Data from: Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein
Data files
Oct 13, 2025 version files 35.56 GB
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RajshekarS_2025_Dryad_Submission.zip
35.56 GB
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README.md
2.30 KB
Abstract
Nucleoli are surrounded by Pericentromeric Heterochromatin (PCH), reflecting a conserved spatial association between the two largest biomolecular condensates in eukaryotic nuclei. Nucleoli are the sites of ribosome synthesis, while the repeat-rich PCH is essential for chromosome segregation, genome stability, and transcriptional silencing, yet the mechanisms for their co-assembly are unclear. Here, we use high-resolution live imaging during Drosophila embryogenesis and reveal that de novo establishment of PCH-nucleolar associations is highly dynamic, as PCH transitions from extending along the nuclear edge to surrounding the nucleolus. Eliminating the nucleolus by removing the ribosomal RNA genes (rDNA) disrupted this process, causing increased PCH compaction followed by its reorganization into a toroidal structure. Further, in embryos lacking rDNA, nucleolar proteins were redistributed into new bodies or ‘neocondensates’, including enrichment in the PCH toroidal hole. Combining these in vivo observations with molecular dynamics simulations based on multiphase wetting theory revealed that nucleolar-PCH associations could be mediated by a hierarchy of interaction strengths between PCH, nucleoli, and proteins with dual affinities for both compartments. We validated this model by identifying such a protein, a DEAD-Box RNA Helicase called Pitchoune, and showed that modulating its affinity for either nucleolar or PCH components alters nucleolar-PCH organization. Together, this study unveils a dynamic program for establishing nucleolar-PCH associations during animal development and demonstrates how interaction hierarchies and dual-affinity molecular linkers co-organize compositionally distinct condensates.
Dataset DOI: 10.5061/dryad.vx0k6dk59
Description of the data and file structure
Dataset Title
Microscopy source data for “Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein.”
Authors
Srivarsha Rajshekar, Omar Adame-Arana, Gaurav Bajpai, Serafin U. Colmenares, Hannah Papoi, Lucy D. Brennan, Shingo Tsukamoto, Samuel Safran, Gary H. Karpen
Corresponding Author Contact
gkarpen@berkeley.edu
First Author Contact
srajshekar@berkeley.edu
Dataset Overview
This dataset contains the source data for all the microscopy images presented in the figures of the associated publication. Data are organized by figure type (main figures and extended data figures).
Associated Publication
Rajshekar S, Adame-Arana O, Bajpai G, Colmenares SU, Papoi H, Brennan LD, Tsukamoto S, Safran S, Karpen GH. Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein. Nature Cell Biology. 2025.
Files and variables
File: RajshekarS_2025_Dryad_Submission.zip
Description: This master dataset contains all the microscopy data used to generate the figures in Rajshekar et al., 2025.
Sub-folders
Main Figures Raw Data: Contains microscopy files corresponding to Figures 1, 2, 4, and 6 in the published article.
Extended Data Figures Raw Data: Contains microscopy files corresponding to Extended Data Figures 1, 2, 3, 5, 6, 7, and 9.
File Nomenclature
Filenames include: (1) Figure and panel number. (2) Experimental condition (e.g., developmental stage, cell type, genetic background). (3) Targeted molecule and fluorophore (e.g., protein of interest with tagged fluorescent protein).
File Format and Access
File types include .czi (Airyscan-processed) or .tif. All files can be accessed using Fiji/ImageJ.
Acquisition Notes
Detailed imaging parameters and methods are available in the Methods section of the associated publication and in the Light Microscopy Reporting Table supplement.