ArticleBMC genomics2010
Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Identification and functional characterization of bidirectional gene pairs and their intergenic regions in cotton.BMC plant biology · 2024Article
- Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.The EMBO journal · 2023Article
- Pathogen Resistance Depending on Jacalin-Dirigent Chimeric Proteins Is Common among Poaceae but Absent in the Dicot Arabidopsis as Evidenced by Analysis of Homologous Single-Domain Proteins.Plants (Basel, Switzerland) · 2022Article
- Core circadian clock and light signaling genes brought into genetic linkage across the green lineage.Plant physiology · 2022Article
- Comprehensive construction strategy of bidirectional green tissue-specific synthetic promoters.Plant biotechnology journal · 2020Article
- Additional Layer of Regulation via Convergent Gene Orientation in Yeasts.Molecular biology and evolution · 2020Article
- Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate.Frontiers in genetics · 2019Article
- The Effects of Transcription Directions of Transgenes and the gypsy Insulators on the Transcript Levels of Transgenes in Transgenic Arabidopsis.Scientific reports · 2017Article
- Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana.Nucleic acids research · 2017Article
- Histone modifications facilitate the coexpression of bidirectional promoters in rice.BMC genomics · 2016Article
- Functional characterization of open chromatin in bidirectional promoters of rice.Scientific reports · 2016Article
- A low-temperature-responsive element involved in the regulation of the Arabidopsis thaliana At1g71850/At1g71860 divergent gene pair.Plant cell reports · 2016Article
- A Novel Candidate Gene for Temperature-Dependent Sex Determination in the Common Snapping Turtle.Genetics · 2016Article
- Integrated mapping and characterization of the gene underlying the okra leaf trait in Gossypium hirsutum L.Journal of experimental botany · 2016Article
- A comparative gene analysis with rice identified orthologous group II HKT genes and their association with Na(+) concentration in bread wheat.BMC plant biology · 2016Article
- Isolation and Functional Characterization of Bidirectional Promoters in Rice.Frontiers in plant science · 2016Article
- Physical mapping of immune-related genes in Yesso scallop (Comparative cytogenetics · 2016Article
- Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.Genome biology · 2015Article
- Suppression of expression between adjacent genes within heterologous modules in yeast.G3 (Bethesda, Md.) · 2014Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn all eukaryotic species examined, genes that are chromosomal neighbours are more similar in their expression than random gene pairs. Currently, it is still unclear how much of this local co-expression is caused by direct transcriptional interactions, and how much is due to shared chromatin environments.
resultsWe analysed neighbouring genes in Arabidopsis thaliana. At large intergenic distances (>400 bp), divergently and convergently transcribed gene pairs show very similar levels of co-expression, mediated most likely by shared chromatin environments. At gene distances below 400 bp, co-expression is strongly enhanced only for divergently transcribed gene pairs, indicating bi-directional transcription from a single promoter. Conversely, co-expression is suppressed for short convergently or uni-directionally transcribed pairs. This suppression points to transcriptional interference concentrated at the 3' end, e.g., in the context of transcription termination.
conclusionsClassifying linked gene pairs by their orientation, we are able to partially tease apart the different levels of regional expression modulation. (i) Regional chromatin characteristics modulate the accessibility for regulation and transcription, regardless of gene orientation; the strength of this chromatin effect can be assessed from divergently or convergently transcribed distant neighbours. (ii) Shared promoter regions up to 400 bp in length enhance the co-expression of close bi-directional neighbours. (iii) Transcriptional interference of close neighbours is concentrated at the 3' ends of genes, and reduces co-expression on average by 40%.
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