EXPERIMENT_TITLE: GSM3905160: Foreskin fibroblasts, Hi-C reversal of senescence rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: 1-2 million of cells were fixed with 1% formaldehyde at room temperature for 10 min. Formaldehyde was quenched with glycine for 10min at room temperature. cells were lysed and digested with MboI overnight with rotation. MboI was then inactivated at 62℃ for 20 minutes. After filling in with biotin-14-dCTP, the fragments were ligated at room temperature for 5.5 hours with rotation. Then reversal of crosslink and DNA purification was done. The biotin-labeled DNA was sheared to 300-500bp with Covaris M220 and then pulled down with Dynabeads MyOne Streptavidin C1 (Life Technology). Sequencing library preparation was performed on beads, including end-repair, dATP tailing and adaptor-ligation. ­­9 cycles of PCR amplification were performed with Extaq (Takara). Finally, size selection was done with AMPure XP beads and fragments ranging from 300bp to 500bp were selected. Truseq
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Heterochromatin remodeling is critical for various cell processes. In particular, the “loss of heterochromatin” phenotype in cellular senescence engages with the progress of aging and age-related disorders. Although biological processes of senescent cells including senescence-associated heterochromatin foci (SAHF) formation, chromosome compaction and entry into senescence have been closely associated with high-order chromatin structure. the relationship between the high-order chromatin organization and the loss of heterochromatin phenotype during senescence has not been fully understood. By using senescent and late senescent fibroblasts induced by DNA damage harboring the “loss of heterochromatin” phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, showed different alterations. Facultative heterochromatin tends to switch from the repressive B-compartment to the active A-compartment, whereas constitutive heterochromatin shows no significant changes at the compartment level but enhanced interactions between themselves. Interestingly, both types show increased chromatin accessibility and gene expression leakage during senescence. Furthermore, increased chromatin accessibility in potential CTCF binding sites accompanies by the establishment of novel loops in constitutive heterochromatin. Finally, we also observed aberrant expression of repetitive elements, including LTR (long terminal repeat) and satellite classes. Overall, facultative and constitutive heterochromatin show multiscale but distinct alterations in the 3D map, meanwhile they also share the same features of increased chromatin accessibility and gene expression leakage. This study provides an epigenomic map of heterochromatin reorganization during senescence. Overall design: We build five cell states including growing, quiescence, senescence, deep senescence with human diploid BJ fibroblasts and carried out Hi-C, ATAC-seq,RNA-seq and ChIP-seq.
SAMPLE_TITLE: Foreskin fibroblasts, Hi-C reversal of senescence rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "foreskin fibroblast"}, {"TAG": "cell line", "VALUE": "human diploid BJ fibroblasts"}, {"TAG": "cell state", "VALUE": "reversal of senescence"}]
Pool_Member_@attributes_sample_title: Foreskin fibroblasts, Hi-C reversal of senescence rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Foreskin fibroblasts, Hi-C reversal of senescence rep1
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