OTX2 regulates CFTR expression during endoderm differentiation and occupies 3' cis-regulatory elements

Area of Science:

• Developmental Biology
• Gene Regulation
• Stem Cell Biology

Background:

• The developmental regulation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene is not well understood.
• Cell-specific mechanisms influence CFTR gene expression, but developmental control remains unclear.

Purpose of the Study:

• To investigate the developmental mechanisms regulating CFTR gene expression.
• To utilize human induced pluripotent stem cells differentiated into airway epithelial cells for studying CFTR regulation.

Main Methods:

• RNA-sequencing (RNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) were employed to analyze gene expression and open chromatin profiles.
• Chromatin studies were conducted in definitive endoderm (DE) and anterior foregut endoderm (AFE) cells.
• The role of OTX2 in regulating CFTR expression was assessed through loss-of-function experiments.

Main Results:

• Alterations in CFTR expression correlated with stage-specific open chromatin profiles.
• Two novel open chromatin regions 3' to the CFTR gene were identified in DE cells.
• OTX2 occupancy at these sites in DE cells was observed, and its loss led to increased CFTR expression and altered histone modifications.

Conclusions:

• A network of cis-regulatory elements recruits OTX2 to the CFTR locus.
• OTX2 influences CFTR expression during early endoderm differentiation.