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124-400: The placement and bonding to form G-quadruplexes is not random and serve very unusual functional purposes. The quadruplex structure is further stabilized by the presence of a cation , especially potassium , which sits in a central channel between each pair of tetrads. They can be formed of DNA , RNA , LNA , and PNA , and may be intramolecular , bimolecular , or tetramolecular. Depending on

248-452: A tautomeric shift from the original damage guanine, 8-oxo-Gua, and represents DNA damage that causes changes in the structure. This form allows for the base excision repair (BER) enzyme OGG1 to bind and remove the oxidative damage with the help of APE1, resulting in an AP site. Moreover, an AP site is a location in DNA that has neither a purine or a pyrimidine base due to DNA damage, they are

372-430: A big potential to modify the genetic control in a host organism. The movement of TEs is a driving force of genome evolution in eukaryotes because their insertion can disrupt gene functions, homologous recombination between TEs can produce duplications, and TE can shuffle exons and regulatory sequences to new locations. Retrotransposons are found mostly in eukaryotes but not found in prokaryotes. Retrotransposons form

496-468: A cell; the helicases WRN and Bloom syndrome protein have a high affinity for resolving DNA G-quadruplexes. The DEAH/RHA helicase, DHX36 , has also been identified as a key G-quadruplex resolvase. In 2009, a metastasis suppressor protein NM23H2 (also known as NME2) was found to directly interact with G-quadruplex in the promoter of the c-myc gene, and transcriptionally regulate c-myc. More recently, NM23H2

620-506: A defined structure that are able to change their location in the genome. TEs are categorized as either as a mechanism that replicates by copy-and-paste or as a mechanism that can be excised from the genome and inserted at a new location. In the human genome, there are three important classes of TEs that make up more than 45% of the human DNA; these classes are The long interspersed nuclear elements (LINEs), The interspersed nuclear elements (SINEs), and endogenous retroviruses. These elements have

744-517: A gain-of-function mechanism, which is when the altered gene product has a new function or new expression of a gene; this has been detected in the C9orf72 (chromosome 9 open reading frame 72). Antisense therapy is the process by which synthesized strands of nucleic acids are used to bind directly and specifically to the mRNA produced by a certain gene, which will inactivate it. Antisense oligonucleotides (ASOs) are commonly used to target C9orf72 RNA of

868-411: A high guanine association became apparent in the early 1960s, through the identification of gel-like substances associated with guanines. More specifically, this research detailed the four-stranded DNA structures with a high association of guanines, which was later identified in eukaryotic telomeric regions of DNA in the 1980s. The importance of discovering G-quadruplex structure was described through

992-492: A high affinity for porphyrin rings which makes them effective anticancer agents. However, TMPyP4 has been limited for used due to its non-selectivity toward cancer cell telomeres and normal double stranded DNA (dsDNA). To address this issue analog of TMPyP4, it was synthesized known as 5Me which targets only G quadruplex DNA which inhibits cancer growth more effectively than TMPyP4. Ligand design and development remains an important field of research into therapeutic reagents due to

1116-520: A huge role in its repair. These enzymes participate in BER to repair certain DNA lesions such as 7,8-dihydro-8-oxoguanine (8-oxoG), which forms under oxidative stress to guanine bases. Guanine (G) bases in G-quadruplex have the lowest redox potential causing it to be more susceptible to the formation of 8-oxoguanine (8-oxoG), an endogenous oxidized DNA base damage in the genome. Due to Guanine having

1240-534: A large portion of the genomes of many eukaryotes. A retrotransposon is a transposable element that transposes through an RNA intermediate. Retrotransposons are composed of DNA , but are transcribed into RNA for transposition, then the RNA transcript is copied back to DNA formation with the help of a specific enzyme called reverse transcriptase. A retrotransposon that carries reverse transcriptase in its sequence can trigger its own transposition but retrotransposons that lack

1364-473: A longer sequence context. In the DNA polymerase stop assay, the formation of a G-quadruplex in a DNA template can act as a roadblock and cause polymerase stalling, which halts the primer extension. The dimethyl sulfate (DMS) followed by the piperidine cleavage assay is based on the fact that the formation of a G-quadruplex will prohibit the N7 guanine methylation caused by DMS, leading to a protection pattern observed at

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1488-414: A lower electron reduction potential than the other nucleotides bases, 8-oxo-2'-deoxyguanosine (8-oxo-dG), is a known major product of DNA oxidation. Its concentration is used as a measurement of oxidative stress within a cell. When DNA undergoes oxidative damage, a possible structural change in guanine, after ionizing radiation, gives rise to an enol form, 8-OH-Gua. This oxidative product is formed through

