Evidence map›Paper›PMID 25798578›Full record

ArticleNature communications2015

SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation.

Dhaval Varshney, Jana Vavrova-Anderson, Andrew J Oler, Victoria H Cowling, Bradley R Cairns, Robert J White

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

Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.

0numbers the graph read from it
0cells of the map it votes in
63citing papers in PubMed
5.6field-weighted citation impact, top 3% 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

63 citing papers in PubMed, 114 citations in OpenAlex.

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  18. Genome assembly of the Pendlebury's roundleaf bat, Hipposideros pendleburyi, revealed the expansion of Tc1/Mariner DNA transposons in Rhinolophoidea.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022
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3 more citing papers are in PubMed but not listed here.

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

6 authors at 4 institutions in 2 countries.

Dhaval Varshney1] College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK [2] The MRC Protein Phosphorylation Unit, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
Jana Vavrova-AndersonCollege of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
Andrew J Oler1] Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA [2] Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.
Victoria H CowlingThe MRC Protein Phosphorylation Unit, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
Bradley R Cairns1] Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA [2] Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.
Robert J White1] College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK [2] Department of Biology, University of York, York YO10 5DD, UK.
University of Glasgow · GBHuntsman Cancer Institute · USUniversity of Dundee · GBUniversity of Utah · US

Funding

Cancer Research UKHoward Hughes Medical InstituteMedical Research Council G0700240Medical Research Council MR/K024213/1Wellcome Trust 073424/Z/03/ZWellcome Trust 097945
6 · The paper itself

Abstract

Short interspersed nuclear elements (SINEs), such as Alu, spread by retrotransposition, which requires their transcripts to be copied into DNA and then inserted into new chromosomal sites. This can lead to genetic damage through insertional mutagenesis and chromosomal rearrangements between non-allelic SINEs at distinct loci. SINE DNA is heavily methylated and this was thought to suppress its accessibility and transcription, thereby protecting against retrotransposition. Here we provide several lines of evidence that methylated SINE DNA is occupied by RNA polymerase III, including the use of high-throughput bisulphite sequencing of ChIP DNA. We find that loss of DNA methylation has little effect on accessibility of SINEs to transcription machinery or their expression in vivo. In contrast, a histone methyltransferase inhibitor selectively promotes SINE expression and occupancy by RNA polymerase III. The data suggest that methylation of histones rather than DNA plays a dominant role in suppressing SINE transcription.

Indexed as

Alu ElementsAnimalsChromatin ImmunoprecipitationDNA-Binding ProteinsDNA MethylationFibroblastsHeLa CellsHigh-Throughput Nucleotide SequencingHistone CodeHistonesHumansMethylationMethyl-CpG-Binding Protein 2MiceRNA Polymerase IIIShort Interspersed Nucleotide ElementsDNA-Binding ProteinsHistonesMBD1 protein, humanMbd1 protein, mouseMBD2 protein, humanMbd2 protein, mouseMethyl-CpG-Binding Protein 2RNA Polymerase IIITranscription Factors

Identifiers

PMID25798578
PMCPMC4382998
OpenAlexW1995229781

What OpenQuestion holds

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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.