Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation (ChIP-seq)

Transcription factors and chromatin modifiers play important roles in programming and reprogramming of cellular states during development. Much is known about the role of these regulators in gene activation, but relatively little is known about the critical process of enhancer silencing during differentiation. Here we show that the H3K4/K9 histone demethylase LSD1 plays an essential role in decommissioning enhancers during differentiation of embryonic stem cells (ESCs). LSD1 occupies enhancers of active genes critical for control of ESC state. However, LSD1 is not essential for maintenance of ESC identity. Instead, ESCs lacking LSD1 activity fail to fully differentiate and ESC-specific enhancers fail to undergo the histone demethylation events associated with differentiation. At enhancers, LSD1 is a component of the NuRD complex, which contains additional subunits that are necessary for ESC differentiation. We propose that the LSD1-NuRD complex decommissions enhancers of the pluripotency program upon differentiation, which is essential for complete shutdown of the ESC gene expression program and the transition to new cell states. This is the ChIP-seq part of the study. NOTE: We are unable to provide the sequencing data for the IgG control sample because it was never generated. The IgG control sample described in Figure 3c of Whyte et al., 2012 served as a control for the co-immunoprecipation and western blot experiments performed and shown in Figure 3. It was not used in sequencing experiments, and therefore was not sequenced and uploaded to GEO. Please inform those requesting this dataset of this fact.