Loss of Krüppel-like factor 9 deregulates both physiological gene expression and development

Area of Science:

• Developmental Biology
• Genetics
• Molecular Biology

Background:

• Krüppel-like factor 9 (Klf9) is a transcription factor regulating stress and endocrine pathways.
• Previous studies analyzed Klf9's transcriptomic effects at a single time point (5 days post-fertilization), coinciding with its lowest expression level.

Purpose of the Study:

• To investigate how the diurnal oscillation of Klf9 expression influences the transcriptomic consequences of Klf9 deficiency.
• To identify time-of-day specific effects of Klf9 loss-of-function on zebrafish development.

Main Methods:

• Bulk RNA sequencing of 5 days post-fertilization zebrafish embryos at three time points capturing Klf9 expression peak and nadir.
• Integration with a single-cell RNA sequencing atlas to map transcriptomic changes to specific cell types.
• Confocal imaging to assess organ morphology in Klf9 mutant zebrafish.

Main Results:

• Klf9 deficiency impacts gene expression robustly across different times of day, but with additional effects observed at the predawn peak.
• The Klf9 mutation is associated with increased mRNA in digestive organs (liver, pancreas, intestine) and decreased mRNA in differentiating neurons and blood.
• Enlarged livers were observed in Klf9 mutant larvae, correlating with increased liver mRNA levels.

Conclusions:

• The transcriptomic effects of Klf9 deficiency are partially dependent on the time of day, with unique impacts at the predawn expression peak.
• Klf9 plays a crucial role in regulating the development of digestive organs, neurons, and blood cells in zebrafish.
• Disruption of Klf9 function leads to liver overgrowth, highlighting its importance in liver development and homeostasis.