Small Cajal body-specific RNA

Last updated
Small Cajal body specific RNA 1
RF00553.png
Predicted secondary structure of Small Cajal body specific RNA 1
Identifiers
SymbolSCARNA1
Rfam RF00553
Other data
RNA type gene, snRNA, snoRNA, scaRNA;
Domain(s) Vertebrata
PDB structures PDBe

Small Cajal body-specific RNAs (scaRNAs) are a class of small nucleolar RNAs (snoRNAs) that specifically localise to the Cajal body, a nuclear organelle (cellular sub-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.

Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, the C/D box snoRNAs, which are associated with methylation, and the H/ACA box snoRNAs, which are associated with pseudouridylation. SnoRNAs are commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes.

Cajal body A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors

Cajal bodies (CBs) also coiled bodies, are spherical nuclear bodies 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. CBs are membrane-less organelles and largely consist of proteins and RNA. They were first reported by Santiago Ramón y Cajal in 1903, who called them nucleolar accessory bodies due to their association with the nucleoli in neuronal cells. They were rediscovered with the use of the electron microscope (EM) and named coiled bodies, according to their appearance as coiled threads on EM images, and later renamed after their discoverer. Research on CBs was accelerated after discovery and cloning of the marker protein p80/Coilin. CBs have been implicated in RNA-related metabolic processes such as the biogenesis, maturation and recycling of snRNPs, histone mRNA processing and telomere maintenance. CBs assemble RNA which is used by telomerase to add nucleotides to the ends of telomeres.

Cell nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.

In cell biology, the nucleus is a membrane-bound organelle found in eukaryotic cells. Eukaryotes usually have a single nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei, and a few others including osteoclasts have many.

Contents

The first scaRNA identified was U85. [1] 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.

Ribosomal RNA RNA component of the ribosome, essential for protein synthesis in all living organisms

Ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome, and is essential for protein synthesis in all living organisms. It constitutes the predominant material within the ribosome, which is approximately 60% rRNA and 40% protein by weight, or 3/5 of ribosome mass. Ribosomes contain two major rRNAs and 50 or more proteins. The ribosomal RNAs form two subunits, the large subunit (LSU) and small subunit (SSU). The LSU rRNA acts as a ribozyme, catalyzing peptide bond formation. The SSU and LSU rRNA sequences are widely used for working out evolutionary relationships among organisms, since they are of ancient origin and are found in all known forms of life.

Nucleolus A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane. Its prime function is the transcription of the nucleolar DNA

The nucleolus is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis. Nucleoli also participate in the formation of signal recognition particles and play a role in the cell's response to stress. Nucleoli are made of proteins, DNA and RNA and form around specific chromosomal regions called nucleolar organizing regions. Malfunction of nucleoli can be the cause of several human conditions called "nucleolopathies" and the nucleolus is being investigated as a target for cancer chemotherapy.

Drosophila scaRNAs

Several studies identified scaRNAs in Drosophila. [1] [2] [3] [4] [5] One of the studies showed that several Drosophila scaRNAs could function equally well in the nucleoplasm of mutant flies that lack Cajal bodies. [4] Further investigation showed that scaRNA pugU6-40 targets U6 snRNA, whose modification occurs in the nucleolus not CB and that pugU1-6 and pug U2-55 guide 2 RNAs: snRNA and 28s rRNA. [5]

<i>Drosophila</i> genus of insects

Drosophila is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many species to linger around overripe or rotting fruit. They should not be confused with the Tephritidae, a related family, which are also called fruit flies ; tephritids feed primarily on unripe or ripe fruit, with many species being regarded as destructive agricultural pests, especially the Mediterranean fruit fly. One species of Drosophila in particular, D. melanogaster, has been heavily used in research in genetics and is a common model organism in developmental biology. The terms "fruit fly" and "Drosophila" are often used synonymously with D. melanogaster in modern biological literature. The entire genus, however, contains more than 1,500 species and is very diverse in appearance, behavior, and breeding habitat.

Small Cajal body-specific RNA 1

In molecular biology, 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 at residue U89.

Molecular biology branch of biology that deals with the molecular basis of biological activity

Molecular biology is a branch of biology that concerns the molecular basis of biological activity between biomolecules in the various systems of a cell, including the interactions between DNA, RNA, proteins and their biosynthesis, as well as the regulation of these interactions. Writing in Nature in 1961, William Astbury described molecular biology as:

...not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and [...] is predominantly three-dimensional and structural – which does not mean, however, that it is merely a refinement of morphology. It must at the same time inquire into genesis and function.

scaRNA1 is a non-coding RNA, which are functional products of genes not translated into proteins. Such RNA molecules usually contain important secondary structure or ligand-binding motifs and are involved in many important biological processes in the cell. [6]

Non-coding RNA class of RNA

A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR.

Gene Basic physical and functional unit of heredity

In biology, a gene is a sequence of nucleotides in DNA or RNA that codes for a molecule that has a function. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life.

Translation (biology) in biology, the process in which cellular ribosomes create proteins

In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or ER synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression.

scaRNA1 belongs to the H/ACA box class of snoRNAs, as it has the predicted hairpin-hinge-hairpin-tail structure, conserved H/ACA-box motifs, and is found associated with GAR1 protein. [7]

Related Research Articles

Small nucleolar RNA U6-53/MBII-28

Small nucleolar RNA U6-53 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

Small Cajal body specific RNA 11

In molecular biology, Small Cajal body specific RNA 11 is a small nucleolar RNA found in Cajal bodies.

Small Cajal body specific RNA 13

In molecular biology, Small Cajal body specific RNA 13 is a small nucleolar RNA found in Cajal bodies and believed to be involved in the pseudouridylation of U2 and U5 spliceosomal RNA.

