Gene silencing (also known as ribonucleic acid [RNA] interference [RNAi] or interfering RNA) was first recognized in plants and is considered one of the most significant discoveries in molecular biology in the last several years. These short-chain ribonucleic acid molecules regulate eukaryotic gene expression. The phenomenon involves a process that promotes RNA transcripts degradation through complementarity between RNA molecules and RNAi transcripts, resulting in the reduction of their translation levels. There are two principal classes of regulatory RNA molecules: small interfering RNAs (siRNA) and microRNAs (miRNA). Both are generated from the cleavage of double-stranded self-complementary RNA hairpins by a DICER enzyme that belongs to the RNase III family. Small RNAs (of about 21–24 nucleotides in size) guide specific effector Argonaute protein to a target nucleotide sequence by complementary base pairing. Thereby, the effector protein complex downregulates the expression of RNA or DNA targets. In plants, cis-regulatory RNAi sequences are involved in defense mechanisms against antagonistic organisms and transposition events, while trans-regulatory sequences participate in growth-related gene expression. siRNA also performs neutral antiviral defense mechanisms and adaptive stress responses. This document is an attempt to scrutinize the RNAi nature in understanding gene downregulation mechanism in plants and some technical applications.
Part of the book: Plant Genomics
Nowadays, it is well known that archaea organisms as well as bacteria show an important range of defense mechanisms. Among others, a unique molecular system called CRISPR/Cas (clustered regularly interspaced short palindromic repeats) helps provide protection (adaptive guided immunity) athwart foreign nucleic acids, including plasmids and viral infections. As a typical immune response, CRISPR system is based on the acquisition of genetic records provided by infectious external agents, and in this sense, a high interference upon a new infection is unchained. In relation to plant research, less than 10 years ago, efforts to understand this peculiar mechanism and the possibility of being used in biotechnological processes have been focused on obtaining atavistic changes in different transformable vegetal specimens by inducing selective mutations into a reading frame that may be translated in a given moment (i.e., ORF; open reading frame). In light of the consideration that one common use of ORFs is to assist gene prediction processes, palindromic repeats are mostly based on the directed mutations via nonhomologous end joining. Although it is true that DNA-free editing techniques are now desirable for molecular crop breeding, CRISPR/Cas as a mutational regulatory system in plant biology may offer better complex genome rearrangements.
Part of the book: Transgenic Crops