ArticleGenome biology2014
Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 38 citations in OpenAlex.
- Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages.International journal of molecular sciences · 2020Pooled it
- Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†.Human molecular genetics · 2015Trial
- The landscape of human p53-regulated long non-coding RNAs reveals critical host gene co-regulation.Molecular oncology · 2023Article
- An Isoxazoloquinone Derivative Inhibits Tumor Growth by Targeting STAT3 and Triggering Its Ubiquitin-Dependent Degradation.Cancers · 2023Article
- Traditional Chinese medicine for transformation of gastric precancerous lesions to gastric cancer: A critical review.World journal of gastrointestinal oncology · 2023Review
- Long non-coding RNA ESCCAL-1/miR-590/LRP6 signaling pathway participates in the progression of esophageal squamous cell carcinoma.Cancer medicine · 2023Article
- Clinical Perspectives of Non-Coding RNA in Oral Inflammatory Diseases and Neuropathic Pain: A Narrative Review.International journal of molecular sciences · 2022Review
- Multidimensional Mutational Profiling of the Indian HNSCC Sub-Population Provides IRAK1, a Novel Driver Gene and Potential Druggable Target.Frontiers in oncology · 2021Article
- Meta-analysis of transcriptome datasets: An alternative method to study IL-6 regulation in coronavirus disease 2019.Computational and structural biotechnology journal · 2021Article
- Master and servant: LINC00152 - a STAT3-induced long noncoding RNA regulates STAT3 in a positive feedback in human multiple myeloma.BMC medical genomics · 2020Article
- Prospects and challenges of multi-omics data integration in toxicology.Archives of toxicology · 2020Review
- Long non-coding RNAs in brain tumours: Focus on recent epigenetic findings in glioma.Journal of cellular and molecular medicine · 2018Review
- A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts.BMC genomics · 2017Article
- STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer.Scientific reports · 2017Article
- Expression Profiling of Long Noncoding RNA Splice Variants in Human Microvascular Endothelial Cells: Lipopolysaccharide EffectsMediators of inflammation · 2017Article
- A Review on Recent Computational Methods for Predicting Noncoding RNAs.BioMed research international · 2017Review
- Evolution of the unspliced transcriptome.BMC evolutionary biology · 2015Article
- Long non-coding RNA MALAT1 regulates hyperglycaemia induced inflammatory process in the endothelial cells.Journal of cellular and molecular medicine · 2015Article
- The Landscape of long noncoding RNA classification.Trends in genetics : TIG · 2015Review
- Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved.RNA (New York, N.Y.) · 2015Article
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe genome is pervasively transcribed but most transcripts do not code for proteins, constituting non-protein-coding RNAs. Despite increasing numbers of functional reports of individual long non-coding RNAs (lncRNAs), assessing the extent of functionality among the non-coding transcriptional output of mammalian cells remains intricate. In the protein-coding world, transcripts differentially expressed in the context of processes essential for the survival of multicellular organisms have been instrumental in the discovery of functionally relevant proteins and their deregulation is frequently associated with diseases. We therefore systematically identified lncRNAs expressed differentially in response to oncologically relevant processes and cell-cycle, p53 and STAT3 pathways, using tiling arrays.
resultsWe found that up to 80% of the pathway-triggered transcriptional responses are non-coding. Among these we identified very large macroRNAs with pathway-specific expression patterns and demonstrated that these are likely continuous transcripts. MacroRNAs contain elements conserved in mammals and sauropsids, which in part exhibit conserved RNA secondary structure. Comparing evolutionary rates of a macroRNA to adjacent protein-coding genes suggests a local action of the transcript. Finally, in different grades of astrocytoma, a tumor disease unrelated to the initially used cell lines, macroRNAs are differentially expressed.
conclusionsIt has been shown previously that the majority of expressed non-ribosomal transcripts are non-coding. We now conclude that differential expression triggered by signaling pathways gives rise to a similar abundance of non-coding content. It is thus unlikely that the prevalence of non-coding transcripts in the cell is a trivial consequence of leaky or random transcription events.
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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.