Evidence map›Paper›PMID 40974823›Full record

ReviewCurrent opinion in structural biology2025

Chromatin higher-order folding as influenced by preferred values of linker DNA.

Zilong Li, Stephanie Portillo-Ledesma, Tamar Schlick

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Current opinion in structural biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Review
  3. Getting gene expression "just right".Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  4. Review
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

3 authors.

Zilong LiDepartment of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA; Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA.
Stephanie Portillo-LedesmaDepartment of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA; Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA.
Tamar SchlickDepartment of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA; Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China. Electronic address: schlick@nyu.edu.

Funding

Bridging Disparate Structural/Functional Scales: Multiscale Modeling of the Chromatin Fiber and RNA Tertiary StructuresR35GM122562 · NIGMS · NEW YORK UNIVERSITY · PI Tamar Schlick · 2017 to 2026
$4.6M
NIGMS NIH HHS R35 GM122562
6 · The paper itself

Abstract

Specific values of nucleosome spacing have long been associated with distinct chromatin organization, but recent studies reveal surprising structural and functional consequences of small changes in regular linker DNA length. This opinion article revisits experimental and modeling studies addressing the classic 10n versus 10n + 5 spacing, highlighting how this 5 bp difference can alter nucleosome orientation, fiber topology, and higher-order chromatin behavior. We underscore how differences in model parameters and system design yield different trends for the effect of linker DNA lengths on chromatin architecture. However, chromatin structure in vivo reflects the heterogeneous nucleosome spacing in combination with other cellular variables like salt conditions, epigenetic marks, and protein and RNA binding, which work together to shape gene folding and direct gene regulation.

Indexed as

ChromatinDNANucleic Acid ConformationAnimalsHumansNucleosomesChromatinDNANucleosomes

Identifiers

PMID40974823
PMCPMC12767869

What OpenQuestion holds

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Registered trials

None linked

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.