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to evaluate the precipitated DNA (Neary & Carless, 2020; Zhang et al., 2006;

Zilberman et al., 2007).

12.5.2.3 REDUCED-REPRESENTATION BISULFITE SEQUENCING (RRBS)

Bisulfite sequencing can be used for obtaining single-nucleotide accuracy

on DNA methylation inside genomic segments generated by using restric­

tion enzymes. Genetic and epigenetic variations can be compared due to

the availability of sequencing and methylation variation within the same

set of loci. The technique depends upon MspI restriction digestion, bisulfite

conversion and sequencing of (40 and 220 base pairs) digested fragments

(Gu et al., 2011). RRBS can be used in the research of plant communities as

well as used on plants without any genomic database (Trucchi et al., 2016;

van Gurp et al., 2016). RRBS has also been utilized in oak (Platt et al., 2015)

and Brassica rapa (Chen et al., 2015) populations.

12.5.3 SMALL RNA SEQUENCING

Small RNAs (sRNAs) are ncRNA molecules that have a role in gene silencing

as well as controls post-transcriptional gene expression. sRNA Sequencing

(sRNA-seq) is a technique that allows for in-depth analysis of small

RNAs, particularly miRNAs and siRNAs. sRNA-Seq is a next-generation

sequencing-based method for miRNA profiling that is presently the most

powerful and efficient technique.

12.6 CHROMATIN MODIFICATION

The dynamic variation of chromatin architecture in a controlled manner,

so that condensed genomic DNA is accessible to regulatory transcription

machinery proteins, and therefore regulate gene expression, the process is

known as chromatin remodeling. The gene expression occurs only when

the chromatin of a cell is “open.” The shift from a repressed to an active

state is facilitated by chromatin modification and remodeling machinery.

Pioneer transcription factors are the foremost to bind to a “closed” promoter

and enhancers, allowing other sequence-specific transcription factors’

easier access to these genomic regions. In conjunction with DNA and

histone protein change, several mechanisms such as chromatin assembly/