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RNA interference



 
 
RNA interference (RNAi) is a system within living cells that helps to control which genes are active and how active they are. Two types of small RNA
RNA

Ribonucleic acid is a type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate....
 molecules – microRNA (miRNA) and small interfering RNA
Small interfering RNA

Small interfering RNA , sometimes known as short interfering RNA or silencing RNA, is a class of 20-25 nucleotide-long RNA#Double-stranded RNA molecules that play a variety of roles in biology....
 (siRNA) – are central to RNA interference. RNAs are the direct products of genes, and these small RNAs can bind to specific other RNAs and either increase or decrease their activity, for example by preventing a messenger RNA
Messenger RNA

Messenger ribonucleic acid is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcription from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes....
 from producing a protein.






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RNA interference (RNAi) is a system within living cells that helps to control which genes are active and how active they are. Two types of small RNA
RNA

Ribonucleic acid is a type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate....
 molecules – microRNA (miRNA) and small interfering RNA
Small interfering RNA

Small interfering RNA , sometimes known as short interfering RNA or silencing RNA, is a class of 20-25 nucleotide-long RNA#Double-stranded RNA molecules that play a variety of roles in biology....
 (siRNA) – are central to RNA interference. RNAs are the direct products of genes, and these small RNAs can bind to specific other RNAs and either increase or decrease their activity, for example by preventing a messenger RNA
Messenger RNA

Messenger ribonucleic acid is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcription from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes....
 from producing a protein. RNA interference has an important role in defending cells against parasitic genes – virus
Virus

A virus is a Optical microscope#Limitations of light microscopes infectious agent that is unable to grow or reproduce outside a host cell . Viruses infect all cellular life....
es and transposon
Transposon

Transposons are sequences of DNA that can move around to different positions within the genome of a single cell , a process called transposition....
s – but also in directing development
Developmental biology

Developmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, cellular differentiation and "morphogenesis," which is the process that gives rise to biological tissues, organ s and anatomy....
 as well as gene expression
Gene expression

Gene expression is the process by which inheritable information from a gene, such as the DNA sequence, is made into a functional gene product, such as protein or RNA....
 in general.

The RNAi pathway is found in many eukaryote
Eukaryote

Animals, plants, fungus, and protists are eukaryotes , organisms whose Cell are organized into complex structures enclosed within Cell membrane....
s including animals and is initiated by the enzyme Dicer
Dicer

Dicer is an endoribonuclease in the RNase III family that cleaves dsRNA and pre-microRNA into short double-stranded RNA fragments called small interfering RNA about 20-25 nucleotides long, usually with a two-base overhang on the 3' end....
, which cleaves long double-stranded RNA molecules into short fragments of ~20 nucleotide
Nucleotide

Nucleotides are molecules that comprise the structural units of RNA and DNA. Additionally, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cell signaling , and are incorporated into important cofactors of enzymatic reactions ....
s. One of the two strands of each fragment, known as the guide strand, is then incorporated into the RNA-induced silencing complex
RNA-induced silencing complex

RNA-induced silencing complex, or RISC, is a multi-protein siRNA complex which cleaves dsRNA and binds short antisense RNA strands which are then able to bind complementary strands....
 (RISC). The most well-studied outcome is post-transcriptional gene silencing, which occurs when the guide strand base pairs with a complementary sequence of a messenger RNA molecule and induces cleavage by Argonaute
Argonaute

For the French ships, see French ship ArgonauteArgonaute proteins are the catalytic components of the RNA-induced silencing complex , the protein complex responsible for the gene silencing phenomenon known as RNA interference ....
, the catalytic component of the RISC complex. This process is known to spread systemically throughout the organism despite initially limited molar concentrations of siRNA.

The selective and robust effect of RNAi on gene expression makes it a valuable research tool, both in cell culture
Cell culture

Cell culture is the process by which prokaryote or eukaryote cells are grown under controlled conditions. In practice the term "cell culture" has come to refer to the culturing of cells derived from multicellular eukaryotes, especially animal cells....
 and in living organisms because synthetic dsRNA introduced into cells can induce suppression of specific genes of interest. RNAi may also be used for large-scale screens that systematically shut down each gene in the cell, which can help identify the components necessary for a particular cellular process or an event such as cell division
Cell division

Cell division is a process by which a cell , called the parent cell, divides into two or more cells, called daughter cells. Cell division is usually a small segment of a larger cell cycle....
. Exploitation of the pathway is also a promising tool in biotechnology
Biotechnology

Biotechnology is technology based on biology, especially when used in agriculture, food science, and medicine. United Nations Convention on Biological Diversity defines biotechnology as:...
 and medicine
Medicine

Medicine is the art and science of healing. It encompasses a range of health care practices evolved to maintain and restore health by the prevention and treatment of illness....
.

Historically, RNA interference was known by other names, including post transcriptional gene silencing
Post transcriptional gene silencing

Post transcriptional gene silencing is a mechanism for sequence-specific RNA degradation in plants similar to RNA interference in other organisms....
, and quelling. Only after these apparently-unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon. In 2006, Andrew Fire
Andrew Fire

Andrew Zachary Fire is an United States of America biologist and Professor of pathology and of genetics at the Stanford University School of Medicine....
 and Craig C. Mello shared the Nobel Prize in Physiology or Medicine
Nobel Prize in Physiology or Medicine

The Nobel Prize in Physiology or Medicine is awarded once a year by the Swedish Karolinska Institutet. It is one of the five Nobel Prizes established by the will of Alfred Nobel in 1895, awarded for outstanding contributions in Nobel Prize in Physics, Nobel Prize in Chemistry, Nobel Prize in Literature, Nobel Peace Prize, and Physiology or Medic...
 for their work on RNA interference in the nematode
Nematode

The "roundworms" or "nematodes" are the most diverse phylum of body cavity, and one of the most diverse of all animals. Nematode species are very difficult to distinguish; over 80,000 have been described, of which over 15,000 are parasite....
 worm C. elegans, which they published in 1998.

Cellular mechanism

2ffl By Domain
RNAi is an RNA-dependent gene silencing
Gene silencing

Gene silencing is a general term describing epigenetic processes of gene regulation. The term gene silencing is generally used to describe the "switching off" of a gene by a mechanism other than genetic modification....
 process that is controlled by the RNA-induced silencing complex
RNA-induced silencing complex

RNA-induced silencing complex, or RISC, is a multi-protein siRNA complex which cleaves dsRNA and binds short antisense RNA strands which are then able to bind complementary strands....
 (RISC) and is initiated by short double-stranded RNA molecules in a cell's cytoplasm
Cytoplasm

The cytoplasm is the part of a Cell that is enclosed within the plasma membrane. In eukaryote cells the cytoplasm contains organelles, such as mitochondrion, that are filled with liquid kept separate from the rest of the cytoplasm by biological membranes....
, where they interact with the catalytic RISC component argonaute
Argonaute

For the French ships, see French ship ArgonauteArgonaute proteins are the catalytic components of the RNA-induced silencing complex , the protein complex responsible for the gene silencing phenomenon known as RNA interference ....
. When the dsRNA is exogenous (coming from infection by a virus
Virus

A virus is a Optical microscope#Limitations of light microscopes infectious agent that is unable to grow or reproduce outside a host cell . Viruses infect all cellular life....
 with an RNA genome or laboratory manipulations), the RNA is imported directly into the cytoplasm and cleaved to short fragments by the enzyme dicer
Dicer

Dicer is an endoribonuclease in the RNase III family that cleaves dsRNA and pre-microRNA into short double-stranded RNA fragments called small interfering RNA about 20-25 nucleotides long, usually with a two-base overhang on the 3' end....
. The initiating dsRNA can also be endogenous (originating in the cell), as in pre-microRNAs expressed from RNA-coding gene
Non-coding RNA

A non-coding RNA is a functional RNA molecule that is not Translation into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA , small non-messenger RNA , functional RNA ....
s in the genome. The primary transcripts from such genes are first processed to form the characteristic stem-loop
Stem-loop

Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same molecule, usually palindrome in nucleotide sequence, base-pair to form a double helix that ends in an unpaired loop....
 structure of pre-miRNA in the nucleus
Cell nucleus

In cell biology, the nucleus , also sometimes referred to as the "control center", is a membrane-enclosed organelle found in all eukaryote cell ....
, then exported to the cytoplasm to be cleaved by dicer. Thus, the two dsRNA pathways, exogenous and endogenous, converge at the RISC complex.

dsRNA cleavage

Exogenous dsRNA initiates RNAi by activating the ribonuclease
Ribonuclease

Ribonuclease is a type of nuclease that catalysis the degradation of RNA into smaller components. Ribonucleases can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the EC 2.7 and 3.1 classes of enzymes....
 protein Dicer
Dicer

Dicer is an endoribonuclease in the RNase III family that cleaves dsRNA and pre-microRNA into short double-stranded RNA fragments called small interfering RNA about 20-25 nucleotides long, usually with a two-base overhang on the 3' end....
, which binds and cleaves double-stranded RNAs (dsRNA)s to produce double-stranded fragments of 20–25 base pair
Base pair

In molecular biology, two nucleotides on opposite complementarity DNA or RNA strands that are connected via hydrogen bonds are called a base pair ....
s with a few unpaired overhang bases on each end. Bioinformatics
Bioinformatics

Bioinformatics is the application of information technology to the field of molecular biology. The term bioinformatics was coined by Paulien Hogeweg in 1978 for the study of informatic processes in biotic systems....
 studies on the genomes of multiple organisms suggest this length maximizes target-gene specificity and minimizes non-specific effects. These short double-stranded fragments are called small interfering RNAs (siRNA
Sírna

S?rna S?eglach , son of Dian, son of Demal, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland....
s). These siRNAs are then separated into single strands and integrated into an active RISC complex. After integration into the RISC, siRNAs base-pair to their target mRNA and induce cleavage of the mRNA, thereby preventing it from being used as a translation
Translation (genetics)

Translation is the first stage of protein biosynthesis . Translation is the production of proteins by decoding mRNA produced in Transcription ....
 template.

Exogenous dsRNA is detected and bound by an effector protein, known as RDE-4 in C. elegans and R2D2 in Drosophila
Drosophila

Drosophila is a genus of small fly, belonging to the family Drosophilidae, whose members are often called "fruit flies" or more appropriately pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many species to linger around overripe or rotting fruit....
, that stimulates dicer activity. This protein only binds long dsRNAs, but the mechanism producing this length specificity is unknown. These RNA-binding proteins then facilitate transfer of cleaved siRNAs to the RISC complex.

This initiation pathway may be amplified by the cell through the synthesis of a population of 'secondary' siRNAs using the dicer-produced initiating or 'primary' siRNAs as templates. These siRNAs are structurally distinct from dicer-produced siRNAs and appear to be produced by an RNA-dependent RNA polymerase
RNA-dependent RNA polymerase

RNA-dependent RNA polymerase , or RNA replicase, is an enzyme that catalyzes the Self-replication of RNA from an RNA template. This is in contrast to a typical RNA polymerase, which catalyzes the transcription_ of RNA from a DNA template....
 (RdRP).

MicroRNA

MicroRNAs (miRNAs) are genomically
Genome

In classical genetics, the genome of a diploid organism including eukarya refers to a full set of chromosomes or genes in a gamete; thereby, a regular somatic cell contains two full sets of genomes....
 encoded non-coding RNA
Non-coding RNA

A non-coding RNA is a functional RNA molecule that is not Translation into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA , small non-messenger RNA , functional RNA ....
s that help regulate gene expression
Gene expression

Gene expression is the process by which inheritable information from a gene, such as the DNA sequence, is made into a functional gene product, such as protein or RNA....
, particularly during development
Developmental biology

Developmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, cellular differentiation and "morphogenesis," which is the process that gives rise to biological tissues, organ s and anatomy....
. The phenomenon of RNA interference, broadly defined, includes the endogenously induced gene silencing effects of miRNAs as well as silencing triggered by foreign dsRNA. Mature miRNAs are structurally similar to siRNAs produced from exogenous dsRNA, but before reaching maturity, miRNAs must first undergo extensive post-transcriptional modification
Post-transcriptional modification

Post-transcriptional modification is a process in cell biology by which, in eukaryotic cells, RNA is converted into RNA. A notable example is the conversion of precursor messenger RNA into mature messenger RNA messenger RNA , which includes splicing and occurs prior to protein synthesis....
. An miRNA is expressed from a much longer RNA-coding gene as a primary transcript
Primary transcript

A primary transcript is an RNA molecule that has not yet undergone any post-transcriptional modification after its transcription . For example, a precursor mRNA is a primary transcript that becomes a messenger RNA after processing, and a primary microRNA transcript becomes a microRNA after processing....
 known as a pri-miRNA which is processed, in the cell nucleus
Cell nucleus

In cell biology, the nucleus , also sometimes referred to as the "control center", is a membrane-enclosed organelle found in all eukaryote cell ....
, to a 70-nucleotide stem-loop
Stem-loop

Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same molecule, usually palindrome in nucleotide sequence, base-pair to form a double helix that ends in an unpaired loop....
 structure called a pre-miRNA by the microprocessor complex. This complex consists of an RNase III
RNase III

RNase III enzymes specifically bind to and cleave double-stranded RNA . There are three subdivisions, known as Class 1, 2, and 3.* Class 1 RNases III are largely found in bacteria, bacteriophage, and some fungi....
 enzyme called Drosha
Drosha

Drosha is a Class 2 RNase III enzyme responsible for initiating the processing of microRNA , or short RNA molecules naturally gene expression by the cell that regulate a wide variety of other genes by interacting with the RNA-induced silencing complex to induce cleavage of base pair messenger RNA ....
 and a dsRNA-binding protein Pasha
Pasha

Pasha or pacha, formerly bashaw, was a high rank in the Ottoman Empire political system, typically granted to governors and generals....
. The dsRNA portion of this pre-miRNA is bound and cleaved by dicer to produce the mature miRNA molecule that can be integrated into the RISC complex; thus, miRNA and siRNA share the same cellular machinery downstream of their initial processing.

The siRNAs derived from long dsRNA precursors differ from miRNAs in that miRNAs, especially those in animals, typically have incomplete base pairing to a target and inhibit the translation of many different mRNAs with similar sequences. In contrast, siRNAs typically base-pair perfectly and induce mRNA cleavage only in a single, specific target. In Drosophila
Drosophila melanogaster

Drosophila melanogaster is a two-winged insect that belongs to the Diptera, the Order of the Fly. The species is commonly known as the Drosophilidae or vinegar fly, and is one of the most commonly used model organisms in biology, including studies in genetics, physiology and Life history theory....
 and C. elegans, miRNA and siRNA are processed by distinct argonaute proteins and dicer enzymes.

RISC activation and catalysis

The active components of an RNA-induced silencing complex
RNA-induced silencing complex

RNA-induced silencing complex, or RISC, is a multi-protein siRNA complex which cleaves dsRNA and binds short antisense RNA strands which are then able to bind complementary strands....
 (RISC) are endonuclease
Endonuclease

Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain, in contrast to exonucleases, which cleave phosphodiester bonds at the end of a polynucleotide chain....
s called argonaute
Argonaute

For the French ships, see French ship ArgonauteArgonaute proteins are the catalytic components of the RNA-induced silencing complex , the protein complex responsible for the gene silencing phenomenon known as RNA interference ....
 proteins, which cleave the target mRNA strand complementary
Complementarity (molecular biology)

In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA and RNA as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalent bond connected via two or three hydrogen bonds....
 to their bound siRNA. As the fragments produced by dicer are double-stranded, they could each in theory produce a functional siRNA. However, only one of the two strands, which is known as the guide strand, binds the argonaute protein and directs gene silencing. The other anti-guide strand or passenger strand is degraded during RISC activation. Although it was first believed that an ATP
Adenosine triphosphate

This article is about the chemical used by cells as an energy carrier. For other uses, see ATP .Adenosine-5'-triphosphate is a multifunctional nucleotide, and plays an important role in cell biology as a coenzyme that is the "molecule unit of currency" of intracellular energy transfer....
-dependent helicase
Helicase

Helicases are a class of proteins vital to all living organisms. They are motor proteins that move directionally along a nucleic acid Phosphodiester bond, separating two Annealing nucleic acid strands using energy derived from nucleotide hydrolysis....
 separated these two strands, the process is actually ATP-independent and performed directly by the protein components of RISC. The strand selected as the guide tends to be the one whose 5' end is least paired to its complement, but strand selection is unaffected by the direction in which dicer cleaves the dsRNA before RISC incorporation. Instead, the R2D2 protein may serve as the differentiating factor by binding the more-stable 5' end of the passenger strand.

