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E-GEOD-76616 - Genome-wide analyses in neuronal cells reveal that USF transcription factors regulate lysosomal gene expression [ChIP-chip]
Released on 8 January 2016, last updated on 17 January 2016
The upstream stimulating factors (USFs) USF1 and USF2 are ubiquitously expressed transcription factors 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 response 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 preparations. 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 arrays using a neuronal cell line subsequently revealed that knockdown of USFs deregulated lysosomal gene expression. Altered expression was validated by quantitative RT-PCR, supporting the conclusion that USFs regulate lysosomal gene expression. Furthermore, USFs knockdown slightly increased LysoTracker 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. ChIP-chip analysis of USF1 and NF-Y in mouse brain cortex. To identify downstream targets of USF1 and NF-Y in neuronal cells, they were chromatin-immunoprecipitated from mouse brain cortical lysates. The obtained chromatin DNAs were labeled with biotin and hybridized on Affymetrix Mouse Promoter 1.0R Array.
ChIP-chip by tiling array
Tomoyuki Yamanaka <firstname.lastname@example.org>, N Nukina, T Yamanaka