An organoid-based CRISPR-Cas9 screen for regulators of intestinal epithelial maturation and cell fate

Generation of functionally mature organs requires exquisite control of transcriptional programs governing cell state transitions during development. Despite advances in understanding the behavior of adult intestinal stem cells and their progeny, the transcriptional regulators that control the emergence of the mature intestinal phenotype remain largely unknown. Using mouse fetal and adult small intestinal organoids, we uncover transcriptional differences between the fetal and adult state and identify rare adult-like cells present in fetal organoids. This suggests that fetal organoids have an inherent potential to mature, which is locked by a regulatory program. By implementing a CRISPR-Cas9 screen targeting transcriptional regulators expressed in fetal organoids, we establish Smarca4 and Smarcc1 as important factors safeguarding the immature progenitor state. Our approach demonstrates the utility of organoid models in the identification of factors regulating cell fate and state transitions during tissue maturation and reveals that SMARCA4 and SMARCC1 prevent precocious differentiation during intestinal development.

Automated summary

By studying mouse fetal and adult small intestinal organoids, it was found that rare adult-like cells exist in fetal organoids, suggesting that fetal organoids have the potential to mature but are regulated by certain factors. Through a CRISPR-Cas9 screen, Smarca4 and Smarcc1 were identified as important factors for maintaining the immature progenitor state. This study demonstrates the usefulness of organoid models in identifying factors regulating cell fate and state transitions during tissue maturation and reveals the role of SMARCA4 and SMARCC1 in preventing precocious differentiation during intestinal development.