Genome-wide ChIP-seq and RNA-seq analyses of Pou3f1 during mouse pluripotent stem cell neural fate commitment.

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This process is regulated by the coordination of extrinsic signals and intrinsic programs. However, how the coordination is achieved to ensure proper neural fate commitment is largely unknown. Here, taking advantage of genome-wide ChIP-sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) analyses, we demonstrate that the transcriptional factor Pou3f1 is an upstream activator of neural-promoting genes, and it is able to repress neural-inhibitory signals as well. Further studies revealed that Pou3f1 could directly bind neural lineage genes like Sox2 and downstream targets of neural inhibition signaling such as BMP and Wnt. Our results thus identify Pou3f1 as a critical dual-regulator of the intrinsic transcription factors and the extrinsic cellular signals during neural fate commitment. 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ChIP-seq data processing The ChIP-seq reads were mapp"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Genome-wide ChIP-seq and RNA-seq analyses of Pou3f1 during mouse pluripotent", "f genome-wide ChIP-sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) analyses, we demonstrate that the", "IP-sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) analyses, we demonstrate that the transcrip", "pressed (Pou3f1-OE) cells were collected for RNA-seq analysis, and Pou3f1 ChIP-seq was performed"], "order_basis": "paper_text_order:0", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["IP-seq and RNA-seq analyses of Pou3f1 during mouse pluripotent stem cell neural fate commitment", "and methods Cell culture and differentiation Mouse embryonic stem cells (mESCs) (R1 and R1/E) w", "maintained on a layer of mitomycin C-treated mouse embryonic fibroblast feeder cells in standar", "standard medium supplemented with 1000 U/mL mouse leukemia inhibitory factor (LIF). 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