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Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea

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Title Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea
 
Creator Bhatia, Himanshi
Khemka, Niraj
Jain, Mukesh
Garg, Rohini
 
Subject bisulphite-sequencing
chickpea
methylation
 
Description Accepted date: 30 May 2018
DNA methylation is widely known to regulate gene expression in eukaryotes. Here, we unraveled DNA methylation patterns in cultivated chickpea to understand the regulation of gene expression in different organs. We analyzed the methylation pattern in leaf tissue of wild chickpea too, and compared it with cultivated chickpea. Our analysis indicated abundant CG methylation within gene-body and CHH methylation in intergenic regions of the chickpea genome in all the organs examined. Analysis of differentially methylated regions (DMRs) demonstrated a higher number of CG context DMRs in wild chickpea and CHH context DMRs in cultivated chickpea. We observed increased preponderance of hypermethylated DMRs in the promoter regions and hypomethylated DMRs in the genic regions in cultivated chickpea. Genomic location and context of the DMRs correlated well with expression of proximal genes. Our results put forth a positive correlation of promoter hypermethylation with increased transcript abundance via identification of DMR-associated genes involved in flower development in cultivated chickpea. The atypical correlation observed between promoter hypermethylation and increased transcript abundance might be dependent on 24-nt small RNAs and transcription factors binding to the promoter region. This study provides novel insights into DNA methylation patterns in chickpea and their role in regulation of gene expression.
This project was funded by the Department of Biotechnology, Government of India, New Delhi (BT/AB/
NIPGR/SEED BIOLOGY/2012). HB acknowledges National Post-Doctoral Fellowship Award by the Science
and Engineering Research Board, Department of Science and Technology, Government of India, New Delhi.
NK acknowledges BINC Fellowship by the Department of Biotechnology, Government of India, New Delhi. RG
acknowledges INSPIRE Faculty Award from the Department of Science and Technology, Government of India,
New Delhi. We are thankful to Dr. Vikash Kumar Singh for his help in gene expression data analysis.
 
Date 2018-07-10T05:04:47Z
2018-07-10T05:04:47Z
2018
 
Type Article
 
Identifier Scientific Reports 8(1): 9704
2045-2322
http://223.31.159.10:8080/jspui/handle/123456789/868
https://www.nature.com/articles/s41598-018-27979-w
https://doi.org/10.1038/s41598-018-27979-w
 
Language en_US
 
Format application/pdf
 
Publisher Springer Nature