Protecting genes from RNA silencing by destroying aberrant transcripts

Abstract

Gene expression is intensively regulated at the transcript level. It is the rate of transcription and the rate of degradation that together determine the steady-state level of a specific transcript. A whole-genome study indicates that the half-life of Arabidopsis transcripts varies from 0.2 to >24 h, indicating large variations in the turnover rate of specific transcripts, which is related to their biological functions [1]. While RNA polymerase II is responsible for mRNA production in all eukaryotic organisms, a large repertoire of ribonucleases are involved in mRNA decay [2]. Different components in the RNA degradation pathway usually target specific sets of transcripts. The specificity can be at least partly accounted for by the presence of RNA motifs within the 3′ UTR regions and RNA binding proteins that recognize them. In Arabidopsis, mRNAs targeted for degradation are first deadenylated and subjected to digestion by at least two major classes of exonucleases [3]. The exosome performs 3′5′ degradation, whereas the XRN4 exonuclease acts on further decapped transcripts and digests them from the 5′ end.Both animals and plants utilize small RNAs for posttranscriptional gene silencing (PTGS) and/or transcriptional gene silencing (TGS). Evolutionarily, small RNA-mediated gene silencing is believed to function in defense against foreign nucleic acids, whether they are from viruses, transposons or transgenes. In Arabidopsis, small RNAs are usually 2124 nucleotides in length. Different classes of small RNAs (sRNA) all require a double stranded RNA (dsRNA) precursor that is diced into small fragments by the RNase III-class DICER enzymes. The DICER protein functions like a ruler to determine the size of small RNA products. For example, siRNA generated by DCL2 are usually 22-nt long and siRNA by DCL4 are 21-nt long. When the guide strand of double stranded sRNAs are loaded into ARGONAUTE (AGO) proteins and form the RNA-induced silencing complex (RISC), the RISC complex binds to complementary transcripts, resulting in transcript cleavage or translational inhibition. The cleaved transcript can also be converted into dsRNAs by the RNA-dependent RNA polymerases (RDRs) and produce so-called secondary small interfering RNAs, which increases siRNA levels and ensures silencing.The dsRNA precursor can be generated from different sources. MicroRNA (miRNA) genes produce transcripts that form hairpin-loop structures and are processed into mature miRNAs by DCL1. In other cases, aberrant transcripts are sensed by the cell and converted into dsRNAs by RDRs. For example, TRANS-ACTING SIRNA (TAS) genes are targets of miRNAs. The cleaved transcripts by the