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113-410: Cis -regulatory elements ( CREs ) or cis -regulatory modules ( CRMs ) are regions of non-coding DNA which regulate the transcription of neighboring genes . CREs are vital components of genetic regulatory networks , which in turn control morphogenesis , the development of anatomy , and other aspects of embryonic development , studied in evolutionary developmental biology . CREs are found in

226-435: 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 . 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. Pigmentation patterns provide one of

339-539: A DNA sequence with transcription factor binding sites which are clustered into modular structures, including -but not limited to- locus control regions, promoters, enhancers, silencers, boundary control elements and other modulators. Cis -regulatory modules can be divided into three classes; enhancers , which regulate gene expression positively; insulators , which work indirectly by interacting with other nearby cis -regulatory modules; and silencers that turn off expression of genes. The design of cis -regulatory modules

452-433: A causal mutation. (The association is referred to as tight linkage disequilibrium .) About 12% of these polymorphisms are found in coding regions; about 40% are located in introns; and most of the rest are found in intergenic regions, including regulatory sequences. Enhancer (genetics) In genetics , an enhancer is a short (50–1500 bp ) region of DNA that can be bound by proteins ( activators ) to increase

565-487: A cell line, and one year later also in vivo. In eukaryotic cells the structure of the chromatin complex of DNA is folded in a way that functionally mimics the supercoiled state characteristic of prokaryotic DNA, so although the enhancer DNA may be far from the gene in a linear way, it is spatially close to the promoter and gene. This allows it to interact with the general transcription factors and RNA polymerase II . The same mechanism holds true for silencers in

678-452: A century and it is likely that they are more abundant than coding DNA. Telomeres are regions of repetitive DNA at the end of a chromosome , which provide protection from chromosomal deterioration during DNA replication . Recent studies have shown that telomeres function to aid in its own stability. Telomeric repeat-containing RNA (TERRA) are transcripts derived from telomeres. TERRA has been shown to maintain telomerase activity and lengthen

791-513: 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 transcription factor Fox1. Early in development, Fox1-driven Nodal expression establishes

904-450: A different spatial regions of the embryo, of gene expression will be under the control of different cis -regulatory modules. The design of regulatory modules help in producing feedback , feed forward , and cross-regulatory loops. Cis -regulatory modules can regulate their target genes over large distances. Several models have been proposed to describe the way that these modules may communicate with their target gene promoter. These include

1017-515: A eukaryotic enhancer was in the immunoglobulin heavy chain gene in 1983. This enhancer, located in the large intron , provided an explanation for the transcriptional activation of rearranged Vh gene promoters while unrearranged Vh promoters remained inactive. Lately, enhancers have been shown to be involved in certain medical conditions, for example, myelosuppression . Since 2022, scientists have used artificial intelligence to design synthetic enhancers and applied them in animal systems, first in

1130-491: 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

1243-415: A human cell ) generally bind to specific motifs on an enhancer and a small combination of these enhancer-bound transcription factors, when brought close to a promoter by a DNA loop, govern level of transcription of the target gene. Mediator (a complex usually consisting of about 26 proteins in an interacting structure) communicates regulatory signals from enhancer DNA-bound transcription factors directly to

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1356-419: A large amount of developmental information processing. Cis -regulatory modules are non-random clusters at their specified target site that contain transcription factor binding sites. The original definition presented cis-regulatory modules as enhancers of cis-acting DNA, which increased the rate of transcription from a linked promoter . However, this definition has changed to define cis -regulatory modules as

1469-403: A large proportion of the genomic sequences in many species. Alu sequences , classified as a short interspersed nuclear element, are the most abundant mobile elements in the human genome. Some examples have been found of SINEs exerting transcriptional control of some protein-encoding genes. Endogenous retrovirus sequences are the product of reverse transcription of retrovirus genomes into

1582-410: A lot still remains unknown. Additionally, the regulation of chromatin structure and nuclear organization also play a role in determining and controlling the function of cis-regulatory modules. Thus gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output). The challenge

1695-565: A number of transcription factors can bind and regulate expression of nearby genes and regulate their transcription rates. They are labeled as cis because they are typically located on the same DNA strand as the genes they control as opposed to trans , which refers to effects on genes not located on the same strand or farther away, such as transcription factors. One cis -regulatory element can regulate several genes, and conversely, one gene can have several cis -regulatory modules. Cis -regulatory modules carry out their function by integrating

1808-456: 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 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

