Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells.

Massimiliano Manzo, Christina Ambrosi, Tuncay Baubec

Open access · greenAbstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

–field-weighted citation impact, top 96% 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

1 citing paper in PubMed, 1 citations in OpenAlex.

Downregulated Reprimo by LINC00467 participates in the growth and metastasis of gastric cancer.Bioengineered · 2022
Article

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 at 2 institutions in 1 country.

Massimiliano ManzoDepartment of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.

Christina AmbrosiDepartment of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.

Tuncay BaubecDepartment of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland. tuncay.baubec@uzh.ch.

Life Science Zurich · CHUniversity of Zurich · CH

Funding

Swiss National Science Foundation 157488

6 · The paper itself

Abstract

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is currently the method of choice to determine binding sites of chromatin-associated factors in a genome-wide manner. Here, we describe a method to investigate the binding preferences of mammalian DNA methyltransferases (DNMT) based on ChIP-seq using biotin-tagging. Stringent ChIP of DNMT proteins based on the strong interaction between biotin and avidin circumvents limitations arising from low antibody specificity and ensures reproducible enrichment. DNMT-bound DNA fragments are ligated to sequencing adaptors, amplified and sequenced on a high-throughput sequencing instrument. Bioinformatic analysis gives valuable information about the binding preferences of DNMTs genome-wide and around promoter regions. This method is unconventional due to the use of genetically engineered cells; however, it allows specific and reliable determination of DNMT binding.

Indexed as

DNA MethylationGenome-Wide Association StudyProtein Array AnalysisAnimalsAvidinBinding SitesBiotinChromatinDNADNA Modification MethylasesHumansPromoter Regions, GeneticSoftwareAvidinBiotinChromatinDNADNA Modification MethylasesChIP-seqCpG islandsDNA methyltransferasesImmunoprecipitationIn vivo biotinylationNext-generation sequencing

Identifiers

PMID29605852

DOI10.1007/978-1-4939-7768-0_9

PMCPMC7611273

OpenAlexW2795356708

What OpenQuestion holds

Textmetadata

LicenceTDM

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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.