ArticleMolecular systems biology2014
Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions.
Article in Molecular systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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Who cites it
64 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons.Nucleic acids research · 2016Pooled it
- Nanopore full-length sequencing reveals Nudt21 knockdown drives genome-wide 3'UTR shortening and transcriptome reprogramming in mouse hepatocytes.BMC genomics · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Article
- Nuclear export is a limiting factor in eukaryotic mRNA metabolism.PLoS computational biology · 2024Article
- Review
- Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability.Science advances · 2023Article
- stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies.Genomics, proteomics & bioinformatics · 2023Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- A non-canonical Puf3p-binding sequence regulates CAT5/COQ7 mRNA under both fermentable and respiratory conditions in budding yeast.PloS one · 2023Article
- 3' Untranslated Regions Are Modular Entities That Determine Polyadenylation Profiles.Molecular and cellular biology · 2022Article
- A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.RNA biology · 2021Article
- Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish.Genome research · 2021Article
- Proteinopathies as Hallmarks of Impaired Gene Expression, Proteostasis and Mitochondrial Function in Amyotrophic Lateral Sclerosis.Frontiers in neuroscience · 2021Review
- Alternative polyadenylation of mRNA and its role in cancer.Genes & diseases · 2021Review
- Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data.Frontiers in genetics · 2021Article
- Article
- Mitochondrial Biogenesis Is Positively Regulated by Casein Kinase I Hrr25 Through Phosphorylation of Puf3 inGenetics · 2020Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
Recent research has uncovered extensive variability in the boundaries of transcript isoforms, yet the functional consequences of this variation remain largely unexplored. Here, we systematically discriminate between the molecular phenotypes of overlapping coding and non-coding transcriptional events from each genic locus using a novel genome-wide, nucleotide-resolution technique to quantify the half-lives of 3' transcript isoforms in yeast. Our results reveal widespread differences in stability among isoforms for hundreds of genes in a single condition, and that variation of even a single nucleotide in the 3' untranslated region (UTR) can affect transcript stability. While previous instances of negative associations between 3' UTR length and transcript stability have been reported, here, we find that shorter isoforms are not necessarily more stable. We demonstrate the role of RNA-protein interactions in conditioning isoform-specific stability, showing that PUF3 binds and destabilizes specific polyadenylation isoforms. Our findings indicate that although the functional elements of a gene are encoded in DNA sequence, the selective incorporation of these elements into RNA through transcript boundary variation allows a single gene to have diverse functional consequences.
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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.