ArticleMethods in enzymology2021
A computational pipeline to infer alternative poly-adenylation from 3' sequencing data.
Article in Methods in enzymology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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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.
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Who cites it
3 citing papers in PubMed, 4 citations in OpenAlex.
- Post-genome-wide association study variant-to-function challenges in asthma research.The Journal of allergy and clinical immunology · 2026Review
- NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1.Journal of neuro-oncology · 2023Article
- Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites.Science advances · 2023Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
An increasing number of investigations have established alternative polyadenylation (APA) as a key mechanism of gene regulation through altering the length of 3' untranslated region (UTR) and generating distinct mRNA termini. Further, appreciation for the significance of APA in disease contexts propelled the development of several 3' sequencing techniques. While these RNA sequencing technologies have advanced APA analysis, the intrinsic limitation of 3' read coverage and lack of appropriate computational tools constrain precise mapping and quantification of polyadenylation sites. Notably, Poly(A)-ClickSeq (PAC-seq) overcomes limiting factors such as poly(A) enrichment and 3' linker ligation steps using click-chemistry. Here we provide an updated PolyA-miner protocol, a computational approach to analyze PAC-seq or other 3'-Seq datasets. As a key practical constraint, we also provide a detailed account on the impact of sequencing depth on the number of detected polyadenylation sites and APA changes. This protocol is also updated to handle unique molecular identifiers used to address PCR duplication potentially observed in PAC-seq.
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Registered trials
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