USF2 and TFEB compete in regulating lysosomal and autophagy genes

• Published in: Nature communications Vol. 15; no. 1; pp. 8334 - 17
• Main Authors: Kim, Jaebeom, Yu, Young Suk, Choi, Yehwa, Lee, Do Hui, Han, Soobin, Kwon, Junhee, Noda, Taichi, Ikawa, Masahito, Kim, Dongha, Kim, Hyunkyung, Ballabio, Andrea, Kim, Keun Il, Baek, Sung Hee
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 27.09.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 14/19; 14/28; 42/41; 42/89; 45; 45/15; 45/90; 45/91; 631/337/100; 631/337/176; 631/337/572; 631/80/39; 82/29; 82/58; 82/80; 96/1; 96/109; Acetylation; Animals; Autophagy; Autophagy - genetics; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors - genetics; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors - metabolism; Chromatin; Competition; Gene expression; Gene Expression Regulation; Gene silencing; Genes; Glycogen Synthase Kinase 3 beta - genetics; Glycogen Synthase Kinase 3 beta - metabolism; HEK293 Cells; HeLa Cells; Histone deacetylase; Histone Deacetylase 1 - genetics; Histone Deacetylase 1 - metabolism; Histones; Histones - metabolism; Homeostasis; Humanities and Social Sciences; Humans; Lysosomes - metabolism; Mice; multidisciplinary; NuRD protein; Nutrients; Phosphorylation; Promoter Regions, Genetic; Protein deficiency; Protein interaction; Science; Science (multidisciplinary); Upstream stimulating factor 2; Upstream Stimulatory Factors - genetics; Upstream Stimulatory Factors - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-52600-2

Autophagy, a highly conserved self-digestion process crucial for cellular homeostasis, is triggered by various environmental signals, including nutrient scarcity. The regulation of lysosomal and autophagy-related processes is pivotal to maintaining cellular homeostasis and basal metabolism. The consequences of disrupting or diminishing lysosomal and autophagy systems have been investigated; however, information on the implications of hyperactivating lysosomal and autophagy genes on homeostasis is limited. Here, we present a mechanism of transcriptional repression involving upstream stimulatory factor 2 (USF2), which inhibits lysosomal and autophagy genes under nutrient-rich conditions. We find that USF2, together with HDAC1, binds to the CLEAR motif within lysosomal genes, thereby diminishing histone H3K27 acetylation, restricting chromatin accessibility, and downregulating lysosomal gene expression. Under starvation, USF2 competes with transcription factor EB (TFEB), a master transcriptional activator of lysosomal and autophagy genes, to bind to target gene promoters in a phosphorylation-dependent manner. The GSK3β-mediated phosphorylation of the USF2 S155 site governs USF2 DNA-binding activity, which is involved in lysosomal gene repression. These findings have potential applications in the treatment of protein aggregation-associated diseases, including α1-antitrypsin deficiency. Notably, USF2 repression is a promising therapeutic strategy for lysosomal and autophagy-related diseases. Here, the authors show that USF2 epigenetically represses autophagy and lysosomal genes by recruiting NuRD complex and competing with TFEB. USF2 depletion enhances these processes, offering a potential therapeutic strategy for aggregate diseases.