Evidence map›Paper›PMID 40790224›Full record

ArticleGenome biology2025

Common cell lysis procedures distort ribosome profiling analyses of gene expression.

Aoife O'Connell, Alla D Fedorova, Patrick B F O'Connor, Alexander V Zhdanov, Pavel V Baranov, Gary Loughran, Dmitry E Andreev

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 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. 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

7 authors.

Aoife O'ConnellSchool of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Alla D FedorovaEIRNA Bio Ltd, Bioinnovation Hub, Food Science & Technology Building, College Road, Cork, Ireland.
Patrick B F O'ConnorEIRNA Bio Ltd, Bioinnovation Hub, Food Science & Technology Building, College Road, Cork, Ireland.
Alexander V ZhdanoviEd Hub and School of Pharmacy, University College Cork, Cork, Ireland.
Pavel V BaranovSchool of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Gary LoughranEIRNA Bio Ltd, Bioinnovation Hub, Food Science & Technology Building, College Road, Cork, Ireland. gary.loughran@eirnabio.com.
Dmitry E AndreevShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia. cycloheximide@yandex.ru.

Funding

Irish Research Council Enterprise Partnership Studentship Award EPSPG/2020/461Russian Science Foundation 20-14-00121Science Foundation Ireland Frontiers for the Future Award 20/FFP-A/8929
6 · The paper itself

Abstract

Ribosome profiling is a powerful technique used to study gene expression on a transcriptome-wide scale. It involves sequencing of mRNA fragments protected by ribosomes from ribonuclease digestion. The initial steps commonly involve cell lysis followed by centrifugation and ribonuclease digestion. We find that centrifugation depletes 329 translated mRNAs in HEK293T cells. Many of these mRNAs encode cytoskeleton proteins. This suggests that the expression of a subset of mRNAs may be significantly underestimated in most ribosome profiling experiments. We show that omitting the centrifugation step after cell lysis can resolve this issue.

Indexed as

Gene Expression ProfilingRibosomesCentrifugationHEK293 CellsHumansProtein BiosynthesisRibosome ProfilingRNA, MessengerTranscriptomeRNA, MessengerCytoskeletonGene expressionInsoluble fractionLysisNascent peptidePolysome profilingRiboseqRibosome profiling

Identifiers

PMID40790224
PMCPMC12341276

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.