ArticleNucleic acids research2017
Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 37 citations in OpenAlex.
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- WRKY transcription factors and OBERON histone-binding proteins form complexes to balance plant growth and stress tolerance.The EMBO journal · 2023Article
- Chromosome-level genome assembly ofFrontiers in plant science · 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
- MS1/MMD1 homologues in the moss Physcomitrium patens are required for male and female gametogenesis.The New phytologist · 2022Article
- The 3D architecture of the pepper genome and its relationship to function and evolution.Nature communications · 2022Article
- Positively selected genes in the hoary bat (PeerJ · 2022Article
- Global Changes in AsexualMicroorganisms · 2021Article
- Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology.Frontiers in plant science · 2021Review
- Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance.Genome biology and evolution · 2020Article
- Subnuclear gene positioning through lamina association affects copper tolerance.Nature communications · 2020Article
- Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure.Nature plants · 2020Article
- MS1, a direct target of MS188, regulates the expression of key sporophytic pollen coat protein genes in Arabidopsis.Journal of experimental botany · 2020Article
- EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes.Bioinformatics (Oxford, England) · 2020Article
- Investigation of the genes associated with a male sterility mutant (msm) in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq.Molecular genetics and genomics : MGG · 2020Article
- Evolutionary and functional patterns of shared gene neighbourhood in fungi.Nature microbiology · 2019Article
- Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize.International journal of molecular sciences · 2019Article
- Transcriptome Profiling and Genome-Wide Association Studies RevealFrontiers in plant science · 2019Article
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Authors and funding
8 authors at 5 institutions in 3 countries.
Funding
Abstract
Co-expression of physically linked genes occurs surprisingly frequently in eukaryotes. Such chromosomal clustering may confer a selective advantage as it enables coordinated gene regulation at the chromatin level. We studied the chromosomal organization of genes involved in male reproductive development in Arabidopsis thaliana. We developed an in-silico tool to identify physical clusters of co-regulated genes from gene expression data. We identified 17 clusters (96 genes) involved in stamen development and acting downstream of the transcriptional activator MS1 (MALE STERILITY 1), which contains a PHD domain associated with chromatin re-organization. The clusters exhibited little gene homology or promoter element similarity, and largely overlapped with reported repressive histone marks. Experiments on a subset of the clusters suggested a link between expression activation and chromatin conformation: qRT-PCR and mRNA in situ hybridization showed that the clustered genes were up-regulated within 48 h after MS1 induction; out of 14 chromatin-remodeling mutants studied, expression of clustered genes was consistently down-regulated only in hta9/hta11, previously associated with metabolic cluster activation; DNA fluorescence in situ hybridization confirmed that transcriptional activation of the clustered genes was correlated with open chromatin conformation. Stamen development thus appears to involve transcriptional activation of physically clustered genes through chromatin de-condensation.
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