Journal of Biosciences

, Volume 39, Issue 3, pp 365–380

miRNAting control of DNA methylation

Article

DOI: 10.1007/s12038-014-9437-9

Cite this article as:
Jha, A. & Shankar, R. J Biosci (2014) 39: 365. doi:10.1007/s12038-014-9437-9

Abstract

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.

Keywords

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

Abbreviations

AGO

argonaute

GFF

General Feature Format

GO

gene ontology

ncRNA

non-coding RNA

NGS

next-generation sequencing

RdDM

RNA-dependent DNA methylation

RDR2

RNA-dependent RNA polymerase 2

siRNA

small interfering RNA

SVR

support vector regression

TFBS

transcription factor binding site

Supplementary material

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

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

Personalised recommendations