Evidence map›Paper›PMID 34734265›Full record

ArticleNucleic acids research2022

HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein.

Fatema-Zahra M Rashid, Eike Mahlandt, Michiel van der Vaart, Daphne E C Boer, Monica Varela Alvarez, Bram Henneman, Daan J W Brocken, Patrick Voskamp, Anneloes J Blok, Thomas S Shimizu and 5 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.3field-weighted citation impact, top 43% of its field
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

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
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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

15 authors at 4 institutions in 1 country.

Fatema-Zahra M RashidMacromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands.
Eike MahlandtMolecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands.
Michiel van der VaartAnimal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands.
Daphne E C BoerDepartment of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands.
Monica Varela AlvarezAnimal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands.
Bram HennemanMacromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands.
Daan J W BrockenMacromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands.
Patrick VoskampBiophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands.
Anneloes J BlokMacromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands.
Thomas S ShimizuSystems Biology, AMOLF Institute, Amsterdam 1098XG, The Netherlands.
Annemarie H MeijerAnimal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands.
Martijn S LuijsterburgDepartment of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands.
Joachim GoedhartMolecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands.ORCID 0000-0002-0630-3825
Frédéric G E CrémazyMacromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands.
Remus T DameMacromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands.ORCID 0000-0001-9863-1692
Leiden University · NLLeiden University Medical Center · NLNetherlands Institute for Neuroscience · NLInstitute for Atomic and Molecular Physics · NL

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.

Indexed as

AnimalsBacterial ProteinsBiological AssayCell LineCloning, MolecularDNA, BacterialDNA-Binding ProteinsDNA ReplicationFluorescent DyesGene ExpressionGenetic VectorsMicroscopy, FluorescenceStaining and LabelingBacterial ProteinsDNA, BacterialDNA-Binding ProteinsFluorescent Dyes

Identifiers

PMID34734265
PMCPMC8789088
OpenAlexW3210052648

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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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.