ArticleNucleic acids research2018
An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 44 citations in OpenAlex.
- Regulation of gene expression by alternative polyadenylation in health and disease.Nature reviews. Genetics · 2026Review
- PolyA-GLM: A comprehensive framework forComputational and structural biotechnology journal · 2026Article
- mTOR signaling networks: mechanistic insights and translational frontiers in disease therapeutics.Signal transduction and targeted therapy · 2025Review
- Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025Review
- IPScan: Detecting novel intronic PolyAdenylation events with RNA-seq data.PLoS computational biology · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Exploring transcriptome plasticity at the intersection of cell signaling, metabolism and computational biology.Experimental & molecular medicine · 2025Article
- Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes.NAR genomics and bioinformatics · 2025Review
- mTORC1, the maestro of cell metabolism and growth.Genes & development · 2025Review
- Review
- Iron homeostasis and ferroptosis in human diseases: mechanisms and therapeutic prospects.Signal transduction and targeted therapy · 2024Review
- Dichotomous intronic polyadenylation profiles reveal multifaceted gene functions in the pan-cancer transcriptome.Experimental & molecular medicine · 2024Article
- The emerging theme of 3'UTR mRNA isoform regulation in reprogramming of cell metabolism.Biochemical Society transactions · 2023Review
- CEBPG suppresses ferroptosis through transcriptional control of SLC7A11 in ovarian cancer.Journal of translational medicine · 2023Article
- Regulation of the hypertonic stress response by the 3' mRNA cleavage and polyadenylation complex.Genetics · 2023Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing.International journal of molecular sciences · 2022Article
- APA-Scan: detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.BMC bioinformatics · 2022Article
- In silico model for miRNA-mediated regulatory network in cancer.Briefings in bioinformatics · 2021Article
- Alternative polyadenylation: methods, mechanism, function, and role in cancer.Journal of experimental & clinical cancer research : CR · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
3'-untranslated regions (UTRs) can vary through the use of alternative polyadenylation sites during pre-mRNA processing. Multiple publically available pipelines combining high profiling technologies and bioinformatics tools have been developed to catalog changes in 3'-UTR lengths. In our recent RNA-seq experiments using cells with hyper-activated mammalian target of rapamycin (mTOR), we found that cellular mTOR activation leads to transcriptome-wide alternative polyadenylation (APA), resulting in the activation of multiple cellular pathways. Here, we developed a novel bioinformatics algorithm, IntMAP, which integrates RNA-Seq and PolyA Site (PAS)-Seq data for a comprehensive characterization of APA events. By applying IntMAP to the datasets from cells with hyper-activated mTOR, we identified novel APA events that could otherwise not be identified by either profiling method alone. Several transcription factors including Cebpg (CCAAT/enhancer binding protein gamma) were among the newly discovered APA transcripts, indicating that diverse transcriptional networks may be regulated by mTOR-coordinated APA. The prevention of APA in Cebpg using the CRISPR/cas9-mediated genome editing tool showed that mTOR-driven 3'-UTR shortening in Cebpg is critical in protecting cells from endoplasmic reticulum (ER) stress. Taken together, we present IntMAP as a new bioinformatics algorithm for APA analysis by which we expand our understanding of the physiological role of mTOR-coordinated APA events to ER stress response. IntMAP toolbox is available at http://compbio.cs.umn.edu/IntMAP/.
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Registered trials
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.