From Wikipedia,
the free encyclopedia.
A non-coding RNA (ncRNA)
is any
RNA molecule that functions
without being
translated into a
protein. A commonly used
synonym is small RNA (sRNA).
Less-frequently used synonyms are
non-messenger RNA (nmRNA), small
non-messenger RNA (snmRNA), and
functional RNA (fRNA). The
DNA sequence from which a
non-coding RNA is transcribed as
the end product is often called an
RNA gene or non-coding RNA
gene (see
gene).
The most prominent examples of
non-coding RNAs are transfer
RNA (tRNA) and
ribosomal RNA (rRNA),
both of which are involved in the
process of translation and gene
expression. However, since the
late 1990s, many new non-coding
RNAs have been found, and thus
non-coding RNAs may play a much
more significant role than
previously thought.
Human
mitochondrial genome contains
24 RNA genes: 2 for 23S and 16S
rRNR subunits of mitochondrial
ribosomes. Nuclear genome
contains c.a. 3000 RNA genes (less
than 10% of total gene number). To
identify RNA genes in sequenced
DNA is very difficult. In addition
to the RNA genes there are many
related
pseudogene/gene fragments.
Types (families) of non-coding
RNAs
Transfer RNA
Transfer RNA (tRNA) is
RNA that transfers a specific
amino acid to a growing
polypeptide chain at the ribosomal
site of
protein biosynthesis during
translation.
Ribosomal RNA
Ribosomal RNA (rRNA) is the
primary constituent of
ribosomes. Ribosomes are the
protein-manufacturing
organelles of cells and exist
in the
cytoplasm. rRNA is transcribed
from DNA, like all RNA. Ribosomal
proteins are transported into the
nucleus and assembled together
with rRNA before being transported
through the
nuclear membrane. This type of
RNA makes up the vast majority of
RNA found in a typical cell. While
proteins are also present in the
ribosomes, solely rRNA is able to
form peptides. Therefore ribosome
often is referred to as
ribozyme.
There are 2 mitochondrial (23S
and 16S) molecules and 4 types of
cytoplasmic rRNA (28S, 5.8S, 5S
(large ribosome subunit) and 18S
(small subunit)). 28S, 5.8S and
18S rRNAs are encoded by a
single transcription unit
organized into 5 clusters (each
has 30-40 repeats) on the
13,14,15, 21 and 22
chromosomes. 5S occurs in
tandem arrays (~200-300 true 5S
genes and many dispersed pseudoges),
the largest one on the chromosome
1q41-42.
Cytomplasmic rRNA genes are
highly repetitive because of huge
demand of ribosomes for protein
synthesis (gene dosage) in
the cell.
Untranslated regions of mRNAs
Many non-coding RNAs are
structural elements in the
untranslated regions of
mRNAs (i.e. cis-regulatory
RNAs), for example
riboswitches and the
SECIS element.
Small nuclear RNA
Small nuclear RNA (snRNA) is a
class of small RNA molecules that
are found within the nucleus of
eukaryotic cells. They are
involved in a variety of important
processes such as RNA splicing
(removal of
introns from hnRNA) and
maintaining the
telomeres. They are always
associated with specific proteins,
and the complexes are referred to
as
small nuclear ribonucleoproteins
(snRNP) or sometimes as snurps.
Small nucleolar RNA
Small nucleolar RNA (snoRNA) is
a class of small RNA molecules
that are involved in chemical
modifications of ribosomal RNAs (rRNAs)
and other RNA genes, for example
by
methylation. snoRNAs are a
component in the small nucleolar
ribonucleoprotein (snoRNP), which
contains snoRNA and proteins. The
snoRNA guides the snoRNP complex
to the modification site of the
target RNA gene via sequences in
the snoRNA that hybridize to the
target site. The proteins then
catalyze modification of the RNA
gene.
microRNA
microRNA (also miRNA) are RNA
genes that are the reverse
complement of another gene's mRNA
transcript and inhibit the
expression of the target gene.
See
miRNA.
gRNAs
gRNAs (for guide RNA) are RNA
genes that function in RNA
editing. Thus far, RNA editing has
been found only in the
mitochondria of
kinetoplastids, in which mRNAs
are edited by inserting or
deleting stretches of
uridylates (Us). The gRNA
forms part of the editosome
and contains sequences that
hybridize to matching sequences in
the mRNA, to guide the mRNA
modifications.
The term "guide RNA" is also
sometimes used generically to mean
any RNA gene that guides an
RNA/protein complex via
hybridization of matching
sequences.
efference RNA
Efference RNA (eRNA)
is derived from
intron sequences of genes or
from non-coding DNA. The function
is assumed to be regulation of
translational activity by
interference with the
transcription apparatus or target
proteins of the translated peptide
in question, or by providing a
concentration-based measure of
protein expression, basically
introducing a fine-tuned
analog element in gene
regulation as opposed to the
digital on-or-off regulation
by
promoters. Research into the
role of eRNAs is only beginning,
but they could theoretically be
able to explain much of the
molecular fundament of
biodiversity, which has so far
eluded genetics.
Signal recognition particle
RNA
The
signal recognition particle (SRP)
is an RNA-protein complex present
in the cytoplasm of cells that
binds to the mRNA of proteins that
are destined for secretion from
the cell. The RNA component of the
SRP in eukaryotes is called 4.5S
RNA.
pRNA
At least one species of
DNA-containing
phages, phi-29, uses a complex
of six identical short RNA
sequences as mechanical components
(utilizing ATP for energy) of its
DNA packaging machinery. How
common this phenomenon is has yet
to be determined.
tmRNA
tmRNA has a complex structure
with tRNA-like and mRNA-like
regions. It has currently only
been found in
bacteria, but is ubiquitous in
all bacteria. tmRNA recognizes
ribosomes that have trouble
translating or reading an mRNA and
stall, leaving an unfinished
protein that may be detrimental to
the cell. tmRNA acts like a
tRNA first, and then an
mRNA that encodes a peptide
tag. The ribosome translates this
mRNA region of tmRNA and attaches
the encoded peptide tag to the
C-terminus of the unfinished
protein. This attached tag targets
the protein for destruction or
proteolysis.
How tmRNA works
External
-
The Rfam Database A curated
list of hundreds of families of
related ncRNAs. Each family
includes a multiple
alignment of known members,
and predicted homologs in a
large genome database. The
definition of "family" is a
pragmatic one, the goal being to
lead to high-quality
annotations. Thus, some families
are quite broad (e.g. all tRNAs
are in one family, as of 2004),
while some families are quite
narrow (e.g. there are many
microRNA families, one for each
type).
-
Non-coding RNA database
