RNA Activators of Stress Kinase PKR within Human Genes That Control Splicing or Translation Create Novel Targets for Hereditary Diseases

Figure 1. The RNA activator of PKR in human IFNG mRNA. The cis-acting 203-nucleotide element within human IFNG mRNA that activates PKR, to strongly attenuate its own translation, is composed of the entire 5′-UTR and 78 nucleotides of the open reading frame. Secondary structure was determined by T1, U2, and V1 nuclease sensitivity mapping, in-line structure probing in the absence or presence of recombinant PKR and by directed mutagenesis. The pseudoknot structure of the RNA activator of PKR contains the pseudoknot stem, three helices S1, S2, and S3, and kink-turn K. The AUG start codon is boxed. Mutations shown to affect its ability to activate PKR are indicated in color [15,16].

Figure 2. The RNA activator of PKR in human TNF pre-mRNA. (A) The 104-nucleotide element within human TNF pre-mRNA that strongly activates PKR, thereby potently enhancing splicing into mature TNF mRNA, is located within the 3′-UTR [13]. Secondary structure was determined by T1, U2, and V1 nuclease sensitivity mapping, in-line structure probing in the absence or presence of recombinant PKR and by directed mutagenesis. The pseudoknot structure of the RNA activator of PKR contains pseudoknot stems P1 and P2, three helices S1, S2, and S3, and linker lin. Mutations shown to affect its ability to activate PKR are indicated in color [14]. (B) In the folded RNA structure [14], pseudoknot stems P1 and P2, three helices S1, S2, and S3, and linker lin are shown in color.

Figure 3. The RNA activator of PKR within human β-globin pre-mRNA. (A) The 124-nucleotide element within human β-globin pre-mRNA that strongly activates PKR, thereby greatly enhancing splicing into mature mRNA, is composed of the entire 5′-UTR and first 74 nucleotides of the open reading frame within exon 1. Secondary structure was determined by in-line structure probing in the absence or presence of recombinant PKR and by directed mutagenesis. The core of the RNA activator of PKR contains the S1a:S1b helix. Mutations shown to affect ability to activate PKR are indicated in color [17]. (B) The silencer of PKR activation is composed of 5 nucleotides of S1c located within the first 10 nucleotides of exon 2. Displacement of strand S1b from strand S1a by the S1c silencer element upon excision of intron 1. Mutation of nucleotides in red color (S1c) abrogates silencing of the ability to activate PKR after intron 1 is spliced out [17].