Evidence map›Paper›PMID 27025842›Full record

ArticleGenome biology2016

Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets.

Aurélien A Sérandour, Stéphane Avner, Elise A Mahé, Thierry Madigou, Sylvain Guibert, Michaël Weber, Gilles Salbert

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

Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
1.9field-weighted citation impact, top 14% 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

6 citing papers in PubMed, 14 citations in OpenAlex.

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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

7 authors at 2 institutions in 2 countries.

Aurélien A SérandourEMBL, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
Stéphane AvnerCNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.
Elise A MahéCNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.
Thierry MadigouCNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.
Sylvain GuibertCNRS, Université de Strasbourg, UMR7242, Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, Illkirch cedex, 67412, France.
Michaël WeberCNRS, Université de Strasbourg, UMR7242, Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, Illkirch cedex, 67412, France.
Gilles SalbertCNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France. gilles.salbert@univ-rennes1.fr.ORCID http://orcid.org/0000-0001-6115-4140
Centre National de la Recherche Scientifique · FREuropean Molecular Biology Organization · DE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Conventional techniques for single-base resolution mapping of epigenetic modifications of DNA such as 5-hydroxymethylcytosine (5hmC) rely on the sequencing of bisulfite-modified DNA. Here we present an alternative approach called SCL-exo which combines selective chemical labeling (SCL) of 5hmC in genomic DNA with exonuclease (exo) digestion of the bead-trapped modified DNA molecules. Associated with a straightforward bioinformatic analysis, this new procedure provides an unbiased and fast method for mapping this epigenetic mark at high resolution. Implemented on mouse genomic DNA from in vitro-differentiated neural precursor cells, SCL-exo sheds light on an intrinsic lack of conservation of hydroxymethylated CpGs across vertebrates.

Indexed as

5-MethylcytosineAnimalsCells, CulturedCpG IslandsCytosineDNADNA MethylationEmbryonic Stem CellsEpigenesis, GeneticEpigenomicsExonucleasesMiceSequence Analysis, DNAStaining and Labeling5-hydroxymethylcytosine5-MethylcytosineCytosineDNAExonucleases5hmC5-hydroxymethylcytosineSelective chemical labelingSingle-CpG resolution

Identifiers

PMID27025842
PMCPMC4810514
OpenAlexW2335089565

What OpenQuestion holds

Textmetadata
LicenceCC BY
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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.