title: Genome-wide analyses in neuronal cells reveal that upstream transcription factors regulate lysosomal gene expression.
abstract: The upstream transcription factors (USFs) USF1 and USF2 are ubiquitously expressed transcription factors that are characterized by a conserved basic helix-loop-helix/leucine zipper DNA-binding domain. They form homo- or heterodimers, and recognize E-box motifs to modulate gene expression. They are known to regulate diverse cellular functions, including the cell cycle, immune responses and glucose/lipid metabolism, but their roles in neuronal cells remain to be clarified. Here, we performed chromatin immunoprecipitation of USF1 from mouse brain cortex. Subsequent promoter array analysis (ChIP-chip) indicated that USF1 exclusively bound to the CACGTG E-box motifs in the proximal promoter regions. Importantly, functional annotation of the USF1-binding targets revealed an enrichment of genes related to lysosomal functions. Gene expression array analysis using a neuronal cell line subsequently revealed that knockdown of USFs de-regulated lysosomal gene expression. Altered expression was validated by quantitative RT-PCR, supporting the conclusion that USFs regulate lysosomal gene expression. Furthermore, USF knockdown slightly increased LysoTracker Red staining, implying a role for USFs in modulating lysosomal homeostasis. Together, our comprehensive genome-scale analyses identified lysosomal genes as targets of USFs in neuronal cells, suggesting a potential additional pathway of lysosomal regulation.
  
  
  METHODS
  The data for the gene expression array and ChIP-chip have been submitted to the Gene Expression Omnibus (GEO) under accession numbers GSE76615 and GSE76616, respectively.
authors.affiliation: Laboratory of Structural Neuropathology, Doshisha University Graduate School of Brain Science, Kyoto, Japan.|Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.|Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan.|Laboratory for Molecular Mechanisms of Thalamus Development, RIKEN Brain Science Institute, Saitama, Japan.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Yamanaka
authors.affiliation: Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.
authors.forename: Asako
authors.initials: A
authors.lastname: Tosaki
authors.affiliation: Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.|Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Kurosawa
authors.affiliation: Laboratory for Molecular Mechanisms of Thalamus Development, RIKEN Brain Science Institute, Saitama, Japan.
authors.forename: Tomomi
authors.initials: T
authors.lastname: Shimogori
authors.affiliation: Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan.
authors.forename: Nobutaka
authors.initials: N
authors.lastname: Hattori
authors.affiliation: Laboratory of Structural Neuropathology, Doshisha University Graduate School of Brain Science, Kyoto, Japan.|Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.|Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan.|Laboratory for Molecular Mechanisms of Thalamus Development, RIKEN Brain Science Institute, Saitama, Japan.
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Nukina
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D002460:Cell Line; D002540:Cerebral Cortex / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D024721:E-Box Elements; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D055106:Genome-Wide Association Study; D008247:Lysosomes / Q000235:genetics* / Q000378:metabolism*; D008297:Male; D051379:Mice; D008808:Mice, Inbred CBA; D009474:Neurons / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D051720:Upstream Stimulatory Factors / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*
chemical_list: D051720:Upstream Stimulatory Factors; C497183:Usf1 protein, mouse; C497186:Usf2 protein, mouse
keywords: chromatin immunoprecipitation; lysosome; microarray; neuron; transcription factor