ArticleNucleic acids research2020
Integrative network analysis identifies cell-specific trans regulators of m6A.
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 63 papers.
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Who cites it
63 citing papers in PubMed, 97 citations in OpenAlex.
- Identification of Chronic Stress-Related Biomarkers for Potential Diagnosis and Treatment of Osteoporosis: An Integrated Multi-omic and Clinical Data Analysis.Therapeutic innovation & regulatory science · 2026Article
- A Dual-Responsive Claringbullite-Like Nanozyme for Inhibition of Non-Small Cell Lung Cancer Progression.Small methods · 2026Article
- Integrative multi-omics analysis defines a macrophage-associated phospholipid metabolism signature linked to immune remodeling and prognosis in lung adenocarcinoma.Respiratory research · 2026Article
- TRA2A negatively regulates HIV-1-induced macrophage pyroptosis by mediating TXNIP expression in an m6A-dependent manner.Cell death discovery · 2026Article
- Integrative systems biology and drug repurposing reveal key regulatory hubs and a prognostic signature in gastric cancer.Discover oncology · 2026Article
- Intermittent fasting inhibits Tp53-driven glioma through gut microbiota-mediated methionine-mNature communications · 2026Article
- Gut microbiota induces immune-related alterations in gene expression, RNA methylation, and metabolism in glioblastoma revealed by single-cell and spatial multi-omics.Frontiers in immunology · 2026Article
- RNA-triggered innate immunity: friend and foe.Frontiers in genetics · 2026Review
- Systematic evaluation of tools used for single-cell mCommunications biology · 2025Article
- CAPRIN1 specifically mediates mCommunications biology · 2025Article
- WTAP-mediated mScience China. Life sciences · 2025Article
- Block sparse Bayes-based fuzzy system for RNA N6-methyladenosine sites prediction.PLoS computational biology · 2025Article
- RNA-interactome capture identifies SRSF3 as a key protein for herpesviral gene expression.PNAS nexus · 2025Article
- Emerging Orchestrator of Ecological Adaptation: mMolecular ecology · 2025Review
- Metagenomics and transcriptomics analysis of aspartame's impact on gut microbiota and glioblastoma progression in a mouse model.Scientific reports · 2025Article
- Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types.Genomics, proteomics & bioinformatics · 2024Article
- Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level.Genomics, proteomics & bioinformatics · 2024Article
- Regulatory roles of N6-methyladenosine (mCancer gene therapy · 2024Review
- Cap-related modifications of RNA regulate binding to IFIT proteins.RNA (New York, N.Y.) · 2024Article
- Decoding the specificity of mMolecular therapy : the journal of the American Society of Gene Therapy · 2024Review
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
N6-methyladenosine (m6A) is a reversible and dynamic RNA modification in eukaryotes. However, how cells establish cell-specific m6A methylomes is still poorly understood. Here, we developed a computational framework to systematically identify cell-specific trans regulators of m6A through integrating gene expressions, binding targets and binding motifs of large number of RNA binding proteins (RBPs) with a co-methylation network constructed using large-scale m6A methylomes across diverse cell states. We applied the framework and successfully identified 32 high-confidence m6A regulators that modulated the variable m6A sites away from stop codons in a cell-specific manner. To validate them, we knocked down three regulators respectively and found two of them (TRA2A and CAPRIN1) selectively promoted the methylations of the m6A sites co-localized with their binding targets on RNAs through physical interactions with the m6A writers. Knockdown of TRA2A increased the stabilities of the RNAs with TRA2A bound near the m6A sites and decreased the viability of cells. The successful identification of m6A regulators demonstrates a powerful and widely applicable strategy to elucidate the cell-specific m6A regulators. Additionally, our discovery of pervasive trans-acting regulating of m6A provides novel insights into the mechanisms by which spatial and temporal dynamics of m6A methylomes are established.
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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.