ArticleBMC bioinformatics2006
In silico discovery of human natural antisense transcripts.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations.Non-coding RNA · 2021Review
- Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications.BMC plant biology · 2018Article
- In silico analysis of endogenous siRNAs associated transposable elements and NATs in Schistosoma japonicum reveals their putative roles during reproductive development.Parasitology research · 2018Article
- Development of genodynamic metrics for exploring the biophysics of DNA polymorphisms.Journal of computational biology and bioinformatics research · 2014Article
- Effect of siRNA with an asymmetric RNA/dTdT overhang on RNA interference activity.Nucleic acid therapeutics · 2014Article
- Emerging landscape of non-coding RNAs in oral health and disease.Oral diseases · 2014Review
- Conserved expression of natural antisense transcripts in mammals.BMC genomics · 2013Article
- A genome-wide investigation of expression characteristics of natural antisense transcripts in liver and muscle samples of pigs.PloS one · 2012Article
- Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci.Frontiers in genetics · 2012Article
- Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model.PloS one · 2011Article
- Transcriptome of small regulatory RNAs in the development of the zoonotic parasite Trichinella spiralis.PloS one · 2011Article
- Regulation of Emx2 expression by antisense transcripts in murine cortico-cerebral precursors.PloS one · 2010Article
- Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.Nucleic acids research · 2010Article
- Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.Nucleic acids research · 2008Article
- Bioinformatics in China: a personal perspective.PLoS computational biology · 2008Review
- Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes.Genome biology · 2008Article
- antiCODE: a natural sense-antisense transcripts database.BMC bioinformatics · 2007Article
- Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).BMC genomics · 2007Article
- Localizing hotspots of antisense transcription.Nucleic acids research · 2007Article
- Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms.EMBO reports · 2006Review
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSeveral high-throughput searches for potential natural antisense transcripts (NATs) have been performed recently, but most of the reports were focused on cis type. A thorough in silico analysis of human transcripts will help expand our knowledge of NATs.
resultsWe have identified 568 NATs from human RefSeq RNA sequences. Among them, 403 NATs are reported for the first time, and at least 157 novel NATs are trans type. According to the pairing region of a sense and antisense RNA pair, hNATs are divided into 6 classes, of which about 87% involve 5' or 3' UTR sequences, supporting the regulatory role of UTRs. Among a total of 535 NAT pairs related with splice variants, 77.4% (414/535) have their pairing regions affected or completely eliminated by alternative splicing, suggesting significant relationship of alternative splicing and antisense-directed regulation. The extensive occurrence of splice variants in hNATs and other multiple pairing patterns results in a one-to-many relationship, allowing the formation of complex regulation networks. Based on microarray data from Stanford Microarray Database, two hNAT pairs were found to display significant inverse expression patterns before and after insulin injection.
conclusionNATs might carry out more extensive and complex functions than previously thought. Combined with endogenous micro RNAs, hNATs could be regarded as a special group of transcripts contributing to the complex regulation networks.
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