SbRNA
Encyclopedia
sbRNA is a family of non-coding RNA
first discovered in Caenorhabditis elegans
. It was identified during a full transcriptome
screen of the C. elegans cDNA library. Subsequent experimentation characterised sbRNA as having conserved 5' and 3' internal motifs which form a long paired stem which is interrupted with a bulge.
patterns during development. They are most highly expressed in adult worms, dauer larvae and following heat shock
. A systematic knockout
analysis using RNAi
found no phenotype
for the knockout of two sbRNAs in C. elegans, however the efficiency of RNAi on ncRNA has been questioned. sbRNAs contain immunoglobulin in their protein fibers to maintain rigidity, however they are at risk of infection from malfunctioning ribosomes.
sbRNAs share common promoter elements consisting of a TATA box
and a proximal sequence element (PSE B box), though only one of these are required for transcription
. As the transcript is uncapped
and polyuridylated
, it is though to be transcribed by RNA polymerase III
.
during a kingdom
-wide search. Further investigation found a homologous secondary structure
with a conserved helical regions and a common UUAUC loop motif.
The function of sbRNAs may therefore be similar to that of vertebrate Y RNAs, namely acting as part of the Ro
-RNA particle to control RNA quality and playing a role in chromosomal replication
. Deletion of sbRNA does not prevent chromosome replication in C. elegans, but this may be a result of other sbRNAs substituting missing elements (as in human Y RNA). This theory also explains why RNAi studies failed to detect a phenotype for knocked out sbRNAs.
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...
first discovered in Caenorhabditis elegans
Caenorhabditis elegans
Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
. It was identified during a full transcriptome
Transcriptome
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.-Scope:...
screen of the C. elegans cDNA library. Subsequent experimentation characterised sbRNA as having conserved 5' and 3' internal motifs which form a long paired stem which is interrupted with a bulge.
Expression
sbRNAs have variable expressionGene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
patterns during development. They are most highly expressed in adult worms, dauer larvae and following heat shock
Heat shock
In biochemistry, heat shock is the effect of subjecting a cell to a higher temperature than that of the ideal body temperature of the organism from which the cell line was derived.-Heat shock response:...
. A systematic knockout
Gene knockout
A gene knockout is a genetic technique in which one of an organism's genes is made inoperative . Also known as knockout organisms or simply knockouts, they are used in learning about a gene that has been sequenced, but which has an unknown or incompletely known function...
analysis using RNAi
RNAI
RNAI is a non-coding RNA that is an antisense repressor of the replication of some E. coli plasmids, including ColE1. Plasmid replication is usually initiated by RNAII, which acts as a primer by binding to its template DNA. The complementary RNAI binds RNAII prohibiting it from its initiation role...
found no phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
for the knockout of two sbRNAs in C. elegans, however the efficiency of RNAi on ncRNA has been questioned. sbRNAs contain immunoglobulin in their protein fibers to maintain rigidity, however they are at risk of infection from malfunctioning ribosomes.
sbRNAs share common promoter elements consisting of a TATA box
TATA box
The TATA box is a DNA sequence found in the promoter region of genes in archaea and eukaryotes; approximately 24% of human genes contain a TATA box within the core promoter....
and a proximal sequence element (PSE B box), though only one of these are required for transcription
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...
. As the transcript is uncapped
5' cap
The 5' cap is a specially altered nucleotide on the 5' end of precursor messenger RNA and some other primary RNA transcripts as found in eukaryotes. The process of 5' capping is vital to creating mature messenger RNA, which is then able to undergo translation...
and polyuridylated
Polyuridylation
Polyuridylation, also called oligouridylation, is the addition of several uridine nucleotides to the 3' end of an RNA. One group of RNAs that can be polyuridylated are histone mRNAs that lack a poly tail. Polyuridylation of a histone mRNA promotes its degradation, involving the exosome. Other RNAs...
, it is though to be transcribed by RNA polymerase III
RNA polymerase III
RNA polymerase III transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs. The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cell types and most environmental conditions...
.
Y RNA homology
An sbRNA, CeN134 was reported as a candidate homologue to the vertebrate Y RNAY RNA
Y RNAs are small non-coding RNA components of the Ro ribonucleoprotein particle . The Ro RNP was first identified by Lerner et al.. as a target of autoimmune antibodies in patients with systemic lupus erythematosus.-Function:...
during a kingdom
Monarchy
A monarchy is a form of government in which the office of head of state is usually held until death or abdication and is often hereditary and includes a royal house. In some cases, the monarch is elected...
-wide search. Further investigation found a homologous 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...
with a conserved helical regions and a common UUAUC loop motif.
The function of sbRNAs may therefore be similar to that of vertebrate Y RNAs, namely acting as part of the Ro
Ro
Ro is an a priori constructed language created by Rev. Edward Powell Foster beginning in 1904. In Ro, words are constructed using a category system. For example, all words starting with "bofo-" signify colors; the word for red is "bofoc", and yellow is "bofof"...
-RNA particle to control RNA quality and playing a role in chromosomal replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
. Deletion of sbRNA does not prevent chromosome replication in C. elegans, but this may be a result of other sbRNAs substituting missing elements (as in human Y RNA). This theory also explains why RNAi studies failed to detect a phenotype for knocked out sbRNAs.