EXPERIMENT_TITLE: GSM4194454: 60 min-Hi-C-r2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed as previously described (Lieberman-Aiden et al. 2009). Briefly, U2OS cells (2 × 106) were cross-linked with formaldehyde. Chromatin was digested with a restriction enzyme Hind III (NEB), biotinylated with biotin-ATP (Life Technologies), and then ligated with T4 DNA ligase (NEB). DNA was purified and sheared with Covaris LE220 instrument (Covaris). Biotinylated DNA interactions were pulled down with Dynabeads MyOne Streptavin T1 Beads (Life Technologies) and ligated with indexed Illumina Truseq adapters. Amplified libraries were sequenced with Illumina Novoseq platform using the S4 flow cell.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: During mitosis, transcription of genomic DNA is dramatically reduced, before its reactivation occurs during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. In combination with EU-RNA-seq and Hi-C analyses, we show that, during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers harboring mitotic H3K4me1 are associated with cell type-specific transcription factor motifs and mitotic activation of cell identity genes. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC binding factors (CTCF) in anaphase/telophase. This increase may play a role in the establishment of topologically associating domains (TADs). Together, our results show that the genome is reorganized in sequential order, in which histone methylations occur first in prometaphase, histone acetylation and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. Our results provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division. Overall design: Hi-C during mitosis-G1 in U2OS cells
SAMPLE_TITLE: 60 min-Hi-C-r2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "U2OS osteosarcoma cell line"}, {"TAG": "cell line", "VALUE": "U2OS"}, {"TAG": "cell cycle phase", "VALUE": "Cytokinesis"}]
Pool_Member_@attributes_sample_title: 60 min-Hi-C-r2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: 60 min-Hi-C-r2
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