Genome-wide Bisulphite-sequencing Reveals Organ-specific Methylation Patterns in Chickpea

Overview

Journal Sci Rep

Specialty Science

Date 2018 Jun 28

PMID 29946142

Citations 16

Authors

Himanshi Bhatia

Niraj Khemka

Mukesh Jain

Rohini Garg

Affiliations

Soon will be listed here.

Abstract

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.

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References

Takuno S, Gaut B . Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol Biol Evol. 2011; 29(1):219-27. DOI: 10.1093/molbev/msr188. View

Struhl K . Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell. 1999; 98(1):1-4. DOI: 10.1016/S0092-8674(00)80599-1. View

Matzke M, Mosher R . RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet. 2014; 15(6):394-408. DOI: 10.1038/nrg3683. View

Wada Y, Miyamoto K, Kusano T, Sano H . Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants. Mol Genet Genomics. 2004; 271(6):658-66. DOI: 10.1007/s00438-004-1018-4. View

Varshney R, Song C, Saxena R, Azam S, Yu S, Sharpe A . Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol. 2013; 31(3):240-6. DOI: 10.1038/nbt.2491. View

Karam Teixeira F, Colot V . Gene body DNA methylation in plants: a means to an end or an end to a means?. EMBO J. 2009; 28(8):997-8. PMC: 2683714. DOI: 10.1038/emboj.2009.87. View

Filion G, Zhenilo S, Salozhin S, Yamada D, Prokhortchouk E, Defossez P . A family of human zinc finger proteins that bind methylated DNA and repress transcription. Mol Cell Biol. 2005; 26(1):169-81. PMC: 1317629. DOI: 10.1128/MCB.26.1.169-181.2006. View

Chen K, Rajewsky N . The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet. 2007; 8(2):93-103. DOI: 10.1038/nrg1990. View

Waterhouse P, Hellens R . Plant biology: Coding in non-coding RNAs. Nature. 2015; 520(7545):41-2. DOI: 10.1038/nature14378. View

10.

Garg R, Patel R, Jhanwar S, Priya P, Bhattacharjee A, Yadav G . Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol. 2011; 156(4):1661-78. PMC: 3149962. DOI: 10.1104/pp.111.178616. View

11.

Chodavarapu R, Feng S, Bernatavichute Y, Chen P, Stroud H, Yu Y . Relationship between nucleosome positioning and DNA methylation. Nature. 2010; 466(7304):388-92. PMC: 2964354. DOI: 10.1038/nature09147. View

12.

Song Q, Lu X, Li Q, Chen H, Hu X, Ma B . Genome-wide analysis of DNA methylation in soybean. Mol Plant. 2013; 6(6):1961-74. DOI: 10.1093/mp/sst123. View

13.

Pikaard C, Mittelsten Scheid O . Epigenetic regulation in plants. Cold Spring Harb Perspect Biol. 2014; 6(12):a019315. PMC: 4292151. DOI: 10.1101/cshperspect.a019315. View

14.

Li X, Zhu J, Hu F, Ge S, Ye M, Xiang H . Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics. 2012; 13:300. PMC: 3447678. DOI: 10.1186/1471-2164-13-300. View

15.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S . TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4):R36. PMC: 4053844. DOI: 10.1186/gb-2013-14-4-r36. View

16.

Liu Y, Olanrewaju Y, Zheng Y, Hashimoto H, Blumenthal R, Zhang X . Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res. 2014; 42(8):4859-67. PMC: 4005678. DOI: 10.1093/nar/gku134. View

17.

Garg R, Singh V, Singh Rajkumar M, Kumar V, Jain M . Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with seed development and seed size/weight determination in chickpea. Plant J. 2017; 91(6):1088-1107. DOI: 10.1111/tpj.13621. View

18.

Krueger F, Andrews S . Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011; 27(11):1571-2. PMC: 3102221. DOI: 10.1093/bioinformatics/btr167. View

19.

Kim K, El Baidouri M, Abernathy B, Iwata-Otsubo A, Chavarro C, Gonzales M . A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean. Plant Physiol. 2015; 168(4):1433-47. PMC: 4528746. DOI: 10.1104/pp.15.00408. View

20.

Law J, Jacobsen S . Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010; 11(3):204-20. PMC: 3034103. DOI: 10.1038/nrg2719. View