title: Riches of phenotype computationally extracted from microbial colonies.
abstract: The genetic, epigenetic, and physiological differences among cells in clonal microbial colonies are underexplored opportunities for discovery. A recently developed genetic assay reveals that transient losses of heterochromatic repression, a heritable form of gene silencing, occur throughout the growth of Saccharomyces colonies. This assay requires analyzing two-color fluorescence patterns in yeast colonies, which is qualitatively appealing but quantitatively challenging. In this paper, we developed a suite of automated image processing, visualization, and classification algorithms (MORPHE) that facilitated the analysis of heterochromatin dynamics in the context of colonial growth and that can be broadly adapted to many colony-based assays in Saccharomyces and other microbes. Using the features that were automatically extracted from fluorescence images, our classification method distinguished loss-of-silencing patterns between mutants and wild type with unprecedented precision. Application of MORPHE revealed subtle but significant differences in the stability of heterochromatic repression between various environmental conditions, revealed that haploid cells experienced higher rates of silencing loss than diploids, and uncovered the unexpected contribution of a sirtuin to heterochromatin dynamics.
authors.affiliation: Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720;
authors.forename: Tzu-Yu
authors.initials: TY
authors.lastname: Liu
authors.affiliation: Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720;
authors.forename: Anne E
authors.initials: AE
authors.lastname: Dodson
authors.affiliation: Department of Statistics, University of California, Berkeley, CA 94720;
authors.forename: Jonathan
authors.initials: J
authors.lastname: Terhorst
authors.affiliation: Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720; Department of Statistics, University of California, Berkeley, CA 94720; Department of Integrative Biology, University of California, Berkeley, CA 94720 jrine@berkeley.edu yss@berkeley.edu.
authors.forename: Yun S
authors.initials: YS
authors.lastname: Song
authors.affiliation: Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; jrine@berkeley.edu yss@berkeley.edu.
authors.forename: Jasper
authors.initials: J
authors.lastname: Rine
mesh_terms: D000465:Algorithms; D001681:Biological Assay; D015966:Gene Expression Regulation, Fungal; D020868:Gene Silencing; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000096:biosynthesis / Q000235:genetics; D007091:Image Processing, Computer-Assisted; D010641:Phenotype; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*
chemical_list: D049452:Green Fluorescent Proteins
keywords: epigenetics; feature extraction; heterochromatin dynamics; image segmentation