Functional Characteristics of Genome-wide Rice Transcriptomes Responded to Gamma Radiation
0
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
Genome-wide transcriptomic profiles disclose physiomes or phenomes associatedwith diverse phenotypes in plants. Some transcriptomes associated with DNA damage response(DDR) in Arabidopsis are used for phytodosimetry of ionizing radiation (IR). This study revealsfunctional characteristics of genome-wide rice transcriptomes after gamma irradiation. Biologicalpathway analysis demonstrated that some genes responsible for histone modification and chromatinremodeling were notably affected in association with transcriptional regulation in rice after gammairradiation. Gene ontology (GO) enrichment analysis further showed that the GO terms representingstimulus or stress were enriched commonly in both Arabidopsis and rice after gamma irradiation,while the cell cycle was more conspicuous in rice. In addition, the transcriptomic profile in riceafter gamma irradiation revealed a substantial difference in expression of DDR genes comparedto that in Arabidopsis, having about two times more genes downregulated than those upregulated. These results suggest that rice transcriptomes responded to gamma radiation should be functionallyverified before being used for phytodosimetry of IR or correlated with diverse phenotypes aftergamma irradiation.
Abstract
Genome-wide transcriptomic profiles disclose physiomes or phenomes associatedwith diverse phenotypes in plants. Some transcriptomes associated with DNA damage response(DDR) in Arabidopsis are used for phytodosimetry of ionizing radiation (IR). This study revealsfunctional characteristics of genome-wide rice transcriptomes after gamma irradiation. Biologicalpathway analysis demonstrated that some genes responsible for histone modification and chromatinremodeling were notably affected in association with transcriptional regulation in rice after gammairradiation. Gene ontology (GO) enrichment analysis further showed that the GO terms representingstimulus or stress were enriched commonly in both Arabidopsis and rice after gamma irradiation,while the cell cycle was more conspicuous in rice. In addition, the transcriptomic profile in riceafter gamma irradiation revealed a substantial difference in expression of DDR genes comparedto that in Arabidopsis, having about two times more genes downregulated than those upregulated. These results suggest that rice transcriptomes responded to gamma radiation should be functionallyverified before being used for phytodosimetry of IR or correlated with diverse phenotypes aftergamma irradiation.
참고문헌 (14)
- Eschbach V, "Different replication protein A complexes of Arabidopsis thaliana have different DNA-binding properties as a function of heterotrimer composition", Plant Cell Physiol, 44, pp.1460~1472 (2014)
- Hsu SK, "RNA-Seq analysis of diverse rice genotypes to identify the genes controlling coleoptile growth during submerged germination", Front. Plant Sci, 8, pp.762~ (2017)
- Kim JE, "Characterization of non-CG genomic hypomethylation associated with gamma-ray-induced suppression of CMT3 transcription in Arabidopsis thaliana", Radiat. Res, 180, pp.638~648 (2013)
- Kim JH, "Integrated analysis of diverse transcriptomic data Arabidopsis reveals genetic markers that reliably and reproducibly respond to ionizing radiation", Gene, 518, pp.273~279 (2013)
- 김진홍, "Confirmation of no Causal Relationship between Genome-wide DNA Methylation and Transcriptome Changes after Gamma Irradiation", 방사선산업학회지, 11(4), pp.181~187 (2017), (사)한국방사선산업학회[DOI]
- Kim JH, "Ionizing radiation manifesting DNA damage response in plants: An overview of DNA damage signaling and repair mechanisms in plants", Plant Sci, 278, pp.44~53 (2019)
- Mondal S, "Characterization of histone modifications associated with DNA damage repair genes upon exposure to gamma rays in Arabidopsis seedling", J. Radiat. Res, 57, pp.646~654 (2016)
- Ryu TH, "SOG1-dependent NAC103 modulates the DNA damage response as a transcriptional regulator in Arabidopsis", Plant J, 98, pp.83~96 (2019)
- Ryu TH, "Transcriptome- based biological dosimetry of gamma radiation in Arabidopsis using DNA damage response genes", J. Environ. Radioactiv, 181, pp.94~101 (2018)
- Takehisa H, "Transcriptome monitoring visualizes growth stage-dependent nutrient status dynamics in rice under field conditions", Plant J, 97, pp.1048~1060 (2019)
- Tian T, "agriGO v2. 0 : a GO analysis toolkit for the agricultural community, 2017 update", Nucleic Acids Res, 45, pp.W122~W129 (2017)
- Trapnell C, "TopHat : discovering splice junctions with RNA-Seq", Bioinformatics, 25, pp.1105~1111 (2009)
- Trapnell C, "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks", Nat. Protoc, 7, pp.562~578 (2012)
- Usadel B, "A guide to using MapMan to visualize and compare Omics data in plants : a case study in the crop species, Maize", Plant Cell Environ, 32, pp.1211~1229 (2009)