ArticleBMC genomics2019
Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 34 citations in OpenAlex.
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- Genome-wide identification and expression pattern analysis under drought stress of PHD family genes in alfalfa (Medicago sativa).BMC genomics · 2025Article
- Zinc and its binding proteins: essential roles and therapeutic potential.Archives of toxicology · 2025Review
- Transcriptome wide identification, characterization and expression analysis of PHD gene family inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Differential gene expression during floral transition in pineapple.Plant direct · 2023Article
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- PHD finger proteins function in plant development and abiotic stress responses: an overview.Frontiers in plant science · 2023Review
- Identification of the Genes Encoding B3 Domain-Containing Proteins Related to Vernalization ofGenes · 2022Article
- MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression.The Plant journal : for cell and molecular biology · 2022Article
- A Large-Scale Genomic Association Analysis Identifies the Candidate Genes Regulating Salt Tolerance in Cucumber (International journal of molecular sciences · 2022Article
- C2H2 Zinc Finger Proteins Response to Abiotic Stress in Plants.International journal of molecular sciences · 2022Review
- Genetic and Physiological Responses to Heat Stress inFrontiers in plant science · 2022Review
- Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.).BMC plant biology · 2021Article
- Genome-wide analysis of PHD finger gene family and identification of potential miRNA and their PHD finger gene specific targets inNon-coding RNA research · 2020Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundPlant homeodomain (PHD) finger proteins are widely present in all eukaryotes and play important roles in chromatin remodeling and transcriptional regulation. The PHD finger can specifically bind a number of histone modifications as an "epigenome reader", and mediate the activation or repression of underlying genes. Many PHD finger genes have been characterized in animals, but only few studies were conducted on plant PHD finger genes to this day. Brassica rapa (AA, 2n = 20) is an economically important vegetal, oilseed and fodder crop, and also a good model crop for functional and evolutionary studies of important gene families among Brassica species due to its close relationship to Arabidopsis thaliana.
resultsWe identified a total of 145 putative PHD finger proteins containing 233 PHD domains from the current version of B. rapa genome database. Gene ontology analysis showed that 67.7% of them were predicted to be located in nucleus, and 91.3% were predicted to be involved in protein binding activity. Phylogenetic, gene structure, and additional domain analyses clustered them into different groups and subgroups, reflecting their diverse functional roles during plant growth and development. Chromosomal location analysis showed that they were unevenly distributed on the 10 B. rapa chromosomes. Expression analysis from RNA-Seq data showed that 55.7% of them were constitutively expressed in all the tested tissues or organs with relatively higher expression levels reflecting their important housekeeping roles in plant growth and development, while several other members were identified as preferentially expressed in specific tissues or organs. Expression analysis of a subset of 18 B. rapa PHD finger genes under drought and salt stresses showed that all these tested members were responsive to the two abiotic stress treatments.
conclusionsOur results reveal that the PHD finger genes play diverse roles in plant growth and development, and can serve as a source of candidate genes for genetic engineering and improvement of Brassica crops against abiotic stresses. This study provides valuable information and lays the foundation for further functional determination of PHD finger genes across the Brassica species.
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