The U4 small nuclear Ribo-Nucleic Acid (U4 snRNA) is a
non-coding RNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not Translation (genetics), 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 imp ...
component of the major or U2-dependent
spliceosome
A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs ( snRNA) and numerous proteins. Small nuclear RNA (snRNA) molecules bind to sp ...
– a
eukaryotic
The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...
molecular machine
Molecular machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switch ...
involved in the splicing of pre-messenger RNA (pre-
mRNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein.
mRNA is ...
). It forms a duplex with
U6, and with each splicing round, it is displaced from the U6 snRNA (and the spliceosome) in an ATP-dependent manner, allowing U6 to re-fold and create the
active site
In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the ''binding s ...
for
splicing catalysis. A recycling process involving protein Brr2 releases U4 from U6, while protein
Prp24 re-anneals U4 and U6. The
crystal structure
In crystallography, crystal structure is a description of ordered arrangement of atoms, ions, or molecules in a crystalline material. Ordered structures occur from intrinsic nature of constituent particles to form symmetric patterns that repeat ...
of a 5′
stem-loop
Stem-loops are nucleic acid Biomolecular structure, secondary structural elements which form via intramolecular base pairing in single-stranded DNA or RNA. They are also referred to as hairpins or hairpin loops. A stem-loop occurs when two regi ...
of U4 in complex with a binding protein has been solved.
Biological role
The U4 snRNA has been shown to exist in a number of different formats including: bound to proteins as a small nuclear Ribo-Nuclear Protein
snRNP
snRNPs (pronounced "snurps"), 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- ...
,
involved with the U6 snRNA in the di-snRNP,
as well as involved with both the U6 snRNA and the U5 snRNA in the tri-snRNP.
The different formats have been proposed to coincide with different temporal events in the activity of the penta-snRNP,
or as intermediates in the step-wise model of spliceosome assembly and activity.
The U4 snRNA (and its likely analog snR14 in Yeast
) has been shown not to participate directly in the specific catalytic activities of the splicing reaction,
and is proposed instead to act as a regulator of the U6 snRNA. The U4 snRNA inhibits spliceosome activity during assembly by complementary base pairing between the U6 snRNA in two highly conserved stem regions.
It is suggested that this base-pairing interaction prevents the U6 snRNA from assembling with the U2 snRNA into the conformation required for catalytic activity.
If the U4 snRNA is degraded and thereby removed from the spliceosome, splicing is effectively halted.
The U4 and U6 snRNAs are demonstratively required for splicing in vitro.
Structure
left, 200px, Figure 1. Naked U4 putative secondary structure.
400px, Figure 2. Putative U4/U6 base pairing secondary structure.
The U4 snRNA secondary structure is suggested to alter depending on its interaction with the U6 snRNA.
Several experiments involving
X-ray crystallography
X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring th ...
,
NMR
Nuclear magnetic resonance (NMR) is a physical phenomenon in which atomic nucleus, nuclei in a strong constant magnetic field are disturbed by a weak oscillating magnetic field (in the near and far field, near field) and respond by producing ...
,
and chemical modification
RNA structure probing
Experimental approaches of determining the structure of nucleic acids, such as RNA and DNA, can be largely classified into biophysical and biochemical methods. Biophysical methods use the fundamental physical properties of molecules for structur ...
indicate that U4 snRNA secondary structure contains several conserved motifs,
which serve structural as well as intermediary roles in establishing interactions with other splicing components. The putative U4/U6 snRNA base pairing secondary structure shown in Figure 2., is conserved across a diverse set of organisms suggesting the splicing machinery's ancient origins.
It has been shown previously that a highly conserved Kinked-loop participates in specific protein interactions.
Interactions
The U4 snRNA must be displaced from U6 snRNA in an ATP dependent process involving the protein Brr2 - before the spliceosome is made active.
A cycle has been proposed including both Brr2 as well as the protein prp24 which selectively re-anneals U4 to the U6 snRNA.
A ring of Sm proteins surround a conserved region of the U4 snRNA near the 3' end which are expected to promote favorable interactions between the different snRNPs as well as possibly protect the U4 snRNA from degradation by
RNAse
Ribonuclease (commonly abbreviated RNase) is a type of nuclease that catalyzes the degradation of RNA into smaller components. Ribonucleases can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the ...
enzymes.
Over 100 proteins have been identified that participate in spliceosomal pathway, several proteins of varying size are also known to interact with the U4 snRNP.
References
Further reading
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External links
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{{DEFAULTSORT:U4 Spliceosomal Rna
Small nuclear RNA
Spliceosome
RNA splicing