RNA

Ribonucleic acid or RNA is a nucleic acid made from a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell RNA is usually single stranded, while DNA is usually double stranded. RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom), and in RNA the nucleotide uracil substitutes for thymine, which is present in DNA.

RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. Some of these RNA-processing enzymes contain RNA as part of their structures. RNA is also central to the translation of some RNAs into proteins. In this process, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can and read messenger RNAs and translate the information they carry into proteins. It has also been known since the 1990s that several types of RNA regulate which genes are active.

Structure

Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, generally adenine (A), cytosine (C), guanine (G) or uracil (U). A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.^[1] However other interactions are possible, such as a group of adenine bases binding to each other in a bulge,^[2] or the GNRA tetraloop that has a guanine%u2013adenine base-pair.^[1]

Chemical structure of RNA

An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar. The presence of this functional group enforces the C3'-endo sugar conformation (as opposed to the C2'-endo conformation of the deoxyribose sugar in DNA) that causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA.^[3] This results in a very deep and narrow major groove and a shallow and wide minor groove.^[4] A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone.^[5]

RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil),^[6] but there are numerous modified bases and sugars in mature RNAs. Pseudouridine (%u03A8), in which the linkage between uracil and ribose is changed from a C%u2013N bond to a C%u2013C bond, and ribothymidine (T), are found in various places (most notably in the T%u03A8C loop of tRNA).^[7] Another notable modified base is hypoxanthine, a deaminated guanine base whose nucleoside is called inosine. Inosine plays a key role in the wobble hypothesis of the genetic code.^[8] There are nearly 100 other naturally occurring modified nucleosides,^[9] of which pseudouridine and nucleosides with 2'-O-methylribose are the most common.^[10] The specific roles of many of these modifications in RNA are not fully understood. However, it is notable that in ribosomal RNA, many of the post-transcriptional modifications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function.^[11]

Secondary structure of an RNA from a telomerase

The functional form of single stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements which are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges and internal loops.^[12] There has been a significant amount of research directed at the RNA structure prediction problem.

Comparison with DNA

RNA and DNA differ in three main ways. First, unlike DNA which is double-stranded, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. Second, while DNA contains deoxyribose, RNA contains ribose, (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA, whereas RNA has two hydroxyl groups). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Third, the complementary nucleotide to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine.^[13]

Like DNA, most biologically active RNAs including tRNA, rRNA, snRNAs and other non-coding RNAs are extensively base paired to form double stranded helices. Structural analysis of these RNAs have revealed that they are highly structured. Unlike DNA, this structure is not long double-stranded helices but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis, like enzymes.^[14] For instance, determination of the structure of the ribosome%u2014an enzyme that catalyzes peptide bond formation%u2014revealed that its active site is composed entirely of RNA.^[15]

Synthesis

Synthesis of RNA is usually catalyzed by an enzyme%u2014RNA polymerase%u2014using DNA as a template. Initiation of synthesis begins with the binding of the enzyme to a promoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the helicase activity of the enzyme. The enzyme then progresses along the template strand in the 3%u2019 to 5%u2019 direction, synthesizing a complementary RNA molecule with elongation occurring in the 5%u2019 to 3%u2019 direction. The DNA sequence also dictates where termination of RNA synthesis will occur.^[16]

There are also a number of RNA-dependent RNA polymerases as well that use RNA as their template for synthesis of a new strand of RNA. For instance, a number of RNA viruses (such as poliovirus) use this type of enzyme to replicate their genetic material.^[17] Also, it is known that RNA-dependent RNA polymerases are required for the RNA interference pathway in many organisms.^[18]

Types of RNA

Overview

Messenger RNA (mRNA) is the RNA that carries information from DNA to the ribosome sites of protein synthesis (translation) in the cell. The coding sequence of the mRNA determines the amino acid sequence in the protein that is produced.^[19]

RNA genes are genes that encode RNA which is not translated into a protein, known as non-coding RNA or small RNA. Non-coding RNAs can also derive from introns.^[20] 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.^[13] There are also non-coding RNAs involved in gene regulation, RNA processing and other roles. Certain RNAs are able to catalyse chemical reactions such as cutting and ligating other RNA molecules,^[21] and the catalysis of peptide bond formation in the ribosome;^[15] these are known as ribozymes.

Double-stranded RNA (dsRNA) is RNA with two complementary strands, similar to the DNA found in all cells. dsRNA forms the genetic material of some viruses (double-stranded RNA viruses). In eukaryotes, long double-stranded RNA such as viral RNA can trigger RNA interference, where short dsRNA molecules called siRNAs (small interfering RNAs) can silence the expression of genes.^[22]

In translation

Messenger RNA (mRNA) carries information about a protein sequence to the ribosomes, the protein synthesis factories in the cell. It is coded so that every three nucleotides (a codon) correspond to one amino acid. In eukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA. This removes its introns%u2014non-coding sections of the pre-mRNA. The mRNA is then exported from the nucleus to the cytoplasm, where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA. In prokaryotic cells, which do not have nucleus and cytoplasm compartments, mRNA can bind to ribosomes while it is being transcribed from DNA. After a certain amount of time the message degrades into its component nucleotides with the assistance of ribonucleases.^[19]

Transfer RNA (tRNA) is a small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and an anticodon region for codon recognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding.^[20]

Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5.8S, 28S and 5S rRNA. Three of the rRNA molecules are synthesized in the nucleolus, and one is synthesized elsewhere. In the cytoplasm, ribosomal RNA and protein combine to form a nucleoprotein called a ribosome. The ribosome binds mRNA and carries out protein synthesis. Several ribosomes may be attached to a single mRNA at any time.^[19] rRNA is extremely abundant and makes up 80% of the 10 mg/ml RNA found in a typical eukaryotic cytoplasm.^[23]