1921-410: A number of unique RNA genes that produce catalytic RNAs . Noncoding genes account for only a few percent of prokaryotic genomes but they can represent a vastly higher fraction in eukaryotic genomes. In humans, the noncoding genes take up at least 6% of the genome, largely because there are hundreds of copies of ribosomal RNA genes. Protein-coding genes occupy about 38% of the genome; a fraction that

2034-540: A powerful tool to direct gene products to particular cell types in order to treat disease by activating beneficial genes or by halting aberrant cell states. Since 2022, artificial intelligence and transfer learning strategies have led to a better understanding of the features of regulatory DNA sequences, the prediction, and the design of synthetic enhancers. Building on work in cell culture, synthetic enhancers were successfully applied to entire living organisms in 2023. Using deep neural networks , scientists simulated

2147-609: A profound effect on phenotype by altering gene expression . Mutations arising within a CRE can generate expression variance by changing the way TFs bind. Tighter or looser binding of regulatory proteins will lead to up- or down-regulated transcription. The function of a gene regulatory network depends on the architecture of the nodes , whose function is dependent on the multiple cis -regulatory modules. The layout of cis -regulatory modules can provide enough information to generate spatial and temporal patterns of gene expression. During development each domain, where each domain represents

2260-404: A result, inflammation reprograms cells, altering their interactions with the rest of tissue and with the immune system. In cancer, proteins that control NF-κB activity are dysregulated, permitting malignant cells to decrease their dependence on interactions with local tissue, and hindering their surveillance by the immune system . Synthetic regulatory elements such as enhancers promise to be

2373-414: A simple repeat such as ATC. There are about 350,000 STRs in the human genome and they are scattered throughout the genome with an average length of about 25 repeats. Variations in the number of STR repeats can cause genetic diseases when they lie within a gene but most of these regions appear to be non-functional junk DNA where the number of repeats can vary considerably from individual to individual. This

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2486-414: A single enhancer sometimes fails to drive the complete pattern of expression, whereas the presence of both enhancers permits normal gene expression. One theme of research in evolutionary developmental biology ("evo-devo") is investigating the role of enhancers and other cis-regulatory elements in producing morphological changes via developmental differences between species. Recent work has investigated

2599-797: A singular product or more. For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed. The most efficient way for an organism to regulate gene expression is at the transcriptional level. CREs function to control transcription by acting nearby or within a gene. The most well characterized types of CREs are enhancers and promoters . Both of these sequence elements are structural regions of DNA that serve as transcriptional regulators . Cis -regulatory modules are one of several types of functional regulatory elements . Regulatory elements are binding sites for transcription factors, which are involved in gene regulation. Cis -regulatory modules perform

2712-467: A study of brain cortical neurons, 24,937 loops were found, bringing enhancers to their target promoters. Multiple enhancers, each often at tens or hundreds of thousands of nucleotides distant from their target genes, loop to their target gene promoters and can coordinate with each other to control the expression of their common target gene. The schematic illustration in this section shows an enhancer looping around to come into close physical proximity with

2825-464: A substantial proportion of the genome. In humans, for example, introns in protein-coding genes cover 37% of the genome. Combining that with about 1% coding sequences means that protein-coding genes occupy about 38% of the human genome. The calculations for noncoding genes are more complicated because there is considerable dispute over the total number of noncoding genes but taking only the well-defined examples means that noncoding genes occupy at least 6% of

2938-647: 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 that will differentiate into the node (also referred to as the primitive node ). The PEE turns on Nodal expression in response to

3051-503: Is a product of the various operations performed on it. Common operations include the OR gate – this design indicates that in an output will be given when either input is given [3], and the AND gate – in this design two different regulatory factors are necessary to make sure that a positive output results. "Toggle Switches" – This design occurs when the signal ligand is absent while the transcription factor

3164-502: Is considerable controversy in the scientific literature. The nonfunctional DNA in bacterial genomes is mostly located in the intergenic fraction of non-coding DNA but in eukaryotic genomes it may also be found within introns . There are many examples of functional DNA elements in non-coding DNA, and it is erroneous to equate non-coding DNA with junk DNA. Genome-wide association studies (GWAS) identify linkages between alleles and observable traits such as phenotypes and diseases. Most of

3277-432: Is currently without an explained origin is expected to have found its origin in transposable elements that were active so long ago (> 200 million years) that random mutations have rendered them unrecognizable. Genome size variation in at least two kinds of plants is mostly the result of retrotransposon sequences. Highly repetitive DNA consists of short stretches of DNA that are repeated many times in tandem (one after

