ArticleNucleic acids research2020
Alternative proteins are functional regulators in cell reprogramming by PKA activation.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Therapeutic potential of astrocyte transdifferentiated neurons.Neural regeneration research · 2026Article
- An expanded reference catalog of translated open reading frames for biomedical research.Nucleic acids research · 2026Article
- Chasing the Ghost Proteome in the Dark Matter.Molecular & cellular proteomics : MCP · 2025Review
- Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides.Biochemical Society transactions · 2023Review
- Metabolic Modeling Identifies a Novel Molecular Type of Glioblastoma Associated with Good Prognosis.Metabolites · 2023Article
- Re-evaluating the impact of alternative RNA splicing on proteomic diversity.Frontiers in genetics · 2023Review
- Activation of orphan receptor GPR132 induces cell differentiation in acute myeloid leukemia.Cell death & disease · 2022Article
- Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival.Nature communications · 2022Article
- Long noncoding RNA NONMMUT015745 inhibits doxorubicin-mediated cardiomyocyte apoptosis by regulating Rab2A-p53 axis.Cell death discovery · 2022Article
- Application of Small Molecules in the Central Nervous System Direct Neuronal Reprogramming.Frontiers in bioengineering and biotechnology · 2022Review
- Natural Products-Based Nanoformulations: A New Approach Targeting CSCs to Cancer Therapy.International journal of nanomedicine · 2022Review
- Understanding small ORF diversity through a comprehensive transcription feature classification.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Review
- The role and mechanism of long non-coding RNA H19 in stem cell osteogenic differentiation.Molecular medicine (Cambridge, Mass.) · 2021Review
- In-depth proteomics analysis of sentinel lymph nodes from individuals with endometrial cancer.Cell reports. Medicine · 2021Article
- OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes.Nucleic acids research · 2021Article
- Path to Clonal Theranostics in Luminal Breast Cancers.Frontiers in oncology · 2021Article
- Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs.Frontiers in cell and developmental biology · 2021Review
- Immunogenomic Profiling Demonstrate AC003092.1 as an Immune-Related eRNA in Glioblastoma Multiforme.Frontiers in genetics · 2021Article
- Comprehensive Analysis of Survival-Related lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Gastric Cancer.Frontiers in genetics · 2021Article
- SARS-Cov-2 Interactome with Human Ghost Proteome: A Neglected World Encompassing a Wealth of Biological Data.Microorganisms · 2020Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial-mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies.
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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 Socratic graph.