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

• Published in: PloS one Vol. 17; no. 1; p. e0262488
• Main Authors: Igata, Tomoka, Tanaka, Hiroshi, Etoh, Kan, Hong, Seonghyeon, Tani, Naoki, Koga, Tomoaki, Nakao, Mitsuyoshi
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 27-01-2022; Public Library of Science (PLoS)
• Subjects: Aging; Animals; Antibodies; ATP citrate lyase; Biology; Biology and Life Sciences; Cell cycle; Cell division; Cell Nucleolus - genetics; Cell Proliferation - genetics; Cells; Cellular Senescence - genetics; Chromatin; Chromatin - genetics; Cyclin-dependent kinase; Cyclin-Dependent Kinase Inhibitor p16 - genetics; DNA methylation; DNA Replication - genetics; Down-Regulation - genetics; Embryology; Enzyme inhibitors; Epigenomics - methods; Experiments; Female; Fibroblasts; Fibroblasts - physiology; Gene expression; Gene Expression - genetics; Gene Expression Regulation - genetics; Genes; Genetic aspects; Genetic transcription; Homeobox; Homeodomain Proteins - genetics; Humans; Immunoprecipitation; INK4a protein; Kinases; Lysine; Male; Mass spectrometry; Mass spectroscopy; Metabolism; Mice; Mice, Inbred C57BL; Mitochondria; Mitochondria - genetics; Muscles; Nucleoli; Nucleolus organizer region; p16 Protein; Physiological aspects; Proteins; Proteomics; Reagents; Repressor Proteins - genetics; Research and Analysis Methods; Ribonucleic acid; RNA; RNA, Ribosomal - genetics; RNA-mediated interference; rRNA; Senescence; Skeletal muscle; Transcription; Transcription Initiation Site - physiology; Up-Regulation - genetics; Zinc finger proteins; Japan; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0262488

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.