Evidence map›Paper›PMID 38094247›Full record

ArticleiScience2023

Epitranscriptome analysis of NAD-capped RNA by spike-in-based normalization and prediction of chronological age.

Dean Li, Shuwen Ge, Yandong Liu, Miaomiao Pan, Xueting Wang, Guojing Han, Sili Zou, Rui Liu, Kongyan Niu, Chao Zhao and 2 more

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

Article in iScience, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.9field-weighted citation impact, top 24% 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

4 citing papers in PubMed, 7 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
  4. 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

12 authors at 4 institutions in 1 country.

Dean LiInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Pudong, Shanghai 201210, China.
Shuwen GeInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Pudong, Shanghai 201210, China.
Yandong LiuDepartment of Vascular and Endovascular Surgery, Chang Zheng Hospital, Naval Medical University, Shanghai 200003, China.
Miaomiao PanNational Clinical Research Center for Aging and Medicine, Huashan Hospital, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 131 Dong An Road, Shanghai 200032, China.
Xueting WangInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Pudong, Shanghai 201210, China.
Guojing HanDepartment of Vascular and Endovascular Surgery, Chang Zheng Hospital, Naval Medical University, Shanghai 200003, China.
Sili ZouDepartment of Vascular and Endovascular Surgery, Chang Zheng Hospital, Naval Medical University, Shanghai 200003, China.
Rui LiuSinglera Genomics, 500 Fu Rong Hua Road, Pudong, Shanghai 201204, China.
Kongyan NiuInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Pudong, Shanghai 201210, China.
Chao ZhaoNational Clinical Research Center for Aging and Medicine, Huashan Hospital, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 131 Dong An Road, Shanghai 200032, China.
Nan LiuInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Pudong, Shanghai 201210, China.
Lefeng QuDepartment of Vascular and Endovascular Surgery, Chang Zheng Hospital, Naval Medical University, Shanghai 200003, China.
Second Military Medical University · CNShanghai Institute of Organic Chemistry · CNShanghai Medical College of Fudan University · CNSinotech Genomics (China) · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Nicotinamide adenine dinucleotide (NAD) can be used as an initiating nucleotide in RNA transcription to produce NAD-capped RNA (NAD-RNA). RNA modification by NAD that links metabolite with expressed transcript is a poorly studied epitranscriptomic modification. Current NAD-RNA profiling methods involve multi-steps of chemo-enzymatic labeling and affinity-based enrichment, thus presenting a critical analytical challenge to remove unwanted variations, particularly batch effects. Here, we propose a computational framework, enONE, to remove unwanted variations. We demonstrate that designed spike-in RNA, together with modular normalization procedures and evaluation metrics, can mitigate technical noise, empowering quantitative and comparative assessment of NAD-RNA across different datasets. Using enONE and a human aging cohort, we reveal age-associated features of NAD-capping and further develop an accurate RNA-based aging clock that combines signatures from both transcriptome and NAD-modified epitranscriptome. enONE facilitates the discovery of NAD-RNA responsive to physiological changes, laying an important foundation for functional investigations into this modification.

Indexed as

Computational bioinformaticsMethodology in biological sciencesSequence analysisTranscriptomics

Identifiers

PMID38094247
PMCPMC10716591
OpenAlexW4388902645

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.