1612-405: A main driving role to generate genetic novelty and natural genome editing. Works of science fiction illustrate concerns about the availability of genome sequences. Michael Crichton's 1990 novel Jurassic Park and the subsequent film tell the story of a billionaire who creates a theme park of cloned dinosaurs on a remote island, with disastrous outcomes. A geneticist extracts dinosaur DNA from

1736-413: A major role in shaping the genome. Duplication may range from extension of short tandem repeats , to duplication of a cluster of genes, and all the way to duplication of entire chromosomes or even entire genomes . Such duplications are probably fundamental to the creation of genetic novelty. Horizontal gene transfer is invoked to explain how there is often an extreme similarity between small portions of

1860-467: A major theme of the book. The 1997 film Gattaca is set in a futurist society where genomes of children are engineered to contain the most ideal combination of their parents' traits, and metrics such as risk of heart disease and predicted life expectancy are documented for each person based on their genome. People conceived outside of the eugenics program, known as "In-Valids" suffer discrimination and are relegated to menial occupations. The protagonist of

1984-428: A new site. This cut-and-paste mechanism typically reinserts transposons near their original location (within 100 kb). DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C. elegans . Genome size is the total number of the DNA base pairs in one copy of a haploid genome. Genome size varies widely across species. Invertebrates have small genomes, this

2108-404: A positive or negative manner. The c-kit oncogene deals with a pathway that encodes an RTK, which was shown to have elevated expression levels in certain types of cancer. The rich guanine sequence of this promoter region has shown the ability to form a variety of quadruplexes. Current research on this pathway is focusing on discovering the biological function of this specific quadruplex formation on

2232-461: A propensity to form g-quadruplexes, are located at the terminal ends of chromosomes and help maintain genome integrity by protecting these vulnerable terminal ends from instability. These telomeric regions are characterized by long regions of double-stranded CCCTAA:TTAGGG repeats. The repeats end with a 3’ protrusion of between 10 and 50 single-stranded TTAGGG repeats. The heterodimeric complex ribonucleoprotein enzyme telomerase adds TTAGGG repeats at

2356-438: A quadruplex folding rule have been performed, which have identified 376,000 Putative Quadruplex Sequences (PQS) in the human genome , although not all of these probably form in vivo . A similar studies have identified putative G-quadruplexes in prokaryotes , namely the bacterium E. coli . There are several possible models for how quadruplexes could influence gene activity, either by upregulation or downregulation . One model

2480-465: A quadruplex formed entirely from a single strand is called an intramolecular quadruplex. Depending on how the individual runs of guanine bases are arranged in a bimolecular or intramolecular quadruplex, a quadruplex can adopt one of a number of topologies with varying loop configurations. If all strands of DNA proceed in the same direction, the quadruplex is termed parallel. For intramolecular quadruplexes, this means that any loop regions present must be of

2604-415: A reference, whereas analyses of coverage depth and mapping topology can provide details regarding structural variations such as chromosomal translocations and segmental duplications. DNA sequences that carry the instructions to make proteins are referred to as coding sequences. The proportion of the genome occupied by coding sequences varies widely. A larger genome does not necessarily contain more genes, and

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2728-487: A reverse transcriptase must use reverse transcriptase synthesized by another retrotransposon. Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome. Retrotransposons can be divided into long terminal repeats (LTRs) and non-long terminal repeats (Non-LTRs). Long terminal repeats (LTRs) are derived from ancient retroviral infections, so they encode proteins related to retroviral proteins including gag (structural proteins of

2852-580: A role in meiosis . However, as currently used in molecular biology, the term G4 can mean G-quadruplexes of any molecularity. Longer sequences, which contain two contiguous runs of three or more guanine bases, where the guanine regions are separated by one or more bases, only require two such sequences to provide enough guanine bases to form a quadruplex. These structures, formed from two separate G-rich strands, are termed bimolecular quadruplexes. Finally, sequences which contain four distinct runs of guanine bases can form stable quadruplex structures by themselves, and

2976-753: A single G-quadruplex sequence. However, a cationic porphyrin known as TMPyP4 is able to bind to the C9orf72 GGGGCC repeat region, which causes the G-quadruplex repeat region to unfold and lose its interactions with proteins causing it to lose its functionality. Small-molecule ligands, composed primarily of lead, can target GGGGCC repeat regions as well and ultimately decreased both repeat-associated non-ATG translation and RNA foci in neuron cells derived from patients with Amyotrophic lateral sclerosis (ALS). This provides evidence that small-molecule ligands are an effective and efficient process to target GGGGCC regions, and that specificity for small-molecule ligand binding

