RNA classification

Well two weeks ago in Science, two reports came out about yet another species of small RNA ... rasiRNA ... uhm i mean piRNA (OK they haven't harmonized their nomenclature yet).

So here is a brief review of the types of RNA:

- mRNA (messenger RNA). These are the RNAs that encode polypeptide chains.
- rRNA (ribosomal RNA). These form the core structure of the ribosome. The ribosome is the enzyme that translates the tri-nucleotides, to amino acids. In this way it synthesizes (or "translates") proteins from mRNAs.
- tRNAs (transfer RNA). These are used by the ribosome to translate the tri-nucleotie. On one end a loop displaying the complement of the tri-nucleotide is displayed, on the other end is the corresponding amino acids. So if you think about it tRNAs are responsible for coupling the tri-nucleotide to the amino acid.
- snRNA (small nuclear RNA). These form the core components of the splicesome, an enzyme that catalyses the splicing of mRNA.
- snoRNA (small nucleolar RNA). These strange critters help to process and assemble a variety of RNAs such as rRNAs.
- siRNA (small interfering RNA). These are processed from long double stranded RNAs, mostly exogenous in origin (exogenous = originates from outside the entity, in this case the cell) but occasionally are produced from endogenous transcripts (endogenous = originates from the same entity, in this case the cell's genome). The 21-23 nucleotide fragments are then used by the RNAi (RNA interference) pathway to turn off the expression of any single stranded RNA that the siRNA can base pair with. The machine that mediates RNAi is the RISC (RNAi Induced Silencing Complex), which includes the siRNA, a protein called Argonaute, and some other factors.
- miRNA (micro RNA). These are processed from short nearly double stranded small hairpin RNAs (shRNA) that are produced from endogenously transcribed RNAs. Like siRNAs, miRNAs are 21-23 nucleotides in length and are used by RNAi and the RISC machinery to inhibit mRNA transcription.
- rasiRNA (repeat associated small interfering RNA). These small RNAs (24-29 nucleotides in length) are produced from endogenous transcripts in fruit flies and seem to silence. Unlike siRNA, rasi RNA they are highly enriched in germline cells (sperm+oocyte) and form a complex similar to the RISC complex except the main protein involved is Piwi, a member of the Argonaute family of proteins. It seems like rasiRNAs function to inhibit bits of selfish DNA that copy themselves and multiply within the genome. These "selfish genes" are called retrotransposons.
- piRNA (piwi interacting RNA). Similar to rasiRNA, piRNAs are 25-31 nucleotides in length and produced from endogenous genes in mammalian cells. Along with Piwi, they form the piRNA complex (piRC) and act to. Unlike siRNA and miRNA, piRNA (and rasiRNA?) are not processed from a double stranded RNA precursor. For the moment the role of piRNAs is not clear, but like rasiRNA, these are highly enriched in germ cells. It is possible that they may regulate selfish genes, but there wasn't enough info in the paper ... I'm sure we'll find out soon what their targets are.

Ref:

rasiRNA
Vasily V. Vagin, Alla Sigova, Chengjian Li, Hervé Seitz, Vladimir Gvozdev, and Phillip D. Zamore
A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline
Science (2006) 313:320 - 324

piRNA
Nelson C. Lau, Anita G. Seto, Jinkuk Kim, Satomi Kuramochi-Miyagawa, Toru Nakano, David P. Bartel, and Robert E. Kingston
Characterization of the piRNA Complex from Rat Testes
Science (2006) 313:363 - 367