Analysis of DNA methylome and transcriptome profiling following Gibberellin A3 (GA3) foliar application in Nicotiana tabacum L.
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The present work investigated a comprehensive genome-wide landscape of DNA methylome and its relationship with transcriptome upon gibberellin A3 (GA3) foliar application under practical field conditions in solanaceae model, Nicotiana tabacum L. Methylated DNA Immunoprecipitation-Sequencing (MeDIP-Seq) analysis uncovered over 82% (18,456) of differential methylated regions (DMRs) in intergenic-region. Within protein-coding region, 2339 and 1685 of identified DMRs were observed in genebody- and promoter-region, respectively. Microarray study revealed 7032 differential expressed genes (DEGs) with 3507 and 3525 genes displaying up- and down-regulation, respectively. Integration analysis revealed 520 unique non-redundant annotated DMRs overlapping with DEGs. Our results indicated that GA3 induced DNA hypo- as well as hyper-methylation were associated with both gene-silencing and -activation. No complete biasness or correlation was observed in either of the promoter- or genebody-regions, which otherwise showed an overall trend towards GA3 induced global DNA hypo-methylation. Taken together, our results suggested that differential DNA methylation mediated by GA3 may only play a permissive role in regulating the gene expression.
KeywordsNicotiana tabacum GA3 Microarray DNA methylation and MeDIP-Seq
Differential Expressed Genes
Differential Methylated Regions
Methylated DNA Immunoprecipitation
We would like to acknowledge Dr. C.C. Lakshmanan [Head, Corporate R&D, ITC Limited, ITC Life Science and Technology Centre (LSTC)] for his consistent support. Our appreciation is extended to Prof. Sanjeev Galande [Head, Centre of Excellence in Epigenetics, Indian Institute of Science Education and Research (IISER), Pune, India] for providing his valuable inputs on MeDIP-Seq experiment. Nucleome Informatics Private Limited, Hyderabad, India and Genotypic Technology Private Limited, Bengaluru, India are acknowledged for performing the MeDIP-Seq and microarray processing and data analysis, respectively. We would also like to acknowledge EpigenDx Hopkinton, MA, USA for carrying out tNGBS assays. Editorial and useful tips from the in-house manuscript committee of LSTC-ITC are well appreciated. Overall support from team Agriscience, ITC-LSTC is greatly acknowledged. We also acknowledge the field-workers at Northern Light Soil (NLS) region, Rajahmundry, Andhra Pradesh (A.P.), India for providing their consistent help and support during field experiments and sample collections.
Compliance with ethical standards
Conflict of interest
The authors declare that there are no conflict of interest. The content of this manuscript does not necessarily reflect the views or policies of the ITC-LSTC.
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