Piwi-interacting RNA
Encyclopedia
Piwi-interacting RNA is the largest class of small non-coding RNA
molecules that is expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi
proteins. These piRNA complexes have been linked to both epigenetic and post-transcriptional gene silencing of retrotransposon
s and other genetic elements in germ line cells, particularly those in spermatogenesis
. They are distinct from microRNA (miRNA) in size (26–31 nt rather than 21–24 nt), lack of sequence conservation, and increased complexity.
It remains unclear how piRNAs are generated, but potential methods have been suggested, and it is certain their biogenesis pathway is distinct from miRNA and siRNA
, while rasiRNA
s are a piRNA subspecies.
piRNAs have been identified in both vertebrates and invertebrates, and although biogenesis
and modes of action do vary somewhat between species
, a number of features are conserved. piRNAs have no clear secondary structure
motifs, the length of a piRNA is, by definition, between 26 and 31 nucleotide
s, and the bias for a 5’ uridine
is common to piRNAs in both vertebrates and invertebrates. piRNAs in Caenorhabditis elegans
have a 5’ monophosphate and a 3’ modification that acts to block either the 2’ or 3’ oxygen, and this has also been confirmed to exist in Drosophila melanogaster
, zebrafish, mice
and rats
. This 3’ modification is a 2’-O-methylation; the reason for this modification is not clear, but it has been suggested to increase piRNA stability.
It is thought that there are many hundreds of thousands of different piRNA species found in mammals. Thus far, over 50,000 unique piRNA sequences have been discovered in mice and more than 13,000 in D. melanogaster.
; these clusters may contain as few as ten or up to many thousands of piRNAs and can vary in size from one to one hundred kb. While the clustering of piRNAs is highly conserved across species, the sequences are not. While D. melanogaster and vertebrate piRNAs have been located in areas lacking any protein coding genes
, piRNAs in C. elegans have been identified amidst protein coding genes.
In mammals, piRNAs are found both in testes and ovaries , although they only seem to be required in males . In invertebrates, piRNAs have been detected in both the male
and female
germline
s .
At the cellular level, piRNAs have been found within both nuclei
and cytoplasm
, suggesting that piRNA pathways may function in both of these areas and, therefore, may have multiple effects.
The biogenesis
of piRNAs is not yet fully understood, although possible mechanisms have been proposed. piRNAs show a significant strand bias, that is, they are derived from one strand of DNA
only, and this may indicate that they are the product of long single stranded precursor molecules. A primary processing pathway is suggested to be the only pathway used to produce pachytene piRNAs; in this mechanism, piRNA precusors are transcribe
d resulting in piRNAs with a tendency to target 5’ uridine
s. Also proposed is a ‘Ping Pong’ mechanism wherein primary piRNAs recognise their complementary targets and cause the recruitment of piwi
proteins. This results in the cleavage
of the transcript at a point ten nucleotide
s from the 5’ end of the primary piRNA, producing the secondary piRNA. These secondary piRNAs are targeted toward sequences that possess an adenine
at the tenth position. Since the piRNA involved in the ping pong cycle directs its attacks on transposon transcripts, the ping pong cycle acts only at the level of transcription
. One or both of these mechanisms may be acting in different species
; C. elegans
, for instance, does have piRNAs, but does not appear to use the ping pong mechanism at all.
A significant number of piRNAs identified in zebrafish and D.melanogaster
contain adenine at their tenth position, and this has been interpreted as possible evidence of a conserved
biosynthetic mechanism
across species. Ping-pong signatures have been identified in very primitive animals such as sponges and cnidarians, pointing to the existence of the ping-pong cycle already in the early branches of metazoans .
function over species
contributes to the difficulty in establishing the functionality of piRNAs. However, like other small RNAs, piRNAs are thought to be involved in gene silencing
, specifically the silencing of transposon
s. The majority of piRNAs are antisense to transposon sequences, suggesting that transposons are the piRNA target. In mammals it appears that the activity of piRNAs in transposon silencing is most important during the development of the embryo
, and in both C. elegans
and humans, piRNAs are necessary for spermatogenesis
.
RNA silencing
piRNA has a role in RNA silencing
via the formation of an RNA-induced silencing complex
(RISC). piRNAs interact with piwi
proteins that are part of a family of proteins called the Argonaute
s. These are active in the testes of mammals and are required for germ-cell and stem-cell development in invertebrate
s. Three piwi subfamily proteins - MIWI, MIWI2 and MILI - have been found to be essential for spermatogenesis in mice. piRNAs direct the piwi proteins to their transposon targets. A decrease or absence of PIWI protein expression
is correlated with an increased expression of transposons. Transposons have a high potential to cause deleterious effect on their host, and, in fact, mutations in piRNA pathways are found to reduce fertility
in D.melanogaster
. However, piRNA pathway mutations in mice do not demonstrate reduced fertility; this may indicate redundancies to the piRNA system. Further, it is thought that piRNA and endogenous
small interfering RNA
(endo-siRNA) may have comparable and even redundant functionality in transposon control in mammalian oocytes.
piRNAs appear to have an impact on particular methyltransferase
s that perform the methylation
s which are required to recognise and silence transposons, but this relationship is not well understood.
