Evidence map›Paper›PMID 40989927›Full record

ArticleAccess microbiology2025

Direct RNA sequencing reveals m6A modifications and isoform changes in SARS-CoV-2-infected HEK cells.

Ilhan Cem Duru, Zlatka Plavec, Anne Ylinen, Pia Laine, Martyn James, Lotta Riihimäki, Sarah J Butcher, Maria Anastasina, Petri Auvinen

Abstract read
In one paragraph

Article in Access microbiology, 2025. 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
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. 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.

Ilhan Cem DuruInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.ORCID https://orcid.org/0000-0003-3409-5215
Zlatka PlavecInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
Anne YlinenInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
Pia LaineInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
Martyn JamesInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
Lotta RiihimäkiInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
Sarah J ButcherInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
Maria AnastasinaInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
Petri AuvinenInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection triggers complex host responses, including alterations in RNA transcription and modification. Understanding these changes is crucial for elucidating viral pathogenesis and identifying potential therapeutic targets. We used direct RNA sequencing to comprehensively profile the transcriptomic and epitranscriptomic landscapes of human HEK-AT cells infected with SARS-CoV-2 at 8 h post-infection, compared to mock controls. We analysed viral and host transcriptomes, focusing on gene and transcript expression, isoform usage and RNA m6A modifications. Viral RNA sequencing reads showed 3' end-biassed coverage indicative of subgenomic RNA synthesis, with high expression of

Indexed as

COVID-19direct RNA sequencingRNA methylationSARS-CoV-2

Identifiers

PMID40989927
PMCPMC12451313

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.