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.

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]

Types (families) of non-coding RNAs

Transfer RNA

Main article: 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.

Ribosomal RNA

Main article: 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 (23S and 16S) rRNA molecules [2] 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 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.

Cytoplasmic rRNA genes are highly repetitive because of huge demand of ribosomes for protein synthesis ('gene dosage') in the cell.

Small nuclear RNA and small nucleolar RNA

Main articles: Small nuclear RNA and snoRNA

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 RNA

Main article: Cajal Body specific RNA

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.

microRNA

Main article: miRNA

microRNA (also miRNA) are RNA genes that are the reverse complement of portions of another gene's mRNA transcript and inhibit the expression of the target gene.

gRNAs

Main article: 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 (e.g. snoRNAs).

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 in its infancy.

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

Promoter RNAs (pRNA) are RNAs that correspond to promoter regions and act as a scaffolding to bind the antisense strand of promoter directed siRNAs resulting in epigenetic remodeling and siRNA directed transcriptional gene silencing in human cells.

tmRNA

Main article: 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

Untranslated regions of mRNAs

Main articles: Five prime untranslated region and Three prime untranslated region

Messenger RNA (mRNA) contains non-coding regions (UTRs) at its ends which include riboswitches and the SECIS element. Although UTRs do not code for protein, mRNA is not considered to be non-coding RNA.

External links

• [3] 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).

• Non-coding RNA database
• EumiR prediction of microRNA precursors based on Support Vector Machine.
• HairpinFetcher Prediction and analysis of hairpin forming potential in nucleic acids.
• RNA@IGIB group at the Institute of Genomics and Integrative Biology working on functional noncoding RNA biology.
• Wikiomics/RNA Provides links to a variety of ncRNA analysis tools for structure prediction, sequence alignment and homology search.
• miRacle Provides target search for microRNAs and other small non-coding RNAs based on an algorithm which incorporates RNA secondary structure.

Major families of biochemicals
Peptides | Amino acids | Nucleic acids | Carbohydrates | Lipids | Terpenes | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | Glycosides
Analogues of nucleic acids:	Types of Nucleic Acids	Analogues of nucleic acids:
Nucleobases:	Purine (Adenine, Guanine) | Pyrimidine (Uracil, Thymine, Cytosine)
Nucleosides:	Adenosine/Deoxyadenosine | Guanosine/Deoxyguanosine | Uridine | Thymidine | Cytidine/Deoxycytidine
Nucleotides:	monophosphates (AMP, UMP, GMP, CMP) | diphosphates (ADP, UDP, GDP, CDP) | triphosphates (ATP, UTP, GTP, CTP) | cyclic (cAMP, cGMP, cADPR)
Deoxynucleotides:	monophosphates (dAMP, TMP, dGMP, dCMP) | diphosphates (dADP, TDP, dGDP, dCDP) | triphosphates (dATP, TTP, dGTP, dCTP)
Ribonucleic acids:	RNA | mRNA | piRNA | tRNA | rRNA | ncRNA | gRNA | shRNA | siRNA | snRNA | miRNA | snoRNA
Deoxyribonucleic acids:	DNA | mtDNA | cDNA | plasmid | Cosmid | BAC | YAC | HAC
Analogues of nucleic acids:	GNA | PNA | TNA | Morpholino | LNA

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