Small Cajal body specific RNA 14

In molecular biology, Small Cajal body specific RNA 14 is a small nucleolar RNA found in Cajal bodies.

Small Cajal body specific RNA 15

Small Cajal body specific RNA 15 is a small nucleolar RNA found in Cajal bodies and believed to be involved in the pseudouridylation of U1 spliceosomal RNA.

Small Cajal body specific RNA 16

Small Cajal body specific RNA 16 is a small nucleolar RNA found in Cajal bodies and believed to be involved in the pseudouridylation of U1 spliceosomal RNA.

Small Cajal body specific RNA 17

Small Cajal body-specific RNA 17 is a type of small nuclear RNA which localises to the cajal bodies and proposed to guide the modification of RNA polymerase II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12.

Small Cajal body specific RNA 18

small Cajal body-specific RNA 18 is a type of small nuclear RNA which localises to the cajal bodies and proposed to guide the modification of RNA polymerase II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12.

Small Cajal body specific RNA 23

Small Cajal body specific RNA 23 is a small nucleolar RNA found in Cajal bodies and believed to be involved in the pseudouridylation of U1 spliceosomal RNA.

Small Cajal body specific RNA 24

Small Cajal body specific RNA 24 is a small nucleolar RNA found in Cajal bodies and believed to be involved in the pseudouridylation of U6 spliceosomal RNA.

Small Cajal body specific RNA 4

In molecular biology, small Cajal body specific RNA 4 is believed to be a guide RNA of the H/ACA box class, since it has the predicted hairpin-hinge-hairpin-tail structure, conserved H/ACA-box motifs, and is found associated with GAR1. In particular, ACA26 is predicted to guide the pseudouridylation of residues U39 and U41 in U2 snRNA. Such scaRNAs are a specific class of small nuclear RNAs that localise to the Cajal bodies and guide the modification of RNA polymerase II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12.

Small Cajal body specific RNA 6

Small Cajal body specific RNA 6 is a small nucleolar RNA found in Cajal bodies and believed to be involved in the pseudouridylation of U5 spliceosomal RNA.

Small Cajal body specific RNA 8

Small Cajal body specific RNA 8 is a small nucleolar RNA found in Cajal bodies and believed to be involved in the pseudouridylation of U2 spliceosomal RNA.

Small nucleolar RNA psi18S-1854

Small nucleolar RNA psi28S-3327 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a 'guide RNA'.

Small nucleolar RNA psi28S-1192

Small nucleolar RNA psi28S-1192 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a 'guide RNA'.

Small nucleolar RNA psi28S-3327

Small nucleolar RNA psi28S-3327 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a 'guide RNA'.

Small nucleolar RNA SNORA61

Small nucleolar RNA SNORA61 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a 'guide RNA'. ACA61 was originally cloned from HeLa cells and belongs to the H/ACA box class of snoRNAs as it has the predicted hairpin-hinge-hairpin-tail structure, has the conserved H/ACA-box motifs and is found associated with GAR1 protein. snoRNA ACA61 is predicted to guide the pseudouridylation of U2495 of 28S ribosomal RNA (rRNA). Pseudouridylation is the to the different isomeric form pseudouridine.

Small Cajal body specific RNA 20

In molecular biology, Small Cajal body specific RNA 20 is a small nucleolar RNA found in Cajal bodies and believed to be involved in the pseudouridylation of U12 minor spliceosomal RNA.

Small Cajal body specific RNA 21

In molecular biology, Small Cajal body specific RNA 21 is a small nucleolar RNA found in Cajal bodies and believed to be involved in the pseudouridylation of U12 minor spliceosomal RNA.

Small nucleolar RNA SNORA11

Small nucleolar RNA SNORA11 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA).

References

  1. 1 2 Jády BE, Kiss T (February 2001). "A small nucleolar guide RNA functions both in 2'-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA". The EMBO Journal. 20 (3): 541–51. doi:10.1093/emboj/20.3.541. PMC   133463 . PMID   11157760.
  2. ↑ Tortoriello G, Accardo MC, Scialò F, Angrisani A, Turano M, Furia M (May 2009). "A novel Drosophila antisense scaRNA with a predicted guide function". Gene. 436 (1–2): 56–65. doi:10.1016/j.gene.2009.02.005. PMID   19230845.
  3. ↑ Tycowski KT, Shu MD, Kukoyi A, Steitz JA (April 2009). "A conserved WD40 protein binds the Cajal body localization signal of scaRNP particles". Molecular Cell. 34 (1): 47–57. doi:10.1016/j.molcel.2009.02.020. PMC   2700737 . PMID   19285445.
  4. 1 2 Deryusheva S, Gall JG (December 2009). "Small Cajal body-specific RNAs of Drosophila function in the absence of Cajal bodies". Molecular Biology of the Cell. 20 (24): 5250–9. doi:10.1091/mbc.E09-09-0777. PMC   2793299 . PMID   19846657.
  5. 1 2 Deryusheva S, Gall JG (December 2013). "Novel small Cajal-body-specific RNAs identified in Drosophila: probing guide RNA function". RNA. 19 (12): 1802–14. doi:10.1261/rna.042028.113. PMC   3884663 . PMID   24149844.
  6. ↑ Darzacq X, Jády BE, Verheggen C, Kiss AM, Bertrand E, Kiss T (June 2002). "Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs". The EMBO Journal. 21 (11): 2746–56. doi:10.1093/emboj/21.11.2746. PMC   126017 . PMID   12032087.
  7. ↑ Kiss AM, Jády BE, Bertrand E, Kiss T (July 2004). "Human box H/ACA pseudouridylation guide RNA machinery". Molecular and Cellular Biology. 24 (13): 5797–807. doi:10.1128/MCB.24.13.5797-5807.2004. PMC   480876 . PMID   15199136.
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