The structural basis for binding of RNA to the argonaute protein was examined by X-ray crystallography
X-ray crystallography

X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and scatters into many different directions....
 of the binding domain of an RNA-bound argonaute protein. Here, the phosphorylated
Phosphorylation

Phosphorylation is the addition of a phosphate group to a protein or other organic molecule. Protein phosphorylation in particular plays a significant role in a wide range of cellular processes....
 5' end of the RNA strand enters a conserved
Conservation (genetics)

Conservation may refer to:* Conservation genetics - "an interdisciplinary science that aims to apply genetic methods to the conservation and restoration of biodiversity."...
 basic surface pocket
Binding site

In biochemistry, a binding site is a region on a protein, DNA, or RNA to which specific other molecules and ions — in this context collectively called Ligand , or more specifically, protein ligands — form a chemical bond....
 and makes contacts through a divalent
Divalent

In chemistry, divalent anions are atoms or radicals with 2 additional electrons when compared to their elemental state ; for instance, S2- is the sulfide anion....
 cation (an atom with two positive charges) such as magnesium
Magnesium

Magnesium is a chemical element with the symbol Mg, atomic number 12, atomic weight 24.3050 and common oxidation number +2.Magnesium, an alkaline earth metal, is the ninth most abundance of the chemical elements in the universe by mass....
 and by aromatic
Aromaticity

Aromaticity is a chemical property in which a conjugated system ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone....
 stacking
Stacking (chemistry)

Stacking in supramolecular chemistry refers to a stacked arrangement of aromatic molecules, which interact through aromatic interactions. The most popular example of a stacked system is found for consecutive base pairs in DNA....
 (a process that allows more than one atom to share an electron by passing it back and forth) between the 5' nucleotide in the siRNA and a conserved tyrosine
Tyrosine

Tyrosine or 4-hydroxyphenylalanine, is one of the 20 amino acids that are used by cell to protein biosynthesis proteins. This is a non-essential amino acid and it is found in casein....
 residue. This site is thought to form a nucleation site for the binding of the siRNA to its mRNA target.

It is not understood how the activated RISC complex locates complementary mRNAs within the cell. Although the cleavage process has been proposed to be linked to translation
Translation (genetics)

Translation is the first stage of protein biosynthesis . Translation is the production of proteins by decoding mRNA produced in Transcription ....
, translation of the mRNA target is not essential for RNAi-mediated degradation. Indeed, RNAi may be more effective against mRNA targets that are not translated. Argonaute proteins, the catalytic components of RISC, are localized to specific regions in the cytoplasm
Cytoplasm

The cytoplasm is the part of a Cell that is enclosed within the plasma membrane. In eukaryote cells the cytoplasm contains organelles, such as mitochondrion, that are filled with liquid kept separate from the rest of the cytoplasm by biological membranes....
 called P-bodies
P-bodies

Processing bodies are regions within the cytoplasm of the eukaryotic cell consisting of many enzymes involved in mRNA turnover. P bodies are likely the site of miRNA action, as miRNA-targeted mRNAs are recruited to P bodies and degraded or sequestered from translation machinery....
 (also cytoplasmic bodies or GW bodies), which are regions with high rates of mRNA decay; miRNA activity is also clustered in P-bodies. Disruption of P-bodies decreases the efficiency of RNA interference, suggesting that they are the site of a critical step in the RNAi process.

Transcriptional silencing

Components of the RNA interference pathway are also used in many eukaryotes in the maintenance of the organisation and structure of their genome
Genome

In classical genetics, the genome of a diploid organism including eukarya refers to a full set of chromosomes or genes in a gamete; thereby, a regular somatic cell contains two full sets of genomes....
s. Modification of histone
Histone

In biology, histones are the chief protein components of chromatin. They act as spools around which DNA winds, and they play a role in gene regulation....
s and associated induction of heterochromatin
Heterochromatin

Heterochromatin is a tightly packed form of DNA. Its major characteristic is that transcription is limited. As such, it is a means to control gene expression, through regulation of the transcription initiation....
 formation serves to downregulate genes pre-transcriptionally
Transcription (genetics)

Transcription is the synthesis of RNA under the direction of DNA. RNA synthesis, or transcription, is the process of transcribing DNA nucleotide sequence information into RNA sequence information....
; this process is referred to as RNA-induced transcriptional silencing
RNA-induced transcriptional silencing

RNA-induced transcriptional silencing is a form of RNA interference by which short RNA molecules - such as small interfering RNA - trigger the downregulation of transcription of a particular gene or genome region....
 (RITS), and is carried out by a complex of proteins called the RITS complex. In fission yeast this complex contains argonaute
Argonaute

For the French ships, see French ship ArgonauteArgonaute proteins are the catalytic components of the RNA-induced silencing complex , the protein complex responsible for the gene silencing phenomenon known as RNA interference ....
, a chromodomain
Chromodomain

A chromodomain a is protein structural domain of about 40-50 amino acid residues commonly found in proteins associated with the remodeling and manipulation of chromatin....
 protein Chp1, and a protein called Tas3 of unknown function. As a consequence, the induction and spread of heterochromatic regions requires the argonaute and RdRP proteins. Indeed, deletion of these genes in the fission yeast S. pombe
Schizosaccharomyces pombe

Schizosaccharomyces pombe, also called "fission yeast", is a species of yeast. It is used as a model organism in molecular biology and cell biology....
 disrupts histone methylation
Histone methylation

Histone methylation is the modification of certain amino acids in a histone protein by the addition of one, two, or three methyl groups....
 and centromere
Centromere

A centromere is a region of DNA typically found near the middle of a chromosome where two sister chromatids come in contact. It is involved in cell division as the point of mitotic spindle....
 formation, causing slow or stalled anaphase
Anaphase

Anaphase, is from the ancient Greek ??? and f?s?? , is the stage of mitosis when chromosomes separate in a eukaryote cell . Each chromatid moves to opposite poles of the cell, the opposite ends of the mitotic spindle, near the microtubule organizing centers....
 during cell division
Cell division

Cell division is a process by which a cell , called the parent cell, divides into two or more cells, called daughter cells. Cell division is usually a small segment of a larger cell cycle....
. In some cases, similar processes associated with histone modification have been observed to transcriptionally upregulate genes.

The mechanism by which the RITS complex induces heterochromatin formation and organization is not well understood, and most studies have focused on the mating-type region
Mating-type region

The mating-type region is a specialized region in the genomes of some yeast and other fungi, usually organized into heterochromatin and possessing unique histone methylation patterns....
 in fission yeast, which may not be representative of activities in other genomic regions or organisms. In maintenance of existing heterochromatin regions, RITS forms a complex with siRNAs complementary
Complementarity (molecular biology)

In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA and RNA as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalent bond connected via two or three hydrogen bonds....
 to the local genes and stably binds local methylated histones, acting co-transcriptionally to degrade any nascent pre-mRNA transcripts that are initiated by RNA polymerase
RNA polymerase

RNA polymerase is an enzyme that produces RNA. In cell s, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called Transcription ....
. The formation of such a heterochromatin region, though not its maintenance, is dicer-dependent, presumably because dicer is required to generate the initial complement of siRNAs that target subsequent transcripts. Heterochromatin maintenance has been suggested to function as a self-reinforcing feedback loop, as new siRNAs are formed from the occasional nascent transcripts by RdRP for incorporation into local RITS complexes. The relevance of observations from fission yeast mating-type regions and centromeres to mammal
Mammal

Mammals are a class of vertebrate animals whose name is derived from their distinctive feature, mammary glands, with which they feed their young....
s is not clear, as heterochromatin maintenance in mammalian cells may be independent of the components of the RNAi pathway.