3390-425: Is much higher than the coding region because genes contain large introns. The total number of noncoding genes in the human genome is controversial. Some scientists think that there are only about 5,000 noncoding genes while others believe that there may be more than 100,000 (see the article on Non-coding RNA ). The difference is largely due to debate over the number of lncRNA genes. Promoters are DNA segments near

3503-404: Is not powerful enough to eliminate them (see Nearly neutral theory of molecular evolution ). The human genome contains about 15,000 pseudogenes derived from protein-coding genes and an unknown number derived from noncoding genes. They may cover a substantial fraction of the genome (~5%) since many of them contain former intron sequences. Pseudogenes are junk DNA by definition and they evolve at

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3616-492: Is only about one eighth the size of the human genome, yet seems to have a comparable number of genes. Genes take up about 30% of the pufferfish genome and the coding DNA is about 10%. (Non-coding DNA = 90%.) The reduced size of the pufferfish genome is due to a reduction in the length of introns and less repetitive DNA. Utricularia gibba , a bladderwort plant, has a very small nuclear genome (100.7 Mb) compared to most plants. It likely evolved from an ancestral genome that

3729-414: 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. Establishing body axes is a critical step in animal development. During mouse embryonic development, Nodal , a transforming growth factor-beta superfamily ligand,

3842-430: Is present; this transcription factor ends up acting as a dominant repressor. However, once the signal ligand is present the transcription factor's role as repressor is eliminated and transcription can occur. Other Boolean logic operations can occur as well, such as sequence specific transcriptional repressors, which when they bind to the cis -regulatory module lead to an output of zero. Additionally, besides influence from

3955-480: Is specified early in development by Gata4 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,

4068-414: Is subject to a greater or lesser number of false-positive identifications. 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 as green fluorescent protein or lacZ to determine

4181-649: Is such that transcription factors and epigenetic modifications serve as inputs, and the output of the module is the command given to the transcription machinery, which in turn determines the rate of gene transcription or whether it is turned on or off . There are two types of transcription factor inputs: those that determine when the target gene is to be expressed and those that serve as functional drivers , which come into play only during specific situations during development. These inputs can come from different time points, can represent different signal ligands, or can come from different domains or lineages of cells. However,

4294-547: Is to predict GRFs. This challenge still remains unsolved. In general, gene-regulation functions do not use Boolean logic , although in some cases the approximation of the Boolean logic is still very useful. Within the assumption of the Boolean logic, principles guiding the operation of these modules includes the design of the module which determines the regulatory function. In relation to development, these modules can generate both positive and negative outputs. The output of each module

4407-462: Is unclear because it is difficult to distinguish between spurious transcription factor binding sites and those that are functional. The binding characteristics of typical DNA-binding proteins were characterized in the 1970s and the biochemical properties of transcription factors predict that in cells with large genomes, the majority of binding sites will not be biologically functional. Many regulatory sequences occur near promoters, usually upstream of

4520-491: Is why these length differences are used extensively in DNA fingerprinting . Junk DNA is DNA that has no biologically relevant function such as pseudogenes and fragments of once active transposons. Bacteria and viral genomes have very little junk DNA but some eukaryotic genomes may have a substantial amount of junk DNA. The exact amount of nonfunctional DNA in humans and other species with large genomes has not been determined and there

4633-664: The exonic region of an unrelated gene and they may act on genes on another chromosome . Enhancers are bound by p300-CBP and their location can be predicted by ChIP-seq against this family of coactivators. Gene expression in mammals is regulated by many cis-regulatory elements , including core promoters and promoter-proximal elements that are located near the transcription start sites of genes. Core promoters are sufficient to direct transcription initiation, but generally have low basal activity. Other important cis-regulatory modules are localized in DNA regions that are distant from

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4746-448: 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

4859-510: The mediator complex , which recruits polymerase II and the general transcription factors which then begin transcribing the genes. 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. That is one reason that introns polymorphisms may have effects although they are not translated . Enhancers can also be found at

4972-427: The transcription initiation site to affect transcription, as some have been found located 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 as first shown by in vivo competition experiments. Subsequently, molecular studies showed direct interactions with transcription factors and cofactors, including

5085-445: 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 , which is activated by wingless expression at all of the pigmented locations. Thus, in the evolution of

5198-416: The 1960s and their general characteristics were worked out in the 1970s by studying specific transcription factors in bacteria and bacteriophage . Promoters and regulatory sequences represent an abundant class of noncoding DNA but they mostly consist of a collection of relatively short sequences so they do not take up a very large fraction of the genome. The exact amount of regulatory DNA in mammalian genome

