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. Database The data for the gene expression array and ChIP‐chip have been submitted to the Gene Expression Omnibus (GEO) under accession numbers http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76615 and http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76616, respectively.

Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y

“…1 D), which may be simply reflecting the CpG richness around TSSs. The proximal CCAAT motif-enrichment was not observed for genes picked up randomly or those dysregulated by knockdown of other transcription factors, USF1/2 27 , whereas USF1/2-binding E-box motifs were enriched in the latter case (Supplementary Fig. S2 E,F).…”

“…We next examined whether the difference in NF-Y-transcriptome is due to the difference in NF-Y-binding in these cells. For this purpose, we analyzed three sequence data for chromatin immunoprecipitation (ChIP-seq) of NF-Y from different types of cells; undifferentiated ES (ES-UD) 14 , neurally differentiated ES (ES-ND) 30 , and HeLa-S3 cells 31 ; as well as our previous ChIP-chip data for mouse brain cortex 27 . We identified 600–1400 of potential NF-Y target genes that contain ChIP peak(s) within 2 Kbp to their TSSs (Fig.…”

Histone deacetylase inhibitor apicidin increases expression of the α‐secretase ADAM10 through transcription factor USF1‐mediated mechanisms

“…USF1 also up‐regulates expression of APP and BDNF genes (51, 52), the latter of which is involved in memory formation and synaptic activity (53, 54). Of interest, USF1 binding to CACGTG E‐box motifs regulates lysosomal gene expression in neuronal cells (55). Deregulated autophagy that is associated with lysosomal activity has also been suggested in the pathology of AD (56).…”

Differential roles of NF-Y transcription factor in ER chaperone expression and neuronal maintenance in the CNS

“…To our knowledge, this is the first report describing the cell type-specific role of ubiquitous transcription factor in the CNS. Because neuronal significance has been reported for other ubiquitous factors 3 4 5 6 7 8 9 10 , further studies focusing on these factors may provide additional mechanisms underlying generation/maintenance of various types of neurons in the CNS. This could also lead to identification of novel mechanisms underlying cell/tissue-specific degeneration often observed in many neurodegenerative diseases and novel therapeutic targets for these diseases.…”

“…Neuronal type-specific transcription factors, called master factors, have been shown to play critical roles in generation and maintenance of the neurons by transcribing specific sets of genes 1 . On the other hands, recent observations identified significance of ubiquitous transcription factors in neuronal differentiation and maintenance 2 3 4 5 6 7 8 9 10 . However, it is still uncertain whether the ubiquitous factors have conserved or differential roles in multiple types of CNS neurons.…”