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

Area of Science:

• Molecular Biology
• Neuroscience
• Cell Biology

Background:

• The transcription factor NF-Y (Nuclear Factor Y) is vital for cell-cycle progression.
• NF-Y also plays a critical role in endoplasmic reticulum (ER) homeostasis, particularly in neuronal cells.
• The distinct transcriptomic modulation by NF-Y in different cell types remains unclear.

Purpose of the Study:

• To investigate whether NF-Y modulates different transcriptomes to mediate distinct cellular functions in neuronal cells.
• To compare NF-Y's transcriptomic targets in neuronal cells with those in non-neuronal cells.

Main Methods:

• NF-Y was knocked down in neuro2a neuroblastoma and mouse brain striatal cells.
• Gene expression profiling was performed to analyze transcriptomic changes.
• Chromatin immunoprecipitation (ChIP) and RNA sequencing (RNA-seq) were used to analyze DNA binding and splicing.

Main Results:

• Down-regulated genes in neuronal cells were enriched for ER function genes, contrasting with cell cycle genes found in HeLa and embryonic stem cells.
• Clustering analysis revealed distinct functional clusters of down-regulated genes.
• Transcriptomic differences were correlated with NF-YA splicing, not NF-Y DNA binding.

Conclusions:

• Neuronal cells exhibit a unique transcriptome where NF-Y predominantly modulates ER-related genes.
• Alterations in NF-YA splicing may underlie cell type-specific gene modulation by NF-Y.