5311-429: The 1960s. Prokaryotic genomes contain genes for a number of other noncoding RNAs but noncoding RNA genes are much more common in eukaryotes. Typical classes of noncoding genes in eukaryotes include genes for small nuclear RNAs (snRNAs), small nucleolar RNAs (sno RNAs), microRNAs (miRNAs), short interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), and long noncoding RNAs (lncRNAs). In addition, there are

5424-479: The 5' end of the gene where transcription begins. They are the sites where RNA polymerase binds to initiate RNA synthesis. Every gene has a noncoding promoter. Regulatory elements are sites that control the transcription of a nearby gene. They are almost always sequences where transcription factors bind to DNA and these transcription factors can either activate transcription (activators) or repress transcription (repressors). Regulatory elements were discovered in

5537-412: The DNA scanning model, the DNA sequence looping model and the facilitated tracking model. In the DNA scanning model, the transcription factor and cofactor complex form at the cis -regulatory module and then continues to move along the DNA sequence until it finds the target gene promoter. In the looping model, the transcription factor binds to the cis -regulatory module, which then causes the looping of

5650-630: The DNA sequence and allows for the interaction with the target gene promoter. The transcription factor- cis -regulatory module complex causes the looping of the DNA sequence slowly towards the target promoter and forms a stable looped configuration. The facilitated tracking model combines parts of the two previous models. Besides experimentally determining CRMs, there are various bioinformatics algorithms for predicting them. Most algorithms try to search for significant combinations of transcription factor binding sites ( DNA binding sites ) in promoter sequences of co-expressed genes. More advanced methods combine

5763-502: The GADD45G enhancer in humans may contribute to an increase of certain neuronal populations and to forebrain expansion in humans. The development, differentiation and growth of cells and tissues require precisely regulated patterns of gene expression . Enhancers work as cis-regulatory elements to mediate both spatial and temporal control of development by turning on transcription in specific cells and/or repressing it in other cells. Thus,

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5876-518: The RNA polymerase II (pol II) enzyme bound to the promoter. Enhancers, when active, are generally transcribed from both strands of DNA with RNA polymerases acting in two different directions, producing two Enhancer RNAs (eRNAs) as illustrated in the Figure. Like mRNAs , these eRNAs are usually protected by their 5′ cap . An inactive enhancer may be bound by an inactive transcription factor. Phosphorylation of

5989-431: The active transcription factors and the associated co-factors at a specific time and place in the cell where this information is read and an output is given. CREs are often but not always upstream of the transcription site. CREs contrast with trans-regulatory elements (TREs) . TREs code for transcription factors. The genome of an organism contains anywhere from a few hundred to thousands of different genes, all encoding

6102-420: The amount of cells that transcribe a gene, but it does not affect the rate of transcription. Rheostatic response model describes cis-regulatory modules as regulators of the initiation rate of transcription of its associated gene. Promoters are CREs consisting of relatively short sequences of DNA which include the site where transcription is initiated and the region approximately 35 bp upstream or downstream from

6215-637: The appropriate set of TFs, and in the proper order, can RNA polymerase bind and begin transcribing the gene. Enhancers are CREs that influence (enhance) the transcription of genes on the same molecule of DNA and can be found upstream, downstream, within the introns , or even relatively far away from the gene they regulate. Multiple enhancers can act in a coordinated fashion to regulate transcription of one gene. A number of genome-wide sequencing projects have revealed that enhancers are often transcribed to long non-coding RNA (lncRNA) or enhancer RNA (eRNA), whose changes in levels frequently correlate with those of

6328-410: The arrangement could cancel out the function. Functional flexible cis -regulatory modules are called billboards. Their transcriptional output is the summation effect of the bound transcription factors. Enhancers affect the probability of a gene being activated, but have little or no effect on rate. The Binary response model acts like an on/off switch for transcription. This model will increase or decrease

6441-430: The associations are between single-nucleotide polymorphisms (SNPs) and the trait being examined and most of these SNPs are located in non-functional DNA. The association establishes a linkage that helps map the DNA region responsible for the trait but it does not necessarily identify the mutations causing the disease or phenotypic difference. SNPs that are tightly linked to traits are the ones most likely to identify

6554-414: The bacterial genome has a function. The amount of coding DNA in eukaryotes is usually a much smaller fraction of the genome because eukaryotic genomes contain large amounts of repetitive DNA not found in prokaryotes. The human genome contains somewhere between 1–2% coding DNA. The exact number is not known because there are disputes over the number of functional coding exons and over the total size of

