The hierarchical packing of euchromatin domains can be described as multiplicative cascades

Abstract

The genome is packed into the cell nucleus in the form of chromatin. Biochemical approaches have revealed that chromatin is packed within domains, which group into larger domains, and so forth. Such hierarchical packing is equally visible in super-resolution microscopy images of large-scale chromatin organization. While previous work has suggested that chromatin is partitioned into distinct domains via microphase separation, it is unclear how these domains organize into this hierarchical packing. A particular challenge is to find an image analysis approach that fully incorporates such hierarchical packing, so that hypothetical governing mechanisms of euchromatin packing can be compared against the results of such an analysis. Here, we obtain 3D STED super-resolution images from pluripotent zebrafish embryos labeled with improved DNA fluorescence stains, and demonstrate how the hierarchical packing of euchromatin in these images can be described as multiplicative cascades. Multiplicative cascades are an established theoretical concept to describe the placement of ever-smaller structures within bigger structures. Importantly, these cascades can generate artificial image data by applying a single rule again and again, and can be fully specified using only four parameters. Here, we show how the typical patterns of euchromatin organization are reflected in the values of these four parameters. Specifically, we can pinpoint the values required to mimic a microphase-separated state of euchromatin. We suggest that the concept of multiplicative cascades can also be applied to images of other types of chromatin. Here, cascade parameters could serve as test quantities to assess whether microphase separation or other theoretical models accurately reproduce the hierarchical packing of chromatin.

Fluorescence-based super-resolution-microscopy strategies for chromatin studies

“…5 ) (Lau et al 2012 ). The photon budget and signal-to-noise ratio can be maximised by (i) minimising the contact of the fluorophore with water (Maillard et al 2021 ); (ii) properly storing the fluorophore; (iii) adding photoprotective agents to the mounting media for fixed samples or (when non-toxic) to the medium in live-cell applications (Gong et al 2019 ; Noa et al 2021 ); (iv) applying adaptive-illumination strategies; (v) optimising laser-excitation powers, preventing unnecessary high bleaching; and (vi) using phenol-red-free media when imaging in the red. Other sample optimisations not specific to SRM, such as labelling artefacts, are reviewed by, e.g.…”