Small Cajal body-specific RNA
Encyclopedia
Small Cajal body-specific RNAs (scaRNAs) are a class of small nucleolar RNAs (snoRNAs) which specifically localise to the Cajal body
, a nuclear
organelle
involved in the biogenesis of small nuclear ribonucleoproteins
(snRNPs or snurps). ScaRNAs guide the modification (methylation
and pseudouridylation) of RNA polymerase II
transcribed
spliceosomal
RNAs U1
, U2
, U4
, U5
and U12
.
The first scaRNA identified was U85 . It is unlike typical snoRNAs in that it is a composite C/D box and H/ACA box snoRNAs and can guide both pseudouridylation and 2'-O-methylation. Not all scaRNAs are composite C/D and H/ACA box snoRNA and most scaRNAs are structurally and functionally indistinguishable from snoRNAs directing ribosomal RNA
(rRNA) modification in the nucleolus
.
, Small Cajal body specific RNA 1 (also known as scaRNA1 or ACA35) is a small nucleolar RNA found in Cajal bodies
and believed to be involved in the pseudouridylation
of U2 spliceosomal RNA
.
scaRNA1 is a non-coding RNA
, which are functional products of gene
but not translated into a protein
. Such RNA molecules usually contain important secondary structure
or ligand
binding motifs
and are involved in many important biological processes in the cell. More specifically, scaRNAs are a class of small nuclear RNA
s that localise to the Cajal bodies
and guide the modification of RNA polymerase II
transcribed spliceosomal
RNAs U1
, U2
, U4
, U5
and U12
.
scaRNA1 belongs to the H/ACA box class of guide RNAs, as it has the predicted hairpin-hinge-hairpin-tail structure, conserved H/ACA-box motifs and is found associated with GAR1 protein. It is predicted to guide pseudouridylation of the U2 spliceosomal RNA
at residue U89.
Cajal body
Cajal bodies are spherical sub-organelles of 0.3-1.0 µm in diameter found in the nucleus of proliferative cells like embryonic cells and tumor cells, or metabolically active cells like neurons. In contrast to cytoplasmic organelles, CBs lack any phospholipid membrane which would separate their...
, a nuclear
Cell nucleus
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...
organelle
Organelle
In cell biology, an organelle is a specialized subunit within a cell that has a specific function, and is usually separately enclosed within its own lipid bilayer....
involved in the biogenesis of small nuclear ribonucleoproteins
SnRNP
snRNPs , or small nuclear ribonucleoproteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs...
(snRNPs or snurps). ScaRNAs guide the modification (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...
and pseudouridylation) of RNA polymerase II
RNA polymerase II
RNA polymerase II is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase...
transcribed
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
spliceosomal
Spliceosome
A spliceosome is a complex of snRNA and protein subunits that removes introns from a transcribed pre-mRNA segment. This process is generally referred to as splicing.-Composition:...
RNAs U1
U1 spliceosomal RNA
U1 spliceosomal RNA is the small nuclear RNA component of U1 snRNP , an RNA-protein complex that combines with other snRNPs, unmodified pre-mRNA, and various other proteins to assemble a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs...
, U2
U2 spliceosomal RNA
U2 spliceosomal RNA is a small nuclear RNA component of the spliceosome . Complementary binding between U2 snRNA and the branchpoint sequence of the intron results in the bulging out of an unpaired adenosine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice...
, U4
U4 spliceosomal RNA
The U4 small nuclear Ribo-Nucleic Acid is a non-coding RNA component of the major or U2-dependent spliceosome – a eukaryotic molecular machine involved in the splicing of pre-messenger RNA...
, U5
U5 spliceosomal RNA
U5 RNA is a non-coding RNA that is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm...
and U12
U12 minor spliceosomal RNA
U12 minor spliceosomal RNA is formed from U12 small nuclear , together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns. Although the U12 sequence is very divergent from that of U2, the two are...
.
The first scaRNA identified was U85 . It is unlike typical snoRNAs in that it is a composite C/D box and H/ACA box snoRNAs and can guide both pseudouridylation and 2'-O-methylation. Not all scaRNAs are composite C/D and H/ACA box snoRNA and most scaRNAs are structurally and functionally indistinguishable from snoRNAs directing 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) modification 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...
