ArticleNucleic acids research2021
TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 35 citations in OpenAlex.
- PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2026Article
- Target-site dynamics explain a large share of apparent microRNA differential expression.RNA (New York, N.Y.) · 2026Article
- PolyA_DB v4: systematic polyA site identification and isoform annotation in human and mouse genomes using 3' end and long-read sequencing data.Nucleic acids research · 2026Article
- Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025Review
- Identification of microprotein-coding intronic polyadenylation isoforms and function in genotoxic anticancer drug response.Genome biology · 2025Article
- Altered polyadenylation site usage in SERPINA1 3'UTR in response to cellular stress affects A1AT protein expression.Scientific reports · 2025Article
- Alternative mRNA polyadenylation regulates macrophage hyperactivation via the autophagy pathway.Cellular & molecular immunology · 2024Article
- Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA.American journal of human genetics · 2024Article
- Downregulation of CPSF6 leads to global mRNA 3' UTR shortening and enhanced antiviral immune responses.PLoS pathogens · 2024Article
- Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing.Nature communications · 2023Article
- Post-transcriptional control of haemostatic genes: mechanisms and emerging therapeutic concepts in thrombo-inflammatory disorders.Cardiovascular research · 2023Review
- Known sequence features explain half of all human gene ends.NAR genomics and bioinformatics · 2023Article
- 3'UTR Diversity: Expanding Repertoire of RNA Alterations in Human mRNAs.Molecules and cells · 2023Review
- CFIm-mediated alternative polyadenylation safeguards the development of mammalian pre-implantation embryos.Stem cell reports · 2023Article
- Context-specific regulation and function of mRNA alternative polyadenylation.Nature reviews. Molecular cell biology · 2022Review
- Review
- Leveraging omic features with F3UTER enables identification of unannotated 3'UTRs for synaptic genes.Nature communications · 2022Article
- FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research.Scientific data · 2022Article
- scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution.Nucleic acids research · 2022Article
- APAview: A web-based platform for alternative polyadenylation analyses in hematological cancers.Frontiers in genetics · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3' end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3' end maturation is closely linked to transcription, RNA processing and even epigenetic (histone/DNA/RNA) modifications. Here, we present TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), a resource cataloging the dynamic landscape of APA after depletion of >170 proteins involved in various facets of transcriptional, co- and post-transcriptional gene regulation, epigenetic modifications and further processes. TREND-DB visualizes the dynamics of transcriptome 3' end diversification (TREND) in a highly interactive manner; it provides a global APA network map and allows interrogating genes affected by specific APA-regulators and vice versa. It also permits condition-specific functional enrichment analyses of APA-affected genes, which suggest wide biological and clinical relevance across all RNAi conditions. The implementation of the UCSC Genome Browser provides additional customizable layers of gene regulation accounting for individual transcript isoforms (e.g. epigenetics, miRNA-binding sites and RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps identify their diagnostic and therapeutic potential.
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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.