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20-September-2008 09:29:09 - coding RNA Srna redirects here. For the Croatian footballer, see Darijo Srna. A non-coding RNA ncRNA is any RNA molecule that is not translated into a protein. A previously used synonym, particularly with bacteria, was small RNA sRNA. However, some ncRNAs are very large e.g. Xist. Less-frequently used synonyms are non-messenger RNA nmRNA, small non-messenger RNA snmRNA, or functional RNA fRNA. The DNA sequence from which a non-coding RNA is transcribed as the end product is often called an RNA gene or non-coding RNA gene see gene. Non-coding RNA genes include transfer RNA tRNA and ribosomal RNA rRNA, small RNAs such as snoRNAs, microRNAs, siRNAs and piRNAs and lastly long ncRNAs that include examples such as Xist, Evf, Air, CTN and PINK. The number of ncRNAs encoded within the genome is unknown, however recent transcriptomic and microarray studies suggest the existence of over 30,000 long ncRNAs and at least as many small regulatory RNAs within the mouse genome alone. Since most of the newly identified ncRNAs have not been validated for their function, it is possible that the majority of them are meaningless e.g. non-functional or truncated transcript. One of the major findings of the 2007 ENCODE Pilot Project was that nearly the entire genome may be represented in primary transcripts that extensively overlap and include many non-protein-coding regions.1 Contents 1 The evaluation of ncRNA has changed radically 2 Newfound role - as regulators of various types 2.1 Possible role as the most basic encodings for memory and behaviour 3 Distinction between functional RNA fRNA and ncRNA 4 Untranslated regions of mRNAs 5 See also 6 References 7 External links The evaluation of ncRNA has changed radically It was formerly believed that the main role for RNA was to code for protein, though there were the recognized exceptions of rRNA ribosomal, and tRNA transfer. It was assumed that any leftover ncRNA which served none of those roles must usually be mere junk coding.clarify Some might conceivably be coopted later by chance in the course of evolution, but it was otherwise assumed to be useless. There began to be signs that this was not true, e.g. with the paper by Brannan et al. 1990.2 Then by 2001, Mattick3 had claimed that in fact this applied to more than 97% of the RNA produced from DNA. See also later works by Mattick and others.456 Given this imbalance, it became clear that ncRNA must be playing other important roles; but what? Newfound role - as regulators of various types It has been becoming increasingly clear that cross-interactions between genes play a crucial role, and the importance of ncRNA for this task is explored in some detail in the table below. Rather less obvious is ncRNA's postulated role in how the brain deals with non-trivial thought processes, as follows: Possible role as the most basic encodings for memory and behaviour In developing his theory of cognitive development, the late Professor Piaget based his explanations on abstract constructs called schemes. That leaves open just what these schemes might be in physical terms, though he did briefly consider the possibility of RNA in 1967.7 Such roles for RNA fell out of favour by about 1980 partly because any such RNA was seen only as some sort of protein-producing adjunct to synaptic change. Meanwhile, based on some work8 from the 1970s, Traill 20059 argued that some sort of linear coding must underlie memory at least for advanced thinking10, and that RNA is the only plausible candidate. Such an action-or-memory-encoding role need not conflict with the aforementioned regulator role. In fact thought itself might be seen as a special case of internal regulation.11 Moreover this connection was perhaps already implied in the 1950s by Ross Ashby when he argued that recursive elaborations to a simple homeostat could yield a brainlike system.12. Distinction between functional RNA fRNA and ncRNA The term ncRNA has been used, in addition to its above definition, to describe regions of mRNA that are functional at the RNA level, i.e. they have a biological function other than coding for protein even though they are on a protein-coding mRNA, for example riboswitches and the SECIS element. They may even overlap with protein-coding sequence and are thus dual-functional: at the RNA level and at the protein level e.g. SgrS RNA and RNAIII. However, these conflict with the Sequence Ontology's definition of ncRNA, which requires that a RNA does not contain any protein-coding sequence in order to be labeled ncRNA. Several publications131415 have started using the term functional RNA fRNA, as opposed to ncRNA, to describe regions functional at the RNA level that may or may not be stand-alone RNA transcripts. Therefore, every ncRNA is a fRNA, but there exist fRNA such as riboswitches, SECIS elements, and other cis-regulatory regions that are not ncRNA. Yet the term fRNA could also include mRNA as