ArticleBMC genomics2013
Divergent transcription is associated with promoters of transcriptional regulators.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed, 105 citations in OpenAlex.
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- Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae.Nucleic acids research · 2025Article
- EZH2 specifically regulates ISL1 during embryonic urinary tract formation.Scientific reports · 2024Article
- Molecular models of bidirectional promoter regulation.Current opinion in structural biology · 2024Review
- Proteasome Inhibition Reprograms Chromatin Landscape in Breast Cancer.Cancer research communications · 2024Article
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- RNA-based therapeutics to treat human fungal infections.Trends in microbiology · 2022Review
- Long non-coding RNAs mediate cerebral vascular pathologies after CNS injuries.Neurochemistry international · 2021Review
- Pneumocystis Mating-Type Locus and Sexual Cycle during Infection.Microbiology and molecular biology reviews : MMBR · 2021Review
- The cardiac translational landscape reveals that micropeptides are new players involved in cardiomyocyte hypertrophy.Molecular therapy : the journal of the American Society of Gene Therapy · 2021Article
- Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage.Genome research · 2021Article
- A Comprehensive Toolbox to Analyze Enhancer-Promoter Functions.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation.The Journal of experimental medicine · 2020Article
- The Role of Long Non-Coding RNAs in Intracranial Aneurysms and Subarachnoid Hemorrhage.Life (Basel, Switzerland) · 2020Review
- Associating divergent lncRNAs with target genes by integrating genome sequence, gene expression and chromatin accessibility data.NAR genomics and bioinformatics · 2020Article
- Long non-coding RNA LncKdm2b regulates cortical neuronal differentiation by cis-activating Kdm2b.Protein & cell · 2020Article
- Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.Communications biology · 2020Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDivergent transcription is a wide-spread phenomenon in mammals. For instance, short bidirectional transcripts are a hallmark of active promoters, while longer transcripts can be detected antisense from active genes in conditions where the RNA degradation machinery is inhibited. Moreover, many described long non-coding RNAs (lncRNAs) are transcribed antisense from coding gene promoters. However, the general significance of divergent lncRNA/mRNA gene pair transcription is still poorly understood. Here, we used strand-specific RNA-seq with high sequencing depth to thoroughly identify antisense transcripts from coding gene promoters in primary mouse tissues.
resultsWe found that a substantial fraction of coding-gene promoters sustain divergent transcription of long non-coding RNA (lncRNA)/mRNA gene pairs. Strikingly, upstream antisense transcription is significantly associated with genes related to transcriptional regulation and development. Their promoters share several characteristics with those of transcriptional developmental genes, including very large CpG islands, high degree of conservation and epigenetic regulation in ES cells. In-depth analysis revealed a unique GC skew profile at these promoter regions, while the associated coding genes were found to have large first exons, two genomic features that might enforce bidirectional transcription. Finally, genes associated with antisense transcription harbor specific H3K79me2 epigenetic marking and RNA polymerase II enrichment profiles linked to an intensified rate of early transcriptional elongation.
conclusionsWe concluded that promoters of a class of transcription regulators are characterized by a specialized transcriptional control mechanism, which is directly coupled to relaxed bidirectional transcription.
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