Evidence map›Paper›PMID 35388081›Full record

ArticleScientific reports2022

scTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs.

Kooper V Hunt, Sean M Burnard, Ellise A Roper, Danielle R Bond, Matthew D Dun, Nicole M Verrills, Anoop K Enjeti, Heather J Lee

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

Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
1.6field-weighted citation impact, top 16% 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

14 citing papers in PubMed, 19 citations in OpenAlex.

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  9. Machine learning to detect the SINEs of cancer.Science translational medicine · 2024
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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

8 authors at 2 institutions in 1 country.

Kooper V HuntSchool of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
Sean M BurnardSchool of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
Ellise A RoperSchool of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
Danielle R BondSchool of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
Matthew D DunSchool of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
Nicole M VerrillsSchool of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
Anoop K EnjetiSchool of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
Heather J LeeSchool of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia. Heather.Lee@newcastle.edu.au.
University of Newcastle Australia · AUHunter Medical Research Institute · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Global changes in DNA methylation are observed in development and disease, and single-cell analyses are highlighting the heterogeneous regulation of these processes. However, technical challenges associated with single-cell analysis of DNA methylation limit these studies. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of average DNA methylation levels. By targeting high-copy SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of loci covered in each scTEM-seq library. Parallel transcriptome analysis is also performed to link global DNA methylation estimates with gene expression. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary AML cells. Our method reveals global DNA methylation heterogeneity induced by decitabine treatment of KG1a cells associated with altered expression of immune process genes. We also compare global DNA methylation estimates to expression of transposable elements and find a predominance of negative correlations. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated cells. By linking global DNA methylation heterogeneity with transcription, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.

Indexed as

DNA Transposable ElementsLeukemia, Myeloid, AcuteDecitabineDNA MethylationEpigenesis, GeneticHumansSingle-Cell AnalysisDecitabineDNA Transposable Elements

Identifiers

PMID35388081
PMCPMC8986802
OpenAlexW4223450044

What OpenQuestion holds

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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.