3100-404: A single, linear molecule of DNA, but some are made up of a circular DNA molecule. Prokaryotes and eukaryotes have DNA genomes. Archaea and most bacteria have a single circular chromosome , however, some bacterial species have linear or multiple chromosomes. If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, and if

3224-424: A vocabulary into which genome fits systematically. It is very difficult to come up with a precise definition of "genome." It usually refers to the DNA (or sometimes RNA) molecules that carry the genetic information in an organism but sometimes it is difficult to decide which molecules to include in the definition; for example, bacteria usually have one or two large DNA molecules ( chromosomes ) that contain all of

3348-595: Is a distinctive feature of G-quadruplex structure. Another approach for detection of G-quadruplexes includes nanopore -based methods. Firstly, it was shown that biological nanopores can detect G-quadruplexes based on size exclusion and specific interaction of G-quadruplex and protein nanocavity. The novel approach combines solid-state nanopores and DNA nanotechnology for label-free detection of G-quadruplexes, for their mapping on dsDNA, and for monitoring G-quadruplex formation. G-quadruplexes have been implicated in neurological disorders through two main mechanisms. The first

3472-447: Is a feasible goal for the scientific community. Metal complexes have a number of features that make them particularly suitable as G4 DNA binders and therefore as potential drugs. While the metal plays largely a structural role in most G4 binders, there are also examples where it interacts directly with G4s by electrostatic interactions or direct coordination with nucleobases. Cation Too Many Requests If you report this error to

3596-486: Is a widely expressed protein coded by the FMR1 gene that binds to G-quadruplex secondary structures in neurons and is involved in synaptic plasticity . FMRP acts as a negative regulator of translation, and its binding stabilizes G-quadruplex structures in mRNA transcripts, inhibiting ribosome elongation of mRNA in the neuron's dendrite and controlling the timing of the transcript's expression. Mutations of this gene can cause

3720-485: Is also correlated to a small number of transposable elements. Fish and Amphibians have intermediate-size genomes, and birds have relatively small genomes but it has been suggested that birds lost a substantial portion of their genomes during the phase of transition to flight.  Before this loss, DNA methylation allows the adequate expansion of the genome. In humans, the nuclear genome comprises approximately 3.1 billion nucleotides of DNA, divided into 24 linear molecules,

3844-497: Is also directly regulated through promoter G-quadruplex by interaction with the transcription factor NM23H2 where epigenetic modifications were dependent on NM23H2-G-quadruplex association. Recently, hTERT epigenetic regulation reported to be mediated through interaction of hTERT promoter G-quadruplex with the telomeric factor TRF2. Another gene pathway deals with the VEGF gene, Vascular Endothelial Growth Factor, which remains involved in

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3968-438: Is an enzyme responsible for the promotion and the formation of G-quadruplex structures. APE1 is mainly in charge of repairing damage caused to AP sites through the BER pathway. APE1 is considered to be very crucial as AP site damage is known to be the most recurring type of endogenous damage to DNA. The oxidation of certain purine bases, like guanine, forms oxidized nucleotides that impairs DNA function by mismatching nucleotides in

4092-432: Is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes. Long interspersed elements (LINEs) encode genes for reverse transcriptase and endonuclease, making them autonomous transposable elements. The human genome has around 500,000 LINEs, taking around 17% of the genome. Short interspersed elements (SINEs) are usually less than 500 base pairs and are non-autonomous, so they rely on

4216-444: Is carried in plasmids . For this, the word genome should not be used as a synonym of chromosome . Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from Jack jumper ants and an asexual nemotode , which each have only one pair, to a fern species that has 720 pairs. It is surprising the amount of DNA that eukaryotic genomes contain compared to other genomes. The amount

4340-564: Is even more than what is necessary for DNA protein-coding and noncoding genes due to the fact that eukaryotic genomes show as much as 64,000-fold variation in their sizes. However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs). A typical human cell has two copies of each of 22 autosomes , one inherited from each parent, plus two sex chromosomes , making it diploid. Gametes , such as ova, sperm, spores, and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to