this is RNA coding for protein and hence is functional. Additionally artificially evolved RNAs also fall under the fRNA umbrella term. Some publications16 state that the terms ncRNA and fRNA are nearly synonymous. Untranslated regions of mRNAs Main articles: Five prime untranslated region and Three prime untranslated region Messenger RNA mRNA contains non-coding regions at its ends called UTRs which include riboswitches and the SECIS element. Although UTRs do not code for protein, mRNA is not considered to be non-coding RNA. Many of the functional elements in UTRs are cis-regulatory elements. See also Ribozyme List of RNAs References ^ George M. Weinstock 2007. ENCODE: More genomic empowerment. Genome Research 17: 667-668. doi:10.1101/gr.6534207. PMID 17567987. ^ Brannan, C.I., E.C.Dees, R.S.Ingram S.M.Tilghman 1990. The product of the H19 gene may function as an RNA. Molecular and Cellular Biology, 101, 28-36. ^ Mattick, J.S. 2001 Noncoding RNAs: the architects of eukaryotic complexity. EMBO Reports 211, 986-991. http://emboreports.npgjournals.com/cgi/content/full/2/11/986 ^ Mattick, J.S., M.J.Gagen 2001. The evolution of controlled multitask gene networks: The role of introns and other noncoding RNAs in the development of complex organisms. Mol. Biol. Evol. 189, 1611-1630. Review http://mbe.oupjournals.org/cgi/content/full/18/9/1611 ^ Mattick, J.S. 2003. Challenging the dogma: The hidden layer of non-protein-coding RNAs on complex organisms Bioessays. 25, 930-939.1 ^ Mattick, J.S. 2004. The hidden genetic program of complex organisms, Scientific American. 2914, 30-37. 2 ^ Piaget, J. 1967/1971. Biology and Knowledge. Chicago University Press, and Edinburgh University Press. ^ Traill, R.R. 1976 / 2007. Short papers and letters on the 'linear micro-element' theory of mental mechanism; and related questions of scientific method. Ondwelle: Melbourne. 3 ^ Traill, R.R. 2005/2008 Thinking by molecule, synapse, or both? - From Piaget's schema, to the selecting/ing of ncRNA. Ondwelle: Melbourne. http://www.ondwelle.com/OSM02.pdf ^ For advanced thinking such as logic, symbolism, and speaking the traditional synaptic mechanisms taken alone do not offer any explanation at all. Piaget's account does offer a plausible explanatory framework, and that seems consistent with ncRNA capabilities plus some other technical issues. ^ or in other words, this notion of physical regulation being closely related to mental regulation looks very like the concept of psychosomatic effects. - Traill, R.R. 2005, see above - pp.3 and 21.4 ^ Ashby, W.R. 1952 / 1960. Design for a Brain. Chapman Hall: London. ^ Richard J. Carter, Inna Dubchak, Stephen R. Holbrook 2001. A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Research 29 19: 3928-3938. ^ Jakob Skou Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, David Haussler 2006. Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. PLOS Computational Biology 2 4: e33. doi:10.1371/journal.pcbi.0020033. ^ Tomas Babak, Benjamin J Blencowe, Timothy R Hughes 2007. Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinformatics 8 8: 33. doi:10.1186/1471-2105-8-21. ^ Sean Eddy 2001. Non-coding RNA genes and the modern RNA world. Nature Reviews Genetics 2 2: 919-929. doi:10.1038/35103511. External links Comprehensive database of mammalian ncRNAs The Rfam Database 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. Wikiomics/RNA Provides links to a variety of ncRNA analysis tools for structure prediction, sequence alignment and homology search. ncRNA databaseNONCODE is a brand-new database of all kinds of noncoding RNAs except tRNAs and rRNAs. v d e Types of nucleic acids Constituents Nucleobases | Nucleosides | Nucleotides | Deoxynucleotides Ribonucleic acids RNA | mRNA pre-mRNA/hnRNA | tRNA | rRNA | aRNA | gRNA | miRNA | ncRNA | piRNA | shRNA | siRNA | snRNA | snoRNA | stRNA | ta-siRNA | tmRNA Deoxyribonucleic acids DNA | cDNA | gDNA | msDNA | mtDNA Nucleic acid analogues GNA | LNA | PNA | TNA | morpholino Cloning vectors phagemid | plasmid | lambda phage | cosmid | P1 phage | fosmid | BAC | YAC | HAC Major families of biochemicals Saccharides | Carbohydrates | Glycosides | | Amino acids | Peptides | Proteins | Glycoproteins | | Lipids | Terpenes | Steroids | Carotenoids Alkaloids | Nucleobases | Nucleic acids | | Enzyme cofactors | Flavonoids | Polyketides | Tetrapyrroles Retrieved from http://en..org/wiki/Non-coding_RNA Categories: RNA | Molecular geneticsHidden category: articles needing clarification Views Article Discussion this page History Personal tools Log in / create account Navigation Main page Contents Featured content Current events Random article Search Go Search Interaction Community portal Recent changes Contact Donate to Help Toolbox What links here Related changes Upload file Special pages Printable version Permanent link Cite this page Languages Deutsch Italiano 한국어 日本語 اردو 中文 This page was last modified on 6 August 2008, at 15:27
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