Gene silencing
Encyclopedia
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. That is, a gene which would be expressed (turned on) under normal circumstances is switched off by machinery in the cell.
Gene
s are regulated at either the transcriptional
or post-transcriptional level.
Transcriptional gene silencing is the result of histone
modifications, creating an environment of heterochromatin
around a gene that makes it inaccessible to transcriptional machinery (RNA polymerase
, transcription factors, etc.).
Post-transcriptional gene silencing is the result of mRNA
of a particular gene being destroyed or blocked. The destruction of the mRNA prevents translation
to form an active gene product (in most cases, a protein
). A common mechanism of post-transcriptional gene silencing is RNAi
.
Both transcriptional and post-transcriptional gene silencing are used to regulate endogenous genes. Mechanisms of gene silencing also protect the organism's genome from transposon
s and virus
es. Gene silencing thus may be part of an ancient immune system protecting from such infectious DNA
elements.
Genes may be silenced by DNA methylation
during meiosis
, as in the filamentous fungus Neurospora crassa
.
Transcriptional Gene Silencing:
Post-transcriptional Gene Silencing:
Meiotic gene silencing:
Cellular components of gene silencing:
Ribozyme and antisense technology are the two approaches used to exact post transcriptional gene silencing in order to suppress a gene of interest.
Gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s are regulated at either the transcriptional
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...
or post-transcriptional level.
Transcriptional gene silencing is the result of histone
Histone
In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation...
modifications, creating an environment of heterochromatin
Heterochromatin
Heterochromatin is a tightly packed form of DNA, which comes in different varieties. These varieties lie on a continuum between the two extremes of constitutive and facultative heterochromatin...
around a gene that makes it inaccessible to transcriptional machinery (RNA polymerase
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
, transcription factors, etc.).
Post-transcriptional gene silencing is the result of mRNA
Messenger RNA
Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein...
of a particular gene being destroyed or blocked. The destruction of the mRNA prevents translation
Translation
Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. Whereas interpreting undoubtedly antedates writing, translation began only after the appearance of written literature; there exist partial translations of the Sumerian Epic of...
to form an active gene product (in most cases, a protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
). A common mechanism of post-transcriptional gene silencing is RNAi
RNAI
RNAI is a non-coding RNA that is an antisense repressor of the replication of some E. coli plasmids, including ColE1. Plasmid replication is usually initiated by RNAII, which acts as a primer by binding to its template DNA. The complementary RNAI binds RNAII prohibiting it from its initiation role...
.
Both transcriptional and post-transcriptional gene silencing are used to regulate endogenous genes. Mechanisms of gene silencing also protect the organism's genome from 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 and virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
es. Gene silencing thus may be part of an ancient immune system protecting from such infectious 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...
elements.
Genes may be silenced by DNA methylation
DNA methylation
DNA methylation is a biochemical process that is important for normal development in higher organisms. It involves the addition of a methyl group to the 5 position of the cytosine pyrimidine ring or the number 6 nitrogen of the adenine purine ring...
during meiosis
Meiosis
Meiosis is a special type of cell division necessary for sexual reproduction. The cells produced by meiosis are gametes or spores. The animals' gametes are called sperm and egg cells....
, as in the filamentous fungus 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. The first published account of this fungus was from an infestation of French bakeries in 1843. N...
.
Specific studies of gene silencing
There are several more terms related to specific topics of gene silencing:Transcriptional Gene Silencing:
- Genomic Imprinting
- ParamutationParamutationIn epigenetics, paramutation is an interaction between two alleles of a single locus, resulting in a heritable change of one allele that is induced by the other allele...
- Transposon silencing
- Transgene silencing
- Transcriptional gene silencing
- position effectPosition effectPosition effect is the effect on the expression of a gene when its location in a chromosome is changed, often by translocation. This has been well described in Drosophila with respect to eye color and is known as position effect variegation ....
- RNA-directed DNA methylationRNA-Directed DNA MethylationRNA-directed DNA methylation is an epigenetic process first elucidated in plants whereby small double-stranded RNAs are processed to guide methylation to complementary DNA loci...
Post-transcriptional Gene Silencing:
- RNA interferenceRNA interferenceRNA interference is a process within living cells that moderates the activity of their genes. Historically, it was known by other names, including co-suppression, post transcriptional gene silencing , and quelling. Only after these apparently unrelated processes were fully understood did it become...
- Nonsense mediated decayNonsense mediated decayNonsense-mediated decay is a cellular mechanism of mRNA surveillance that functions to detect nonsense mutations and prevent the expression of truncated or erroneous proteins. Following transcription, precursor mRNA undergoes an assemblage of ribonucleoprotein components followed by regulatory...
Meiotic gene silencing:
- TransvectionTransvection (genetics)Transvection is an epigenetic phenomenon that results from an interaction between an allele on one chromosome and the corresponding allele on the homologous chromosome. Transvection can lead to either gene activation or repression...
- Meiotic silencing of unpaired DNA
Cellular components of gene silencing:
- HistoneHistoneIn biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation...
s - ChromatinChromatinChromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene...
and heterochromatinHeterochromatinHeterochromatin is a tightly packed form of DNA, which comes in different varieties. These varieties lie on a continuum between the two extremes of constitutive and facultative heterochromatin... - MicroRNA
- siRNASmall interfering RNASmall 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...
- dsRNA
- DicerDicerDicer is an endoribonuclease in the RNase III family that cleaves double-stranded RNA 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...
- TransposonTransposonTransposable 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
Ribozyme and antisense technology are the two approaches used to exact post transcriptional gene silencing in order to suppress a gene of interest.
External links
- RNAiAtlas - database of siRNA libraries and their target analysis results
- Science project: Transgenic apple varieties Approaches to preventing outcrossing – possible effects on micro-organisms
- Research project: New Cost-effective method for gene silencing