4464-492: Is facilitated by active DNA demethylation , a process that entails the DNA base excision repair pathway. This pathway is employed in the erasure of CpG methylation (5mC) in primordial germ cells. The erasure of 5mC occurs via its conversion to 5-hydroxymethylcytosine (5hmC) driven by high levels of the ten-eleven dioxygenase enzymes TET1 and TET2 . Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to

4588-440: Is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice , a mouse , the plant Arabidopsis thaliana , the puffer fish , and the bacteria E. coli . In December 2013, scientists first sequenced the entire genome of a Neanderthal , an extinct species of humans . The genome

4712-401: Is rather exceptional, eukaryotes generally have these features in their genes and their genomes contain variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is composed of repetitive DNA. High-throughput technology makes sequencing to assemble new genomes accessible to everyone. Sequence polymorphisms are typically discovered by comparing resequenced isolates to

4836-408: Is responsible for maintaining length of telomeres and is involved in around 85% of all cancers . This is an active target of drug discovery, including telomestatin . Quadruplexes are present in locations other than at the telomere . Analysis of human, chimpanzee, mouse and rat genomes showed enormous number of potential G-quadruplex (pG4)-forming sequences in non-telomeric regions. A large number of

4960-562: Is shown below, with G-quadruplex formation in or near a promoter blocking transcription of the gene, and hence de-activating it. In another model, quadruplex formed at the non-coding DNA strand helps to maintain an open conformation of the coding DNA strand and enhance an expression of the respective gene. It has been suggested that quadruplex formation plays a role in immunoglobulin heavy chain switching. As cells have evolved mechanisms for resolving (i.e., unwinding) quadruplexes that form. Quadruplex formation may be potentially damaging for

5084-462: Is the complete list of the nucleotides (A, C, G, and T for DNA genomes) that make up all the chromosomes of an individual or a species. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity. In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish

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5208-416: Is the fluidity in the position of the loops to better associate with the ligand side chains. TMPyP4, a cationic porphyrin, is a more well known G4 binding ligand that helps to repress c-Myc.  The way in which TMPyP4 binds to G4's is similar to MM41, with the ring stacking onto the external G-quartet and side chains associating to the loops of G4's. When designing ligands to be bound to G-quadruplexes,

5332-410: Is the same for all vertebrates ) consists of many repeats of the sequenced (TTAGGG), and the quadruplexes formed by this structure can be in bead-like structures of 5 nm to 8 nm in size and have been well studied by NMR , TEM and X-ray crystal structure determination. The formation of these quadruplexes in telomeres has been shown to decrease the activity of the enzyme telomerase , which

5456-523: Is through expansions of G-repeats within genes that lead to the formation of G-quadruplex structures that directly cause disease, as is the case with the C9orf72 gene and amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD). The second mechanism is through mutations that affect the expression of G-quadruplex binding proteins, as seen in the fragile X mental retardation gene 1 (FMR1) gene and Fragile X Syndrome . The C9orf72 gene codes for

5580-421: Is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multi-cellular organisms (see developmental biology ). The work is both in vivo and in silico . There are many enormous differences in size in genomes, specially mentioned before in

5704-407: Is unlikely that all pG4s would form in vivo. The proto-oncogene c-myc forms a quadruplex in a nuclease hypersensitive region critical for gene activity. Other genes shown to form G-quadruplexes in their promoter regions include the chicken β-globin gene , human ubiquitin -ligase RFP2, and the proto-oncogenes c-kit , bcl-2 , VEGF , H-ras and N-ras . Genome -wide surveys based on

5828-601: The Genoscope in Paris. Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity. The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service, to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA.LAND at the New York Genome Center , an example both of

5952-406: The economies of scale and of citizen science . Viral genomes can be composed of either RNA or DNA. The genomes of RNA viruses can be either single-stranded RNA or double-stranded RNA , and may contain one or more separate RNA molecules (segments: monopartit or multipartit genome). DNA viruses can have either single-stranded or double-stranded genomes. Most DNA virus genomes are composed of

6076-455: The mitochondria . In addition, algae and plants have chloroplast DNA. Most textbooks make a distinction between the nuclear genome and the organelle (mitochondria and chloroplast) genomes so when they speak of, say, the human genome, they are only referring to the genetic material in the nucleus. This is the most common use of 'genome' in the scientific literature. Most eukaryotes are diploid , meaning that there are two of each chromosome in

6200-418: The thermodynamics of molecular crowding indicate that the antiparallel g-quadruplex is stabilized by molecular crowding. This effect seems to be mediated by alteration of the hydration of the DNA and its effect on Hoogsteen base pair bonding. These quadruplexes seemed to readily occur at the ends of chromosome . In addition, the propensity of g-quadruplex formation during transcription in RNA sequences with

