Non-coding RNA Totally Explained

Everything about Ncrna totally explained

A non-coding RNA (ncRNA) is any RNA molecule that isn't translated into a protein. A previously used synonym, particularly with bacteria, was small RNA (sRNA). However, some ncRNAs are very large (for example 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's possible that the majority of them are meaningless (for example 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."

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 mRNA (messenger), and tRNA (transfer). It was assumed that any leftover ncRNA which served none of those roles must usually be mere "junk" coding. 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 wasn't true, for example with the paper by Brannan et al. (1990). Then by 2001, Mattick 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. —— 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. Such roles for RNA fell out of favour by about 1980 (partly because any such RNA was seen only as some sort of adjunct to synaptic change). Meanwhile, based on some work from the 1970s, Traill (2005) argued that some sort of linear coding must underlie memory (at least for advanced thinking), and that RNA is the only plausible candidate.
Such an action-or-memory-encoding role need not conflict with the abovementioned "regulator" role. In fact "thought" itself might be seen as a special case of internal regulation. (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.)

Types of non-coding RNAs

Universal
rRNA	Main: Ribosomal RNA	Ribosomal RNA (rRNA) is the primary constituent of ribosomes. Ribosomes are the protein-manufacturing organelles of cells and exist in the cytoplasm. rRNA is transcribed from DNA, like all RNA. Ribosomal proteins are transported into the nucleus and assembled together with rRNA before being transported through the nuclear membrane. This type of RNA makes up the vast majority of RNA found in a typical cell. While proteins are also present in the ribosomes, solely rRNA is able to form peptides. Therefore ribosomes, having a catalytic function, are a form of ribozyme. Mammalian cells have 2 mitochondrial (12S and 16S) rRNA molecules (External Link) and 4 types of cytoplasmic rRNA (28S, 5.8S, 5S (large ribosome subunit) and 18S (small subunit)). 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit 45S organized into 5 clusters (each has 30-40 repeats) on the 13,14,15,21,and 22 chromosomes. These are transcribed by RNA polymerase I. 5S occurs in tandem arrays (~200-300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. 5S rRNA is transcribed by RNA polymerase III. rRNA genes are highly repetitive because of huge demand of ribosomes for protein synthesis ('gene dosage') in the cell.
tRNA	Main: Transfer RNA	Transfer RNA (tRNA) is RNA that transfers the correct amino acid to a growing polypeptide chain at the ribosomal site of protein biosynthesis during translation.
SRP	Main: signal recognition particle	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 Eubacteria is called 4.5S RNA, in Eukaryotes 7SL RNA.
Prokaryotic
sRNA		Regulatory
6S	Main: 6S RNA	A regulatory hairpin that binds to RNA Polymerase
tmRNA	Main: 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
Eukaryotic
miRNA	Main: microRNA	microRNA (also miRNA) are RNA genes that are the reverse complement of portions of another gene's mRNA transcript and alter the expression of one or several genes through RNA interference. They are around 21-23 base pairs long in the mature form, single-stranded, and are integrated into the RNA-induced silencing complex (RISC).
snRNA	Main: Small nuclear RNA and Small nucleolar RNA	Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the nucleus of eukaryotic cells. Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that guide chemical modifications (methylation or pseudouridylation) of ribosomal RNAs (rRNAs) and other RNA genes. Small Cajal Body specific RNAs (scaRNAs) are a class of small RNA molecules similar to snoRNAs which specifically localize in the Cajal body, a nuclear organelle involved in the biogenesis of snRNPs. U85 is the first scaRNA ever described. Unlike typical snoRNAs, U85 scaRNA can guide both pseudouridylation and 2'-O-methylation.
Large ncRNA	Main: Large ncRNA	Large ncRNA are mRNA-like (Pol II, spliced and polyadenylated) and perform regulatory roles. Several have been characterised: Xist and TSIX regulate X chromosome inactivation AIR and H19 are paternal and maternal imprited genes which repress Igfr2 and igf2 on their respecive clusters, respectively HOTAIR transcribed from HOXC cluster inhibits late HOXD Evf CTN PINK
gRNA	Main: Guide RNA	gRNAs (for guide RNA) are RNA genes that function in RNA editing. Thus far, gRNA mediated 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. Other types of RNA editing are found in many eukaryotes, including humans. 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 (for example snoRNAs).
piRNA	Main: Piwi-interacting RNA	Piwi-interacting RNAs (piRNA) are active in ovaries and testes in animals, and cause gene silencing by interacting with Piwi proteins. They are similar to miRNAs, but somewhat longer and don't use dicer.

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, for example they've a biological function other than coding for protein even though they're 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 (for example SgrS RNA and RNAIII). However, these conflict with the Sequence Ontology's definition of ncRNA

, which requires that a RNA doesn't contain any protein-coding sequence in order to be labeled ncRNA.
Several publications 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 publications state that the terms ncRNA and fRNA are nearly synonymous.

Untranslated regions of mRNAs

Messenger RNA (mRNA) contains non-coding regions at its ends (called UTRs) which include riboswitches and the SECIS element. Although UTRs don't code for protein, mRNA isn't considered to be non-coding RNA. Many of the functional elements in UTRs are cis-regulatory elements.

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