Liu Tzu-Yu, Dodson Anne E, Terhorst Jonathan, Song Yun S, Rine Jasper
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 Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720;
Proc Natl Acad Sci U S A. 2016 May 17;113(20):E2822-31. doi: 10.1073/pnas.1523295113. Epub 2016 May 2.
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.
克隆微生物菌落中细胞间的遗传、表观遗传和生理差异是尚未充分探索的发现机会。最近开发的一种遗传检测方法表明，在酿酒酵母菌落的整个生长过程中，都会发生异染色质抑制（一种可遗传的基因沉默形式）的短暂丧失。该检测需要分析酵母菌落中的双色荧光模式，这在定性方面很有吸引力，但在定量方面具有挑战性。在本文中，我们开发了一套自动化的图像处理、可视化和分类算法（MORPHE），这些算法有助于在菌落生长的背景下分析异染色质动力学，并且可以广泛应用于酿酒酵母和其他微生物中许多基于菌落的检测。利用从荧光图像中自动提取的特征，我们的分类方法以前所未有的精度区分了突变体和野生型之间的沉默丧失模式。MORPHE的应用揭示了不同环境条件下异染色质抑制稳定性的细微但显著的差异，表明单倍体细胞比二倍体细胞经历更高的沉默丧失率，并揭示了一种沉默调节蛋白对异染色质动力学的意外贡献。
