Transcription organizes euchromatin via microphase separation

Abstract

In eukaryotes, DNA is packed inside the cell nucleus in the form of chromatin, which consists of DNA, proteins such as histones, and RNA. Euchromatin, which is permissive for transcription, is spatially organized into transcriptionally inactive domains interspersed with pockets of transcriptional activity. While transcription and RNA have been implicated in euchromatin organization, it remains unclear how their interplay forms and maintains transcription pockets. Here we combine theory and experiment to analyze the dynamics of euchromatin organization as pluripotent zebrafish cells exit mitosis and begin transcription. We show that accumulation of RNA induces formation of transcription pockets which displace transcriptionally inactive chromatin. We propose that the accumulating RNA recruits RNA-binding proteins that together tend to separate from transcriptionally inactive euchromatin. Full phase separation is prevented because RNA remains tethered to transcribed euchromatin through RNA polymerases. Instead, smaller scale microphases emerge that do not grow further and form the typical pattern of euchromatin organization.

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

“…It appears that the different nuclei form a continuum of euchromatin organization patterns, and the smooth, intermediate, and coarse organization patterns are placed at different positions within this continuum. Such a continuum is in line with previous work, where it was seen that chromatin organization is established progressively after cell division [ 16 , 21 ]. The observed inverse relationship suggests that the progressive establishment of distinct euchromatin domains (increasing C DNA ) is correlated with more fine-grained structuring (decreasing L corr ).…”

“…To assess large-scale euchromatin organization, we recorded 3D STED super-resolution microscopy data from nuclei of pluripotent cells in zebrafish embryos. At the pluripotent stage of development (late blastula), these cells exhibit a euchromatin-only nuclear organization and are distributed throughout the cell cycle [ 16 – 18 ]. Both aspects have proven beneficial for the study of large-scale euchromatin organization by STED super-resolution microscopy in our previous work [ 16 , 19 ].…”

“…At the pluripotent stage of development (late blastula), these cells exhibit a euchromatin-only nuclear organization and are distributed throughout the cell cycle [ 16 – 18 ]. Both aspects have proven beneficial for the study of large-scale euchromatin organization by STED super-resolution microscopy in our previous work [ 16 , 19 ]. To further improve image quality, we assessed the performance of STED-capable fluorogenic DNA stains that recently became commercially available.…”

“…To illustrate this continuum, we display three typical patterns of organization, which we refer to as smooth, intermediate, and coarse ( Fig 2A ). Based on our previous work, these typical euchromatin patterns can be related to different states of chromatin in the nucleus [ 16 ]. The smooth pattern corresponds to a mixed state, which is found early in the cell cycle when transcription has not yet recommenced.…”

“…We have recently addressed the internal patterning of euchromatin in relation to transcription activity, and proposed that a fine-grained pattern of euchromatin domains is established and maintained in line with a microphase-separated state of a microemulsion [ 16 ]. During our work with super-resolution images of euchromatin organization, it has become increasingly apparent that euchromatin also exhibits a hierarchical packing of domains.…”