Crosstalk with RNA editing

The type of RNA editing
RNA editing

The term RNA editing describes those molecular processes in which the information content in an RNA molecule is altered through a chemical change in the base makeup....
 that is most prevalent in higher eukaryotes converts adenosine
Adenosine

Adenosine is a nucleoside composed of a molecule of adenine attached to a ribose sugar molecule moiety via a ?-N9-glycosidic bond....
 nucleotides into inosine
Inosine

Inosine is a nucleoside that is formed when hypoxanthine is attached to a ribose ring via a ?-N9-glycosidic bond.Inosine is commonly found in tRNAs and is essential for proper translation of the genetic code in wobble base pairs....
 in dsRNAs via the enzyme adenosine deaminase
Adenosine deaminase

Adenosine deaminase is an enzyme involved in Purine#Metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues....
 (ADAR). It was originally proposed in 2000 that the RNAi and A?I RNA editing pathways might compete for a common dsRNA substrate. Indeed, some pre-miRNAs do undergo A?I RNA editing, and this mechanism may regulate the processing and expression of mature miRNAs. Furthermore, at least one mammalian ADAR can sequester siRNAs from RNAi pathway components. Further support for this model comes from studies on ADAR-null C. elegans strains indicating that A?I RNA editing may counteract RNAi silencing of endogenous genes and transgenes.

Variation among organisms

Organisms vary in their ability to take up foreign dsRNA and use it in the RNAi pathway. The effects of RNA interference can be both systemic and heritable in plants and C. elegans, although not in Drosophila
Drosophila

Drosophila is a genus of small fly, belonging to the family Drosophilidae, whose members are often called "fruit flies" or more appropriately pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many species to linger around overripe or rotting fruit....
 or mammal
Mammal

Mammals are a class of vertebrate animals whose name is derived from their distinctive feature, mammary glands, with which they feed their young....
s. In plants, RNAi is thought to propagate by the transfer of siRNAs between cells through plasmodesmata
Plasmodesmata

Plasmodesmata are microscopic channels which traverse the cell wall of plant cells and enable transport and communication between them. Plants having plasmodesmata include the highest derived charophyceans, Charales and Coleochaetales, as well as all embryophytes, better known as land plants....
 (channels in the cell walls that enable communication and transport). The heritability comes from methylation
DNA methylation

DNA methylation is a type of chemical modification of DNA that can be inherited and subsequently removed without changing the original DNA sequence....
 of promoters targeted by RNAi; the new methylation pattern is copied in each new generation of the cell. A broad general distinction between plants and animals lies in the targeting of endogenously produced miRNAs; in plants, miRNAs are usually perfectly or nearly perfectly complementary to their target genes and induce direct mRNA cleavage by RISC, while animals' miRNAs tend to be more divergent in sequence and induce translational repression. This translational effect may be produced by inhibiting the interactions of translation initiation factor
Eukaryotic initiation factor

Eukaryotic initiation factors are proteins used in eukaryotic translation. There exist many more eukaryotic initiation factors than prokaryotic initiation factors due to greater biological complexity....
s with the messenger RNA's polyadenine tail
Polyadenylation

Polyadenylation is the addition of a poly tail, a stretch of RNA where all the nucleobase are adenines, onto an RNA molecule. In eukaryotes, polyadenylation is part of the process that produces mature messenger RNA for translation ....
.

Some eukaryotic protozoa such as Leishmania major
Leishmania major

Leishmania major is a species of Leishmania.It is associated with Zoonosis cutaneous leishmaniasis.The genome has been sequenced....
 and Trypanosoma cruzi
Trypanosoma cruzi

Trypanosoma cruzi is a species of parasite euglenoid trypanosomes. The species causes the trypanosomiasis diseases in humans and animals in United States....
 lack the RNAi pathway entirely. Most or all of the components are also missing in some fungi, most notably the model organism
Model organism

A model organism is a species that is extensively studied to understand particular biology phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms....
 Saccharomyces cerevisiae
Saccharomyces cerevisiae

Saccharomyces cerevisiae is a species of budding yeast. It is perhaps the most useful yeast owing to its use since ancient times in baking and brewing....
. That certain ascomycetes and basidiomycetes are missing RNA interference pathways indicates that proteins required for RNA silencing have been lost independently from many fungal lineages
Lineage (evolution)

An evolutionary lineage is a sequence of species, that form a line of descent, each new species the direct result of speciation from an immediate ancestral species....
, possibly due to the evolution of a novel pathway with similar function, or to the lack of selective advantage in certain niche
Ecological niche

In ecology, a niche is a term describing the relational position of a species or population in its ecosystem to each other; e.g. a dolphin will be in another ecological niche to one that travels in a different school.....
s.

Related prokaryotic systems

Gene expression in prokaryotes is influenced by an RNA-based system similar in some respects to RNAi. Here, RNA-encoding genes control mRNA abundance or translation by producing a complementary RNA that binds to an mRNA by base pairing. However these regulatory RNAs are not generally considered to be analogous to miRNAs because the dicer enzyme is not involved. It has been suggested that CRISPR
CRISPR

CRISPR are direct repeats found in the DNA of many bacteria and archaea. These repeats range in size from 24 to 48 base pairs. They usually show some dyad symmetry but are not truly palindromic....
 systems in prokaryotes are analogous to eukaryotic RNA interference systems, although none of the protein components are orthologous
Homology (biology)

In evolutionary biology, homology refers to any similarity between characteristics that is due to their common descent. The word homologous derives from the ancient Greek ??????e??, 'to agree'....
.

Biological functions


Immunity

RNA interference is a vital part of the immune response to virus
Virus

A virus is a Optical microscope#Limitations of light microscopes infectious agent that is unable to grow or reproduce outside a host cell . Viruses infect all cellular life....
es and other foreign genetic material
Gênes

G?nes is the name of a d?partement in France of the First French Empire in present Italy. It was named after the city Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa....
, especially in plants where it may also prevent self-propagation by transposon
Transposon

Transposons are sequences of DNA that can move around to different positions within the genome of a single cell , a process called transposition....
s. Plants such as Arabidopsis thaliana
Arabidopsis thaliana

Arabidopsis thaliana , is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, Arabidopsis is popular as a model organism in plant biology and genetics....
 express multiple dicer homologs
Homology (biology)

In evolutionary biology, homology refers to any similarity between characteristics that is due to their common descent. The word homologous derives from the ancient Greek ??????e??, 'to agree'....
 that are specialized to react differently when the plant is exposed to different types of viruses. Even before the RNAi pathway was fully understood, it was known that induced gene silencing in plants could spread throughout the plant in a systemic effect, and could be transferred from stock to scion plants via grafting
Grafting

Grafting is a method of asexual plant propagation widely used in agriculture and horticulture where the tissues of one plant are encouraged to fuse with those of another....
. This phenomenon has since been recognized as a feature of the plant adaptive immune system, and allows the entire plant to respond to a virus after an initial localized encounter. In response, many plant viruses have evolved elaborate mechanisms that suppress the RNAi response in plant cells. These include viral proteins that bind short double-stranded RNA fragments with single-stranded overhang ends, such as those produced by the action of dicer. Some plant genomes also express endogenous siRNAs in response to infection by specific types of bacteria
Bacteria

The Bacteria are a large group of unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals....
. These effects may be part of a generalized response to pathogens that downregulates any metabolic processes in the host that aid the infection process.

Although animals generally express fewer variants of the dicer enzyme than plants, RNAi in some animals has also been shown to produce an antiviral response. In both juvenile and adult Drosophila, RNA interference is important in antiviral innate immunity and is active against pathogens such as Drosophila X virus
Drosophila X virus

Drosophila X virus is a virus that can infect fruit fly of the genus Drosophila and is commonly used to study innate immunity in the common model organism Drosophila melanogaster....
. A similar role in immunity may operate in C. elegans, as argonaute proteins are upregulated in response to viruses and worms that overexpress components of the RNAi pathway are resistant to viral infection.

