Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.

Yunrui Qiu, Shuming Liu, Lin Xingcheng, Ilona Christy Unarta, Xuhui Huang, Bin Zhang

Abstract readPreprint

In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

Updated by
Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.2026

5 · Who and what money

Authors and funding

6 authors.

Yunrui QiuDepartment of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0009-0003-2200-0490

Shuming LiuDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID 0000-0002-8569-5520

Lin XingchengDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID 0000-0002-9378-6174

Ilona Christy UnartaDepartment of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0002-5014-0234

Xuhui HuangDepartment of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0002-7119-9358

Bin ZhangDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID 0000-0002-3685-7503

Funding

Probing and Perturbing Transcriptional Condensates with Multiscale Modeling and Deep LearningR35GM133580 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Bin Zhang · 2019 to 2026

$3.1M

NIGMS NIH HHS R35 GM133580

6 · The paper itself

Abstract

Chromatin organization is essential for DNA packaging and gene regulation in eukaryotic genomes. While significant progresses have been made, the exact atomistic arrangement of nucleosomes remains controversial. Using a well-calibrated residue-level coarse-grained model and advanced dynamics modeling techniques, particularly the non-Markovian dynamics model, we map the free energy landscape of tetra-nucleosome systems, identify both metastable conformations and intermediate states in folding pathways, and quantify the folding kinetics. Our findings show that chromatin with Significance: Atomic structures of chromatin have become increasingly accessible, largely through cryo-EM techniques. Nonetheless, these approaches often face limitations in addressing how intrinsic

Identifiers

PMID39605526

DOI10.1101/2024.11.15.623891

PMCPMC11601296

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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.