What are enhancers and silencers?
What are enhancers transcribed into?
How do enhancers regulate gene transcription?
What are the spheres of the regulatory elements?
Where is the gene regulation located?
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Where are enhancers located?
Enhancers can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or thousands of nucleotides away. When a DNA -bending protein binds to the enhancer, the shape of the DNA changes, which allows interactions between the activators and transcription factors to occur.
What are enhancers and silencers in transcription?
A cis-regulatory sequence that increases the activity of a gene when bound by transcription factors is called an enhancer, while a sequence that causes a decrease in gene activity is called a silencer.
Are enhancers only upstream?
Second, while it is known that they regulate genes in cis, their location relative to their target gene (or genes) is highly variable: namely, enhancers can be found upstream or downstream of genes but also within introns.
Do bacteria have enhancers and silencers?
Once thought to be unique to eukaryotes, enhancer-like elements have been discovered in a wide variety of bacteria. The regulatory proteins that bind to these bacterial enhancers must contact RNA polymerase to activate transcription.
Can enhancers be found on introns?
Enhancers can also be found within introns. 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.
Can enhancers be downstream?
Transcription factors can bind to enhancer sequences located upstream or downstream from an associated gene, resulting in stimulation or enhancement of transcription of the related gene.
What are promoters and enhancers?
Enhancers and promoters are gene-regulatory elements. They are stretches of DNA that help in both eukaryotic and prokaryotic transcription. The promoters are known to initiate transcription, and the enhancers increase the level of transcription.
How do enhancers work in transcription?
Enhancers are short regulatory elements of accessible DNA that help establish the transcriptional program of cells by increasing transcription of target genes. They are bound by transcription factors, co-regulators, and RNA polymerase II (RNAP II).
What sorts of sequences are found upstream of eukaryotic genes?
Promoter sequences are DNA sequences that define where transcription of a gene by RNA polymerase begins. Promoter sequences are typically located directly upstream or at the 5' end of the transcription initiation site.
What is the function of DNA enhancers and silencers?
Enhancers function as a "turn on" switch in gene expression and will activate the promoter region of a particular gene while silencers act as the "turn off" switch. Though these two regulatory elements work against each other, both sequence types affect the promoter region in very similar ways.
Are silencers in eukaryotes and prokaryotes?
In prokaryotes, silencers are known as operators, found in many genes such as lac operon and trp operon. In eukaryotes, the following genes have been demonstrated to contain silencers: Human β globin gene.
Do enhancers have a TATA box?
These studies revealed transcriptional enhancers that are specific for promoters that contain either DPE or TATA box elements. Thus, the core promoter not only mediates the initiation of transcription, but also functions as a regulatory element.
What is the function of DNA enhancers and silencers?
Enhancers function as a "turn on" switch in gene expression and will activate the promoter region of a particular gene while silencers act as the "turn off" switch. Though these two regulatory elements work against each other, both sequence types affect the promoter region in very similar ways.
How do enhancers and silencers affect transcription levels?
Transcription factors that are activators boost a gene's transcription. Repressors decrease transcription. Groups of transcription factor binding sites called enhancers and silencers can turn a gene on/off in specific parts of the body.
What is difference between enhancers and inhibitors?
In the terms of biological chemistry the enhancers are certain chemical compounds that speeds up any biological process or any biochemical reaction. But on the other hand inhibitors are certain chemical compounds that slows down the biological process on any biochemical reaction.
What do you mean by silencer?
silencer. / (ˈsaɪlənsə) / noun. any device designed to reduce noise, esp the tubular device containing baffle plates in the exhaust system of a motor vehicleUS and Canadian name: muffler. a tubular device fitted to the muzzle of a firearm to deaden the report.
What is the difference between an enhancer and a silencer on ... - reddit
I'll explain this as easy as possible: Silencer and Enhancers both bind the DNA. Silencers have the effect that the DNA 'reading' is less effective, there will be a slower/no DNA reading. It surpresses the gene expression.. Enhancers have the effect that the DNA 'reading' is more effective, there will be a faster/improved DNA reading. It accelerates the gene expression.
Silencers, Enhancers, and the Multifunctional Regulatory Genome
Negative regulation of gene expression by transcriptional silencers has been difficult to study due to limited defined examples. A new study by Gisselbrecht et al. has dramatically increased the number of identified silencers and reveals that they are bifunctional regulatory sequences that also act as gene expression-promoting enhancers.
What are enhancers and silencers?
