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Encyclopedia > Small nucleolar RNA

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), or 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). Ribonucleic acid (RNA) is a nucleic acid polymer consisting of covalently bound nucleotides. ... Translation is the second process of protein biosynthesis (part of the overall process of gene expression). ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid —usually in the form of a double helix— that contains the genetic instructions specifying the biological development of all cellular forms of life, and most viruses. ... This stylistic schematic diagram shows a gene in relation to the double helix structure of DNA and to a chromosome (right). ...


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. In cell biology, a mitochondrion is an organelle found in the cells of most eukaryotes. ... Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... A pseudogene is a nucleotide sequences that is similar to a normal gene, but is not expressed as a functional protein. ...

Contents


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. Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of covalently bound nucleotides. ... In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid functional groups. ... An overview of protein synthesis. ...


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. Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... Schematic of typical animal cell, showing subcellular components. ... Cytoplasm is a homogeneous, generally clear jelly-like material that fills cells. ... The nuclear envelope refers to the double membrane of the nucleus that encloses genetic material in eukaryotic cells. ... A ribozyme (from ribonucleic acid enzyme, also called RNA enzyme) is an RNA molecule, that catalyzes a chemical reaction. ...


There are 2 mitochondrial (23S and 16S) rRNA molecules[1]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 pseudogenes), the largest one on the chromosome 1q41-42. Figure 1: Chromosome. ...


Cytoplasmic 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 (see 5'UTR, 3'UTR) of mRNAs (i.e. cis-regulatory RNAs), for example riboswitches and the SECIS element . The interaction of mRNA in a eukaryote cell. ... In molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the genes activity. ... In biology, the SECIS element (SECIS: selenocysteine insertion sequence) is a structural motif (pattern of nucleotides) that directs the cell to translate UGA codons as selenocysteines. ...


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 transcribed by RNA polymerase II or RNA polymerase III. They are involved in a variety of important processes such as RNA splicing (removal of introns from hnRNA), regulation of transcription factors (7SK RNA) or RNA polymerase II (B2 RNA), 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. RNA polymerase II (also called RNAP II and Pol II) transcribes DNA to synthesize precursors of mRNA and most snRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. ... RNA polymerase III (also called RNAP III and Pol III) transcribes DNA to synthesize ribosomal 5S RNA, tRNA and other small RNAs. ... Diagram of the location of introns and exons within a gene. ... In the context of genetics, a transcription factor is a regulatory protein that initiates the transcription of certain genes upon binding with DNA. The binding of a transcription factor to a specific DNA sequence can result in either an increased rate of transcription of the gene, known as activated transcription... RNA polymerase II (also called RNAP II and Pol II) transcribes DNA to synthesize precursors of mRNA and most snRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. ... A telomere is a region of highly repetitive DNA at the end of a chromosome that functions as a disposable buffer. ...


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. snoRNA control the modification of rRNA. They are encoded into the introns of ribosomal proteins and are synthesized by RNA polymerase II. 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 (base pairing) in the snoRNA that hybridize to the target site. The proteins then catalyze modification of the RNA gene. In cell biology, the nucleolus is, strictly speaking, a suborganelle of the nucleus, which is an organelle. ... In biochemistry, methylation refers to the replacement of a hydrogen atom (H) with a methyl group (CH3), regardless of the substrate. ...

  1. snoRNA lines up the RNA-modifying enzyme at the correct position by complementary base pairing
  2. 2'-O-methylated robose causes an invrease in the 3'-endo conformation
  3. Pseudourne (psi) adds another option for H-bonding.
  4. Heavily methylated RNA is protected from hydrolysis. rRNA acts as a ribosozyme by catalyzing its own hydrolysis and splicing.

microRNA

Main article: miRNA

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. In genetics, a miRNA (micro-RNA) is a form of single-stranded RNA which is typically 20-25 nucleotides long, and is thought to regulate the expression of other genes. ...


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. Orders Trypanosomatida Bodonida The kinetoplastids are a group of flagellate protozoa, including a number of parasites responsible for serious diseases in humans and other animals, as well as various forms found in soil and aquatic environments. ... Uracil is one of the four RNA nucleobases, replacing thymine as found in DNA. Just like thymine, uracil can form a base pair with adenine via two hydrogen bonds, but it lacks the methyl group present in thymine. ...


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 in its infancy. Diagram of the location of introns and exons within a gene. ... An analog or analogue signal is any continuously variable signal. ... This article is being considered for deletion in accordance with Wikipedias deletion policy. ... In genetics, a promoter is a DNA sequence that enables a gene to be transcribed. ...


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. The signal recognition particle (SRP) is a protein-RNA complex that recognizes and transports specific proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes. ...


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. A phage (short for bacteriophage, from bacteria and Greek phagein, meaning to eat) is a virus that infects bacteria. ...


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 Subgroups Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular: bacterium) are a major group of living organisms. ... Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... The interaction of mRNA in a eukaryote cell. ... Proteolysis is the directed degradation (digestion) of proteins by cellular enzymes called proteases or by intramolecular digestion. ...


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

 
 

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