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Non-coding RNA

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An RNA gene is any gene that encodes RNA that functions without being translated to a protein. Commonly-used synonyms of "RNA gene" is non-coding RNA (ncRNA) and small RNA (sRNA). Less-frequently used synonyms are non-messenger RNA (nmRNA), small non-messenger RNA (snmRNA) and functional RNA (fRNA).

The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. However, since the late 1990s, many new RNA genes have been found, and RNA genes are believe to play a much more significant role than previously thought. At the same time, they are probably not as significant or numerous as the protein-coding genes.

Types of RNA genes

Transfer RNA (tRNA)

(from above) Transfer RNA, abbreviated tRNA, are short RNA strands that are used to transport individual amino acids to ribosomes and match them up with the three-base codons that describe the sequence of the protein encoded by an mRNA molecule. There is a different tRNA for each codon in the genetic code, and each tRNA is covalently attached to a single specific amino acid by a dedicated enzyme called amino-acyl tRNA synthetase.

Another form of RNA is tRNA, or transfer RNA, which is critical in the process of translation. tRNA is the "adaptor" molecule hypothesized by Francis Crick which would mediate the recognition of the codon sequence in mRNA and allow its translation into the appropriate amino acid.

There are several important features of tRNA to be noted:

  1. anticodon - This is the triplet sequence complementary to the codon for a particular amino acid. For example, the codon for lysine is UUU; the anticodon is AAA. By matching the lysine-charged tRNA with the anticodon AAA to the codon UUU, proper translation may be achieved.
  2. amino-acid - Each tRNA is coupled to an appropriate amino acid. In the example above, a tRNA with the anticodon AAA would be coupled to the amino acid lysine.
  3. base modification - tRNA contains several bases that are not "canonical" bases, i.e., that are modifications from the standard adenine, guanine, cytosine and uracil bases.
  4. CCA tail - The sequence 'CCA' is added to the 3' end of the tRNA molecule. This sequence is important for the recognition of tRNA by enzymes critical in translation.
  5. three-dimensional structure - All tRNAs have a similar L-shaped structure that allows them to fit into P and A sites of the ribosome.

There is a unique tRNA for each amino acid (of which there are 20) in the cell. Prior to translation, each tRNA is "charged" by an amino-acyl tRNA synthetase enzyme. There is a different tRNA synthetase for each amino acid, but NOT for each codon. Recognition is not mediated primarily by the anticodon, which would require 64 separate tRNA synthetases, but rather by other sites in the tRNA, especially critical sequences near the 3' end of the molecule.

The synthetase hydrolizes ATP to bind the appropriate amino acid to the 3' hydroxyl of the tRNA molecule. It also mediates a proofreading reaction to ensure high fidelity of tRNA charging; if the tRNA is found to be improperly charged, the amino acid-tRNA bond is hydrolized.

See translation for more on the role of tRNA in this process.

Ribosomal RNA (rRNA)

Ribosomal RNA, abbreviated rRNA, is the primary constituent of ribosomes. Ribosomes are the protein-manufacturing organelles of living cells, and exist in the cell's cytoplasm. rRNA is transcribed from DNA like all RNA, and in eukaryotes it is processed in the nucleolus before being transported through the nuclear membrane. This type of RNA makes up the vast majority of RNA found in a typical cell (~95%).


Small nuclear RNA

Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the nucleus of eukaryotic cells. They are involved in a variety of important processes such as RNA splicing (removal of the introns from hnRNA) and maintaining the telomeres. They are always associated with specific proteins and the complexes are referred to as small nuclear ribonucleoproteins (snRNP) or sometimes as snurps.

Small nucleolar RNA

Small nucleolar RNA (snoRNA) is a class of small RNA molecules that are involved in chemical modifications of ribosomal RNAs (rRNAs) and other RNA genes, for example by methylation. snoRNAs are a component in the small nucleolar ribonucleoprotein (snoRNP), which contains snoRNA and proteins. The snoRNA guides the snoRNP complex to the modification site of the target RNA gene through sequences in the snoRNA that hybridize to the target site. The proteins then catalyze the modification of the RNA gene.

microRNA

microRNA (also miRNA) are RNA genes that are believed to negative regulate the expression of genes by targeting the gene's mRNA transcripts for RNA interference. The microRNA precursor (the immediate transcript of the microRNA gene) has a 20- to 25-nucleotide sequence whose reverse complement is repeated within the precursor. This causes the two sequences to bind together, forming a 20-25 nucleotide double-stranded region. It is believed that an enzyme (Dicer) excises the dsRNA segment, producing the mature microRNA. The mature microRNA then targets targets mRNAs that contain sequences similar to itself, and those mRNAs are degraded or translation of them is repressed in a process related to that of RNA interference. It is also possible that microRNAs affect mRNAs in other ways, or that they directly target genomic DNA for some process.

The first microRNAs to be discovered were let-7 and lin-4 in C. elegans, which are involved in development. microRNAs have been discovered in plants (Arabidopsis and rice), mice, humans and fruit flies, although relatively experimental work has been carried out on them thus far.

See miRNA.

gRNAs

gRNAs (for guide RNA) are RNA genes that function in RNA editing. RNA editing is a process found thus far only in the mitochondria of Kinetoplastids, in which mRNAs are edited by inserting or deleting stretches of uridylates (Us). The gRNA forms a part of the editosome, and contains sequences that hybridize to matching sequences in the mRNA, in order to guide the mRNA modifications.

The term "guide RNA" is also sometimes used generically to mean any RNA gene that guides an RNA/protein complex through hybridization of matching sequences.

Signal recognition particle RNA

The signal recognition particle (SRP) is an RNA-protein complex present in the cytoplasm of cells that binds to the mRNA of proteins which are intended for secretion from the cell. The RNA component of the SRP in eukaryotes is called 4.5S RNA.