Loss of the transcription repressor ZHX3 induces senescence-associated gene expression and mitochondrial-nucleolar activation.

Tomoka Igata,Seonghyeon Hong,Naoki Tani,Tomoaki Koga,Hiroshi Tanaka,Kan Etoh,Mitsuyoshi Nakao,Wei Cui

doi:10.1371/journal.pone.0262488

Abstract

Cellular senescence is accompanied by metabolic and epigenomic remodeling, but the transcriptional mechanism of this process is unclear. Our previous RNA interference-based screen of chromatin factors found that lysine methyltransferases including SETD8 and NSD2 inhibited the senescence program in cultured fibroblasts. Here, we report that loss of the zinc finger and homeobox protein 3 (ZHX3), a ubiquitously expressed transcription repressor, induced senescence-associated gene expression and mitochondrial–nucleolar activation. Chromatin immunoprecipitation–sequencing analyses of growing cells revealed that ZHX3 was enriched at the transcription start sites of senescence-associated genes such as the cyclin-dependent kinase inhibitor (ARF-p16INK4a) gene and ribosomal RNA (rRNA) coding genes. ZHX3 expression was consistently downregulated in cells with replicative or oncogene-induced senescence. Mass spectrometry-based proteomics identified 28 proteins that interacted with ZHX3, including ATP citrate lyase and RNA metabolism proteins. Loss of ZHX3 or ZHX3-interaction partners by knockdown similarly induced the expression of p16INK4a and rRNA genes. Zhx3-knockout mice showed upregulation of p16INK4a in the testes, thymus and skeletal muscle tissues, together with relatively short survival periods in males. These data suggested that ZHX3 plays an essential role in transcriptional control to prevent cellular senescence.

Highlights

Cellular senescence is characterized by persistent growth arrest, senescence-associated (SA)-βgalactosidase positivity and the senescence-associated secretory phenotype, which plays important roles in tissue development, tumor suppression and aging in vivo [1,2,3,4]
Levels of transcription for cyclin-dependent kinase inhibitor (p16INK4a), inflammatory cytokines (IL-1A/1B) and nucleolus-related ribosomal RNA genes were upregulated in zinc finger and homeobox protein 3 (ZHX3)-KD cells (Fig 1F; p14ARF results shown in S1D Fig)
RNA interference-based screening revealed that loss of the transcription repressor ZHX3 induced cellular senescence in human fibroblasts

Summary

Introduction

Cellular senescence is characterized by persistent growth arrest, senescence-associated (SA)-βgalactosidase positivity and the senescence-associated secretory phenotype, which plays important roles in tissue development, tumor suppression and aging in vivo [1,2,3,4]. The senescent cells exhibit enlarged cell size and increased protein content due to the remodeling of various metabolic pathways including protein synthesis and degradation, and mitochondrial oxidative phosphorylation (OXPHOS) [1, 5]. Senescent cells have higher activities in ribosome biogenesis and OXPHOS than proliferating cells [7,8,9,10,11]. Metabolic stresses such as loss of proteostasis and mitochondrial dysfunction lead to senescent state [1]. Several lines of evidence suggest that metabolic and epigenomic remodeling cooperatively create these features of senescent cells [4], it is still undetermined whether such reprogram is a cause or consequence of cellular senescence

Methods

Results

Conclusion