, or 72h
SAMPLE_TITLE: HIC_K562_0360min_biorep4_techrep2_seqrep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "K562"}, {"TAG": "cell line", "VALUE": "K562"}, {"TAG": "cell type", "VALUE": "Human leukemia"}, {"TAG": "genotype", "VALUE": "WT"}, {"TAG": "treatment", "VALUE": "PMA (megakaryocyte differentiation)"}]
Pool_Member_@attributes_sample_title: HIC_K562_0360min_biorep4_techrep2_seqrep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HIC_K562_0360min_biorep4_techrep2_seqrep2
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