The role of RNA interference in mammalian innate immunity is poorly understood, and relatively little data is available. However, the existence of viruses that encode genes able to suppress the RNAi response in mammalian cells may be evidence in favour of an RNAi-dependent mammalian immune response. However, this hypothesis of RNAi-mediated immunity in mammals has been challenged as poorly substantiated. Alternative functions for RNAi in mammalian viruses also exist, such as miRNAs expressed by the herpes virus
Herpes virus

In colloquial use, herpes virus refers to the herpes simplex virus, particularly when transmitted sexually.In scientific use, herpesvirus refers to a virus of the family herpesviridae....
 that may act as heterochromatin
Heterochromatin

Heterochromatin is a tightly packed form of DNA. Its major characteristic is that transcription is limited. As such, it is a means to control gene expression, through regulation of the transcription initiation....
 organization triggers to mediate viral latency.

Downregulation of genes

Endogenously expressed miRNA
Mirna

Mirna may refer to:people* Mirna * Mirna Jukic, a bronze medal winner in swimming* Mirna Khayat, a Lebanese music video director* Mirna Macur, a Slovenian social researcher...
s, including both intron
Intron

Introns, derived from the term "intragenic regions" and also called intervening sequence , are DNA regions in a gene that are not translated into proteins....
ic and intergenic
Intergenic region

An Intergenic region is a stretch of DNA sequences located between Gene_cluster of genes that contain few or no genes. Occasionally some intergenic DNA acts to control genes close by, but most of it has no currently known function....
 miRNAs, are most important in translational repression
Translation (genetics)

Translation is the first stage of protein biosynthesis . Translation is the production of proteins by decoding mRNA produced in Transcription ....
 and in the regulation of development
Developmental biology

Developmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, cellular differentiation and "morphogenesis," which is the process that gives rise to biological tissues, organ s and anatomy....
, especially on the timing of morphogenesis
Morphogenesis

Morphogenesis , is the physical process that gives rise to the shape of an organism. It is one of three fundamental aspects of developmental biology along with the control of cell growth and cellular differentiation....
 and the maintenance of undifferentiated or incompletely differentiated cell types such as stem cell
Stem cell

Stem cells are Cell found in most, if not all, multi-cellular organisms. They are characterized by the ability to renew themselves through Mitosis cell division and Cellular differentiation into a diverse range of specialized cell types....
s. The role of endogenously expressed miRNA in downregulating gene expression
Gene expression

Gene expression is the process by which inheritable information from a gene, such as the DNA sequence, is made into a functional gene product, such as protein or RNA....
 was first described in C. elegans in 1993. In plants this function was discovered when the "JAW microRNA" of Arabidopsis
Arabidopsis thaliana

Arabidopsis thaliana , is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, Arabidopsis is popular as a model organism in plant biology and genetics....
 was shown to be involved in the regulation of several genes that control plant shape. In plants, the majority of genes regulated by miRNAs are transcription factor
Transcription factor

In the field of molecular biology, a transcription factor is a protein that binds to specific DNA sequence and thereby controls the transfer of genetic information from DNA to RNA....
s; thus miRNA activity is particularly wide-ranging and regulates entire gene networks during development by modulating the expression of key regulatory genes, including transcription factors as well as F-box protein
F-box protein

F-box proteins are proteins containing at least one F-box motif, a protein structural motif of about 50 amino acids that mediates protein-protein interactions....
s. In many organisms, including humans, miRNAs have also been linked to the formation of tumor
Tumor

A tumor or tumour is the name for a swelling or lesion formed by an abnormal growth of cells . Tumor is not synonymous with cancer. A tumor can be Benign neoplasm, Carcinoma in situ or malignant, whereas cancer is by definition malignant....
s and dysregulation of the cell cycle
Cell cycle

The cell cycle, or cell-division cycle, is the series of events that take place in a cell leading to its division and duplication . In cells without a nucleus , the cell cycle occurs via a process termed binary fission....
. Here, miRNAs can function as both oncogene
Oncogene

An oncogene is a gene that, when mutated or expressed at high levels, helps turn a normal cell into a cancer cell.Many cells normally undergo a programmed form of death ....
s and tumor suppressors.

Upregulation of genes

RNA sequences (siRNA and miRNA) that are complementary to parts of a promoter can increase gene transcription, a phenomenon dubbed RNA activation
RNAa

Small double-stranded RNA has been found to silence gene expression by an evolutionally conserved mechanism known as RNA interference or RNAi. Such dsRNAs are called small interfering RNAs or siRNA....
. Part of the mechanism for how these RNA upregulate genes is known: dicer
Dicer

Dicer is an endoribonuclease in the RNase III family that cleaves dsRNA and pre-microRNA into short double-stranded RNA fragments called small interfering RNA about 20-25 nucleotides long, usually with a two-base overhang on the 3' end....
 and argonaute
Argonaute

For the French ships, see French ship ArgonauteArgonaute proteins are the catalytic components of the RNA-induced silencing complex , the protein complex responsible for the gene silencing phenomenon known as RNA interference ....
 are involved, and there is histone demethylation
Histone methylation

Histone methylation is the modification of certain amino acids in a histone protein by the addition of one, two, or three methyl groups....
.

Evolution

Based on parsimony-based
Computational phylogenetics

Computational phylogenetics is the application of computational algorithms, methods and programs to Phylogenetics analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa....
 phylogenetic analysis, the most recent common ancestor
Most recent common ancestor

In genetics, the most recent common ancestor of any set of organisms is the most recent individual from which all organisms in the group are directly Common descent....
 of all eukaryote
Eukaryote

Animals, plants, fungus, and protists are eukaryotes , organisms whose Cell are organized into complex structures enclosed within Cell membrane....
s most likely already possessed an early RNA interference pathway; the absence of the pathway in certain eukaryotes is thought to be a derived characteristic. This ancestral RNAi system probably contained at least one dicer
Dicer

Dicer is an endoribonuclease in the RNase III family that cleaves dsRNA and pre-microRNA into short double-stranded RNA fragments called small interfering RNA about 20-25 nucleotides long, usually with a two-base overhang on the 3' end....
-like protein, one argonaute
Argonaute

For the French ships, see French ship ArgonauteArgonaute proteins are the catalytic components of the RNA-induced silencing complex , the protein complex responsible for the gene silencing phenomenon known as RNA interference ....
, one PIWI protein, and an RNA-dependent RNA polymerase
RNA-dependent RNA polymerase

RNA-dependent RNA polymerase , or RNA replicase, is an enzyme that catalyzes the Self-replication of RNA from an RNA template. This is in contrast to a typical RNA polymerase, which catalyzes the transcription_ of RNA from a DNA template....
 that may have also played other cellular roles. A large-scale comparative genomics
Comparative genomics

Comparative genomics is the study of the relationship of genome structure and function across different biological species or Strain . Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary processes that act on genomes....
 study likewise indicates that the eukaryotic crown group
Crown group

A crown group is the smallest monophyletic group, or "clade", to contain the last common ancestor of all members, and all of that ancestor's descendants....
 already possessed these components, which may then have had closer functional associations with generalized RNA degradation systems such as the exosome
Exosome complex

The exosome complex is a multi-protein Protein complex, capable of degrading various types of RNAs. Exosome complexes can be found in both eukaryotic cells and archaea, while in bacteria a simpler complex called the degradosome carries out similar functions....
. This study also suggests that the RNA-binding argonaute protein family, which is shared among eukaryotes, most archaea, and at least some bacteria (such as Aquifex aeolicus
Aquifex aeolicus

Aquifex aeolicus is a rod-shaped bacterium with a length of 2 to 6 micrometres and a diameter of around half a micrometer. It is one of a handful of species in the Aquificae phylum, an unusual group of thermophilia bacteria that are thought to be some of the oldest species of bacteria....
), is homologous to and originally evolved from components of the translation initiation
Translation (genetics)

Translation is the first stage of protein biosynthesis . Translation is the production of proteins by decoding mRNA produced in Transcription ....
 system.