6324-423: The 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon , Methanococcus jannaschii , was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of complete genome sequences

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6448-533: The 3’ end of DNA strands. At these 3’ end protrusions, the G-rich overhang can form secondary structures such as G-quadruplexes if the overhang is longer than four TTAGGG repeats. The presence of these structures prevent telomere elongation by the telomerase complex. Telomeric repeats in a variety of organisms have been shown to form these quadruplex structures in vitro , and subsequently they have also been shown to form in vivo . The human telomeric repeat (which

6572-519: The CD experiments under non-G-quadruplex stabilizing (Li+) and G-quadruplex stabilizing conditions (such as K+ or with G-quadruplex ligands), and scan toward the far-UV region (180–230 nm). Likewise, the thermostability of the G-quadruplex structure can be identified by observing the UV signal at 295 nm. Upon G-quadruplex melting, the UV absorbance at 295 nm decreases, leading to a hypochromic shift that

6696-532: The DNA G-quadruplex region after piperidine cleavage. The topology of the G-quadruplex structure can be determined by monitoring the positive or negative circular dichroism (CD) signals at specific wavelengths. Parallel G-quadruplexes have negative and positive CD signals at 240 and 262 nm, respectively, whereas antiparallel G-quadruplexes place these signals at 262 and 295 nm, respectively. To verify G-quadruplex formation, one should also perform

6820-618: The First International G-quadruplex Meeting held in April 2007 in Louisville, Kentucky. In 2006, the prevalence of G-quadruplexes within gene promoters of several bacterial genomes was reported predicting G-quadruplex-mediated gene regulation. With the abundance of G-quadruplexes in vivo , these structures hold a biologically relevant role through interactions with the promoter regions of oncogenes and

6944-504: The G 4 C 2 repeats in DNA have the ability to form mixed parallel-antiparallel G-quadruplex structures as well. These RNA transcripts containing G 4 C 2 repeats were shown to bind and separate a wide variety of proteins, including nucleolin . Nucleolin is involved in the synthesis and maturation of ribosomes within the nucleus, and separation of nucleolin by the mutated RNA transcripts impairs nucleolar function and ribosomal RNA synthesis. Fragile X mental retardation protein (FMRP)

7068-515: The G-quadruplex GGGGCC expansion repeat region, which has lowered the toxicity in cellular models of C9orf72. ASOs have previously been used to restore normal phenotypes in other neurological diseases that have gain-of-function mechanisms, the only difference is that it was used in the absence of G-quadruplex expansion repeat regions. The G-quadruplex decoy strategy is another promising approach for targeting cancer cells by exploiting

7192-529: The G4 loops and the ligand side chains can align. Identifying and predicting sequences which have the capacity to form quadruplexes is an important tool in further understanding their role. Generally, a simple pattern match is used for searching for possible intrastrand quadruplex forming sequences: d(G 3+ N 1-7 G 3+ N 1-7 G 3+ N 1-7 G 3+ ), where N is any nucleotide base (including guanine ). This rule has been widely used in on-line algorithms . Although

7316-682: The Wikimedia System Administrators, please include the details below. Request from 172.68.168.226 via cp1108 cp1108, Varnish XID 219242962 Upstream caches: cp1108 int Error: 429, Too Many Requests at Thu, 28 Nov 2024 07:51:26 GMT Genome In the fields of molecular biology and genetics , a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses ). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of

7440-489: The abundance of G-quadruplexes and their multiple conformational differences. One type of ligand involving a Quindoline derivative, SYUIQ-05, utilizes the stabilization of G-quadruplexes in promoter regions to inhibit the production of both the c-Myc protein product and the human telomerase reverse transcriptase (hTERT). This main pathway of targeting this region results in the lack of telomerase elongation, leading to arrested cell development. Further research remains necessary for

7564-577: The abundant guanine sequence in the promoter region of this specific pathway. The cyclin-dependent cell cycle checkpoint kinase inhibitor-1 CDKN1A (also known as p21) gene harbours promoter G-quadruplex. Interaction of this G-quadruplex with TRF2 (also known as TERF2) resulted in epigenetic regulation of p21, which was tested using the G-quadruplex-binding ligand 360A. Hypoxia inducible factor 1ɑ, HIF-1ɑ, remains involved in cancer signaling through its binding to Hypoxia Response Element, HRE, in

