Evidence map›Paper›PMID 26484232›Full record

ArticleGenomics data2015

Genome-wide mapping of hot spots of DNA double-strand breaks in human cells as a tool for epigenetic studies and cancer genomics.

N A Tchurikov, O V Kretova, D M Fedoseeva, V R Chechetkin, M A Gorbacheva, A V Snezhkina, I R Alembekov, G I Kravatskaya, Y V Kravatsky

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

Article in Genomics data, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.5field-weighted citation impact, top 34% 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

5 citing papers in PubMed, 9 citations in OpenAlex.

  1. Review
  2. Review
  3. Mutational load in carotid body tumor.BMC medical genomics · 2019
    Article
  4. Article
  5. Fragility Extraordinaire: Unsolved Mysteries of Chromosome Fragile Sites.Advances in experimental medicine and biology · 2017
    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

9 authors at 1 institution in 1 country.

N A TchurikovEngelhardt Institute of Molecular Biology, Moscow, Russia.
O V KretovaEngelhardt Institute of Molecular Biology, Moscow, Russia.
D M FedoseevaEngelhardt Institute of Molecular Biology, Moscow, Russia.
V R ChechetkinEngelhardt Institute of Molecular Biology, Moscow, Russia.
M A GorbachevaEngelhardt Institute of Molecular Biology, Moscow, Russia.
A V SnezhkinaEngelhardt Institute of Molecular Biology, Moscow, Russia.
I R AlembekovEngelhardt Institute of Molecular Biology, Moscow, Russia.
G I KravatskayaEngelhardt Institute of Molecular Biology, Moscow, Russia.
Y V KravatskyEngelhardt Institute of Molecular Biology, Moscow, Russia.
Engelhardt Institute of Molecular Biology · RU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Hot spots of DNA double-strand breaks (DSBs) are associated with coordinated expression of genes in chromosomal domains (Tchurikov et al., 2011 [1]; 2013). These 50-150-kb DNA domains (denoted "forum domains") can be visualized by separation of undigested chromosomal DNA in pulsed-field agarose gels (Tchurikov et al., 1988; 1992) and used for genome-wide mapping of the DSBs that produce them. Recently, we described nine hot spots of DSBs in human rDNA genes and observed that, in rDNA units, the hot spots coincide with CTCF binding sites and H3K4me3 marks (Tchurikov et al., 2014), suggesting a role for DSBs in active transcription. Here we have used Illumina sequencing to map DSBs in chromosomes of human HEK293T cells, and describe in detail the experimental design and bioinformatics analysis of the data deposited in the Gene Expression Omnibus with accession number GSE53811 and associated with the study published in DNA Research (Kravatsky et al., 2015). Our data indicate that H3K4me3 marks often coincide with hot spots of DSBs in HEK293T cells and that the mapping of these hot spots is important for cancer genomic studies.

Indexed as

BioinformaticsDouble-strand breaksFragile sitesH3K4me3 marksHEK293T

Identifiers

PMID26484232
PMCPMC4583641
OpenAlexW2106038951

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.