Journal of Biosciences

, Volume 39, Issue 3, pp 365–380 | Cite as

miRNAting control of DNA methylation

  • Ashwani Jha
  • Ravi ShankarEmail author


DNA methylation is a type of epigenetic modification where a methyl group is added to the cytosine or adenine residue of a given DNA sequence. It has been observed that DNA methylation is achieved by some collaborative agglomeration of certain proteins and non-coding RNAs. The assembly of IDN2 and its homologous proteins with siRNAs recruits the enzyme DRM2, which adds a methyl group at certain cytosine residues within the DNA sequence. In this study, it was found that de novo DNA methylation might be regulated by miRNAs through systematic targeting of the genes involved in DNA methylation. A comprehensive genome-wide and system-level study of miRNA targeting, transcription factors, DNA-methylation-causing genes and their target genes has provided a clear picture of an interconnected relationship of all these factors which regulate DNA methylation in Arabidopsis. The study has identified a DNA methylation system that is controlled by four different genes: IDN2, IDNl1, IDNl2 and DRM2. These four genes along with various critical transcription factors appear to be controlled by five different miRNAs. Altogether, DNA methylation appears to be a finely tuned process of opposite control systems of DNA-methylation-causing genes and certain miRNAs pitted against each other.


Bioinformatics de novo DNA methylation expression genome genomic microarray miRNA NGS regulatory network transcription factors 





General Feature Format


gene ontology


non-coding RNA


next-generation sequencing


RNA-dependent DNA methylation


RNA-dependent RNA polymerase 2


small interfering RNA


support vector regression


transcription factor binding site



AJ is thankful to CSIR for his project fellowship. RS is thankful to INSA for his Indo-Australia Visiting Fellowship, during which this work was done. We are thankful to the open source community and all the researchers who provided their valuable data as an open source. We are grateful to Dr RD Singh, CSIR-IHBT, for his valuable inputs in editing this manuscript. Like most of our previous works, this work has also been done completely over open source operating system of Ubuntu Linux. We are thankful to the same Linux community. This study was funded by SERB India through grant number SR/FT/LS-97/2010 and CSIR - 12th Five Year Plan National Project Grant (BSC-0118). IHBT communication number for this MS is 3648.

Supplementary material

12038_2014_9437_MOESM1_ESM.pdf (33 kb)
ESM 1 (PDF 32.8 kb)


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Copyright information

© Indian Academy of Sciences 2014

Authors and Affiliations

  1. 1.Studio of Computational Biology & Bioinformatics, Biotechnology DivisionCSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT)PalampurIndia

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