In gene regulation

Several types of RNA can downregulate gene expression by being complementary to a part of a gene. MicroRNAs (miRNA; 21-22 nt) are found in eukaryotes and act through RNA interference (RNAi), where an effector complex of miRNA and enzymes can break down mRNA which the miRNA is complementary to, block the mRNA from being translated, or cause the promoter to be methylated which generally downregulates the gene.^[24] Some miRNAs upregulate genes instead (RNA activation).^[25] While small interfering RNAs (siRNA; 20-25 nt) are often produced by breakdown of viral RNA, there are also endogenous sources of siRNAs.^[26] siRNAs act through RNA interference in a fashion similar to miRNAs, including RNA activation.^[27] Animals have Piwi-interacting RNAs (piRNA; 29-30 nt) which are active in germline cells and are thought to be a defense against transposons and play a role in gametogenesis.^[28][29] X chromosome inactivation in female mammals is caused by Xist, an RNA which coats one X chromosome, inactivating it.^[30] Antisense RNAs are widespread among bacteria; most downregulate a gene, but a few are activators of transcription.^[31] An mRNA may contain regulatory elements itself, such as riboswitches, in the 5' UTR or 3' UTR; these cis-regulatory elements regulate the activity of that mRNA.^[32]

Uridine to pseudouridine is a common RNA modification.

In RNA processing

Many RNAs are involved in modifying other RNAs. Introns are spliced out of pre-mRNA by spliceosomes, which contain several small nuclear RNAs (snRNA).^[13] RNA can also be altered by having its nucleotides modified to other nucleotides than A, C, G and U. In eukaryotes, modifications of RNA nucleotides are generally directed by small nucleolar RNAs (snoRNA; 60-300 nt),^[20] found in the nucleolus and cajal bodies. snoRNAs associate with enzymes and guide them to a spot on an RNA by basepairing to that RNA. These enzymes then perform the nucleotide modification. rRNAs and tRNAs are extensively modified, but snRNAs and mRNAs can also be the target of base modification.^[33][34]

List of RNAs

Type	Abbr.	Function[35]	Distribution	Ref.
Messenger RNA	mRNA	Codes for protein	All organisms
Ribosomal RNA	rRNA	Translation	All organisms
Transfer RNA	tRNA	Translation	All organisms
Transfer-messenger RNA	tmRNA	Rescuing stalled ribosomes	Bacteria	[36]
Antisense RNA	aRNA	Gene regulation	All organisms	[37]
Small interfering RNA	siRNA	Gene regulation	Most eukaryotes	[38]
MicroRNA	miRNA	Gene regulation	Most eukaryotes	[39]
trans-acting siRNA	tasiRNA	Gene regulation	Plants (Arabidopsis thaliana)	[40]
Piwi-interacting RNA	piRNA	Gene regulation	Animals	[28]
Small nuclear RNA	snRNA	Various	Eukaryotes and archaea	[41]
Small nucleolar RNA	snoRNA	Nucleotide modification of RNAs	Eukaryotes and archaea	[42]
Guide RNA	gRNA	mRNA modification	Kinetoplastid mitochondria	[43]
Ribonuclease P	RNase P	tRNA maturation	All organisms	[44]
Ribonuclease MRP	RNase MRP	rRNA maturation, DNA replication	Eukaryotes	[45]
Y RNA		RNA processing, DNA replication	Animals	[46]
Telomerase RNA		Telomere synthesis	Most eukaryotes	[47]
Signal recognition particle RNA		Protein export	All organisms	[48]
Retrotransposon		Self-propagating	Eukaryotes and some bacteria	[49]
Viroid		Self-propagating	Infected plants	[50]
Viral genome		Information carrier	Double-stranded RNA viruses, positive-sense RNA viruses, negative-sense RNA viruses, most satellite viruses and reverse transcribing viruses

Discovery

Nucleic acids were discovered in 1868 by Friedrich Miescher, who called the material 'nuclein' since it was found in the nucleus.^[51] It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis had been suspected since 1939, based on experiments carried out by Torbjörn Caspersson, Jean Brachet and Jack Schultz.^[52] Gerard Marbaix isolated the first messenger RNA, for rabbit hemoglobin, and found it induced the synthesis of hemoglobin after injection into oocytes.^[53] Severo Ochoa won the 1959 Nobel Prize in Medicine after he discovered how RNA is synthesized.^[54] The sequence of the 77 nucleotides of a yeast RNA was found by Robert W. Holley in 1965,^[55] winning Holley the 1968 Nobel Prize in Medicine. Carl Woese realised RNA can be catalytic in 1967 and proposed the earliest forms of life relied on RNA both to carry genetic information and to catalyze biochemical reactions%u2014an RNA world.^[56][57] In 1976, Walter Fiers and his team at the University of Ghent determined the first complete nucleotide sequence of an RNA virus genome, that of bacteriophage MS2.^[58] In the early 1990s it was found that introduced genes can silence homologous endogenous genes in plants.^[59] At about the same time, 22 nt long RNAs, now known as microRNAs, were found to have a role in the development of C. elegans.^[60] The discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, particularly to silence oncogenes and viral genes.^[61] There is no such drug on the market, but there is promising research on using siRNAs to downregulate genes through RNA interference.^[62]

• Genetics
• Molecular biology
• Phosphoramidite
• Quantification of nucleic acids
• RNA Ontology Consortium
• Sequence profiling tool
• RNA extraction