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

9.3.2 SHORT INTERFERING RNA

Short interfering RNAs (siRNA) are the small RNAs having a key role in

gene silencing (Thakur, 2003). Three kinds of siRNAs with lengths of 21, 22,

and 24 nucleotides have been shown to play critical roles in developmental

processes and immunity generation in plants (Wu et al., 2020). Initially, the

majority of siRNAs are generated as short 3’ duplexes by the enzymatic

activity of endonucleases from the Dicer family, acting upon long dsRNA

(Baulcombe, 2005). Then, through sequence complementarity with target

transcripts, one strand of the duplex is loaded into the Argonaute proteins,

which collectively regulate the gene expression of the target gene (He et

al., 2019). siRNAs assign many proteins which modify DNA and histones,

namely cytosine methyltransferase, chromomethylase-3 (Ossowski et al.,

2008) and they vigorously modify transcriptionally active chromatin into

transcriptionally inactive chromatin state (Kamthan et al., 2015). Endog­

enous siRNAs are further categorized into several groups such as natural

antisense siRNAs (natsiRNAs), miRNA-induced trans-acting siRNAs

(tasiRNAs), cis-acting siRNAs (casiRNAs), and hc-siRNAs based on the

specific mode of biogenesis and mode of action (Axtell, 2013; Choudhuri,

2009). natsiRNAs are generated by the processing of dsRNAs that were

produced from endogenous RNAs having complementary sequences and

DCL4 or DCL2 protein acts on the precursors to produce 21- or 22-nucleo­

tide long nat-siRNAs, respectively (Medina et al., 2018). Pha-siRNAs are 21

nt long RNAs that are converted form dsRNA with the help of RDRC and

processed with the help of DCL4 (Medina et al., 2008; Vazquez et al., 2004).

Another siRNA especially 24 nt long, that are associated with the triggering

and modification of de novo methylation of desired loci by RNA-directed

DNA Methylation (RdDM) method, are called “heterochromatic siRNAs”

(hc-siRNA) (Chan et al., 2006; Dalakouras & Wassenegger et al., 1994).

In the case of both hc-siRNA and pha-siRNA, Dicer-like proteins (DCL)

recognize the precursor RNAs and cleave them into products of defined

length (Baldrich et al., 2019). All types of siRNAs are remarkably impor­

tant for plant gene regulation. siRNAs that have length 21 nt and 24 nt are

usually involved in the cleavage of messenger RNAs and DNA methylation

(Bologna & Voinnet, 2014; Borges & Martienssen, 2015). Wu et al. (2020)

showed that 22 nt long siRNAs that are quite different from 21 nt siRNAs

and 24 nt siRNAs, effectively repress translation, triggers transitive RNA

interference and amplification of gene silencing but are less effective in

target cleavage. Further study concluded that induction and upregulation