The ancestral function of the RNAi system is generally agreed to have been immune defense against exogenous genetic elements such as transposon
Transposon

Transposons are sequences of DNA that can move around to different positions within the genome of a single cell , a process called transposition....
s and viral
Virus

A virus is a Optical microscope#Limitations of light microscopes infectious agent that is unable to grow or reproduce outside a host cell . Viruses infect all cellular life....
 genomes. Related functions such as histone
Histone

In biology, histones are the chief protein components of chromatin. They act as spools around which DNA winds, and they play a role in gene regulation....
 modification may have already been present in the ancestor of modern eukaryotes, although other functions such as regulation of development by miRNA are thought to have evolved later.

RNA interference genes, as components of the antiviral innate immune system in many eukaryotes, are involved in an evolutionary arms race
Evolutionary arms race

In evolutionary biology, an evolutionary arms race is an evolutionary struggle between competing sets of co-evolution genes that develop adaptation s and counter-adaptations against each other, resembling an arms race....
 with viral genes. Some viruses have evolved mechanisms for suppressing the RNAi response in their host cells, an effect that has been noted particularly for plant viruses. Studies of evolutionary rates in Drosophila have shown that genes in the RNAi pathway are subject to strong directional selection
Directional selection

In population genetics, directional selection occurs when natural selection favors a single phenotype and therefore allele frequency continuously shifts in one direction....
 and are among the fastest-evolving
Evolution

In biology, evolution is change in the heritability trait of a population of organisms from one generation to the next. These changes are caused by a combination of three main processes: variation, reproduction, and selection....
 genes in the Drosophila genome
Genome

In classical genetics, the genome of a diploid organism including eukarya refers to a full set of chromosomes or genes in a gamete; thereby, a regular somatic cell contains two full sets of genomes....
.

Technological applications

Drosophila Melanogaster   Side (aka)

Gene knockdown

The RNA interference pathway is often exploited in experimental biology to study the function of genes in cell culture
Cell culture

Cell culture is the process by which prokaryote or eukaryote cells are grown under controlled conditions. In practice the term "cell culture" has come to refer to the culturing of cells derived from multicellular eukaryotes, especially animal cells....
 and in vivo in model organism
Model organism

A model organism is a species that is extensively studied to understand particular biology phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms....
s. Double-stranded RNA is synthesized with a sequence complementary to a gene of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway. Using this mechanism, researchers can cause a drastic decrease in the expression of a targeted gene. Studying the effects of this decrease can show the physiological role of the gene product. Since RNAi may not totally abolish expression of the gene, this technique is sometimes referred as a "knockdown
Gene knockdown

Gene knockdown refers to techniques by which the gene expression of one or more of an organism's genes is reduced, either through genetic engineering or by treatment with a reagent such as a short DNA or RNA oligonucleotide with a sequence complementary to either an mRNA transcript or a gene....
", to distinguish it from "knockout
Gene knockout

A gene knockout is a genetics technique in which an organism is genetic engineering to carry genes that have been made inoperative . This is done for research purposes....
" procedures in which expression of a gene is entirely eliminated.

Extensive efforts in computational biology
Computational biology

Computational biology is an interdisciplinary field that applies the techniques of computer science, applied mathematics and statistics to address biology problems....
 have been directed toward the design of successful dsRNA reagents that maximize gene knockdown but minimize "off-target" effects. Off-target effects arise when an introduced RNA has a base sequence that can pair with and thus reduce the expression of multiple genes at a time. Such problems occur more frequently when the dsRNA contains repetitive sequences. It has been estimated from studying the genomes of H. sapiens, C. elegans, and S. pombe that about 10% of possible siRNAs will have substantial off-target effects. A multitude of software tools have been developed implementing algorithm
Algorithm

In mathematics, computing, linguistics and related subjects, an algorithm is a sequence of finite instructions, often used for calculation and data processing....
s for the design of general, mammal-specific, and virus-specific siRNAs that are automatically checked for possible cross-reactivity.

Depending on the organism and experimental system, the exogenous RNA may be a long strand designed to be cleaved by dicer, or short RNAs designed to serve as siRNA substrates. In most mammal
Mammal

Mammals are a class of vertebrate animals whose name is derived from their distinctive feature, mammary glands, with which they feed their young....
ian cells, shorter RNAs are used because long double-stranded RNA molecules induce the mammalian interferon
Interferon

Interferons are natural proteins produced by the cells of the immune system of most vertebrates in response to challenges by foreign agents such as viruses, parasites and tumor cells....
 response, a form of innate immunity that reacts nonspecifically to foreign genetic material. Mouse oocyte
Oocyte

An oocyte, ovocyte, or rarely ocyte, is a female gametocyte or germ cell involved in biological reproduction. In other words, it is an immature ovum, or ovum cell....
s and cells from early mouse embryo
Embryo

An embryo is a multicellular organism ploidy eukaryote in its earliest stage of development, from the time of first cell division until birth, Egg , or germination....
s lack this reaction to exogenous dsRNA and are therefore a common model system for studying gene-knockdown effects in mammals. Specialized laboratory techniques have also been developed to improve the utility of RNAi in mammalian systems by avoiding the direct introduction of siRNA, for example, by stable transfection
Transfection

Transfection is the process of introducing nucleic acids into cells by non-viral methods . The term transformation is preferred to describe non-viral DNA transfer in bacteria and non-animal eukaryotic cells such as fungus, algae and plants....
 with a plasmid
Plasmid

File:plasmid .svgA plasmid is an extra-chromosomal DNA molecule separate from the chromosome which is capable of replicating independently of the chromosomal DNA....
 encoding the appropriate sequence from which siRNAs can be transcribed, or by more elaborate lentiviral
Lentivirus

Lentivirus is a genus of slow viruses of the Retroviridae family , characterized by a long incubation period. Lentiviruses can deliver a significant amount of Genetics information into the DNA of the Host , so they are one of the most efficient methods of a Vector ....
 vector systems allowing the inducible activation or deactivation of transcription, known as conditional RNAi.

Functional genomics

Most functional genomics
Functional genomics

Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects to describe gene functions and interactions....
 applications of RNAi in animals have used C. elegans and Drosophila, as these are the common model organism
Model organism

A model organism is a species that is extensively studied to understand particular biology phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms....
s in which RNAi is most effective. C. elegans is particularly useful for RNAi research for two reasons: firstly, the effects of the gene silencing are generally heritable, and secondly because delivery of the dsRNA is extremely simple. Through a mechanism whose details are poorly understood, bacteria such as E. coli
Escherichia coli

'Escherichia coli' , is a Gram negative bacterium that is commonly found in the lower gastrointestinal tract of warm-blooded animals. Most E....
 that carry the desired dsRNA can be fed to the worms and will transfer their RNA payload to the worm via the intestinal tract. This "delivery by feeding" is just as effective at inducing gene silencing as more costly and time-consuming delivery methods, such as soaking the worms in dsRNA solution and injecting dsRNA into the gonads. Although delivery is more difficult in most other organisms, efforts are also underway to undertake large-scale genomic screening applications in cell culture with mammalian cells.

Approaches to the design of genome-wide RNAi libraries can require more sophistication than the design of a single siRNA for a defined set of experimental conditions. Artificial neural network
Artificial neural network

An artificial neural network , often just called a "neural network" , is a mathematical model or computational model based on biological neural networks....
s are frequently used to design siRNA libraries and to predict their likely efficiency at gene knockdown. Mass genomic screening is widely seen as a promising method for genome annotation and has triggered the development of high-throughput screening methods based on microarray
Microarray

Different kinds of biological assays are called microarrays:*DNA microarrays, such as cDNA microarrays and oligonucleotide microarrays*MMChips, for surveillance of microRNA populations...
s. However, the utility of these screens and the ability of techniques developed on model organisms to generalize to even closely-related species has been questioned, for example from C. elegans to related parasitic nematodes.

