Evidence map›Paper›PMID 40131932›Full record

ArticleCell reports2025

Comprehensive nucleoside analysis of archaeal RNA modification profiles reveals an m

Yueh-Lin Tsai, Eric J Wolf, Kristin A Fluke, Ryan T Fuchs, Nan Dai, Sean R Johnson, Zhiyi Sun, Liam Elkins, Brett W Burkhart, Thomas J Santangelo and 1 more

Abstract read
In one paragraph

Article in Cell reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. The Landscape of tRNA Modifications in Archaea.bioRxiv : the preprint server for biology · 2025
    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

11 authors.

Yueh-Lin TsaiNew England Biolabs Inc., Beverly, MA 01915, USA.
Eric J WolfNew England Biolabs Inc., Beverly, MA 01915, USA.
Kristin A FlukeDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
Ryan T FuchsNew England Biolabs Inc., Beverly, MA 01915, USA.
Nan DaiNew England Biolabs Inc., Beverly, MA 01915, USA.
Sean R JohnsonNew England Biolabs Inc., Beverly, MA 01915, USA.
Zhiyi SunNew England Biolabs Inc., Beverly, MA 01915, USA.
Liam ElkinsDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
Brett W BurkhartDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
Thomas J SantangeloDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
Ivan R CorrêaNew England Biolabs Inc., Beverly, MA 01915, USA. Electronic address: correa@neb.com.

Funding

Regulation of Archaeal TranscriptionR35GM143963 · NIGMS · COLORADO STATE UNIVERSITY · PI Thomas James Santangelo · 2022 to 2026
$1.8M
NIGMS NIH HHS R35 GM143963
6 · The paper itself

Abstract

Extremophilic Archaea employ diverse RNA modifications for survival. Our understanding of the modified nucleosides and their functions in Archaea is far from complete. Here, we establish an extensive profile of nucleoside modifications in thermophilic and mesophilic Archaea. Through liquid chromatography-tandem mass spectrometry (LC-MS/MS) and rigorous non-coding RNA depletion, we identify four previously unannotated modifications in archaeal mRNA. Nucleoside analysis conducted on total, large, small, and mRNA-enriched subfractions of hyperthermophile Thermococcus kodakarensis reveals modifications whose relative abundance is dynamically responsive to growth temperatures. To predict archaeal RNA-modifying enzymes, we leverage open-access databases to compare putative functional domains with previously annotated enzymes. Our approach leads to the discovery of a methyltransferase responsible for the installation of m

Indexed as

NucleosidesRNA, ArchaealRNA, Ribosomal, 23SThermococcusMethyltransferasesRNA Processing, Post-TranscriptionalMethyltransferasesNucleosidesRNA, ArchaealRNA, Ribosomal, 23S7-methylguanosinearchaeaCP: Molecular biologyepitranscriptomehyperthermophilemethyltransferaseribosomeRNA modifications

Identifiers

PMID40131932
PMCPMC12124282

What Socratic 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 Socratic graph.