6667-563: The complex pigmentation phenotype , the yellow pigment gene evolved enhancers responsive to the wingless signal and wingless expression evolved at new locations to produce novel wing patterns. Each cell typically contains several hundred of a special class of enhancers that stretch over many kilobases long DNA sequences, called " super-enhancers ". These enhancers contain a large number of binding sites for sequence-specific, inducible transcription factors, and regulate expression of genes involved in cell differentiation. During inflammation ,

6780-502: The definition of strict restrictions among the Transcription Factor Binding Sites (TFBSs) that compose the module in order to decrease the false positives rate. INSECT is designed to be user-friendly since it allows automatic retrieval of sequences and several visualizations and links to third-party tools in order to help users to find those instances that are more likely to be true regulatory sites. INSECT 2.0 algorithm

6893-465: The different logic operations, the output of a "cis"-regulatory module will also be influenced by prior events. 4) Cis -regulatory modules must interact with other regulatory elements. For the most part, even with the presence of functional overlap between cis -regulatory modules of a gene, the modules' inputs and outputs tend to not be the same. While the assumption of Boolean logic is important for systems biology , detailed studies show that in general

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7006-464: The ends of chromosomes. Both prokaryotic and eukarotic genomes are organized into large loops of protein-bound DNA. In eukaryotes, the bases of the loops are called scaffold attachment regions (SARs) and they consist of stretches of DNA that bind an RNA/protein complex to stabilize the loop. There are about 100,000 loops in the human genome and each SAR consists of about 100 bp of DNA, so the total amount of DNA devoted to SARs accounts for about 0.3% of

7119-479: The eukaryotic genome. Silencers are antagonists of enhancers that, when bound to its proper transcription factors called repressors , repress the transcription of the gene. Silencers and enhancers may be in close proximity to each other or may even be in the same region only differentiated by the transcription factor the region binds to. An enhancer may be located upstream or downstream of the gene it regulates. Furthermore, an enhancer does not need to be located near

7232-424: The evolution of DNA sequences to analyze the emergence of features that underly enhancer function. This allowed the design and production of a range of functioning synthetic enhancers for different cell types of the fruit fly brain. A second approach trained artificial intelligence models on single-cell DNA accessibility data and transferred the learned models towards the prediction of enhancers for selected tissues in

7345-588: The expression of genes distant from the gene that was originally transcribed to create them. For example, a transcription factor that regulates a gene on chromosome 6 might itself have been transcribed from a gene on chromosome 11 . The term trans-regulatory is constructed from the Latin root trans , which means "across from". There are cis-regulatory and trans-regulatory elements. Cis-regulatory elements are often binding sites for one or more trans-acting factors. To summarize, cis-regulatory elements are present on

7458-412: The expression of this gene were responsible for pelvic reduction in sticklebacks. Fish expressing only the freshwater allele 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

7571-401: The fruit fly Drosophila melanogaster , 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

7684-481: 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. Similarly, in highly diverged insects (separated by around 350 million years), similar gene expression patterns of several key genes

7797-481: The genome because each centromere can be millions of base pairs in length. In humans, for example, the sequences of all 24 centromeres have been determined and they account for about 6% of the genome. However, it is unlikely that all of this noncoding DNA is essential since there is considerable variation in the total amount of centromeric DNA in different individuals. Centromeres are another example of functional noncoding DNA sequences that have been known for almost half

7910-408: The genome is so much smaller than other genomes, this represents a considerable reduction in the amount of this DNA. The authors of the original 2013 article note that claims of additional functional elements in the non-coding DNA of animals do not seem to apply to plant genomes. According to a New York Times article, during the evolution of this species, "... genetic junk that didn't serve a purpose

8023-424: The genome that are major gene-regulatory elements. Enhancers control cell-type-specific gene expression programs, most often by looping through long distances to come in physical proximity with the promoters of their target genes. While there are hundreds of thousands of enhancer DNA regions, for a particular type of tissue only specific enhancers are brought into proximity with the promoters that they regulate. In

8136-418: The genome. Centromeres are the sites where spindle fibers attach to newly replicated chromosomes in order to segregate them into daughter cells when the cell divides. Each eukaryotic chromosome has a single functional centromere that is seen as a constricted region in a condensed metaphase chromosome. Centromeric DNA consists of a number of repetitive DNA sequences that often take up a significant fraction of

8249-504: The genome. The standard biochemistry and molecular biology textbooks describe non-coding nucleotides in mRNA located between the 5' end of the gene and the translation initiation codon. These regions are called 5'-untranslated regions or 5'-UTRs. Similar regions called 3'-untranslated regions (3'-UTRs) are found at the end of the gene. The 5'-UTRs and 3'UTRs are very short in bacteria but they can be several hundred nucleotides in length in eukaryotes. They contain short elements that control

