Enhancer (genetics)
Encyclopedia
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
, an enhancer is a short region 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...
that can be bound with 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...
s (namely, the trans-acting factors, much like a set of transcription factors) to enhance 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...
levels of 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 (hence the name) in a gene cluster
Gene cluster
A gene cluster is a set of two or more genes that serve to encode for the same or similar products. Because populations from a common ancestor tend to possess the same varieties of gene clusters, they are useful for tracing back recent evolutionary history...
. While enhancers are usually cis-acting, an enhancer does not need to be particularly close to the genes it acts on, and sometimes need not be located on the same chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
.
Enhancer locations
In eukaryotic cells the structure of the chromatinChromatin
Chromatin 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...
complex of DNA is folded in a way that functionally mimics the supercoiled state characteristic of prokaryotic DNA, so that although the enhancer DNA is far from the gene in regard to the number of nucleotides, it is geometrically close to the promoter and gene. This allows it to interact with the general transcription factor
General transcription factor
General transcription factors or basal transcription factors are protein transcription factors that have been shown to be important in the transcription of class II genes to mRNA templates...
s and RNA polymerase II
RNA polymerase II
RNA polymerase II is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase...
.
An enhancer may be located upstream or downstream
Upstream and downstream (DNA)
In molecular biology and genetics, upstream and downstream both refer to a relative position in DNA or RNA. Each strand of DNA or RNA has a 5' end and a 3' end, so named for the carbons on the deoxyribose ring. Relative to the position on the strand, downstream is the region towards the 3' end of...
of the gene it regulates. Furthermore, an enhancer need not be located near to the 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...
initiation site to affect transcription, as some have been found located in several hundred thousand base pairs upstream or downstream of the start site. Enhancers do not act on the promoter region itself, but are bound by activator proteins. These activator proteins interact with the mediator complex
Mediator (coactivator)
Mediator is a multiprotein complex that functions as a transcriptional coactivator. It was discovered by Roger D. Kornberg, winner of the 2006 Nobel Prize in Chemistry...
, which recruits polymerase II and the general transcription factors which then begin transcribing the genes. Enhancers can also be found within intron
Intron
An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final...
s. An enhancer's orientation may even be reversed without affecting its function. Additionally, an enhancer may be excised and inserted elsewhere in the chromosome, and still affect gene transcription. That is one reason that intron polymorphisms
Polymorphism (biology)
Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species — in other words, the occurrence of more than one form or morph...
may have effects although they are not translated.
Theories
Currently, there are two different theories on the information processing that occurs on enhancers:- EnhanceosomeEnhanceosomeThe enhanceosome is a protein complex that binds to the "enhancer" region of a gene, found upstream or downstream, of the promoter, or within a gene. It accelerates the gene's transcription...
s - rely on highly cooperative, coordinated action and can be disabled by single point mutations that move or remove the binding sites of individual proteins. - Flexible billboards - less integrative, multiple proteins independently regulate gene expression and their sum is read in by the basal transcriptional machinery
HACNS1
HACNS1 (also known as CENTG2CENTG2
Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 is an enzyme that in humans is encoded by the AGAP1 gene.-HACNS1:HACNS1 is located in an intron of the gene CENTG2...
and located in the Human Accelerated Region
Human accelerated regions
Human accelerated regions , first described in August 2006, are a set of 49 segments of the human genome which are conserved throughout vertebrate evolution but are strikingly different in humans. They are named HAR1 through HAR49 according to their degree of difference between humans and chimpanzees...
2) is a gene enhancer "that may have contributed to the evolution of the uniquely opposable human
Human
Humans are the only living species in the Homo genus...
thumb
Thumb
The thumb is the first digit of the hand. When a person is standing in the medical anatomical position , the thumb is the lateral-most digit...
, and possibly also modifications in the ankle
Ankle
The ankle joint is formed where the foot and the leg meet. The ankle, or talocrural joint, is a synovial hinge joint that connects the distal ends of the tibia and fibula in the lower limb with the proximal end of the talus bone in the foot...
or foot
Foot
The foot is an anatomical structure found in many vertebrates. It is the terminal portion of a limb which bears weight and allows locomotion. In many animals with feet, the foot is a separate organ at the terminal part of the leg made up of one or more segments or bones, generally including claws...
that allow humans to walk
WALK
WALK may refer to:*WALK , a radio station licensed to East Patchogue, New York, United States*WALK-FM, a radio station licensed to Patchogue, New York, United States...
on two legs". Evidence to date shows that of the 110,000 gene enhancer sequences identified in the human genome
Genome
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....
