Evidence map›Paper›PMID 39535721›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

Global Profiling and Analysis of 5' Monophosphorylated mRNA Decay Intermediates.

Ai-Ping Chen, Wan-Chieh Chen, Bo-Han Hou, Shu-Jen Chou, Ho-Ming Chen

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 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

5 authors.

Ai-Ping ChenInstitute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Wan-Chieh ChenAgricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
Bo-Han HouAgricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
Shu-Jen ChouInstitute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan. sjchou@gate.sinica.edu.tw.
Ho-Ming ChenAgricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan. homing@gate.sinica.edu.tw.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

During RNA turnover, the action of endo- and exo-ribonucleases can yield RNA decay intermediates with specific 5' ends. These RNA decay intermediates have been demonstrated to be the outcome of decapping, microRNA-directed endo-cleavage, or the protected fragments of ribosomes and exon-junction complexes. Therefore, global analysis of RNA decay intermediates can facilitate studies of many RNA decay pathways. In this chapter, we describe a high-throughput sequencing protocol named parallel analysis of RNA ends (PARE), which allows genome-wide profiling of 5' monophosphorylated mRNA decay intermediates from plants or other eukaryotes. Also, we present the tools and scripts necessary for the proper analysis of RNA degradome data obtained from the PARE method. Details and modifications of library construction procedures and bioinformatic analyses to optimize sequencing quality and cope with emerging sequencing platforms and findings are highlighted.

Indexed as

Computational BiologyHigh-Throughput Nucleotide SequencingRNA, MessengerRNA StabilityGene Expression ProfilingSequence Analysis, RNARNA, Messenger5′-3′ RNA decay5′P endDegradome-seqEJC footprintEndonucleolytic cleavagemiRNA targetRibosome footprint

Identifiers

PMID39535721

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.