Enhancers are short motifs that contain binding sites for transcription factors; they activate their target genes without regard to orientation and often over great separations in cis or in trans [ 2 ]. Silencers suppress gene expression [ 3] and/or confine it within specific chromatin boundaries (and thus are also called 'insulators') [ 4 ]. The interplay between these contrasting regulatory elements, their target promoters and epigenetic modifications at all levels of three-dimensional organisation (that is, nucleosomes, chromatin fibres, loops, rosettes, chromosomes and chromosome location) [ 5 – 9] fine-tune expression during development and differentiation. However, the mechanisms involved in this interplay remain elusive, although some can be computationally predicted [ 10 ]. Although enhancers and silencers have apparently opposite effects, accumulating evidence suggests they share more properties than intuition would suggest [ 11 ]. Herein we try to reconcile their apparently disparate modes of action. We suggest they act by tethering their target promoters close to, or distant from, hot spots of nucleoplasmic transcription (known as 'transcription factories') as they produce noncoding transcripts (ncRNAs) [ 12 – 15 ].
What are enhancers transcribed into?
Enhancers are transcribed into RNAs (eRNAs) that do not encode proteins, run the length of the enhancer sequence and appear to stabilise enhancer-promoter interactions [ 11, 24, 27 – 29 ]. eRNAs derived from elements upstream of the Arc promoter depend on the activity of that promoter, as removing the promoter abolishes eRNA production [ 28 ]. β-globin-associated ncRNAs are still produced in the absence of the β-globin promoter [ 28, 30, 31 ]. However, the rate at which eRNAs are turned over, the exact mechanism by which they function and their abundance (relative to the mRNAs they regulate) all remain to be determined.
How do enhancers regulate gene transcription?
The following four models have been proposed to describe gene regulation by enhancers (Figure 1 ). (1) According to the tracking model, a protein loads onto the enhancer and tracks along the chromatin fibre towards the promoter, where it stimulates transcription [ 62 ]. (2) The linking model is similar, but here the loaded protein drives polymerisation of proteins in the direction of the promoter [ 63 ]. (3) In the relocation model, a given gene relocates to compartments in the nucleus where enhancer-promoter interactions (and so transcription) are favoured [ 64, 65 ]. (4) The looping model (which shares features with the relocation model) predicts a direct contact between an enhancer and a relevant promoter that loops out the intervening DNA [ 12, 65, 66] and thus is closely linked to the three-dimensional genome architecture [ 1, 7, 65 ]. Next, activators bound to the enhancer interact with the mediator complex, which recruits RNAPII and general transcription factors to the promoter [ 34, 67 ]. This last model is now favoured, as it readily explains enhancer-promoter interactions in trans [ 18, 68] and is supported by a wealth of experimental data derived from 3C [ 69] and modelling [ 1, 6 – 10, 15 ].
What are the spheres of the regulatory elements?
A simple model for the function of regulatory elements. Spheres A, B and C represent factories rich in different sets of transcription factors and associated halos indicate the probability that promoter 1, 2 or 3 will collide with a factory (red indicates high probability). The low-probability zone immediately around the factory arises because the intrinsic stiffness of the chromatin fibre restricts the formation of very small loops). Curved black arrow indicates collision between promoter and factory that yields a productive initiation. Dashed grey arrows indicate the preferred site of initiation (as factory B is rich in the relevant transcription factors). Blocked red arrows indicate unproductive collisions (as the factory contains few of the relevant factors). (A) Enhancers and silencers. Transcription unit 1 is being transcribed by a polymerase in factory A. This tethers unit 2 in a 'hot zone', where it has a high probability of colliding with a polymerase in factory A (which contains high local concentrations of factors necessary for initiation by promoters 1 and 2 ). As a result, unit 1 acts as an enhancer for unit 2. At the same time, unit 3 is tethered far from factory B (which is rich in the factors required for its initiation). Here unit 1 acts as a silencer of unit 3. (B) Insulator. At a different stage in development, a different constellation of transcription factors are expressed. Chromatin domains containing units 2 and 3 are separated by unit 1 (now transcribed in factory C, which contains low concentrations of the factors required by units 2 and 3 ), so they rarely bind to factory A and interact. Here unit 1 acts as an insulator or barrier.
Where is the gene regulation located?
The first and most studied example of gene regulation by an enhancer is provided by the β-globin locus; here, the locus control region (LCR) is located 40 to 60 kb upstream from the promoter it regulates. The two interact when the chromatin fibre forms new, or rearranges preexisting, loops [ 17, 25 ]. All other cis -regulatory elements in this locus are also in close proximity, where they form an 'active chromatin hub' [ 12, 26 ]. An active chromatin hub, as defined in the β-globin locus paradigm, arises from the three-dimensional clustering of DNA-hypersensitive sites, depends on specific DNA-protein interactions and brings together all essential components for transcriptional activation [ 17 ]. Similarly, in a comprehensive study of the immunoglobulin heavy-chain locus [ 6] (and many other loci), the multitude of preexisting loops and connecting regulatory elements are rearranged to form new ones that interact upon activation. Obviously, most of these conformations (and in fact most seen using chromosome conformation capture (3C)) concern a population of cells and will not be refined until single-cell 3C is developed and implemented.
