45: RNA-dependent mechanics of nucleolar subcompartments

Cheng HH et al., Proceedings of the National Academy of Sciences (PNAS) - Using micropipette aspiration in Xenopus laevis oocyte nuclei, authors show the nucleolar granular component behaves as a liquid while the dense fibrillar component and fibrillar center exhibit RNA-dependent viscoelastic, partially solid-like properties; RNase A fluidizes the DFC and alters interfacial tensions. Key terms: nucleolus, micropipette aspiration, viscoelasticity, RNA, Xenopus laevis.

Study Highlights:
The study adapts micropipette aspiration (MPA) to measure viscoelasticity and interfacial tensions of nucleoli in isolated Xenopus laevis germinal vesicles. The outer granular component (GC) behaves as a Newtonian, liquid-like material, whereas the inner dense fibrillar component (DFC) and fibrillar center (FC) show signatures of a viscoelastic, partially solid-like material. Degrading RNA with RNase A fluidizes the DFC, speeds fusion, and increases apparent DFC–GC interfacial tension. These results link RNA content and processing to spatially varying nucleolar material properties relevant to ribosome maturation.

Conclusion:
Nascent rRNA confers partially solid-like viscoelastic properties to the DFC/FC and modulates interfacial tensions, coupling nucleolar material state to ribosome biogenesis; MPA provides direct in vivo rheological measurements of condensates.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Micropipette aspiration reveals differential RNA-dependent viscoelasticity of nucleolar subcompartments

First author:
Cheng HH

Journal:
Proceedings of the National Academy of Sciences (PNAS)

DOI:
10.1073/pnas.2407423122

Reference:
Cheng HH, Roggeveen JV, Wang H, Stone HA, Shi Z, Brangwynne CP. Micropipette aspiration reveals differential RNA-dependent viscoelasticity of nucleolar subcompartments. Proc Natl Acad Sci U S A. 2025;122(22):e2407423122. doi:10.1073/pnas.2407423122

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/nucleolus-rna-viscoelasticity-ep45

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-06-12.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the spoken content describing nucleolar architecture, MPA methodology, material-property distinctions between GC and DFC/FC, RNA's role in solid-like DFC behavior, RNase A effects, and the implications for ribosome biogenesis, including measured viscosities, interfacial tensions, and fusion dynamics.
- transcript topics: Nucleolus architecture and subcompartments (GC vs DFC/FC); Micropipette aspiration methodology and nonwetting conditions; Material-property division: GC as Newtonian liquid; DFC/FC as viscoelastic solid; RNA dependence of DFC/FC properties; RNase A experiments fluidizing DFC and changing fusion dynamics; Interfacial tensions and inverse capillary velocity measurements

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 1
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- GC is a New...