RNA classification

Well two weeks ago in Science, two reports came out about yet another species of small RNA ... rasiRNA ... uhm ... 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 translation by chewing up any mRNA complementary to the miRNA (or siRNA).
- 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

[Update ...

This post was just an excuse to write about piRNAs and rasiRNAs - also I missed A THIRD PAPER in that very same issue of Science (haven't read it yet but will do so soon).

PZ asks for mtRNA: or mitochondrial mRNA ... these are mRNA transcripts derived from the mitochondrial genome. Don't forget mitos have their own genes, mostly of proteins that can only fold properly within the mitochondria.

Also someone points out tmRNA. This funny critter is thought to be found in prokaryotes (i.e. bacteria). If an mRNA that is being transcribed translated by the ribosome does not contain a stop codon, the ribosome will freeze on the last codon. tmRNA will then enter the ribosome and help dislodge the mRNA and the growing polypeptide.

If I've missed anything let me know. End of update.]

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Nice review, and excellent timing for me personally :)

Technical correction: microRNA's do not (or at least, don't primarily) inhibit "mRNA transcription". Instead, miRNAs seem to primarily work by inhibiting translation - perhaps via the Pbodies you so recently discussed. I also seem to recall that most of the RISC components are not required for this process, but I could be wrong about that.

dlamming,

Absolutely right (it's a typo). Thanks for pointing that out. I'm on my way out now, so I'll correct it tonight. For completeness, I could have also added that in fission yeast, small RNAs (i think they refer to those as miRNA - not sure though) can regulate transcription through the RITS complex and this is involved in silencing telomeric and centromeric genes.

The RNAs involved in pericentromeric heterochromatin formation in fission yeast are also called siRNAs. In this case, siRNAs act as specificity factors that initiate epigenetic chromatin modifications.

Found your blog a few months ago. I keep coming back...nice work.

kscs,

Yes exactly (Danesh Moazeb, who works on the RITS complex, is one floor down). Funny, someone wrote me an email recently asking about nucleosomes and such ... I wrote back a email explaining the basics of histone modifications etc. There was a nice paper recently on mapping nucleosome binding sites ... I guess I'll have to write an entry on the subject - although it's not my field.

Came here from pharyngula - what is mtRNA?

Here are some other examples.

-M1 RNA (RNAse P)
-7SL RNA (signal recognition particle)
-telomerase RNA
-some type I and type II introns that can exist after they
are excised from the ribosomal RNA precursor (ribozymes)
-RNA primers in DNA replication (made by primase)
-many antisense RNAs in prokaryotes: the classic (1970s)
examples are those transcribed from the PRE and PAQ
promoters in bacteriophage lambda (but there are many
others)
-a huge variety of spurious RNAs produced by inappropriate
transcription, transcription of pseudogenes, transcription
of defective transposons, etc. etc. (the EST databases are
full of these)
-non-coding RNAs (ncRNAs) possibly included in the spurious
RNA category (other members of your list might be spurious
as well!)
-viral and bacteriophage RNAs
-transposon RNAs
-if you're going to include mitochondrial RNAs then you
should also include chloroplast RNAs

By Larry Moran (not verified) on 09 Aug 2006 #permalink

I forgot about the guide RNAs required for RNA editing. In some cases these may be the same as snoRNAs but they're not called snoRNAs in prokaryotes (for obvious reasons).

By Larry Moran (not verified) on 09 Aug 2006 #permalink

I was thinking of adding a little something on 7SL RNA. SRP (signal recognition particle) is very connected to protein synthesis (in this case translocated proteins) - seems like many RNA (or ribozyme) mediated events deal with biological processes close to the central dogma (DNA => RNA => protein). Other examples are RNA splicing, ribosomal synthesis (in the case of snoRNA) translation, translational regulation (RNAi) and now transcription (see http://scienceblogs.com/transcript/2006/08/something_for_you_rna_world_… ).

Processes that are further away from the central dogma (cytoskeleton, signal transduction, membrane traffic etc.) tend to not have ribozyme/"special-RNA" mediated events.

Your comment brings up another issue. There are different meanings of the Central Dogma of Molecular Biology. I started to fix the description on Wikipedia but so far only the first few paragraphs are accurate.

It would be fun have a discussion about the Central Dogma. How many people think the original Crick version is correct and how many prefer the distorted Watson version, which Crick called the "sequence hypothesis"?

By Larry Moran (not verified) on 10 Aug 2006 #permalink

If an mRNA that is being transcribed by the ribosome does not contain a stop codon, the ribosome will freeze on the last codon.

it has to be translated instead of transcribed.

BTW, I recommend the following paper to readers who apply RNA interference:

Grimm D et al (2006): Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 441(7092):537-541