Genome-wide mapping to profile histone H3-associated epigenetic marks and chromatin conformation in senescent human stromal cells

Cellular senescence, one of the major driving forces of organismal aging and age-related pathologies, is modulated by interconnected molecular changes. Combinational analysis of high-throughput 'multi-omics' datasets can provide a multi-dimensional and integrated profile of cellular senescence to unravel the heterogeneous aging process with unprecedented throughput and details.Linear chromatin is compacted into eukaryotic nucleus through a complex and multi-layered architecture. Consequently, chromatin conformation in a local or long-distance manner is strongly correlated with gene expression. Epigenetic study approaches such as chromosome conformation capture (3C) technology, together with its variants like 4C/5C/Hi-C, have been well developed to characterize chromatin looping and whole genome structure. DNA-binding proteins, including transcription factors, epigenetic and chromatin modifiers, govern gene expression in a highly intricate manner. To pinpoint the binding sites of DNA-binding proteins is crucial for decoding gene regulatory networks. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a widely used technique to identify DNA regions bound by a specific protein. Information derived from ChIP-seq has tremendously advanced the research of mechanisms of transcription factors, cofactors and histone modifications in regulating gene expression during cellular senescence.