Evidence map›Paper›PMID 38251200›Full record

ArticleMethods and protocols2024

Mapping m

Alice Baek, Asif Rayhan, Ga-Eun Lee, Sarah Golconda, Hannah Yu, Shihyoung Kim, Patrick A Limbach, Balasubrahmanyam Addepalli, Sanggu Kim

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

Article in Methods and protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
1.6field-weighted citation impact, top 18% 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

5 citing papers in PubMed, 7 citations in OpenAlex.

  1. Review
  2. Article
  3. Review
  4. YTHDF1 and YTHDC1 mJournal of virology · 2025
    Article
  5. 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

9 authors at 2 institutions in 1 country.

Alice BaekCenter for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.ORCID 0000-0002-3631-7988
Asif RayhanRieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.
Ga-Eun LeeCenter for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.ORCID 0000-0002-7521-5546
Sarah GolcondaCenter for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.
Hannah YuCenter for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.ORCID 0000-0001-5354-7622
Shihyoung KimCenter for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.
Patrick A LimbachRieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.ORCID 0000-0003-1526-4546
Balasubrahmanyam AddepalliRieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.ORCID 0000-0001-6257-7700
Sanggu KimCenter for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.ORCID 0000-0003-1228-6168
The Ohio State University · USUniversity of Cincinnati · US

Funding

UPLC for Enhanced Mass Spectrometry of Modified RNAsR01GM058843 · NIGMS · UNIVERSITY OF CINCINNATI · PI LIMBACH, PATRICK A · 1999 to 2025
$5.1M
On-site, high-fidelity target sequencing and absolute quantitation for HIV-1 surveillanceR01HG010318 · NHGRI · OHIO STATE UNIVERSITY · PI KIM, SANGGU · 2018 to 2021
$2.9M
High-accuracy, long-range sequencing for HIV-1 genotypingR21HG010108 · NHGRI · OHIO STATE UNIVERSITY · PI KIM, SANGGU · 2018 to 2020
$624k
Mass Spectrometry of Ribosomal RNA:Protein InteractionsR56GM058843 · NIGMS · UNIVERSITY OF CINCINNATI · PI LIMBACH, PATRICK A · 2009 to 2009
$330k
NHGRI NIH HHS R01 HG010318NHGRI NIH HHS R21 HG010108NIGMS NIH HHS R01 GM058843NIGMS NIH HHS R56 GM058843
6 · The paper itself

Abstract

The biological significance of chemical modifications to the ribonucleic acid (RNA) of human immunodeficiency virus type-1 (HIV-1) has been recognized. However, our understanding of the site-specific and context-dependent roles of these chemical modifications remains limited, primarily due to the absence of nucleotide-resolution mapping of modification sites. In this study, we present a method for achieving nucleotide-resolution mapping of chemical modification sites on HIV-1 RNA using liquid chromatography and tandem mass spectrometry (LC-MS/MS). LC-MS/MS, a powerful tool capable of directly analyzing native RNAs, has proven effective for mapping RNA modifications in small RNA molecules, including ribosomal RNA and transfer RNA. However, longer RNAs have posed challenges, such as the 9 Kb HIV-1 virion RNA, due to the complexity of and ambiguity in mass differences among RNase T1-cleaved RNA fragments in LC-MS/MS data. Here, we introduce a new target RNA enrichment method to isolate small local RNA fragments of HIV-1 RNA that potentially harbor site-specific N6-methyladenosine (m

Indexed as

HIV-1mass spectrometryN6-methyladenosine (m6A)oligonucleotide LC–MS/MSRNA modificationtarget RNA enrichment

Identifiers

PMID38251200
PMCPMC10801558
OpenAlexW4390694440

What OpenQuestion holds

Textmetadata
LicenceCC BY
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 OpenQuestion graph.