Riches of phenotype computationally extracted from microbial colonies

Area of Science:

• Microbiology
• Genetics
• Epigenetics

Background:

• Cellular heterogeneity within microbial colonies presents research opportunities.
• Transient losses of heterochromatic repression (gene silencing) occur during Saccharomyces colony growth.
• Existing assays for gene silencing are difficult to quantify.

Purpose of the Study:

• To develop automated algorithms for analyzing heterochromatin dynamics in microbial colonies.
• To enable precise quantification of gene silencing patterns.
• To broadly adapt colony-based assay analysis for Saccharomyces and other microbes.

Main Methods:

• Developed MORPHE, a suite of automated image processing, visualization, and classification algorithms.
• Utilized two-color fluorescence patterns in yeast colonies.
• Extracted features from fluorescence images for classification.

Main Results:

• MORPHE facilitated precise classification of loss-of-silencing patterns between mutants and wild type.
• Identified significant differences in heterochromatic repression stability across environmental conditions.
• Found haploid cells exhibit higher rates of silencing loss than diploids.
• Uncovered a sirtuin's contribution to heterochromatin dynamics.

Conclusions:

• Automated analysis of heterochromatin dynamics is feasible and precise.
• Environmental conditions and cell ploidy impact gene silencing stability.
• Sirtuins play a role in regulating heterochromatin dynamics in yeast colonies.