8362-410: The genomes of germ cells . Mutation within these retro-transcribed sequences can inactivate the viral genome. Over 8% of the human genome is made up of (mostly decayed) endogenous retrovirus sequences, as part of the over 42% fraction that is recognizably derived of retrotransposons, while another 3% can be identified to be the remains of DNA transposons . Much of the remaining half of the genome that

8475-488: The human genome , HACNS1 has undergone the most change during the evolution of humans following the split with the ancestors of chimpanzees . 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

8588-442: The human genome. Pseudogenes are mostly former genes that have become non-functional due to mutation, but the term also refers to inactive DNA sequences that are derived from RNAs produced by functional genes ( processed pseudogenes ). Pseudogenes are only a small fraction of noncoding DNA in prokaryotic genomes because they are eliminated by negative selection. In some eukaryotes, however, pseudogenes can accumulate because selection

8701-464: The human genome. This means that 98–99% of the human genome consists of non-coding DNA and this includes many functional elements such as non-coding genes and regulatory sequences. Genome size in eukaryotes can vary over a wide range, even between closely related species. This puzzling observation was originally known as the C-value Paradox where "C" refers to the haploid genome size. The paradox

8814-487: The information processing that occurs on enhancers: HACNS1 (also known as CENTG2 and located in the Human Accelerated Region 2) is a gene enhancer "that may have contributed to the evolution of the uniquely opposable human thumb , and possibly also modifications in the ankle or foot that allow humans to walk on two legs". Evidence to date shows that of the 110,000 gene enhancer sequences identified in

8927-459: The information processing that they encode and the organization of their transcription factor binding sites. Additionally, cis -regulatory modules are also characterized by the way they affect the probability, proportion, and rate of transcription. Highly cooperative and coordinated cis -regulatory modules are classified as enhanceosomes . The architecture and the arrangement of the transcription factor binding sites are critical because disruption of

9040-468: The initiation of translation (5'-UTRs) and transcription termination (3'-UTRs) as well as regulatory elements that may control mRNA stability, processing, and targeting to different regions of the cell. DNA synthesis begins at specific sites called origins of replication . These are regions of the genome where the DNA replication machinery is assembled and the DNA is unwound to begin DNA synthesis. In most cases, replication proceeds in both directions from

9153-529: The initiation site (bp). In eukaryotes , promoters usually have the following four components: the TATA box , a TFIIB recognition site , an initiator , and the downstream core promoter element . It has been found that a single gene can contain multiple promoter sites. In order to initiate transcription of the downstream gene, a host of DNA-binding proteins called transcription factors (TFs) must bind sequentially to this region. Only once this region has been bound with

9266-1399: The integration site allows the identification of the enhancer sequence. The development of genomic and epigenomic technologies, however, has dramatically changed the outlook for cis-regulatory modules (CRM) discovery. Next-generation sequencing (NGS) methods now enable high-throughput functional CRM discovery assays, and the vastly increasing amounts of available data, including large-scale libraries of transcription factor-binding site (TFBS) motifs , collections of annotated, validated CRMs, and extensive epigenetic data across many cell types, are making accurate computational CRM discovery an attainable goal. An example of NGS-based approach called DNase-seq have enabled identification of nucleosome-depleted, or open chromatin regions, which can contain CRM. More recently techniques such as ATAC-seq have been developed which require less starting material. Nucelosome depleted regions can be identified in vivo through expression of Dam methylase , allowing for greater control of cell-type specific enhancer identification. Computational methods include comparative genomics , clustering of known or predicted TF-binding sites, and supervised machine-learning approaches trained on known CRMs. All of these methods have proven effective for CRM discovery, but each has its own considerations and limitations, and each

9379-421: The introns in other plant genomes. There are noncoding genes, including many copies of ribosomal RNA genes. The genome also contains telomere sequences and centromeres as expected. Much of the repetitive DNA seen in other eukaryotes has been deleted from the bladderwort genome since that lineage split from those of other plants. About 59% of the bladderwort genome consists of transposon-related sequences but since

9492-580: The likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors . Enhancers are cis -acting . They can be located up to 1 Mbp (1,000,000 bp) away from the gene, upstream or downstream from the start site. There are hundreds of thousands of enhancers in the human genome. They are found in both prokaryotes and eukaryotes. Active enhancers typically get transcribed as enhancer or regulatory non-coding RNA, whose expression levels correlate with mRNA levels of target genes. The first discovery of

