The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence

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.

异染色质重塑对多种细胞进程至关重要。具体而言，细胞衰老过程中出现的"异染色质丢失"表型与衰老及衰老相关疾病的进展密切相关。尽管已明确衰老细胞的诸多生物学进程——包括衰老相关异染色质灶（senescence-associated heterochromatin foci, SAHF）形成、染色体凝缩及衰老进程启动——均与高阶染色质结构紧密相关，但衰老过程中高阶染色质组织与异染色质丢失表型之间的关联尚未完全阐明。本研究利用携带"异染色质丢失"表型、由DNA损伤诱导的衰老及晚期衰老成纤维细胞，观察到衰老过程中异染色质的三维结构发生渐进性重排。分别由H3K27me3和H3K9me3标记的兼性异染色质与组成型异染色质，呈现出不同的改变模式：兼性异染色质倾向于从抑制性B区室切换至激活型A区室，而组成型异染色质在区室水平无显著变化，但自身间的相互作用增强。有趣的是，两类异染色质在衰老过程中均表现出染色质可及性升高及基因表达渗漏现象。进一步研究发现，组成型异染色质中潜在CTCF结合位点的染色质可及性增加，并伴随新型环状染色质结构的形成。此外，本研究还观察到包括长末端重复序列（long terminal repeat, LTR）及卫星序列在内的重复元件的异常表达。综上，兼性异染色质与组成型异染色质在三维染色质图谱中呈现出多尺度但各异的改变模式，同时二者也共享染色质可及性升高与基因表达渗漏这一共同特征。本研究绘制了衰老过程中异染色质重塑的表观基因组图谱。整体实验设计：以人类二倍体BJ成纤维细胞为模型，构建增殖期、静息期、衰老期及深度衰老期共5种细胞状态，并分别进行Hi-C、ATAC-seq、RNA-seq及ChIP-seq实验。