, HACNS1 has undergone the most change during the evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
of humans following the split with the ancestors of chimpanzee
Chimpanzee
Chimpanzee, sometimes colloquially chimp, is the common name for the two extant species of ape in the genus Pan. The Congo River forms the boundary between the native habitat of the two species:...
s.
GADD45G
An enhancer near the gene GADD45g has been described that may regulate brain growth in chimpanzees and other mammals, but not in humans. The GADD45G regulator in mice and chimps is active in regions of the brain where cells that form the cortex, ventral forebrain, and thalamus are located and may suppress further neurogenesis. Loss of the GADD45G enhancer in humans may contribute to an increase of certain neuronal populations and to forebrain expansion in humans.Enhancers in Developmental Biology
The development, differentiation and growth of cells and tissues require precisely regulated patterns of gene expressionGene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
. Enhancers work as cis-regulatory element
Cis-regulatory element
A cis-regulatory element or cis-element is a region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA . This term is constructed from the Latin word cis, which means "on the same side as". These cis-regulatory elements are often binding sites for one or...
s to mediate both spatial and temporal control of development by turning on transcription
Transcription
Transcription may refer to:*Transcription , a business which converts speech into a written or electronic text document*Transcription , software which helps convert speech into text transcript...
in specific cells and/or repressing it in other cells. Thus, the particular combination of transcription factors and other DNA-binding proteins in a developing tissue controls which genes will be expressed in that tissue. Enhancers allow the same gene to be used in diverse processes in space and time.
Identification and Characterization
Enhancers can be identified by enhancer trapEnhancer trap
An enhancer trap is a transgenic construction for the identification of enhancers, produced by the fusing of two proteins, genes for which are inserted into the genome. The enhancer trap structure contains a mobile element usually some sort of P element and a reporter gene...
techniques using a reporter gene or by comparative sequence analysis and computational genomics. In genetically tractable models such as the fruit fly 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...
, for example, a reporter construct such as the lacZ gene can be randomly integrated into the genome using a P element transposon. If the reporter gene integrates near an enhancer, its expression will reflect the expression pattern driven by that enhancer. Thus, staining the flies for LacZ expression or activity and cloning the sequence surrounding the integration site can identify the enhancer sequence.
In the comparative genomics approach, sequence conservation of non-coding regions can be indicative of enhancers. Sequences from multiple species are aligned, and conserved regions are identified computationally. Identified sequences can then be attached to a reporter gene such green fluorescent protein
Green fluorescent protein
The green fluorescent protein is a protein composed of 238 amino acid residues that exhibits bright green fluorescence when exposed to blue light. Although many other marine organisms have similar green fluorescent proteins, GFP traditionally refers to the protein first isolated from the...
or lacZ to determine the in vivo pattern of gene expression produced by the enhancer when injected into an embryo. mRNA expression of the reporter can be visualized by in situ hybridization, which provides a more direct measure of enhancer activity, since it is not subjected to the complexities of translation and protein folding. Although much evidence has pointed to sequence conservation for critical developmental enhancers, other work has shown that the function of enhancers can be conserved with little or no primary sequence conservation. For example, the RET enhancers in humans have very little sequence conservation to those in zebrafish, yet both species’ sequences produce nearly identical patterns of reporter gene expression in zebrafish. Additionally, algorithms such as TFSEARCH or JASPAR can be used to identify putative transcription factor binding sites to further characterize an enhancer sequence.
