Y RNAs are small 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...

 components of the Ro ribonucleoprotein particle (Ro RNP). The Ro RNP was first identified by Lerner et al.. as a target of autoimmune antibodies in patients with systemic lupus erythematosus

Systemic lupus erythematosus

Systemic lupus erythematosus , often abbreviated to SLE or lupus, is a systemic autoimmune disease that can affect any part of the body. As occurs in other autoimmune diseases, the immune system attacks the body's cells and tissue, resulting in inflammation and tissue damage...

.

Function

Two functions have been described for Y RNAs in the literature: In one line of evidence, Y RNA appears to function as a repressor of Ro

TRIM21

Tripartite motif-containing protein 21 also known as E3 ubiquitin-protein ligase TRIM21 is a protein that in humans is encoded by the TRIM21 gene. Alternatively spliced transcript variants for this gene have been described but the full-length nature of only one has been determined...

. In its free state, Ro binds to a variety of misfolded RNAs including
misfolded 5S rRNAs, and is thought to act as some sort of quality control mechanism. Crystal structure

Crystal structure

In mineralogy and crystallography, crystal structure is a unique arrangement of atoms or molecules in a crystalline liquid or solid. A crystal structure is composed of a pattern, a set of atoms arranged in a particular way, and a lattice exhibiting long-range order and symmetry...

s of Ro complexed either with Y RNA or another RNA showed that Ro binds single-stranded 3' ends of RNAs relatively nonspecifically, whereas Y RNA binds specifically at a second site that regulates access of other RNAs. In Deinococcus

Deinococcus

The Deinococcus is the one genus of three of the Deinococcales group from the Deinococcus-Thermus phylum highly resistant to environmental hazards.There are 47 species of Deinococcus described according to NCBI on 25 august 2011 :...

, free Ro has also been shown to function in 23S rRNA maturation. In Deinococcus, mutant

Mutant

In biology and especially genetics, a mutant is an individual, organism, or new genetic character, arising or resulting from an instance of mutation, which is a base-pair sequence change within the DNA of a gene or chromosome of an organism resulting in the creation of a new character or trait not...

s lacking Y RNA are viable, and Y RNA appears to be unstable except when complexed with Ro.
Secondly, it has been found that human Y RNAs are functionally required for DNA 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...

. Biochemical fractionation

Fractionation

See also: Fractionated spacecraftFractionation is a separation process in which a certain quantity of a mixture is divided up in a number of smaller quantities in which the composition changes according to a gradient. Fractions are collected based on differences in a specific property of the...

 and reconstitution experiments have established a functional requirement of human Y RNAs for chromosomal

Chromosome

A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...

 DNA replication in isolated vertebrate

Vertebrate

Vertebrates are animals that are members of the subphylum Vertebrata . Vertebrates are the largest group of chordates, with currently about 58,000 species described. Vertebrates include the jawless fishes, bony fishes, sharks and rays, amphibians, reptiles, mammals, and birds...

 cell nuclei in vitro

In vitro

In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...

. Specific degradation of human Y RNAs in vitro, or in intact cells in vivo

In vivo

In vivo is experimentation using a whole, living organism as opposed to a partial or dead organism, or an in vitro controlled environment. Animal testing and clinical trials are two forms of in vivo research...

, have led to an inhibition of chromosomal DNA replication. Interestingly, mutant human Y RNAs lacking the conserved binding site for Ro60 protein still support DNA replication, indicating that binding to Ro protein and promoting DNA replication are two separable functions of Y RNAs. Another study , has shown that Y RNAs are overexpressed in human tumours and required for cell proliferation.

Structure

These small RNAs are predicted to fold into a conserved stem formed by the RNA's 3' and 5' ends and characterized by a single bulged cytosine

Cytosine

Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine . It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached . The nucleoside of cytosine is cytidine...

, these are the known requirements for Ro binding.

Species distribution

Presumptive Y RNA and Ro protein homologs

Homology (biology)

Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...

 have been found in eukaryotes and bacteria

Bacteria

Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

. Humans appear to have four Y RNAs, named hY1, hY3, hY4 and hY5 and also a large number of pseudogenes. C. 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...

has one, named CeY RNA and a large number of sbRNA

SbRNA

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...

s that are postulated to also be Y RNA homologues. The radiation-resistant bacterium Deinococcus radiodurans

Deinococcus radiodurans

Deinococcus radiodurans is an extremophilic bacterium, one of the most radioresistant organisms known. It can survive cold, dehydration, vacuum, and acid, and is therefore known as a polyextremophile and has been listed as the world's toughest bacterium in The Guinness Book Of World Records.-Name...

encodes a homolog of Ro called rsr ("Ro sixty related"), and at least four small RNAs accumulate in Deinococcus under conditions where rsr expression is induced (UV

Ultraviolet

Ultraviolet light is electromagnetic radiation with a wavelength shorter than that of visible light, but longer than X-rays, in the range 10 nm to 400 nm, and energies from 3 eV to 124 eV...

irradiation); one of these RNAs appears to be a Y RNA homolog.