ArticleBMC bioinformatics2009
Searching for bidirectional promoters in Arabidopsis thaliana.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Identification and application of bioparts for plant synthetic biology.Molecules and cells · 2025Review
- Identification and functional characterization of bidirectional gene pairs and their intergenic regions in cotton.BMC plant biology · 2024Article
- Do DEEPER ROOTING 1 Homologs Regulate the Lateral Root Slope Angle in Cucumber (International journal of molecular sciences · 2024Article
- The RiceInternational journal of molecular sciences · 2022Article
- The Hda1 histone deacetylase limits divergent non-coding transcription and restricts transcription initiation frequency.The EMBO journal · 2021Article
- Comprehensive construction strategy of bidirectional green tissue-specific synthetic promoters.Plant biotechnology journal · 2020Article
- Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Plant Defenses Against Pests Driven by a Bidirectional Promoter.Frontiers in plant science · 2019Article
- Structural and Functional Analysis of a Bidirectional Promoter fromInternational journal of molecular sciences · 2018Article
- Processes Underlying a Reproductive Barrier inPlant physiology · 2017Article
- Analysis of Promoters of Arabidopsis thaliana Divergent Gene Pair SERAT3;2 and IDH-III Shows SERAT3;2 Promoter is Nested Within the IDH-III Promoter.Molecular biotechnology · 2017Article
- Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- A phosphate starvation-driven bidirectional promoter as a potential tool for crop improvement and in vitro plant biotechnology.Plant biotechnology journal · 2017Article
- Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations.PloS one · 2017Article
- Functional characterization of open chromatin in bidirectional promoters of rice.Scientific reports · 2016Article
- The intergenic region of the maize defensin-like protein genes Def1 and Def2 functions as an embryo-specific asymmetric bidirectional promoter.Journal of experimental botany · 2016Article
- Isolation and Functional Characterization of Bidirectional Promoters in Rice.Frontiers in plant science · 2016Article
- Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Terminate and make a loop: regulation of transcriptional directionality.Trends in biochemical sciences · 2014Review
- Identification and functional characterization of bidirectional gene pairs and their intergenic regions in maize.BMC genomics · 2014Article
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6 authors.
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Abstract
backgroundA "bidirectional gene pair" is defined as two adjacent genes which are located on opposite strands of DNA with transcription start sites (TSSs) not more than 1000 base pairs apart and the intergenic region between two TSSs is commonly designated as a putative "bidirectional promoter". Individual examples of bidirectional gene pairs have been reported for years, as well as a few genome-wide analyses have been studied in mammalian and human genomes. However, no genome-wide analysis of bidirectional genes for plants has been done. Furthermore, the exact mechanism of this gene organization is still less understood.
resultsWe conducted comprehensive analysis of bidirectional gene pairs through the whole Arabidopsis thaliana genome and identified 2471 bidirectional gene pairs. The analysis shows that bidirectional genes are often coexpressed and tend to be involved in the same biological function. Furthermore, bidirectional gene pairs associated with similar functions seem to have stronger expression correlation. We pay more attention to the regulatory analysis on the intergenic regions between bidirectional genes. Using a hierarchical stochastic language model (HSL) (which is developed by ourselves), we can identify intergenic regions enriched of regulatory elements which are essential for the initiation of transcription. Finally, we picked 27 functionally associated bidirectional gene pairs with their intergenic regions enriched of regulatory elements and hypothesized them to be regulated by bidirectional promoters, some of which have the same orthologs in ancient organisms. More than half of these bidirectional gene pairs are further supported by sharing similar functional categories as these of handful experimental verified bidirectional genes.
conclusionBidirectional gene pairs are concluded also prevalent in plant genome. Promoter analyses of the intergenic regions between bidirectional genes could be a new way to study the bidirectional gene structure, which may provide a important clue for further analysis. Such a method could be applied to other genomes.
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