9605-432: The logic of gene regulation is not Boolean. This means, for example, that in the case of a cis -regulatory module regulated by two transcription factors, experimentally determined gene-regulation functions can not be described by the 16 possible Boolean functions of two variables. Non-Boolean extensions of the gene-regulatory logic have been proposed to correct for this issue. Cis -regulatory modules can be characterized by

9718-531: 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 melanin . Recent work has shown that two enhancers in

9831-465: The neutral rate as expected for junk DNA. Some former pseudogenes have secondarily acquired a function and this leads some scientists to speculate that most pseudogenes are not junk because they have a yet-to-be-discovered function. Transposons and retrotransposons are mobile genetic elements . Retrotransposon repeated sequences , which include long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), account for

9944-458: The number of genes seems to be relatively constant, an issue termed the G-value Paradox . For example, the genome of the unicellular Polychaos dubium (formerly known as Amoeba dubia ) has been reported to contain more than 200 times the amount of DNA in humans (i.e. more than 600 billion pairs of bases vs a bit more than 3 billion in humans). The pufferfish Takifugu rubripes genome

10057-525: The other). The repeat segments are usually between 2 bp and 10 bp but longer ones are known. Highly repetitive DNA is rare in prokaryotes but common in eukaryotes, especially those with large genomes. It is sometimes called satellite DNA . Most of the highly repetitive DNA is found in centromeres and telomeres (see above) and most of it is functional although some might be redundant. The other significant fraction resides in short tandem repeats (STRs; also called microsatellites ) consisting of short stretches of

10170-444: 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. Traditionally, enhancers were identified by enhancer trap techniques using a reporter gene or by comparative sequence analysis and computational genomics. In genetically tractable models such as

10283-509: The parts of a gene that are transcribed into the precursor RNA sequence, but ultimately removed by RNA splicing during the processing to mature RNA. Introns are found in both types of genes: protein-coding genes and noncoding genes. They are present in prokaryotes but they are much more common in eukaryotic genomes. Group I and group II introns take up only a small percentage of the genome when they are present. Spliceosomal introns (see Figure) are only found in eukaryotes and they can represent

10396-427: 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,

10509-419: The promoter of a target gene. The loop is stabilized by a dimer of a connector protein (e.g. dimer of CTCF or YY1 ), with one member of the dimer anchored to its binding motif on the enhancer and the other member anchored to its binding motif on the promoter (represented by the red zigzags in the illustration). Several cell function specific transcription factors (there are about 1,600 transcription factors in

10622-521: The promoter of the gene set of interest. The possible cis-regulatory modules are then statistically analyzed and the significant combinations are graphically represented Active cis -regulatory modules in a genomic sequence have been difficult to identify. Problems in identification arise because often scientists find themselves with a small set of known transcription factors, so it makes it harder to identify statistically significant clusters of transcription factor binding sites. Additionally, high costs limit

10735-473: The relationship between the identified cis -regulatory module and the possible binding set of transcription factors. CRÈME examine clusters of target sites for transcription factors of interest. This program uses a database of confirmed transcription factor binding sites that were annotated across the human genome . A search algorithm is applied to the data set to identify possible combinations of transcription factors, which have binding sites that are close to

10848-420: The replication origin. The main features of replication origins are sequences where specific initiation proteins are bound. A typical replication origin covers about 100-200 base pairs of DNA. Prokaryotes have one origin of replication per chromosome or plasmid but there are usually multiple origins in eukaryotic chromosomes. The human genome contains about 100,000 origins of replication representing about 0.3% of

10961-433: The role of enhancers in morphological changes in threespine stickleback 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 is a homeobox gene involved in posterior limb development in vertebrates. Preliminary genetic analyses indicated that changes in

11074-429: 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. 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

11187-480: The same molecule of DNA as the gene they regulate whereas trans-regulatory elements can regulate genes distant from the gene from which they were transcribed. Non-coding DNA In bacteria , the coding regions typically take up 88% of the genome. The remaining 12% does not encode proteins, but much of it still has biological function through genes where the RNA transcript is functional (non-coding genes) and regulatory sequences, which means that almost all of

11300-477: The search for significant motifs with correlation in gene expression datasets between transcription factors and target genes. Both methods have been implemented, for example, in the ModuleMaster . Other programs created for the identification and prediction of cis -regulatory modules include: INSECT 2.0 is a web server that allows to search Cis-regulatory modules in a genome-wide manner. The program relies on