Epigenetic effects
piRNAs can be transmitted maternally, and based on research in D. melanogaster, piRNAs may be involved in maternally derived epigenetic effects. The activity of specific piRNAs in the epigenetic process also requires interactions between piwi proteins and HP1a, as well as other factors.
Recent discovery also show, the existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: x-ncRNA and its biological implication in Homo sapiens.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
molecules that is expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi
Piwi
The piwi class of genes was originally identified as encoding regulatory proteins responsible for maintaining incomplete differentiation in stem cells and maintaining the stability of cell division rates in germ line cells...
proteins. These piRNA complexes have been linked to both epigenetic and post-transcriptional gene silencing of retrotransposon
Retrotransposon
Retrotransposons are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon. They are particularly abundant in plants, where they are often a principal component of nuclear DNA...
s and other genetic elements in germ line cells, particularly those in spermatogenesis
Spermatogenesis
Spermatogenesis is the process by which male primary germ cells undergo division, and produce a number of cells termed spermatogonia, from which the primary spermatocytes are derived. Each primary spermatocyte divides into two secondary spermatocytes, and each secondary spermatocyte into two...
. They are distinct from microRNA (miRNA) in size (26–31 nt rather than 21–24 nt), lack of sequence conservation, and increased complexity.
It remains unclear how piRNAs are generated, but potential methods have been suggested, and it is certain their biogenesis pathway is distinct from miRNA and siRNA
Sírna
Sírna Sáeglach , son of Dian mac Demal, son of Demal mac Rothechtaid, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland...
, while rasiRNA
RasiRNA
Repeat associated small interfering RNA is a class of small RNA that is involved in the RNA interference pathway. RasiRNA are in fact Piwi-interacting RNAs , which are small RNA molecules that interact with Piwi proteins. Piwi proteins are a clade of the Argonaute family of proteins. In the...
s are a piRNA subspecies.
Characteristics
Biogenesis
Biogenesis is the law that living things come only from other living things, e.g. a spider lays eggs, which develop into spiders. It may also refer to biochemical processes of production in living organisms.-Spontaneous generation:...
and modes of action do vary somewhat between species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
, a number of features are conserved. piRNAs have no clear secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
motifs, the length of a piRNA is, by definition, between 26 and 31 nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s, and the bias for a 5’ uridine
Uridine
Uridine is a molecule that is formed when uracil is attached to a ribose ring via a β-N1-glycosidic bond.If uracil is attached to a deoxyribose ring, it is known as a deoxyuridine....
is common to piRNAs in both vertebrates and invertebrates. piRNAs in Caenorhabditis elegans
Caenorhabditis elegans
Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
have a 5’ monophosphate and a 3’ modification that acts to block either the 2’ or 3’ oxygen, and this has also been confirmed to exist in Drosophila melanogaster
Drosophila melanogaster
Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
, zebrafish, mice
MICE
-Fiction:*Mice , alien species in The Hitchhiker's Guide to the Galaxy*The Mice -Acronyms:* "Meetings, Incentives, Conferencing, Exhibitions", facilities terminology for events...
and rats
RATS
RATS may refer to:* RATS , Regression Analysis of Time Series, a statistical package* Rough Auditing Tool for Security, a computer program...
. This 3’ modification is a 2’-O-methylation; the reason for this modification is not clear, but it has been suggested to increase piRNA stability.
It is thought that there are many hundreds of thousands of different piRNA species found in mammals. Thus far, over 50,000 unique piRNA sequences have been discovered in mice and more than 13,000 in D. melanogaster.
Location
piRNAs are found in clusters throughout the genomeGenome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
; these clusters may contain as few as ten or up to many thousands of piRNAs and can vary in size from one to one hundred kb. While the clustering of piRNAs is highly conserved across species, the sequences are not. While D. melanogaster and vertebrate piRNAs have been located in areas lacking any protein coding genes
Gênes
Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...
, piRNAs in C. elegans have been identified amidst protein coding genes.