Functional genomics using RNAi is a particularly attractive technique for genomic mapping and annotation in plants because many plants are polyploid, which presents substantial challenges for more traditional genetic engineering methods. For example, RNAi has been successfully used for functional genomics studies in bread wheat (which is hexaploid) as well as more common plant model systems Arabidopsis
Arabidopsis thaliana

Arabidopsis thaliana , is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, Arabidopsis is popular as a model organism in plant biology and genetics....
 and maize
Maize

Maize , known as corn in some countries, is a cereal domesticated in Mesoamerica and subsequently spread throughout the American continents....
.

Medicine

It may be possible to exploit RNA interference in therapy. Although it is difficult to introduce long dsRNA strands into mammalian cells due to the interferon
Interferon

Interferons are natural proteins produced by the cells of the immune system of most vertebrates in response to challenges by foreign agents such as viruses, parasites and tumor cells....
 response, the use of short interfering RNA
Sírna

S?rna S?eglach , son of Dian, son of Demal, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland....
 mimics has been more successful. Among the first applications to reach clinical trial
Clinical trial

In health care, clinical trials are conducted to allow safety and efficacy data to be collected for new drugs or devices. These trials can only take place once satisfactory information has been gathered on the quality of the product and its non-clinical safety, and Institutional review board approval is granted in the country where the trial...
s were in the treatment of macular degeneration
Macular degeneration

File:Human eye cross-sectional view grayscale.pngFile:Human eyesight two children and ball normal vision.jpgFile:Human eyesight two children and ball with age-related macular degeneration.jpg...
 and respiratory syncytial virus, RNAi has also been shown to be effective in the reversal of induced liver failure in mouse models.

Other proposed clinical uses center on antiviral therapies, including topical microbicide treatments that use RNAi to treat infection (at Harvard University Medical School; in mice, so far) by herpes simplex virus
Herpes simplex virus

Herpes simplex virus 1 and 2 are two species of the herpes virus family, Herpesviridae, which cause infections in humans. Eight members of herpes virus infect humans to cause a variety of illnesses including cold sores, chickenpox or varicella, shingles or herpes zoster , cytomegalovirus , and various cancers, and can cause brain...
 type 2 and the inhibition of viral gene expression in cancerous cells, knockdown of host receptors and coreceptors for HIV
HIV

Human immunodeficiency virus is a lentivirus that can lead to AIDS , a condition in humans in which the immune system begins to fail, leading to life-threatening opportunistic infections....
, the silencing of hepatitis A
Hepatitis A

Hepatitis A, , is an Acute infectious disease of the liver caused by Hepatitis A virus, which is most commonly transmitted by the fecal-oral route via contaminated food or drinking water....
 and hepatitis B genes, silencing of influenza
Influenza

Influenza, commonly known as the flu, is an infectious disease that affects birds and mammals caused by RNA viruses of the biological family Orthomyxoviridae ....
 gene expression, and inhibition of measles
Measles

Measles is a infection of the respiratory system caused by a virus, specifically a paramyxovirus of the genus Morbillivirus. Morbilliviruses, like other paramyxoviruses, are enveloped, single-stranded, negative-sense RNA viruses....
 viral replication. Potential treatments for neurodegenerative disease
Neurodegenerative disease

Neurodegenerative disease is a condition in which cells of the brain and spinal cord are lost. The brain and spinal cord are composed of neurons that do different functions such as controlling movements, processing sensory information, and making decisions....
s have also been proposed, with particular attention being paid to the polyglutamine diseases such as Huntington's disease
Huntington's disease

Huntington's disease, also called Huntington's Chorea , chorea major, or HD, is a genetics Neurodegenerative disease characterized after onset by uncoordinated, jerky body movements and a decline in some mental abilities....
. RNA interference is also often seen as a promising way to treat cancer
Cancer

Cancer is a class of diseases in which a group of cell display uncontrolled growth , invasion , and sometimes metastasis . These three malignant properties of cancers differentiate them from benign tumors, which are self-limited, do not invade or metastasize....
 by silencing genes differentially upregulated in tumor
Tumor

A tumor or tumour is the name for a swelling or lesion formed by an abnormal growth of cells . Tumor is not synonymous with cancer. A tumor can be Benign neoplasm, Carcinoma in situ or malignant, whereas cancer is by definition malignant....
 cells or genes involved in cell division
Cell division

Cell division is a process by which a cell , called the parent cell, divides into two or more cells, called daughter cells. Cell division is usually a small segment of a larger cell cycle....
. A key area of research in the use of RNAi for clinical applications is the development of a safe delivery method, which to date has involved mainly viral vector
Viral vector

Viral vectors are a tool commonly used by molecular biologists to deliver genetic material into cell s. This process can be performed inside a living organism or in cell culture ....
 systems similar to those suggested for gene therapy
Gene therapy

Gene therapy is the insertion of genes into an individual's cell and Biological tissues to treat a disease, such as a hereditary disease in which a deleterious mutant allele is replaced with a functional one....
.

Despite the proliferation of promising cell culture studies for RNAi-based drugs, some concern has been raised regarding the safety of RNA interference, especially the potential for "off-target" effects in which a gene with a coincidentally similar sequence to the targeted gene is also repressed. A computational genomics study estimated that the error rate of off-target interactions is about 10%. One major study of liver disease in mice led to high death rates in the experimental animals, suggested by researchers to be the result of "oversaturation" of the dsRNA pathway, due to the use of shRNAs that have to be processed in the nucleus and exported to the cytoplasm using an active mechanism. All these are considerations that are under active investigation, to reduce their impact in the potential therapeutic applications for RNAi.

Biotechnology

RNA interference has been used for applications in biotechnology
Biotechnology

Biotechnology is technology based on biology, especially when used in agriculture, food science, and medicine. United Nations Convention on Biological Diversity defines biotechnology as:...
, particularly in the engineering of food plants that produce lower levels of natural plant toxins. Such techniques take advantage of the stable and heritable RNAi phenotype in plant stocks. For example, cotton
Cotton

Cotton is a soft, staple fiber that grows in a form known as a boll around the seeds of the cotton plant a shrub native to tropical and subtropical regions around the world, including the Americas, India and Africa....
 seeds are rich in dietary protein
Protein in nutrition

File:Protein shake.jpgProteins are broken down in the stomach during digestion by enzymes known as proteases into smaller polypeptides to provide amino acids for the organism, including the essential amino acids that the organism cannot biosynthesis itself....
 but naturally contain the toxic terpenoid
Terpenoid

The terpenoids , sometimes called isoprenoids, are a large and diverse class of naturally-occurring organic compound similar to terpenes, derived from five-carbon isoprene units assembled and modified in thousands of ways....
 product gossypol
Gossypol

Gossypol C30H30O8 is a polyphenol derived from the cotton plant . Gossypol is a polyphenolic aldehyde that permeates cells and acts as an inhibitor for several dehydrogenase enzymes....
, making them unsuitable for human consumption. RNAi has been used to produce cotton stocks whose seeds contain reduced levels of delta-cadinene synthase
Delta-cadinene synthase

Delta-cadinene synthase, a sesquiterpene cyclase, is an enzyme expressed in plants that catalysis a cyclization reaction in terpenoid biosynthesis....
, a key enzyme in gossypol production, without affecting the enzyme's production in other parts of the plant, where gossypol is important in preventing damage from plant pests. Similar efforts have been directed toward the reduction of the cyanogenic
Cyanide

A cyanide is any chemical compound that contains the nitrile , which consists of a carbon atom chemical bond to a nitrogen atom. Inorganic cyanides are hydrogen cyanide salts in which cyanide is generally the anion CN-....
 natural product linamarin
Linamarin

Linamarin is a cyanide glucoside found in the leaves and roots of plants such as cassava, lima beans, and flax. Upon exposure to enzymes and gut flora in the human intestine, linamarin and its methylated relative lotaustralin can decompose to the toxic chemical hydrogen cyanide; hence food uses of plants that contain significant quantities of...
 in cassava
Cassava

The cassava, cassadaIn page 25, Darwin says "Mandioca or cassada is likewise cultivated in great quantity."See it also in ,yuca, 'manioc, 'mogo...
 plants.

