EXPERIMENT_TITLE: GSM5417202: U2OS_siCtrl_HiC_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The cross-linked cells were lysed in lysis buffer,fragmentation of the genome using restriction enzymes Hi-C libraries were prepared for sequencing using standard Illumina protocols
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Spatiotemporal regulation of chromatin replication (replication timing, RT) in eukaryotes is critical to maintain the genomic integrity. Here we focused on epigenetic mechanisms in rewiring genomic 3D conformation and replication timing. The results show that the novel lysine ß-hydroxybutyrylation (Kbhb) modifications accelerates chromatin replication without inducing replication defects. This effect was mediated by the NAT10, a novel b-hydroxybutyryl-transferase, through regulating the association of NAT10 and CTCF with chromatin. Depletion of NAT10 and NAT10-mediated Kbhb dramatically reduce chromatin-bound NAT10 and CTCF, resulting in reorganization of genomic 3D conformation with enhanced trans- and cis-interaction in Hi-C matrix, with elevated proportion of A compartments, and with reorganized TADs boundaries. Moreover, reorganization of genomic 3D conformation contributes to rewire replication timing. These results support models in which NAT10-mediated ß-hydroxybutyrylation coordinates genomic 3D conformation reorganization with replication timing alteration, and emphatically address the concept that epigenetic mechanisms reconcile genomic 3D conformation with replication timing. Overall design: Hi-C sequencing was performed in two biological replicates on ß-hydroxybutyrate (BHB) treated control (siCtrl) or NAT10 knock-down (siNAT10) U2OS cells.
SAMPLE_TITLE: U2OS_siCtrl_HiC_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "U2OS cells"}, {"TAG": "cell type", "VALUE": "U2OS cells"}, {"TAG": "genotype", "VALUE": "control"}, {"TAG": "treatment", "VALUE": "untreated"}]
Pool_Member_@attributes_sample_title: U2OS_siCtrl_HiC_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: U2OS_siCtrl_HiC_rep2
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