.
Small Cajal body-specific RNA 1
In molecular biologyMolecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
, Small Cajal body specific RNA 1 (also known as scaRNA1 or ACA35) is a small nucleolar RNA found in Cajal bodies
Cajal body
Cajal bodies are spherical sub-organelles of 0.3-1.0 µm in diameter found in the nucleus of proliferative cells like embryonic cells and tumor cells, or metabolically active cells like neurons. In contrast to cytoplasmic organelles, CBs lack any phospholipid membrane which would separate their...
and believed to be involved in the pseudouridylation
Pseudouridine
Pseudouridine is the C-glycoside isomer of the nucleoside uridine, and it is the most prevalent of the over one hundred different modified nucleosides found in RNA. Ψ is found in all species and in many classes of RNA except mRNA...
of U2 spliceosomal RNA
U2 spliceosomal RNA
U2 spliceosomal RNA is a small nuclear RNA component of the spliceosome . Complementary binding between U2 snRNA and the branchpoint sequence of the intron results in the bulging out of an unpaired adenosine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice...
.
scaRNA1 is a non-coding RNA
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...
, which are functional products of gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
but not translated into a 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...
. Such RNA molecules usually contain important 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...
or ligand
Ligand
In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
binding motifs
Binding site
In biochemistry, a binding site is a region on a protein, DNA, or RNA to which specific other molecules and ions—in this context collectively called ligands—form a chemical bond...
and are involved in many important biological processes in the cell. More specifically, scaRNAs are a class of small nuclear RNA
Small nuclear RNA
Small nuclear ribonucleic acid is a class of small RNA molecules that are found within the nucleus of eukaryotic cells. They are transcribed by RNA polymerase II or RNA polymerase III and are involved in a variety of important processes such as RNA splicing , regulation of transcription factors ...
s that localise to the Cajal bodies
Cajal body
Cajal bodies are spherical sub-organelles of 0.3-1.0 µm in diameter found in the nucleus of proliferative cells like embryonic cells and tumor cells, or metabolically active cells like neurons. In contrast to cytoplasmic organelles, CBs lack any phospholipid membrane which would separate their...
and guide the modification of RNA polymerase II
RNA polymerase II
RNA polymerase II is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase...
transcribed spliceosomal
Spliceosome
A spliceosome is a complex of snRNA and protein subunits that removes introns from a transcribed pre-mRNA segment. This process is generally referred to as splicing.-Composition:...
RNAs U1
U1 spliceosomal RNA
U1 spliceosomal RNA is the small nuclear RNA component of U1 snRNP , an RNA-protein complex that combines with other snRNPs, unmodified pre-mRNA, and various other proteins to assemble a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs...
, U2
U2 spliceosomal RNA
U2 spliceosomal RNA is a small nuclear RNA component of the spliceosome . Complementary binding between U2 snRNA and the branchpoint sequence of the intron results in the bulging out of an unpaired adenosine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice...
, U4
U4 spliceosomal RNA
The U4 small nuclear Ribo-Nucleic Acid is a non-coding RNA component of the major or U2-dependent spliceosome – a eukaryotic molecular machine involved in the splicing of pre-messenger RNA...
, U5
U5 spliceosomal RNA
U5 RNA is a non-coding RNA that is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm...
and U12
U12 minor spliceosomal RNA
U12 minor spliceosomal RNA is formed from U12 small nuclear , together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns. Although the U12 sequence is very divergent from that of U2, the two are...
.
scaRNA1 belongs to the H/ACA box class of guide RNAs, as it has the predicted hairpin-hinge-hairpin-tail structure, conserved H/ACA-box motifs and is found associated with GAR1 protein. It is predicted to guide pseudouridylation of the U2 spliceosomal RNA
U2 spliceosomal RNA
U2 spliceosomal RNA is a small nuclear RNA component of the spliceosome . Complementary binding between U2 snRNA and the branchpoint sequence of the intron results in the bulging out of an unpaired adenosine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice...
at residue U89.