In mammals, piRNAs are found both in testes and ovaries , although they only seem to be required in males . In invertebrates, piRNAs have been detected in both the male
Male
Male refers to the biological sex of an organism, or part of an organism, which produces small mobile gametes, called spermatozoa. Each spermatozoon can fuse with a larger female gamete or ovum, in the process of fertilization...
and female
Female
Female is the sex of an organism, or a part of an organism, which produces non-mobile ova .- Defining characteristics :The ova are defined as the larger gametes in a heterogamous reproduction system, while the smaller, usually motile gamete, the spermatozoon, is produced by the male...
germline
Germline
In biology and genetics, the germline of a mature or developing individual is the line of germ cells that have genetic material that may be passed to a child.For example, gametes such as the sperm or the egg, are part of the germline...
s .
At the cellular level, piRNAs have been found within both nuclei
Cell nucleus
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...
and cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...
, suggesting that piRNA pathways may function in both of these areas and, therefore, may have multiple effects.
Biogenesis
Biogenesis
Biogenesis is the law that living things come only from other living things, e.g. a spider lays eggs, which develop into spiders. It may also refer to biochemical processes of production in living organisms.-Spontaneous generation:...
of piRNAs is not yet fully understood, although possible mechanisms have been proposed. piRNAs show a significant strand bias, that is, they are derived from one strand of DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
only, and this may indicate that they are the product of long single stranded precursor molecules. A primary processing pathway is suggested to be the only pathway used to produce pachytene piRNAs; in this mechanism, piRNA precusors are transcribe
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
d resulting in piRNAs with a tendency to target 5’ uridine
Uridine
Uridine is a molecule that is formed when uracil is attached to a ribose ring via a β-N1-glycosidic bond.If uracil is attached to a deoxyribose ring, it is known as a deoxyuridine....
s. Also proposed is a ‘Ping Pong’ mechanism wherein primary piRNAs recognise their complementary targets and cause the recruitment of piwi
Piwi
The piwi class of genes was originally identified as encoding regulatory proteins responsible for maintaining incomplete differentiation in stem cells and maintaining the stability of cell division rates in germ line cells...
proteins. This results in the cleavage
Bond cleavage
Bond cleavage, or scission, is the splitting of chemical bonds.If the two electrons in a cleaved covalent bond are divided between the products, the process is known as homolytic fission and free redicals are generated by homolytic cleavage the process is known as homolytic fission or homolysis...
of the transcript at a point ten nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s from the 5’ end of the primary piRNA, producing the secondary piRNA. These secondary piRNAs are targeted toward sequences that possess an adenine
Adenine
Adenine is a nucleobase with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate and the cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide , and protein synthesis, as a chemical component of DNA...
at the tenth position. Since the piRNA involved in the ping pong cycle directs its attacks on transposon transcripts, the ping pong cycle acts only at the level of transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
. One or both of these mechanisms may be acting in different species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
; C. elegans
Caenorhabditis elegans
Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
, for instance, does have piRNAs, but does not appear to use the ping pong mechanism at all.
A significant number of piRNAs identified in zebrafish and D.melanogaster
Drosophila melanogaster
Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
contain adenine at their tenth position, and this has been interpreted as possible evidence of a conserved
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...
biosynthetic mechanism
Mechanism (biology)
In biology --and in science in general-- a mechanism is a complex object or, more generally, a process that produces a regular phenomenon. For example, natural selection is one of the mechanisms of biological evolution, other being genetic drift, biased mutation, and gene flow; competition,...
across species. Ping-pong signatures have been identified in very primitive animals such as sponges and cnidarians, pointing to the existence of the ping-pong cycle already in the early branches of metazoans .
Function
The wide variation in piRNA sequences and piwiPiwi
The piwi class of genes was originally identified as encoding regulatory proteins responsible for maintaining incomplete differentiation in stem cells and maintaining the stability of cell division rates in germ line cells...
function over species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
contributes to the difficulty in establishing the functionality of piRNAs. However, like other small RNAs, piRNAs are thought to be involved in 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...
, specifically the silencing of transposon
Transposon
Transposable elements are sequences of DNA that can move or transpose themselves to new positions within the genome of a single cell. The mechanism of transposition can be either "copy and paste" or "cut and paste". Transposition can create phenotypically significant mutations and alter the cell's...
s. The majority of piRNAs are antisense to transposon sequences, suggesting that transposons are the piRNA target. In mammals it appears that the activity of piRNAs in transposon silencing is most important during the development of the embryo
Embryo
An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination...
, and in both C. elegans
Caenorhabditis elegans
Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
and humans, piRNAs are necessary for spermatogenesis
Spermatogenesis
Spermatogenesis is the process by which male primary germ cells undergo division, and produce a number of cells termed spermatogonia, from which the primary spermatocytes are derived. Each primary spermatocyte divides into two secondary spermatocytes, and each secondary spermatocyte into two...
.
