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

We knocked down NF-Y in two types of neuronal cells, neuro2a neuroblastoma cells and sorted brain striatal cells, and performed gene expression profiling. We found that the down-regulated genes preferentially contained NF-Y-binding motifs in their proximal promoters, and notably enriched genes related to ER functions rather than those for cell cycle. These are highly contrast to the profiling data of HeLa and embryonic stem cells in which distinct down-regulation of cell cycle-related genes was observed by NF-Y knockdown. Clustering analysis further identified several functional clusters where populations of the down-regulated genes were highly distinct. Further analyses using chromatin immunoprecipitation and RNA-seq data revealed that transcriptomic difference was not correlated with the DNA binding of NF-Y but with splicing of NF-YA. These data suggest that neuronal cells have a different type of transcriptome in which ER-related genes are dominantly modulated by NF-Y, and imply that NF-YA splicing alteration rather than DNA-binding preference could be involved in this cell type-specific gene modulation. To screen differentially expressed genes in mouse neuro2a cells, the cells were transfected with miR RNAi vectors for NF-YA and NF-YC or an empty vector, and then subjected to microarray analysis using Affymetrix Mouse Gene 1.0 ST Arrays. Obtained microarray data were analyzed using an Agilent GeneSpring GX software to identify differentially expressed genes (DEGs) by gene knockdown.