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. Overall design: Using the ChIP-seq strategy to establish epigenome signatures and generate a wide-spectrum chromatin landscape of senescent human stromal cells, the major components of tissue microenvironment in diverse solid organs. To profile the genomic DNA sequences associated with histone H3-specific alterations including H3K9me3 and H3K36me3, and to identify epigenomes that are highly occupied by these H3 sites but potentially subject to significant changes in the course of cellular senescence. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of human stromal cells. We find that lysine 9 and lysine 36 trimethylation of histone H3 effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect a distinct cellular state between proliferation and senescence or cell cycle arrest, and image overall expression status. Finally, we show that chromatin state can be read in a spatiotemporal and cell lineage-specific manner when systematically taking advantage of ChIP-seq, ATAC-seq and RNA-seq data. This study provides a basic framework for future application of comprehensive chromatin profiling towards characterization of human senescent cells in the course of organismal aging.