The expression of a number of eukaryotic genes is controlled through RNA interference, also known as RNA silencing and posttranscriptional gene silencing (see Chapter 10). Research suggests that as many as 30% of human genes are regulated by RNA interference. RNA interference is widespread in eukaryotes, existing in fungi, plants, and animals. A similar group of small RNA molecules with silencing and activating functions have been detected in prokaryotes. The mechanism of RNA silencing is also widely used as a powerful technique for artificially regulating gene expression in genetically engineered organisms (see Chapter 14).

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RNA interference is triggered by small RNA molecules know as microRNAs (miRNAs) and small interfering RNAs (siRNAs), depending on their origin and mode of action (see Chapter 10). An enzyme called Dicer cleaves and processes double-stranded RNA to produce single-stranded siRNAs or miRNAs 21–25 nucleotides in length, which pair with proteins to form an RNA-induced silencing complex (RISC). The RNA component of the RISC then pairs with complementary base sequences in specific mRNA molecules, most often with sequences in the 3′ UTR of the mRNA. Small interfering RNAs and microRNAs regulate gene expression through at least three distinct mechanisms: (1) cleavage of mRNA, (2) inhibition of translation, or (3) inhibition of transcription (­Figure 12.21).

RNA CLEAVAGE RISCs that contain an siRNA (and some that contain an miRNA) pair with mRNA molecules and cleave the mRNA near the middle of the bound siRNA (Figure 12.21a). This cleavage is carried out by a protein that is sometimes referred to as Slicer. After cleavage, the mRNA is further degraded. Thus, the presence of siRNAs and miRNAs increases the rate at which mRNAs are broken down and decreases the amount of protein produced.

INHIBITION OF TRANSLATION Some miRNAs regulate genes by inhibiting the translation of their complementary mRNAs (Figure 12.21b). For example, an important gene in flower development in Arabidopsis thaliana is APETALA2. The expression of this gene is regulated by an miRNA that base pairs with nucleotides in the coding region of APETALA2 mRNA and inhibits its translation.

TRANSCRIPTIONAL SILENCING Other siRNAs silence transcription by altering chromatin structure. These siRNAs combine with proteins to form a complex called RITS (for RNA-induced transcriptional silencing), which is analogous to RISC (Figure 12.21c). The siRNA component of a RITS then binds to its complementary sequence in DNA or an RNA molecule in the process of being transcribed, where it represses transcription by attracting enzymes that methylate the tails of histone proteins. The addition of these methyl groups to the histones causes them to bind DNA more tightly, restricting the access of proteins and enzymes necessary to carry out transcription (see the sections on histone modification earlier in this chapter).