Enhancers in Invertebrate Segmentation
The enhancers determining early segmentationSegmentation
Segmentation may mean:*Market segmentation, in economics and marketingBiology*A process of morphogenesis that divides a metazoan body into a series of semi-repetitive segments*Segmentation , a series of semi-repetitive segments...
in Drosophila melanogaster embryos are among the best characterized developmental enhancers. In the early fly embryo, the gap gene
Gap gene
A gap gene is a type of gene involved in the development of the segmented embryos of some arthropods. Gap genes are defined by the effect of a mutation in that gene, which causes the loss of contiguous body segments, resembling a gap in the normal body plan...
transcription factors are responsible for activating and repressing a number of segmentation genes, such as the pair rule genes. The gap genes are expressed in blocks along the anterior-posterior axis of the fly along with other maternal effect
Maternal effect
A maternal effect is a situation where the phenotype of an organism is determined not only by the environment it experiences and its genotype, but also by the environment and phenotype of its mother...
transcription factors, thus creating zones within which different combinations of transcription factors are expressed. The pair-rule genes are separated from one another by non-expressing cells. Moreover, the stripes of expression for different pair-rule genes are offset by a few cell diameters from one another. Thus, unique combinations of pair-rule gene expression create spatial domains along the anterior-posterior axis to set up each of the 14 individual segments. The 480 bp enhancer responsible for driving the sharp stripe two of the pair-rule gene even-skipped (eve) has been well-characterized. The enhancer contains 12 different binding sites for maternal and gap gene transcription factors. Activating and repressing sites overlap in sequence. Eve is only expressed in a narrow stripe of cells that contain high concentrations of the activators and low concentration of the repressors for this enhancer sequence. Other enhancer regions drive eve expression in 6 other stripes in the embryo.
Enhancers in Vertebrate Patterning
Establishing body axes is a critical step in animal development. During mouse embryonic development, NodalNodal
Nodal can refer to* Nodal, a protein encoded by the gene NODAL and responsible for left-right asymmetry* Nodal , a novel music composition program...
, a transforming growth factor-beta superfamily ligand, is a key gene involved in patterning both the anterior-posterior axis and the left-right axis of the early embryo. The Nodal gene contains two enhancers: the Proximal Epiblast Enhancer (PEE) and the Asymmetric Enhancer (ASE). The PEE is upstream of the Nodal gene and drives Nodal expression in the portion of the primitive streak
Primitive streak
The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development.-Introduction:...
that will differentiate into the node (also referred to as the primitive node). The PEE turns on Nodal expression in response to a combination of Wnt signaling plus a second, unknown signal; thus, a member of the LEF/TCF transcription factor family likely binds to a TCF binding site in the cells in the node. Diffusion of Nodal away from the node forms a gradient which then patterns the extending anterior-posterior axis of the embryo. The ASE is an intronic enhancer bound by the fork head domain
Fork head domain
The fork head domain is a type of protein domain which is often found in transcription factors and whose purpose is to bind DNA.- Function :...
transcription factor Fox1. Early in development, Fox1-driven Nodal expression establishes the visceral endoderm. Later in development, Fox1 binding to the ASE drives Nodal expression on the left side of the lateral plate mesoderm
Mesoderm
In all bilaterian animals, the mesoderm is one of the three primary germ cell layers in the very early embryo. The other two layers are the ectoderm and endoderm , with the mesoderm as the middle layer between them.The mesoderm forms mesenchyme , mesothelium, non-epithelial blood corpuscles and...
, thus establishing left-right asymmetry necessary for asymmetric organ development in the mesoderm.
Establishing three germ layers during gastrulation
Gastrulation
Gastrulation is a phase early in the embryonic development of most animals, during which the single-layered blastula is reorganized into a trilaminar structure known as the gastrula. These three germ layers are known as the ectoderm, mesoderm, and endoderm.Gastrulation takes place after cleavage...
is another critical step in animal development. Each of the three germ layers has unique patterns of gene expression that promote their differentiation and development. The endoderm
Endoderm
Endoderm is one of the three primary germ cell layers in the very early embryo. The other two layers are the ectoderm and mesoderm , with the endoderm as the intermost layer...
is specified early in development by Gata4
GATA4
Transcription factor GATA-4 is a protein that in humans is encoded by the GATA4 gene.-Interactions:GATA4 has been shown to interact with NKX2-5, TBX5, ZFPM2, Serum response factor and HAND2.HDAC2- External links :...
expression, and Gata4 goes on to direct gut morphogenesis later. Gata4 expression is controlled in the early embryo by an intronic enhancer that binds another forkhead domain transcription factor, FoxA2. Initially the enhancer drives broad gene expression throughout the embryo, but the expression quickly becomes restricted to the endoderm, suggesting that other repressors may be involved in its restriction. Late in development, the same enhancer restricts expression to the tissues that will become the stomach and pancreas. An additional enhancer is responsible for maintaining Gata4 expression in the endoderm during the intermediate stages of gut development.
