Evidence map›Paper›PMID 35907400›Full record

ArticleMolecular cell2022

Molecular organization of the early stages of nucleosome phase separation visualized by cryo-electron tomography.

Meng Zhang, César Díaz-Celis, Bibiana Onoa, Cristhian Cañari-Chumpitaz, Katherinne I Requejo, Jianfang Liu, Michael Vien, Eva Nogales, Gang Ren, Carlos Bustamante

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.

0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

37 citing papers in PubMed.

  1. Article
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  15. In-cell chromatin structure by Cryo-FIB and Cryo-ET.Current opinion in structural biology · 2025
    Review
  16. Review
  17. Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  18. Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Meng ZhangApplied Science and Technology Graduate Group, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
César Díaz-CelisCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
Bibiana OnoaHoward Hughes Medical Institute, University of California, Berkeley, CA, USA.
Cristhian Cañari-ChumpitazDepartment of Chemistry, University of California, Berkeley, CA, USA.
Katherinne I RequejoCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
Jianfang LiuThe Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Michael VienDepartment of Physics, University of California, Berkeley, CA, USA.
Eva NogalesCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Gang RenThe Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. Electronic address: gren@lbl.gov.
Carlos BustamanteCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, CA, USA; Department of Physics, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, CA, USA. Electronic address: carlosjbustamante2@gmail.com.

Funding

STRUCTURAL ANALYSIS OF THE MANNOSE 6-PHOSPHATE RECEPTORSR01DK042667 · NIDDK · MEDICAL COLLEGE OF WISCONSIN · PI DAHMS, NANCY M. · 1997 to 2023
$9.8M
Synaptic Organizers: Dynamic Regulation of Trans-synaptic BridgesR01MH077303 · NIMH · UNIVERSITY OF TEXAS MED BR GALVESTON · PI Gabrielle Rudenko · 2006 to 2026
$8.2M
THE PHYSICAL CHEMISTRY OF NUCLEIC ACIDSR01GM032543 · NIGMS · UNIVERSITY OF OREGON · PI CARLOS Jose BUSTAMANTE · 1985 to 2026
$6.4M
Structural studies of function and regulation of microtubules and transcriptional gene expression machineryR35GM127018 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Eva Nogales · 2018 to 2026
$4.3M
Structure-Function Relationship Studies of the Plasma Lipid Transfer Proteins CETP and PLTPR01HL115153 · NHLBI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI REN, GANG · 2012 to 2021
$3.9M
Improving Quality of Care for Low-Income Pregnant Women through Medicaid Accountable Care Organizations: A Natural ExperimentR01MD017703 · NIMHD · BOSTON UNIVERSITY MEDICAL CAMPUS · PI Megan B. Cole, Sarah Hall Gordon · 2022 to 2026
$3.6M
Lipoprotein Structure and Function by Individual Particle Electron TomographyR01GM104427 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI REN, GANG · 2013 to 2016
$1.3M
Howard Hughes Medical InstituteNHLBI NIH HHS R01 HL115153NIDDK NIH HHS R01 DK042667NIGMS NIH HHS R01 GM032543NIGMS NIH HHS R01 GM104427NIGMS NIH HHS R35 GM127018NIMHD NIH HHS R01 MD017703NIMH NIH HHS R01 MH077303
6 · The paper itself

Abstract

It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.

Indexed as

Electron Microscope TomographyNucleosomesCell NucleusChromatinMetaphaseChromatinNucleosomeschromatincondensatescryo-electron tomographylinker histone H1liquid-liquid phase separationnucleation and growthnucleosomenucleosome arraysspinodal decomposition

Identifiers

PMID35907400
PMCPMC9493104

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.