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7688-412: The blood of ancient mosquitoes and fills in the gaps with DNA from modern species to create several species of dinosaurs. A chaos theorist is asked to give his expert opinion on the safety of engineering an ecosystem with the dinosaurs, and he repeatedly warns that the outcomes of the project will be unpredictable and ultimately uncontrollable. These warnings about the perils of using genomic information are

7812-518: The c-kit pathway, while this quadruplex sequence has been noticed in various species. The RET oncogene functions in the transcription of kinase which has been abundant in certain types of cancer. The guanine rich sequence in the promoter region for this pathway exudes a necessity for baseline transcription of this receptor tyrosine kinase. In certain types of cancers, the RET protein has shown increased expression levels. The research on this pathway suggested

7936-459: The c-myc pathway, plays an integral role in the regulation of a protein product, c-Myc. With this product, the c-Myc protein functions in the processes of apoptosis and cell growth or development and as a transcriptional control on human telomerase reverse transcriptase . Interaction of c-Myc promoter G-quadruplex with NM23H2 was shown to regulate c-Myc in cancer cells in 2009 Regulation of c-myc through Human telomerase reverse transcriptase (hTERT)

8060-482: The cell. This causes replication of damaged and cancerous cells. For therapeutic advances, stabilizing the G-quadruplexes of cancerous cells can inhibit cell growth and replication leading to the cell's death . Along with the association of G-quadruplexes in telomeric regions of DNA, G-quadruplex structures have been identified in various human proto- oncogene promoter regions. The structures most present in

8184-549: The cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and already partially replicated chromosomes. Most prokaryotes have very little repetitive DNA in their genomes. However, some symbiotic bacteria (e.g. Serratia symbiotica ) have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins. Some bacteria have auxiliary genetic material, also part of their genome, which

8308-412: The chromatin, forming acetylated APE1 (AcAPE1). AcAPE1 is very crucial to the BER pathway as it acts as a transcriptional coactivator or corepressor, functioning to load transcription factors (TF) into the site of damage allowing it to regulate the gene expression. AcAPE1 is also very important since it allows APE1 to bind for longer periods of time by delay of its dissociation from the sequence, allowing

8432-478: The chromosomes in the nucleus, organelles such as the chloroplasts and mitochondria have their own DNA. Mitochondria are sometimes said to have their own genome often referred to as the " mitochondrial genome ". The DNA found within the chloroplast may be referred to as the " plastome ". Like the bacteria they originated from, mitochondria and chloroplasts have a circular chromosome. Unlike prokaryotes where exon-intron organization of protein coding genes exists but

8556-455: The co-discoverers of the structure of DNA. Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than a genome sequence and aids in navigating around the genome. The Human Genome Project was organized to map and to sequence the human genome . A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at

8680-415: The complete nucleotide sequence of a viral RNA-genome ( Bacteriophage MS2 ). The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174 , of 5386 base pairs. The first bacterial genome to be sequenced was that of Haemophilus influenzae , completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of

8804-617: The decoy can intercept associated transcription factors and bind them leading to the regulation of gene expression. Decoys have been successfully demonstrated to inhibit oncogenic KRAS in SCID mice leading to reduced tumour growth and increased median survival time. Another commonly used technique is the utilization of small-molecule ligands . These can be used to target G-quadruplex regions that cause neurological disorders. Approximately 1,000 various G-quadruplex ligands exist in which they are able to interact via their aromatic rings ; this allows

8928-445: The details of any particular genes and their products. Researchers compare traits such as karyotype (chromosome number), genome size , gene order, codon usage bias , and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown 2002; Saccone and Pesole 2003; Benfey and Protopapas 2004; Gibson and Muse 2004; Reese 2004; Gregory 2005). Duplications play

9052-672: The development of Fragile X Syndrome, autism , and other neurological disorders. Specifically, Fragile X Syndrome is caused by an increase from 50 to over 200 CGG repeats within exon 13 of the FMR1 gene. This repeat expansion promotes DNA methylation and other epigenetic heterochromatin modifications of FMR1 that prevent the transcription of the gene, leading to pathological low levels of FMRP. Antisense-mediated interventions and small-molecule ligands are common strategies used to target neurological diseases linked to G-quadruplex expansion repeats. Therefore, these techniques are especially advantageous for targeting neurological diseases that have

9176-525: The direction of the strands or parts of a strand that form the tetrads, structures may be described as parallel or antiparallel . G-quadruplex structures can be computationally predicted from DNA or RNA sequence motifs, but their actual structures can be quite varied within and between the motifs, which can number over 100,000 per genome. Their activities in basic genetic processes are an active area of research in telomere, gene regulation, and functional genomics research. The identification of structures with

