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E-GEOD-56838 - Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors [gene expression]

Status
Released on 14 August 2014, last updated on 26 August 2014
Organism
Mus musculus
Samples (15)
Array (1)
Protocols (6)
Description
Cell type-specific master transcription factors (MTFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that all three subunits of the ubiquitous heterotrimeric CCAAT-binding NF-Y complex are required for the maintenance of embryonic stem cell (ESC) identity, and establish NF-Y as a novel component of the core pluripotency network. Genome-wide occupancy and transcriptomic analyses in ESCs and neurons reveal that not only does NF-Y regulate genes with housekeeping functions through cell type-invariant promoter-proximal binding, but also genes required for cell identity by binding to cell type-specific enhancers with MTFs. Mechanistically, NF-Y's distinctive DNA-binding mode promotes MTF binding at enhancers by facilitating a permissive chromatin conformation. Our studies unearth a novel function for NF-Y in promoting chromatin accessibility, and suggest that other proteins with analogous structural and DNA-binding properties may function in similar ways. Genome-wide mapping of NF-YA, NF-YB, and NF-YC subunits of the NF-Y complex in mouse ESCs, and microarray gene expression profiling of control knockdown (KD), NF-YA KD, NF-YB KD, NF-YC KD, and NF-YA/NF-YB/NF-YC triple KD ESCs.
Experiment type
transcription profiling by array 
Contacts
Raja Jothi <jothi@mail.nih.gov>, Andrew J Oldfield, Pengyi Yang
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-56838.idf.txt
Sample and data relationshipE-GEOD-56838.sdrf.txt
Raw data (1)E-GEOD-56838.raw.1.zip
Processed data (1)E-GEOD-56838.processed.1.zip
Array designA-AFFY-45.adf.txt
Links