ArticleGenome biology2020
Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 94 citations in OpenAlex.
- Dietary effects on cytosolic and mitochondrial tRNA abundance and modification patterns across mouse tissues.Genome research · 2026Article
- HENMT1: an RNA methyltransferase in biology and disease.Journal of Zhejiang University. Science. B · 2026Review
- NAT10 promotes gallbladder cancer progression by remodeling cholesterol metabolism via PCSK9 mRNA acetylation.Cell death discovery · 2026Article
- Bidirectional regulation of the ubiquitin-RNA modification axis in cancer.Frontiers in oncology · 2026Review
- The dysregulation score method identifies epigenetic regulator genes that predict cancer prognosis and efficiency of cancer immunotherapy.Molecular therapy. Nucleic acids · 2025Article
- DNA, RNA, and histone methylation regulation enzymes and their crosstalk in colorectal carcinogenesis and progression: a review of molecular mechanisms, clinical implications, and future perspectives.Cellular & molecular biology letters · 2025Review
- Disrupting tRNA modifications to target mitochondrial vulnerabilities in drug-resistant leukemia cells.Blood · 2025Article
- Deciphering RNA modification and post-transcriptional regulation with NetRNApan.Briefings in bioinformatics · 2025Article
- FTO enhances OSCC progression via m⁶A-dependent stabilization of PKM2 mRNA through YTHDF2 modulation.Head & face medicine · 2025Article
- Analysis of the mRNA modification machinery alterations in breast cancer through the SCAN-B cohort.NAR cancer · 2025Article
- ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing.Nucleic acids research · 2025Article
- Quantitative and Multiplexing Analysis of MicroRNAs by Direct Full-Length Sequencing in Nanopores.Journal of the American Chemical Society · 2025Article
- Article
- The three YTHDF paralogs and VIRMA are strong cross-histotype tumor driver candidates among mNAR cancer · 2024Article
- PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals.Cell reports methods · 2024Article
- Variable calling of m6A and associated features in databases: a guide for end-users.Briefings in bioinformatics · 2024Review
- Review
- Discovery, structure, mechanisms, and evolution of protein-only RNase P enzymes.The Journal of biological chemistry · 2024Review
- RNA modifications in physiology and disease: towards clinical applications.Nature reviews. Genetics · 2024Review
- PIWI pathway: bridging acute myeloid leukemia stemness and cellular differentiation.Frontiers in cell and developmental biology · 2024Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification-related proteins (RMPs) may be dysregulated in each cancer type.
resultsHere, we perform a comprehensive annotation and evolutionary analysis of human RMPs, as well as an integrative analysis of their expression patterns across 32 tissues, 10 species, and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. We uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO are not significantly upregulated in most cancer types, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers.
conclusionsOur analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviors that are orchestrated by RNA modifications.
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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.