ArticleBMC genomics2014
Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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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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Who cites it
62 citing papers in PubMed, 101 citations in OpenAlex.
- Human-biasedLife science alliance · 2026Article
- BDNF-DT and BDNF-AS-DT: novel genes in the BDNF locus.Molecular psychiatry · 2026Article
- Natural antisense transcripts as versatile regulators of gene expression.Nature reviews. Genetics · 2024Review
- Article
- Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues.Scientific reports · 2024Article
- The Role of Long Non-Coding RNAs in Cardiovascular Diseases.International journal of molecular sciences · 2023Review
- Functional Roles of lncRNAs in Recurrent Pregnancy Loss: A Review Study.International journal of fertility & sterility · 2023Review
- Native functions of short tandem repeats.eLife · 2023Article
- Emerging concepts involving inhibitory and activating RNA functionalization towards the understanding of microcephaly phenotypes and brain diseases in humans.Frontiers in cell and developmental biology · 2023Review
- Role of Nuclear Non-Canonical Nucleic Acid Structures in Organismal Development and Adaptation to Stress Conditions.Frontiers in genetics · 2022Review
- LncRNAs and Chromatin Modifications Pattern mFrontiers in genetics · 2022Review
- A Novel Regulatory Player in the Innate Immune System: Long Non-Coding RNAs.International journal of molecular sciences · 2021Review
- Bidirectional promoters: an enigmatic genome architecture and their roles in cancers.Molecular biology reports · 2021Review
- Identification of Natural Antisense Transcripts in Mouse Brain and Their Association With Autism Spectrum Disorder Risk Genes.Frontiers in molecular neuroscience · 2021Article
- Compact Bidirectional Promoters for Dual-Gene Expression in a Sleeping Beauty Transposon.International journal of molecular sciences · 2020Article
- Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The Roles of Long Noncoding RNAs HNF1α-AS1 and HNF4α-AS1 in Drug Metabolism and Human Diseases.Non-coding RNA · 2020Review
- Dissecting the transcriptional regulatory networks of promoter-associated noncoding RNAs in development and cancer.Journal of experimental & clinical cancer research : CR · 2020Review
- GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation.Frontiers in genetics · 2020Article
- Differential regulation of CpG island methylation within divergent and unidirectional promoters in colorectal cancer.Cancer science · 2019Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe majority of non-coding RNAs (ncRNAs) involved in mRNA metabolism in mammals have been believed to downregulate the corresponding mRNA expression level in a pre- or post-transcriptional manner by forming short or long ncRNA-mRNA duplex structures. Information on non-duplex-forming long ncRNAs is now also rapidly accumulating. To examine the directional properties of transcription at the whole-genome level, we performed directional RNA-seq analysis of mouse and chimpanzee tissue samples.
resultsWe found that there is only about 1% of the genome where both the top and bottom strands are utilized for transcription, suggesting that RNA-RNA duplexes are not abundantly formed. Focusing on transcription start sites (TSSs) of protein-coding genes revealed that a significant fraction of them contain switching-points that separate antisense- and sense-biased transcription, suggesting that head-to-head transcription is more prevalent than previously thought. More than 90% of head-to-head type promoters contain CpG islands. Moreover, CCG and CGG repeats are significantly enriched in the upstream regions and downstream regions, respectively, of TSSs located in head-to-head type promoters. Genes with tissue-specific promoter-associated ncRNAs (pancRNAs) show a positive correlation between the expression of their pancRNA and mRNA, which is in accord with the proposed role of pancRNA in facultative gene activation, whereas genes with constitutive expression generally lack pancRNAs.
conclusionsWe propose that single-stranded ncRNA resulting from head-to-head transcription at GC-rich sequences regulates tissue-specific gene expression.
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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.