9300-597: The discovery of a single gene target to minimize unwanted reactivity with more efficient antitumor activity. One way of inducing or stabilizing G-quadruplex formation is to introduce a molecule which can bind to the G-quadruplex structure. A number of ligands , which can be both small molecules and proteins , can bind to the G-quadruplex. These ligands can be naturally occurring or synthetic. This has become an increasingly large field of research in genetics, biochemistry, and pharmacology. Cationic porphyrins have been shown to bind intercalatively with G-quadruplexes, as well as

9424-441: The essential genetic material but they also contain smaller extrachromosomal plasmid molecules that carry important genetic information. The definition of 'genome' that is commonly used in the scientific literature is usually restricted to the large chromosomal DNA molecules in bacteria. Eukaryotic genomes are even more difficult to define because almost all eukaryotic species contain nuclear chromosomes plus extra DNA molecules in

9548-599: The first end-to-end human genome sequence in March 2022. The term genome was created in 1920 by Hans Winkler , professor of botany at the University of Hamburg , Germany. The website Oxford Dictionaries and the Online Etymology Dictionary suggest the name is a blend of the words gene and chromosome . However, see omics for a more thorough discussion. A few related -ome words already existed, such as biome and rhizome , forming

9672-411: The formation of a G-quadruplex in the promoter region and an applicable target for therapeutic treatments. Another oncogene pathway involving PDGF-A, platelet-derived growth factor, involves the process of wound healing and function as mitogenic growth factors for cells. High levels of expression of PDGF have been associated with increased cell growth and cancer. The presence of a guanine-rich sequence in

9796-536: The formation of g-quadruplex structures and loading the transcriptional factors onto the AP site G-quadruplex forming sequences are prevalent in eukaryotic cells, especially in telomeres, 5` untranslated strands, and translocation hot spots. G-quadruplexes can inhibit normal cell function, and in healthy cells, are easily and readily unwound by helicase .  However, in cancer cells that have mutated helicase these complexes cannot be unwound and leads to potential damage of

9920-637: The formation of the G-quadruplex. DNA Oxidation Contribution to Diseases Furthermore, the concentration of 8-oxo-dG is a known biomarker of oxidative stress within a cell, and excessive amount of oxidative stress has been linked to carcinogenesis and other diseases. When produced, 8-oxo-dG, has the ability to inactivate OGG1, thus preventing the repair of DNA damage caused by the oxidation of guanine. The possible inactivation allows for un-repaired DNA damages to gather in non-replicating cells, like muscle, and can cause aging as well. Moreover, oxidative DNA damage like 8-oxo-dG contributes to carcinogenesis through

10044-458: The genome such as regulatory sequences (see non-coding DNA ), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome . Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics . The genomes of many organisms have been sequenced and various regions have been annotated. The Human Genome Project

10168-412: The genome where AP site damage occurrence has been significant. Another genome-wide mapping sequencing method known as ChIP-sequencing , was utilized to map both; damage in AP sites, and the enzyme responsible for its repair, AP endonuclease 1 (APE1). Both of these genome-wide mapping sequencing methods, ChIP-sequencing and ARP, have indicated that AP site damage occurrence is nonrandom. AP site damage

10292-406: The genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes . Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes. Recent empirical data suggest an important role of viruses and sub-viral RNA-networks to represent

10416-403: The human genome , many guanine-rich sequences that had the potential to form quadruplexes were discovered. Depending on cell type and cell cycle, mediating factors such as DNA-binding proteins on chromatin , composed of DNA tightly wound around histone proteins, and other environmental conditions and stresses affect the dynamic formation of quadruplexes. For instance, quantitative assessments of

10540-455: The human genome All the cells of an organism originate from a single cell, so they are expected to have identical genomes; however, in some cases, differences arise. Both the process of copying DNA during cell division and exposure to environmental mutagens can result in mutations in somatic cells. In some cases, such mutations lead to cancer because they cause cells to divide more quickly and invade surrounding tissues. In certain lymphocytes in

10664-425: The human genome and 9% of the fruit fly genome. Tandem repeats can be functional. For example, telomeres are composed of the tandem repeat TTAGGG in mammals, and they play an important role in protecting the ends of the chromosome. In other cases, expansions in the number of tandem repeats in exons or introns can cause disease . For example, the human gene huntingtin (Htt) typically contains 6–29 tandem repeats of

