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Biology and Biotechnology of Environmental Stress Tolerance in Plants, Volume 3

and linked to a differently labeled reference specimen as well as used for the

analysis of enhanced signals on DNA microarrays. The use of genome tiling

microarray technology enables for a whole-genome study of proteins bound

to isolated DNA, as well as the construction of a high-resolution genomic

map of protein-binding and protein changes. With the help of computational

and bioinformatic techniques, the enriched and reference channels are then

normalized. The signals are connected with DNA microarray-represented

sections within the genome, reliability criteria are provided, as well as maps

of protein-genome interaction are generated. The technique may be used to

find transcription factor, enhancer, and repressor binding sites, as well as

compare these types of bound proteins in normal and treated samples. With

the decrease in the cost of NGS significantly and identical findings can be

achieved using ChIP-seq, more people are opting for ChIP-seq over ChIP­

chip (Ren et al., 2000).

12.5.2 PROFILING OF DNA METHYLATION IN PLANTS

DNA methylation is an epigenetic alteration that regulates gene expression in

various activities of organisms. It is accurate for each tissue, active, depends

on sequence pattern, as well as inherited across generations, highlighting the

need for profiling DNA methylation to address biological issues. DNA meth­

ylation is detected by either using next-generation sequencing technology or

by microarray hybridization technology.

12.5.2.1 BISULFITE SEQUENCING OF THE WHOLE GENOME (WGBS)

Next-generation sequencing technology is presently being used to build

genomic maps of DNA methylation with single-base clarity. When methyl­

ated cytosines are treated with bisulfite then they get converted to uracil. This

technique compares the treated specimen to a known specimen to identify

the methylated cytosine (Cokus et al., 2008; Kurdyukov & Bullock, 2016).

Whole-genome bisulfite sequencing (WGBS) assesses individual cytosines

inside a query sequence for almost every cytosine within the genome.

12.5.2.2 METHYLATED DNA IMMUNOPRECIPITATION (MEDIP)

The disrupted genomic DNA is pulled down with the help of a 5-methylcyto­

sine-specific antibody. PCR based or microarrays of whole genome are used