ArticleNucleic acids research2023
Low RNA stability signifies increased post-transcriptional regulation of cell identity genes.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 42 citations in OpenAlex.
- Hierarchical interplay between H3K27ac and H3K4me3 in transcriptional regulation.Nature communications · 2026Article
- EnzymeTuning improves enzyme-constrained metabolic modeling and proteome abundance prediction through deep learning.Nature communications · 2026Article
- A dual role of EZH2 in regulating A-to-I RNA editing and mRNA stability through ADAR.Nature communications · 2026Article
- Genomic features associated with sustained mammalian transmission of avian influenza A viruses.Nature microbiology · 2026Article
- Review
- Immune signaling as a determinant of cellular identity and tissue function.Frontiers in immunology · 2026Review
- TNF-α-driven m6A modification disrupts the immunoregulatory function of MSCs by regulating HDAC5-dependent super-enhancers.Cell death & disease · 2025Article
- Targeting AASS alleviates neurotoxicity and improves mitochondrial function in astrocyte models for pyridoxine-dependent epilepsy.Molecular therapy. Nucleic acids · 2025Article
- Transcription factor 4 maintains endothelial cell identity by inhibiting endothelial to mesenchymal transition.Nucleic acids research · 2025Article
- Review
- Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos.Nucleic acids research · 2025Article
- POCALI: Prediction and Insight on CAncer LncRNAs by Integrating Multi-Omics Data with Machine Learning.Small methods · 2025Article
- The immune system in cardiovascular diseases: from basic mechanisms to therapeutic implications.Signal transduction and targeted therapy · 2025Review
- SCIG: Machine learning uncovers cell identity genes in single cells by genetic sequence codes.Nucleic acids research · 2025Article
- Targeting BRD4 ameliorates experimental emphysema by disrupting super-enhancer in polarized alveolar macrophage.Respiratory research · 2025Article
- The detection, function, and therapeutic potential of RNA 2'-O-methylation.The innovation life · 2025Article
- Comparisons between young, aged, and Alzheimer's brains reveal specific expression patterns for a subset of transposons and satellite repeats.Journal of biosciences · 2025Article
- Article
- Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants.BMC plant biology · 2024Article
- 2'-O-methylation at internal sites on mRNA promotes mRNA stability.Molecular cell · 2024Article
Corrections and comments
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Authors and funding
15 authors at 6 institutions in 1 country.
Funding
Abstract
Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g. by super-enhancers and broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, probably due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-sequencing showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run-and-brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.
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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.