Multiscale chromatin dynamics and high entropy in plant iPSC ancestors

Abstract

ABSTRACT Plant protoplasts provide starting material for of inducing pluripotent cell masses that are competent for tissue regeneration in vitro, analogous to animal induced pluripotent stem cells (iPSCs). Dedifferentiation is associated with large-scale chromatin reorganisation and massive transcriptome reprogramming, characterised by stochastic gene expression. How this cellular variability reflects on chromatin organisation in individual cells and what factors influence chromatin transitions during culturing are largely unknown. Here, we used high-throughput imaging and a custom supervised image analysis protocol extracting over 100 chromatin features of cultured protoplasts. The analysis revealed rapid, multiscale dynamics of chromatin patterns with a trajectory that strongly depended on nutrient availability. Decreased abundance in H1 (linker histones) is hallmark of chromatin transitions. We measured a high heterogeneity of chromatin patterns indicating intrinsic entropy as a hallmark of the initial cultures. We further measured an entropy decline over time, and an antagonistic influence by external and intrinsic factors, such as phytohormones and epigenetic modifiers, respectively. Collectively, our study benchmarks an approach to understand the variability and evolution of chromatin patterns underlying plant cell reprogramming in vitro.

Plant phenotyping relevance

植物プロトプラストのクロマチン状態を高スループット画像とカスタム画像解析で定量し、100以上の特徴を抽出・ベンチマークしており、表現型取得法が研究の中心である。

Code and data availability

The paper's chromatin feature datasets (Dryad doi:10.5061/dryad.pnvx0k6wp) and images (BioStudies S-BIAD1157) are paper-specific public assets, but their repository URLs are not among the allowed URLs, so they cannot be listed. The authors' adapted entropy analysis script is publicly available on the authors' GitHub (a