11413-815: The target gene mRNA. Silencers are CREs that can bind transcription regulation factors (proteins) called repressors , thereby preventing transcription of a gene. The term "silencer" can also refer to a region in the 3' untranslated region of messenger RNA, that binds proteins which suppress translation of that mRNA molecule, but this usage is distinct from its use in describing a CRE. Operators are CREs in prokaryotes and some eukaryotes that exist within operons , where they can bind proteins called repressors to affect transcription. CREs have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have

11526-408: The transcription factor NF-κB facilitates remodeling of chromatin in a manner that selectively redistributes cofactors from high-occupancy enhancers, thereby repressing genes involved in maintaining cellular identify whose expression they enhance; at the same time, this F-κB-driven remodeling and redistribution activates other enhancers that guide changes in cellular function through inflammation. As

11639-423: The transcription factor may activate it and that activated transcription factor may then activate the enhancer to which it is bound (see small red star representing phosphorylation of transcription factor bound to enhancer in the illustration). An activated enhancer begins transcription of its RNA before activating transcription of messenger RNA from its target gene. As of 2005 , there are two different theories on

11752-456: The transcription start site of the gene. Some occur within a gene and a few are located downstream of the transcription termination site. In eukaryotes, there are some regulatory sequences that are located at a considerable distance from the promoter region. These distant regulatory sequences are often called enhancers but there is no rigorous definition of enhancer that distinguishes it from other transcription factor binding sites. Introns are

11865-502: The transcription start sites. These include enhancers, silencers , insulators and tethering elements. Among this constellation of elements, enhancers and their associated transcription factors have a leading role in the regulation of gene expression. An enhancer localized in a DNA region distant from the promoter of a gene can have a very large effect on gene expression, with some genes undergoing up to 100-fold increased expression due to an activated enhancer. Enhancers are regions of

11978-530: The use of large whole genome tiling arrays . An example of a cis-acting regulatory sequence is the operator in the lac operon . This DNA sequence is bound by the lac repressor , which, in turn, prevents transcription of the adjacent genes on the same DNA molecule. The lac operator is, thus, considered to "act in cis" on the regulation of the nearby genes. The operator itself does not code for any protein or RNA . In contrast, trans-regulatory elements are diffusible factors, usually proteins, that may modify

12091-437: The vicinity of the genes that they regulate. CREs typically regulate gene transcription by binding to transcription factors . A single transcription factor may bind to many CREs, and hence control the expression of many genes ( pleiotropy ). The Latin prefix cis means "on this side", i.e. on the same molecule of DNA as the gene(s) to be transcribed. CRMs are stretches of DNA , usually 100–1000 DNA base pairs in length, where

12204-531: The visceral endoderm. Later in development, Fox1 binding to the ASE drives Nodal expression on the left side of the lateral plate mesoderm , thus establishing left-right asymmetry necessary for asymmetric organ development in the mesoderm. Establishing three germ layers during gastrulation 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

12317-403: Was 1,500 Mb in size. The bladderwort genome has roughly the same number of genes as other plants but the total amount of coding DNA comes to about 30% of the genome. The remainder of the genome (70% non-coding DNA) consists of promoters and regulatory sequences that are shorter than those in other plant species. The genes contain introns but there are fewer of them and they are smaller than

12430-610: Was expunged, and the necessary stuff was kept." According to Victor Albert of the University of Buffalo, the plant is able to expunge its so-called junk DNA and "have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the junk. Junk is not needed." There are two types of genes : protein coding genes and noncoding genes . Noncoding genes are an important part of non-coding DNA and they include genes for transfer RNA and ribosomal RNA . These genes were discovered in

12543-503: Was found to be regulated through similarly constituted CRMs although these CRMs do not show any appreciable sequence conservation detectable by standard sequence alignment methods such as BLAST . The enhancers determining early segmentation in Drosophila melanogaster embryos are among the best characterized developmental enhancers. In the early fly embryo, the gap gene transcription factors are responsible for activating and repressing

12656-539: Was previously published and the algorithm and theory behind it explained in Stubb uses hidden Markov models to identify statistically significant clusters of transcription factor combinations. It also uses a second related genome to improve the prediction accuracy of the model. Bayesian Networks use an algorithm that combines site predictions and tissue-specific expression data for transcription factors and target genes of interest. This model also uses regression trees to depict

12769-528: Was resolved with the discovery that most of the differences were due to the expansion and contraction of repetitive DNA and not the number of genes. Some researchers speculated that this repetitive DNA was mostly junk DNA . The reasons for the changes in genome size are still being worked out and this problem is called the C-value Enigma. This led to the observation that the number of genes does not seem to correlate with perceived notions of complexity because

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