Abstract SY10-01: Chromatin structure change and aberrant gene expression during senescence
Authors: Narita Masashi 
Published: August 2015

Abstract
Cellular senescence is a highly ‘stable’ state of cell cycle arrest induced by various pathophysiological stimuli, including: telomere dysfunction; abnormal mitotic stress; DNA damage, and; some types of cytokines. Senescent cells typically exhibit distinct morphological changes, including: enlargement of both the cytoplasm and nucleus; prominent nucleoli; and cytoplasmic vacuoles. In addition, a number of biochemical and molecular markers of senescence have been described, which are summarized in our recent review articles.
While it is widely accepted that both of the p53 and p16/RB tumor suppressor pathways are involved in senescence, the precise mechanisms underling the phenotype are still elusive. The senescence phenotype can be heterogeneous and, dependent on the stress or cell type, the ‘quality’ of the phenotype varies. Importantly, several ‘effector mechanisms’ that can modulate the senescence phenotype have been identified, including: senescence associated heterochromatic foci (SAHFs) and epigenetic gene regulation; the DNA damage response (DDR); senescence associated secretory phenotype (SASP); and the autophagy/mTOR pathway. Senescence markers are often associated with senescence effectors, and combinations of these markers and effectors have been useful in extending the concept of the senescence quality, not only within cultured cell models but also to in vivo systems.
We, and others, have previously shown that normal human diploid fibroblasts (HDFs) often exhibit dramatic heterochromatin (HC) alterations during senescence (i.e. SAHFs) in a p16/RB dependent manner and have proposed that SAHF formation is associated with the stability of the phenotype. SAHFs were originally described in oncogene-induced senescence (OIS) and, to a lesser extent, in replicative and DNA damage-induced senescent HDFs. Thus the intensity to which SAHFs are provoked appears to be context dependent. In addition, non-histone chromosomal architectural proteins, HMGA1 and HMGA2, which have been implicated in cancer, are essential structural components of SAHFs. Depletion of HMGA1 in particular disrupts SAHFs almost completely, rendering senescence arrest unstable. We have recently shown that SAHFs are distinct non-overlapping multi-layer structures, in which H3K9me3 (a constitutive HC mark) is enriched in the ‘core’ of SAHFs, surrounded by a layer of H3K27me3 (a facultative HC mark), which separates the core from the transcriptionally active H3K4/36me3 regions. The data also suggest that this multi-layered structure of HC is achieved through a ‘spatial reorganization’ of pre-existing HC without the massive spreading of HC. It was recently reported that Lamin B1, which forms a fibrillar network at nuclear lamina, is down-regulated during senescence. Constitutive HC is often associated with the nuclear envelope in mammals, and our data suggest that the depletion of Lamin B1 disrupts the HC anchoring to nuclear lamina and facilitates its spatial repositioning during senescence. In addition, a series of studies from the Adams laboratory have shown that, as an early event in senescence, translocation of the HIRA histone chaperone complex to PML bodies is required for SAHF formation. Thus SAHF formation appears to involve multiple events and ‘modular processes’. However, how individual gene regulation is associated with SAHFs remains to be elucidated.
The p53 transcription factor is a frequently mutated tumor suppressor. Levels of p53 are typically regulated through its stability, thus, upon stress stimuli, p53 can be up-regulated very quickly. This acutely induced p53 has been used as a major model system for studying genome-wide p53 targets. However, the long-term activation of p53 might be more important in chronic phenotypes such as senescence. We have investigated genome-wide p53 DNA binding profiles in our HDF model, where we can acutely (acute DDR, acDDR) or chronically (OIS) activate p53. Our data suggest that acute- and chronic-p53 profiles are highly distinctive, with the latter being preferentially associated with CpG islands. In addition, our preliminary data suggest that during OIS p53 can also bind uniquely to a region called the epidermal differentiation complex (a tissue specific gene complex, which is heterochromatic in fibroblasts) where the genes are stably silenced. This locus is enriched for both H3K9me3 and Lamin B1, and is primarily located at the nuclear periphery in normal HDFs. During OIS, this locus appears to be internalized and spread in the inter-SAHF space. In addition, some genes within the locus are specifically expressed in OIS cells in a p53-dependent manner, reinforcing the critical role for the spatial reorganization of the genome in gene regulation. Currently we are investigating a functional role for such ‘ectopic’ gene regulation by p53 during senescence.
Citation Format: Masashi Narita. Chromatin structure change and aberrant gene expression during senescence. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr SY10-01. doi:10.1158/1538-7445.AM2015-SY10-01