Small nucleolar RNA U3
Encyclopedia
U3 snoRNA is a non-coding RNA
found predominantly in the nucleolus
.
U3 has C/D box motifs that technically make it a member of the box C/D class of snoRNA
s; however, unlike other C/D box snoRNAs, it has not been shown to direct 2'-O-methylation
of other RNAs.
Rather, U3 is thought to guide site-specific cleavage of ribosomal RNA
(rRNA) during pre-rRNA processing.
The box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure
is characterized by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hyper-methylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein
interactions and are necessary for the rRNA processing functions of U3 snoRNA.
secondary structure determined by chemical mapping of U3A RNA in a purified snoRNP is available. A human
structure model has also been proposed. Four consensus structures specific to metazoa, fungi, plants and basal eukaryotes have been proposed.
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
found predominantly in the nucleolus
Nucleolus
The nucleolus is a non-membrane bound structure composed of proteins and nucleic acids found within the nucleus. Ribosomal RNA is transcribed and assembled within the nucleolus...
.
U3 has C/D box motifs that technically make it a member of the box C/D class of snoRNA
SnoRNA
Small nucleolar RNAs are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs...
s; however, unlike other C/D box snoRNAs, it has not been shown to direct 2'-O-methylation
Methylation
In the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom...
of other RNAs.
Rather, U3 is thought to guide site-specific cleavage of ribosomal RNA
Ribosomal RNA
Ribosomal ribonucleic acid is the RNA component of the ribosome, the enzyme that is the site of protein synthesis in all living cells. Ribosomal RNA provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation by providing peptidyl transferase activity...
(rRNA) during pre-rRNA processing.
The box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
is characterized by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hyper-methylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
interactions and are necessary for the rRNA processing functions of U3 snoRNA.
Species-specific secondary structure models
S. cerevisiaeSaccharomyces cerevisiae
Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...
secondary structure determined by chemical mapping of U3A RNA in a purified snoRNP is available. A human
Human
Humans are the only living species in the Homo genus...
structure model has also been proposed. Four consensus structures specific to metazoa, fungi, plants and basal eukaryotes have been proposed.
See also
- FibrillarinFibrillarinFibrillarin is a component of several ribonucleoproteins including a nucleolar small nuclear ribonucleoprotein and one of the two classes of small nucleolar ribonucleoproteins . SnRNAs function in RNA splicing while snoRNPs function in ribosomal RNA processing.Fibrillarin is associated with U3, U8...
- RCL1RCL1RNA 3'-terminal phosphate cyclase-like protein is an enzyme that in humans is encoded by the RCL1 gene.-See also:* Fibrillarin* Small nucleolar RNA U3* RRP9* UTP6* UTP11L* UTP14A* UTP15-Further reading:...
- RRP9RRP9U3 small nucleolar RNA-interacting protein 2 is a protein that in humans is encoded by the RRP9 gene.-See also:* Fibrillarin* Small nucleolar RNA U3* RCL1* RRP9* UTP6* UTP11L* UTP14A* UTP15-Further reading:...
- UTP6UTP6U3 small nucleolar RNA-associated protein 6 homolog is a protein that in humans is encoded by the UTP6 gene.-See also:* Fibrillarin* Small nucleolar RNA U3* RCL1* RRP9* UTP11L* UTP14A* UTP15-Further reading:...
- UTP11LUTP11LProbable U3 small nucleolar RNA-associated protein 11 is a protein that in humans is encoded by the UTP11L gene.-See also:* Fibrillarin* Small nucleolar RNA U3* RCL1* RRP9* UTP6* UTP14A* UTP15-Further reading:...
- UTP14AUTP14AU3 small nucleolar RNA-associated protein 14 homolog A is a protein that in humans is encoded by the UTP14A gene.-See also:* Fibrillarin* Small nucleolar RNA U3* RCL1* RRP9* UTP6* UTP11L* UTP15-Further reading:...
- UTP15UTP15U3 small nucleolar RNA-associated protein 15 homolog is a protein that in humans is encoded by the UTP15 gene.-See also:* Fibrillarin* Small nucleolar RNA U3* RCL1* RRP9* UTP6* UTP11L* UTP14A-Further reading:...