RNA silencing
piRNA has a role in RNA silencing
RNA silencing
RNA silencing refers to a family of gene silencing effects by which the expression of one or more genes is downregulated or entirely suppressed by the introduction of an antisense RNA molecule...
via the formation of an RNA-induced silencing complex
RNA-induced silencing complex
RNA-Induced Silencing Complex, or RISC, is a multiprotein complex that incorporates one strand of a small interfering RNA or micro RNA . RISC uses the siRNA or miRNA as a template for recognizing complementary mRNA. When it finds a complementary strand, it activates RNase and cleaves the RNA...
(RISC). piRNAs interact with piwi
Piwi
The piwi class of genes was originally identified as encoding regulatory proteins responsible for maintaining incomplete differentiation in stem cells and maintaining the stability of cell division rates in germ line cells...
proteins that are part of a family of proteins called the Argonaute
Argonaute
Argonaute proteins are the catalytic components of the RNA-induced silencing complex , the protein complex responsible for the gene silencing phenomenon known as RNA interference . Argonaute proteins bind different classes of small non-coding RNAs, including microRNAs , small interfering RNAs and...
s. These are active in the testes of mammals and are required for germ-cell and stem-cell development in invertebrate
Invertebrate
An invertebrate is an animal without a backbone. The group includes 97% of all animal species – all animals except those in the chordate subphylum Vertebrata .Invertebrates form a paraphyletic group...
s. Three piwi subfamily proteins - MIWI, MIWI2 and MILI - have been found to be essential for spermatogenesis in mice. piRNAs direct the piwi proteins to their transposon targets. A decrease or absence of PIWI protein expression
Protein expression
Protein expression is a subcomponent of gene expression. It consists of the stages after DNA has been translated into polypeptide chains, which are ultimately folded into proteins...
is correlated with an increased expression of transposons. Transposons have a high potential to cause deleterious effect on their host, and, in fact, mutations in piRNA pathways are found to reduce fertility
Fertility
Fertility is the natural capability of producing offsprings. As a measure, "fertility rate" is the number of children born per couple, person or population. Fertility differs from fecundity, which is defined as the potential for reproduction...
in D.melanogaster
Drosophila melanogaster
Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
. However, piRNA pathway mutations in mice do not demonstrate reduced fertility; this may indicate redundancies to the piRNA system. Further, it is thought that piRNA and endogenous
Endogenous
Endogenous substances are those that originate from within an organism, tissue, or cell. Endogenous retroviruses are caused by ancient infections of germ cells in humans, mammals and other vertebrates...
small interfering RNA
Small interfering RNA
Small interfering RNA , sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 nucleotides in length, that play a variety of roles in biology. The most notable role of siRNA is its involvement in the RNA interference pathway, where it...
(endo-siRNA) may have comparable and even redundant functionality in transposon control in mammalian oocytes.
piRNAs appear to have an impact on particular methyltransferase
Methyltransferase
A methyltransferase is a type of transferase enzyme that transfers a methyl group from a donor to an acceptor.Methylation often occurs on nucleic bases in DNA or amino acids in protein structures...
s that perform the methylation
Methylation
In the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom...
s which are required to recognise and silence transposons, but this relationship is not well understood.
Epigenetic effects
piRNAs can be transmitted maternally, and based on research in D. melanogaster, piRNAs may be involved in maternally derived epigenetic effects. The activity of specific piRNAs in the epigenetic process also requires interactions between piwi proteins and HP1a, as well as other factors.
Recent discovery also show, the existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: x-ncRNA and its biological implication in Homo sapiens.
Investigation
Major advances in the piRNA field have been achieved thanks to the use of next-generation sequencing techniques, such as Solexa and 454. These techniques allow analysis of highly complex and heterogeneus RNA populations like piRNAs. Due to their small size, expression and amplification of small RNAs can be challenging, so specialised PCR-based methods have been developed in response to this difficulty.Further reading
- N.C. Lau et al., "Characterization of the piRNA Complex from Rat Testes," Science 313, 363 (2006)
- V.N. Kim, "Small RNAs Just Got Bigger: Piwi-Interacting RNAs (piRNAs) in Mammalian Testes," Genes Dev. 20, 1993 (2006)
- A. Girard et al., "A Germline-Specific Class of Small RNAs Binds Mammalian Piwi Proteins," Nature 442, 199 (2006)
- S.T. Grivna et al., "A Novel Class of Small RNAs in Mouse Spermatogenic Cells," Genes Dev. 20, 1709 (2006)
- T. Watanabe et al., "Identification and characterization of two novel classes of small RNAs in the mouse germline," Genes Dev. 20, 1732 (2006)
- M.A. Carmell et al., "MIWI2 Is Essential for Spermatogenesis and Repression of Transposons in the Mouse Male Germline," Dev Cell. 12, 503 (2007)
External links
- piRNA Bank A web resource on classified and clustered piRNAs