Transcription organizes euchromatin via microphase separation

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Lennart Hilbert - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics, Max-Planck-Institute for the Physics of Complex Systems, Karlsruhe Institute of Technology (Author)
  • Yuko Sato - , Tokyo Institute of Technology (Author)
  • Ksenia Kuznetsova - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Tommaso Bianucci - , Max Planck Institute of Molecular Cell Biology and Genetics, Max-Planck-Institute for the Physics of Complex Systems (Author)
  • Hiroshi Kimura - , Tokyo Institute of Technology (Author)
  • Frank Jülicher - , Center for Systems Biology Dresden (CSBD), Max-Planck-Institute for the Physics of Complex Systems, TUD Dresden University of Technology, Clusters of Excellence PoL: Physics of Life (Author)
  • Alf Honigmann - , Clusters of Excellence PoL: Physics of Life, Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Vasily Zaburdaev - , Center for Systems Biology Dresden (CSBD), Max-Planck-Institute for the Physics of Complex Systems, Friedrich-Alexander University Erlangen-Nürnberg (Author)
  • Nadine L. Vastenhouw - , Max Planck Institute of Molecular Cell Biology and Genetics, University of Lausanne (Author)

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.

Details

Original languageEnglish
Article number1360
JournalNature communications
Volume12
Issue number1
Publication statusPublished - 1 Dec 2021
Peer-reviewedYes

External IDs

PubMed 33649325
ORCID /0000-0003-0475-3790/work/161889535