Non-coding RNA
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A non-coding RNA (ncRNA) is any RNA molecule that functions without being translated into a protein. A commonly used synonym is small RNA (sRNA). Less-frequently used synonyms are non-messenger RNA (nmRNA), small non-messenger RNA (snmRNA), and functional RNA (fRNA). The DNA sequence from which a non-coding RNA is transcribed is often called an RNA gene or non-coding RNA gene (see gene).
The most prominent examples of non-coding RNAs 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 non-coding RNAs have been found, and thus non-coding RNAs may play a much more significant role than previously thought. Even so, they are probably not as significant or numerous as the proteins.
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Types of non-coding RNAs
Transfer RNA
Transfer RNA (tRNA) is RNA that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein biosynthesis during translation.
Ribosomal RNA
Ribosomal RNA (rRNA) is the primary constituent of ribosomes. Ribosomes are the protein-manufacturing organelles of cells and exist in the cytoplasm and attached to the membrane of the endoplasmic reticulum. 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%). While proteins are also present in the ribosomes, the 23s rRNA forms the active site for peptide bond formation, making that molecule a ribozyme.
Untranslated regions of mRNAs
Many non-coding RNAs are structural elements in the untranslated regions of mRNAs (i.e. cis-regulatory RNAs), for example riboswitches and the SECIS element.
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 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 via sequences in the snoRNA that hybridize to the target site. The proteins then catalyze modification of the RNA gene.
microRNA
microRNA (also miRNA) are RNA genes that are the reverse complement of another gene's mRNA transcript and inhibit the expression of the target gene.
See miRNA.
gRNAs
gRNAs (for guide RNA) are RNA genes that function in RNA editing. Thus far, RNA editing has been found only in the mitochondria of kinetoplastids, in which mRNAs are edited by inserting or deleting stretches of uridylates (Us). The gRNA forms part of the editosome and contains sequences that hybridize to matching sequences in the mRNA, 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 via hybridization of matching sequences.
efference RNA
Efference RNA (eRNA) is derived from intron sequences of genes or from non-coding DNA. The function is assumed to be regulation of translational activity by interference with the transcription apparatus or target proteins of the translated peptide in question, or by providing a concentration-based measure of protein expression, basically introducing a fine-tuned analog element in gene regulation as opposed to the digital on-or-off regulation by promoters. Research into the role of eRNAs is only beginning, but they could theoretically be able to explain much of the molecular fundament of biodiversity, which has so far eluded genetics.
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 that are destined for secretion from the cell. The RNA component of the SRP in eukaryotes is called 4.5S RNA.
pRNA
At least one species of DNA-containing phages, phi-29, uses a complex of six identical short RNA sequences as mechanical components (utilizing ATP for energy) of its DNA packaging machinery. How common this phenomenon is has yet to be determined.
tmRNA
tmRNA has a complex structure with tRNA-like and mRNA-like regions. It has currently only been found in bacteria, but is ubiquitous in all bacteria. tmRNA recognizes ribosomes that have trouble translating or reading an mRNA and stall, leaving an unfinished protein that may be detrimental to the cell. tmRNA acts like a tRNA first, and then an mRNA that encodes a peptide tag. The ribosome translates this mRNA region of tmRNA and attaches the encoded peptide tag to the C-terminus of the unfinished protein. This attached tag targets the protein for destruction or proteolysis. How tmRNA works (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10881189&query_hl=5)
External
- The Rfam Database (http://www.sanger.ac.uk/Software/Rfam/) A curated list of hundreds of families of related ncRNAs. Each family includes a multiple alignment of known members, and predicted homologs in a large genome database. The definition of "family" is a pragmatic one, the goal being to lead to high-quality annotations. Thus, some families are quite broad (e.g. all tRNAs are in one family, as of 2004), while some families are quite narrow (e.g. there are many microRNA families, one for each type).