Trends in Plant Science
ReviewSpecial Issue: Noncoding and small RNAsIntronic noncoding RNAs and splicing
Section snippets
Noncoding RNAs in eukaryotes
The existence of noncoding RNAs (ncRNAs), such as tRNAs and rRNAs, has been known for many decades. Other small, stable RNAs are relatively well characterised and involved in, for example, splicing, ribosome biogenesis, translation and chromosome replication. These RNAs include small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), RNase P and mitochondrial RNA processing (MRP) RNA, signal recognition particle (SRP) RNA, and telomerase RNA (see Glossary for list of RNA species discussed
snoRNAs and their gene organization
The two major classes of snoRNA (box C/D and box H/ACA snoRNAs; see Glossary) are responsible for directing 2′-O-ribose methylation and pseudouridylation of target RNAs, most commonly rRNA and snRNAs. snoRNAs of each class associate with different sets of core proteins to form small nucleolar ribonucleoprotein particles (snoRNPs), which function in modification 5, 6, 7. The organization of snoRNA genes is extremely diverse, both within and among different eukaryotes (Figure 1) [7]. The majority
miRNAs and their gene organization
miRNAs are small ncRNAs of approximately 21–23 nt in length. They regulate gene expression at the post-transcriptional level in animals and plants by base-pairing to target mRNAs 1, 17, 18, 19, 20, 21. miRNAs are produced from primary miRNA (pri-miRNA) transcripts, which fold to form extensively double-stranded stem–loop structures. In animals, processing of the pri-miRNA by the RNase III Drosha occurs in the nucleus and produces an intermediate precursor miRNA (pre-miRNA), which is then
Splicing and intronic snoRNAs
As described above, intron sequences sometimes contain miRNAs and snoRNAs with extensive secondary structures that are recognized by proteins or assemble proteins to form RNPs. The existence of such sequences raises the question of whether RNA folding or RNP formation affects the splicing process or vice versa. Secondary structures in plant and animal introns can affect both splicing efficiency and splice-site selection 41, 42, 43, and therefore snoRNAs or pri-miRNAs have the potential to
Splicing and intronic miRNAs
In animals, several routes for the generation of pri-miRNAs from introns in pre-mRNAs have been described. Processing might occur in a manner that is essentially the same as the processing of intronic snoRNAs, wherein the pri-miRNA is released from the excised and linearised intron lariat (Figure 1a). Alternatively, Drosha might cleave the pre-miRNA from the excised lariat, from the linearised intron or, indeed, from the unspliced pre-mRNA (Figure 1c). Drosha-mediated cleavage of the pri-mRNA
Acknowledgements
This work was supported by the Scottish Government (to J.B. and D.F.M.), the CNRS and L’Agence Nationale de la Recherché (ANR) Blanc project Osmir (to M.E.), and the European Alternative Splicing Network of Excellence (EURASNET) (to J.B.).
Glossary
- Box C/D
- Box C/D snoRNAs contain conserved sequences: box C (GUGAUGA) and D (CUGA), near their 5′ and 3′ ends, respectively.
- Box H/ACA
- Box H/ACA snoRNAs fold into two stem–loop structures in the 5′ and 3′ halves of the RNA. These structures are adjacent to the conserved internal box H (ANANNA) and the 3′-terminal box ACA (ACANNN).
- miRNAs
- microRNAs, small regulatory RNAs.
- ncRNA
- noncoding RNA, does not code for protein.
- pre-miRNA
- precursor miRNA transcript produced by initial processing of pri-miRNA by
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