sbRNA (stem-bulge

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

) is a family of

non-coding RNA A non-coding RNA (ncRNA) is a functional 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-c ...

first discovered in ''

Caenorhabditis elegans ''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' (ro ...

''. It was identified during a full

transcriptome The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The t ...

screen of the ''C. elegans''

cDNA In genetics, complementary DNA (cDNA) is DNA synthesized from a single-stranded RNA (e.g., messenger RNA (mRNA) or microRNA (miRNA)) template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to express a speci ...

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

expression Expression may refer to: Linguistics * Expression (linguistics), a word, phrase, or sentence * Fixed expression, a form of words with a specific meaning * Idiom, a type of fixed expression * Metaphorical expression, a particular word, phrase, o ...

patterns during development. They are most highly expressed in adult worms,

dauer larvae Dauer (German "''die Dauer''", English "the enduring", "the duration" in the meaning of "a length of time",) describes an alternative developmental stage of nematode worms, particularly rhabditids including ''Caenorhabditis elegans'', whereby the l ...

and following

heat shock The heat shock response (HSR) is a cell stress response that increases the number of molecular chaperones to combat the negative effects on proteins caused by stressors such as increased temperatures, oxidative stress, and heavy metals. In a normal ...

. A systematic

knockout A knockout (abbreviated to KO or K.O.) is a fight-ending, winning criterion in several full-contact combat sports, such as boxing, kickboxing, muay thai, mixed martial arts, karate, some forms of taekwondo and other sports involving striking, a ...

analysis using

RNAi RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by double-stranded RNA, through translational or transcriptional repression. Historically, RNAi was known by o ...

found no

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...

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 In molecular biology, the TATA box (also called the Goldberg–Hogness box) is a sequence of DNA found in the core promoter region of genes in archaea and eukaryotes. The bacterial homolog of the TATA box is called the Pribnow box which has ...

and a proximal sequence element (PSE B box), though only one of these is required for

transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...

. As the transcript is uncapped and polyuridylated, it is thought to be transcribed by

RNA polymerase III In eukaryote cells, RNA polymerase III (also called Pol III) is a protein that 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 e ...

Y RNA homology

An sbRNA, ''CeN134'' was reported as a candidate homologue to the vertebrate

Y RNA Y RNAs are small non-coding RNAs. They are components of the Ro60 ribonucleoprotein particle which is a target of autoimmune antibodies in patients with systemic lupus erythematosus. They are also reported to be necessary for DNA replication thro ...

during a

kingdom Kingdom commonly refers to: * A monarchy ruled by a king or queen * Kingdom (biology), a category in biological taxonomy Kingdom may also refer to: Arts and media Television * ''Kingdom'' (British TV series), a 2007 British television drama s ...

-wide search. Further investigation found a homologous

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

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.

Expression

Y RNA homology

See also

References

Further reading