Although no plant products that use RNAi-based genetic engineering
Genetic engineering

Engineering There are a number of ways through which genetic engineering is accomplished. Essentially, the process has five main steps# Isolation of the genes of interest...
 have yet passed the experimental stage, development efforts have successfully reduced the levels of allergen
Allergen

An allergen is a parasite antigen capable of stimulating a type-I hypersensitivity reaction in atopy individuals.Most humans mount significant Immunoglobulin E responses only as a defense against parasitic infections....
s in tomato
Tomato

The Tomato is an herbaceous, usually sprawling plant in the Solanaceae or nightshade family, as are its close cousins Nicotiana, potatoes, aubergine , chilli peppers, and the poisonous Atropa belladonna....
 plants and decreased the precursors of likely carcinogen
Carcinogen

The term carcinogen refers to any substance, radionuclide or radiation that is an agent directly involved in the promotion of cancer or in the increase of its propagation....
s in tobacco
Tobacco

Tobacco is an agricultural product processed from the fresh leaves of plants in the genus Nicotiana. It can be consumed, used as an organic pesticide, and in the form of nicotine tartrate it is used in some medicines....
 plants. Other plant traits that have been engineered in the laboratory include the production of non-narcotic
Narcotic

The term narcotic is believed to have been coined by the Greek physician Galen to refer to agents that benumb or deaden, causing loss of feeling or paralysis....
 natural products by the opium poppy
Opium poppy

The Opium Poppy, Papaver somniferum, is the type of poppy from which opium and many refined opiates, including morphine, thebaine, codeine, papaverine, and noscapine, are extracted....
, resistance to common plant viruses, and fortification of plants such as tomatoes with dietary antioxidant
Antioxidant

An antioxidant is a molecule capable of slowing or preventing the Redox of other molecules. Oxidation is a chemical reaction that transfers electrons from a substance to an oxidizing agent....
s. Previous commercial products, including the Flavr Savr tomato and two cultivar
Cultivar

A cultivar is a cultivated plant that has been selected and given a unique name because of its decorative or useful characteristics; it is usually distinct from similar plants and when Plant propagation it retains those characteristics....
s of ringspot
Papaya ringspot virus

Papaya ringspot virus is a plant pathogenic virus in the genus Potyvirus and the virus family Potyviridae.The virus is an non-enveloped, flexous rod-shaped particle that is between 760-800 nm long and 12 nm in diameter....
-resistant papaya
Papaya

The papaya , is the fruit of the plant Carica papaya, in the genus Carica. It is native to the tropics of the Americas, and was cultivated in Mexico several centuries before the emergence of the Mesoamerica....
, were originally developed using antisense technology but likely exploited the RNAi pathway.

History and discovery

The discovery of RNAi was preceded first by observations of transcriptional inhibition by antisense RNA expressed in transgenic plants, and more directly by reports of unexpected outcomes in experiments performed by plant scientists in the U.S.
United States

The United States of America is a Federal government constitutional republic comprising U.S. state and a federal district. The country is situated mostly in central North America, where its Contiguous United States and Washington, D.C., the Capital districts and territories, lie between the Pacific Ocean and Atlantic Oceans, Borders of the U...
 and The Netherlands in the early 1990s. In an attempt to alter flower
Flower

A flower, sometimes known as a bloom or blossom, is the reproduction structure found in flowering plants . The biological function of a flower is to mediate the union of male sperm with female ovum in order to produce seeds....
 colors in petunia
Petunia

Petunia is a trumpet shaped, widely-cultivated genus of flowering plants of South American origin, in the family Solanaceae. The popular flower got its name from French, which took the word petun 'tobacco' from a Tupi-Guarani language....
s, researchers introduced additional copies of a gene encoding chalcone synthase
Chalcone synthase

Chalcone synthases are a family of polyketide synthase enzymes associated with the production of chalcones, a class of organic compounds found mainly in plants as natural defense mechanisms and as synthetic intermediates, for example in the production of pigments....
, a key enzyme for flower pigmentation into petunia plants of normally pink or violet flower color. The overexpressed gene was expected to result in darker flowers, but instead produced less pigmented, fully or partially white flowers, indicating that the activity of chalcone synthase had been substantially decreased; in fact, both the endogenous genes and the transgenes were downregulated in the white flowers. Soon after, a related event termed quelling was noted in the fungus
Fungus

A fungus is a Eukaryote organism that is a member of the Kingdom Fungi . The fungi are a monophyletic group, also called the Eumycota , that is phylogeny distinct from the morphologically similar slime molds and water molds ....
 Neurospora crassa
Neurospora crassa

Neurospora crassa is a type of red bread mold of the phylum Ascomycota. The genus name, meaning "nerve spore" refers to the characteristic striations on the spores....
, although it was not immediately recognized as related. Further investigation of the phenomenon in plants indicated that the downregulation was due to post-transcriptional inhibition of gene expression via an increased rate of mRNA degradation. This phenomenon was called co-suppression of gene expression, but the molecular mechanism remained unknown.

Not long after, plant virologists working on improving plant resistance to viral diseases observed a similar unexpected phenomenon. While it was known that plants expressing virus-specific proteins showed enhanced tolerance or resistance to viral infection, it was not expected that plants carrying only short, non-coding regions of viral RNA sequences would show similar levels of protection. Researchers believed that viral RNA produced by transgenes could also inhibit viral replication. The reverse experiment, in which short sequences of plant genes were introduced into viruses, showed that the targeted gene was suppressed in an infected plant. This phenomenon was labeled "virus-induced gene silencing" (VIGS), and the set of such phenomena were collectively called post transcriptional gene silencing
Post transcriptional gene silencing

Post transcriptional gene silencing is a mechanism for sequence-specific RNA degradation in plants similar to RNA interference in other organisms....
.

After these initial observations in plants, many laboratories around the world searched for the occurrence of this phenomenon in other organisms. Craig C. Mello and Andrew Fire
Andrew Fire

Andrew Zachary Fire is an United States of America biologist and Professor of pathology and of genetics at the Stanford University School of Medicine....
's 1998 Nature paper reported a potent gene silencing effect after injecting double stranded RNA into C. elegans. In investigating the regulation of muscle protein production, they observed that neither mRNA nor antisense RNA injections had an effect on protein production, but double-stranded RNA successfully silenced the targeted gene. As a result of this work, they coined the term RNAi. Fire and Mello's discovery was particularly notable because it represented the first identification of the causative agent for the phenomenon. Fire and Mello were awarded the Nobel Prize in Physiology or Medicine
Nobel Prize in Physiology or Medicine

The Nobel Prize in Physiology or Medicine is awarded once a year by the Swedish Karolinska Institutet. It is one of the five Nobel Prizes established by the will of Alfred Nobel in 1895, awarded for outstanding contributions in Nobel Prize in Physics, Nobel Prize in Chemistry, Nobel Prize in Literature, Nobel Peace Prize, and Physiology or Medic...
 in 2006 for their work.

External links

  • , from Cambridge University's The Naked Scientists
    The Naked Scientists

    The Naked Scientists is a one-hour audience-interactive science radio talk show, broadcast live by the BBC in the East of England, and internationally as a podcast....
  • , from Nature
    Nature (journal)

    Nature is a prominent scientific journal, first published on 4 November 1869. Although most scientific journals are now highly specialized, Nature is one of the few journals, along with other weekly journals such as Science and Proceedings of the National Academy of Sciences, that still publishes original research articles ac...
  • – A 15 minute video of the Nova
    NOVA (TV series)

    Nova is a popular science television series from the United States produced by WGBH-TV Boston. It can be seen on the Public Broadcasting Service in the United States, and in more than 100 other countries....
     broadcast that aired on PBS, July 26, 2005* RNA interference (RNAi) experiments and bioinformatics in C. elegans for education. From the Dolan DNA Learning Center of Cold Spring Harbor Laboratory.
  • , from NY Times
    The New York Times

    The New York Times is an American daily newspaper published in New York City. The largest metropolitan newspaper in the United States, "The Gray Lady"?named for its staid appearance and style?is regarded as a national newspaper of record....
  • , a collection of free articles about RNAi as a therapeutic strategy.