High-resolution Hi-C reveals increased chromatin looping with senescence associated with hypomethylation and retrotransposon derepression [Hi-C]

This study presents the highest-resolution chromatin map of cellular senescence to date, shedding light on how genomic architecture is altered with this damaging phenotype. Senescence, a driver of aging, is a pro-inflammatory state of proliferative arrest caused by DNA damage; it is associated with epigenetic changes, including those to chromatin organization. We created ~3kb Hi-C contact maps of proliferating, quiescent, and replicative senescent lung fibroblasts, and also compared these to oncogene-induced senescence. Our findings confirm a loss of heterochromatin, with a shift towards the A compartment and A subcompartments. We establish a novel loop analysis framework, revealing the ~six times more unique loops with senescence, which lose methylation at their anchors. Additionally, we present a custom long-read reference genome highlighting structural changes supporting retrotransposon derepression, particularly at a defined ‘hotspot’. These architectural changes contribute to senescence, as they promote cell cycle arrest and inflammation, as well as epigenetic drift. To investigate the role of genomic structure in cellular senescence we generated Hi-C data, total RNA-seq, and long-read DNA sequencing for proliferating and late replicative senescent human diploid lung fibroblasts (LF1). We also generated Hi-C and total RNA-seq for quiescent cells. We compared the proliferating, quiescent, and senescent cell data to determine characteristic architectural features of senescence.

本研究构建了目前分辨率最高的细胞衰老染色质图谱，揭示了该损伤性表型下基因组架构的改变机制。衰老是衰老进程的驱动因素，是由DNA损伤引发的增殖停滞促炎状态，与包括染色质组织异常在内的表观遗传改变密切相关。我们针对增殖态、静息态及复制性衰老的肺成纤维细胞构建了约3kb分辨率的Hi-C（High-throughput Chromosome Conformation Capture）接触图谱，并将其与癌基因诱导性衰老样本进行了对比。本研究结果证实了异染色质丢失现象，且染色质区室发生向A区室及A亚区室的偏移。我们开发了全新的染色质环状结构分析框架，发现衰老样本中独特染色质环状结构的数量增至原有约6倍，且其锚定区域发生甲基化丢失。此外，我们构建了定制化长读长参考基因组，该基因组可凸显支持逆转录转座子去抑制的结构变异，尤其在特定的"热点"区域。这些架构改变通过促进细胞周期停滞、炎症反应及表观遗传漂移，参与细胞衰老进程。为探究基因组架构在细胞衰老中的作用，我们针对增殖态及晚期复制性衰老的人二倍体肺成纤维细胞（LF1）生成了Hi-C、总RNA测序（total RNA-seq）及长读长DNA测序（long-read DNA sequencing）数据；同时针对静息态细胞生成了Hi-C及总RNA测序数据。我们通过对比增殖态、静息态及衰老细胞的测序数据，解析了细胞衰老的特征性基因组架构特征。