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miRNAting control of DNA methylation

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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.

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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

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Acknowledgements

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.

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  1. Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176 061, India

    Ashwani Jha & Ravi Shankar

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  1. Ashwani Jha
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  2. Ravi Shankar
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Correspondence to Ravi Shankar.

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Corresponding editor: UTPAL NATH

[Jha A and Shankar R 2014 miRNAting control of DNA methylation. J. Biosci. 39 1–15] DOI 10.1007/s12038-014-9437-9

Supplementary materials pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/jun2014/supp/Jha.pdf

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Jha, A., Shankar, R. miRNAting control of DNA methylation. J Biosci 39, 365–380 (2014). https://doi.org/10.1007/s12038-014-9437-9

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