ArticleRNA (New York, N.Y.)2013
Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression.
Article in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
74 citing papers in PubMed, 112 citations in OpenAlex.
- Intron retention in health and amyotrophic lateral sclerosis.Brain : a journal of neurology · 2026Review
- SP1 antagonizes H3K27me3 to shape chromatin landscapes for RNA polymerase II recruitment during gastrulation.Nucleic acids research · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- The bidirectional interplay between RNA processing and mechanotransduction.Cell reports · 2025Review
- The regulation and function of post-transcriptional RNA splicing.Nature reviews. Genetics · 2025Review
- Article
- EFTUD2 is a promising diagnostic and prognostic indicator involved in the tumor immune microenvironment and glycolysis of lung adenocarcinoma.Frontiers in oncology · 2025Article
- Protocol for mapping RNA G-quadruplex for chromatin-bound RNA using d-rG4-seq.STAR protocols · 2024Article
- Regulation of Alternative Splicing of Lipid Metabolism Genes in Sepsis-Induced Liver Damage by RNA-Binding Proteins.Inflammation · 2024Article
- Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing.Molecular cell · 2024Review
- PRPF40A induces inclusion of exons in GC-rich regions important for human myeloid cell differentiation.Nucleic acids research · 2024Article
- DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3'-end of genes and involved in the recycling of cleavage factors.Nature communications · 2024Article
- G-quadruplex folding in Xist RNA antagonizes PRC2 activity for stepwise regulation of X chromosome inactivation.Molecular cell · 2024Article
- Article
- Genome-wide kinetic profiling of pre-mRNA 3' end cleavage.RNA (New York, N.Y.) · 2024Article
- Improved enzymatic labeling of fluorescent in situ hybridization probes applied to the visualization of retained introns in cells.RNA (New York, N.Y.) · 2023Article
- Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts.Nature structural & molecular biology · 2023Article
- Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.Molecular cell · 2022Article
- Article
- Over-activation of EFTUD2 correlates with tumor propagation and poor survival outcomes in hepatocellular carcinoma.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2022Article
14 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
6 authors at 2 institutions in 1 country.
Funding
Abstract
The expression of eukaryotic mRNAs is achieved though an intricate series of molecular processes that provide many steps for regulating the production of a final gene product. However, the relationships between individual steps in mRNA biosynthesis and the rates at which they occur are poorly understood. By applying RNA-seq to chromatin-associated and soluble nucleoplasmic fractions of RNA from Lipid A-stimulated macrophages, we examined the timing of exon ligation and transcript release from chromatin relative to the induction of transcription. We find that for a subset of genes in the Lipid A response, the ligation of certain exon pairs is delayed relative to the synthesis of the complete transcript. In contrast, 3' end cleavage and polyadenylation occur rapidly once transcription extends through the cleavage site. Our data indicate that these transcripts with delayed splicing are not released from the chromatin fraction until all the introns have been excised. These unusual kinetics result in a chromatin-associated pool of completely transcribed and 3'-processed transcripts that are not yet fully spliced. We also find that long introns containing repressed exons that will be excluded from the final mRNA are excised particularly slowly relative to other introns in a transcript. These results indicate that the kinetics of splicing and transcript release contribute to the timing of expression for multiple genes of the inflammatory response.
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What OpenQuestion holds
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.