Evidence map›Paper›PMID 38293098›Full record

ArticlebioRxiv : the preprint server for biology2024

Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers.

Jee Min Kim, Claudia C Carcamo, Sina Jazani, Zepei Xie, Xinyu A Feng, Maryam Yamadi, Matthew Poyton, Katie L Holland, Jonathan B Grimm, Luke D Lavis and 2 more

Abstract readPreprint
PubMed Full text at PMC Publisher
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

5 · Who and what money

Authors and funding

12 authors.

Jee Min KimDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
Claudia C CarcamoDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID 0000-0002-2646-188X
Sina JazaniDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID 0000-0002-4184-4803
Zepei XieDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0002-4069-9835
Xinyu A FengDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0001-5862-1983
Maryam YamadiDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0001-7080-5566
Matthew PoytonDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0003-1261-2138
Katie L HollandJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
Jonathan B GrimmJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
Luke D LavisJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.ORCID 0000-0002-0789-6343
Taekjip HaDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID 0000-0003-2195-6258
Carl WuDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0001-6933-5763

Funding

BIOCHEMISTRY, CELLULAR AND MOLECULAR BIOLOGY PROGRAMT32GM007445 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI GREEN, RACHEL · 1985 to 2021
$24.1M
Cellular and Molecular BiologyT32GM141804 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI John Kim · 2021 to 2026
$5.1M
Single Molecule Studies of Nucleic Acids RemodelingR35GM122569 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Taekjip Ha · 2017 to 2026
$3.5M
Dynamic association of transcription initiation proteins with chromatin at single-molecule resolution in living yeastR01GM132290 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI WU, CARL · 2019 to 2022
$1.8M
Lumicks C-Trap for a Core FacilityS10OD025221 · OD · JOHNS HOPKINS UNIVERSITY · PI KUO, SCOT CHARLES · 2019 to 2019
$597k
NIGMS NIH HHS R01 GM132290NIGMS NIH HHS R35 GM122569NIGMS NIH HHS T32 GM007445NIGMS NIH HHS T32 GM141804NIH HHS S10 OD025221
6 · The paper itself

Abstract

Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/sec on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.

Identifiers

PMID38293098
PMCPMC10827135

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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.