Multiple enhancers promote developmental robustness
Some genes involved in critical developmental processes contain multiple enhancers of overlapping function. Secondary enhancers, or “shadow enhancers,” may be found many kilobases away from the primary enhancer (“primary” usually refers to the first enhancer discovered, which is often closer to the gene it regulates). On its own, each enhancer drives nearly identical patterns of gene expression. Are the two enhancers truly redundant? Recent work has shown that multiple enhancers allow fruit flies to survive environmental perturbations, such as an increase in temperature. When raised at an elevated temperature, a single enhancer sometimes fails to drive the complete pattern of expression, whereas the presence of both enhancers permits normal gene expression.Enhancers and the evolution of developmental mechanisms
One theme of research in evolutionary developmental biologyEvolutionary developmental biology
Evolutionary developmental biology is a field of biology that compares the developmental processes of different organisms to determine the ancestral relationship between them, and to discover how developmental processes evolved...
(“evo-devo”) is investigating the role of enhancers and other cis-regulatory elements in producing morphological changes via developmental differences between species.
Stickleback PitX1
Recent work has investigated the role of enhancers in morphological changes in threespine sticklebackStickleback
The Gasterosteidae are a family of fish including the sticklebacks. FishBase currently recognises sixteen species in the family, grouped in five genera. However several of the species have a number of recognised subspecies, and the taxonomy of the family is thought to be in need of revision...
fish. Sticklebacks exist in both marine and freshwater environments, but sticklebacks in many freshwater populations have completely lost their pelvic fins (appendages homologous to the posterior limb of tetrapods). Pitx1
PITX1
Pituitary homeobox 1 is a protein that in humans is encoded by the PITX1 gene.-Interactions:PITX1 has been shown to interact with Pituitary-specific positive transcription factor 1.-Further reading:...
is a homeobox
Homeobox
A homeobox is a DNA sequence found within genes that are involved in the regulation of patterns of anatomical development in animals, fungi and plants.- Discovery :...
gene involved in posterior limb development in vertebrates. Preliminary genetic analyses indicated that changes in the expression of this gene were responsible for pelvic reduction in sticklebacks. Fish expressing only the freshwater allele
Allele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...
of Pitx1 do not have pelvic spines, whereas fish expressing a marine allele retain pelvic spines. A more thorough characterization showed that a 500 base pair enhancer sequence is responsible for turning on Pitx1 expression in the posterior fin bud. This enhancer is located near a chromosomal fragile site--a sequence of DNA that is likely to be broken and thus more likely to be mutated as a result of imprecise DNA repair
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...
. This fragile site has caused repeated, independent losses of the enhancer responsible for driving PitX1 expression in the pelvic spines in isolated freshwater population, and without this enhancer, freshwater fish fail to develop pelvic spines.
Enhancers in Drosophila wing pattern evolution
Pigmentation patterns provide one of the most striking and easily scored differences between different species of animals. Pigmentation of the Drosophila wing has proven to be a particularly amenable system for studying the development of complex pigmentation phenotypes. The Drosophila guttifera wing has 12 dark pigmentation spots and 4 lighter gray intervein patches. Pigment spots arise from expression of the yellow gene, whose product produces black melaninMelanin
Melanin is a pigment that is ubiquitous in nature, being found in most organisms . In animals melanin pigments are derivatives of the amino acid tyrosine. The most common form of biological melanin is eumelanin, a brown-black polymer of dihydroxyindole carboxylic acids, and their reduced forms...
. Recent work has shown that two enhancers in the yellow gene produce gene expression in precisely this pattern – the vein spot enhancer drives reporter gene expression in the 12 spots, and the intervein shade enhancer drives reporter expression in the 4 distinct patches. These two enhancers are responsive to the Wnt signaling pathway
Wnt signaling pathway
The Wnt signaling pathway is a network of proteins best known for their roles in embryogenesis and cancer, but also involved in normal physiological processes in adult animals.-Discovery:...
, which is activated by ‘’wingless’’ expression at all of the pigmented locations. Thus, in the evolution of the complex pigmentation phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
, the yellow pigment gene evolved enhancers responsive to the wingless signal and wingless expression evolved at new locations to produce novel wing patterns.