10788-517: The human immune system, V(D)J recombination generates different genomic sequences such that each cell produces a unique antibody or T cell receptors. During meiosis , diploid cells divide twice to produce haploid germ cells. During this process, recombination results in a reshuffling of the genetic material from homologous chromosomes so each gamete has a unique genome. Genome-wide reprogramming in mouse primordial germ cells involves epigenetic imprint erasure leading to totipotency . Reprogramming

10912-492: The ligands have a higher affinity for parallel folded G-quadruplexes.  It has been found that ligands with smaller side chains bind better to the quadruplex because smaller ligands have more concentrated electron density . Furthermore, the hydrogen bonds of ligands with smaller side chains are shorter and therefore stronger. Ligands with mobile side chains, ones that are able to rotate around its center chromophore, associate more strongly to G-quadruplexes because conformation of

11036-545: The mitochondria begin to decline, which can lead to the formation of many diseases such as Alzheimer's disease (AD). These G-quadruplex structures are said to be formed in the promoter regions of DNA through superhelicity, which favors the unwinding of the double helical structure of DNA and in turn loops the strands to form G-quadruplex structures in guanine rich regions. The BER pathway is signalled when it indicates an oxidative DNA base damage, where structures like, 8-Oxoguanine-DNA glycosylase 1 (OGG1), APE1 and G-quadruplex play

11160-479: The modulation of gene expression, or the induction of mutations. On the condition that 8-oxo-dG is repaired by BER, parts of the repair protein is left behind which can lead to epigenetic alterations, or the modulation of gene expression. Upon insertion of 8-oxo-dG into thymidine kinase gene of humans, it was determine that if 8-oxo-dG was left unchecked and not repaired by BER, it can lead to frequent mutations and eventually carcinogenesis. AP endonuclease 1 (APE1)

11284-453: The molecule telomestatin . The binding of ligands to G-quadruplexes is vital for anti-cancer pursuits because G-quadruplexes are found typically at translocation hot spots.  MM41, a ligand that binds selectively for a quadruplex on the BCL-2 promoter, is shaped with a central core and 4 side chains branching sterically out.  The shape of the ligand is vital because it closely matches

11408-505: The most prevalent type of endogenous DNA damage in cells. AP sites can be generated spontaneously or after the cleavage of modified bases, like 8-OH-Gua. The generation of an AP site enables the melting of the duplex DNA to unmask the PQS, adopting a G-quadruplex fold. With the use of genome-wide ChIP-sequencing analyses, cell-based assays, and in vitro biochemical analyses, a connection has been made between oxidized DNA base-derived AP sites, and

11532-476: The multicellular eukaryotic genomes. Much of this is due to the differing abundances of transposable elements, which evolve by creating new copies of themselves in the chromosomes. Eukaryote genomes often contain many thousands of copies of these elements, most of which have acquired mutations that make them defective. Here is a table of some significant or representative genomes. See #See also for lists of sequenced genomes. Initial sequencing and analysis of

11656-528: The non-telomeric G-quadruplexes were found within gene promoters, and were conserved across the species. Similarly, large number of G-quadruplexes were found in the E. coli and hundreds of other microbial genomes. Here also, like vertebrates G-quadruplexes were enriched within gene promoters. In addition, there was found more than one-billion-year conserved G-quadruplex locus in plants and algae, in gene encoding large subunit of RNA polymerase II. Although these studies predicted G-quadruplex-mediated gene regulation, it

11780-433: The nucleic acid sequences involved in tetrad formation determines how the quadruplex folds. Short sequences, consisting of only a single contiguous run of three or more guanine bases, require four individual strands to form a quadruplex. Such a quadruplex is described as tetramolecular, reflecting the requirement of four separate strands. The term G4 DNA was originally reserved for these tetramolecular structures that might play

11904-795: The nucleotides CAG (encoding a polyglutamine tract). An expansion to over 36 repeats results in Huntington's disease , a neurodegenerative disease. Twenty human disorders are known to result from similar tandem repeat expansions in various genes. The mechanism by which proteins with expanded polygulatamine tracts cause death of neurons is not fully understood. One possibility is that the proteins fail to fold properly and avoid degradation, instead accumulating in aggregates that also sequester important transcription factors, thereby altering gene expression. Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion. Transposable elements (TEs) are sequences of DNA with

12028-426: The nucleus but the 'genome' refers to only one copy of each chromosome. Some eukaryotes have distinctive sex chromosomes, such as the X and Y chromosomes of mammals, so the technical definition of the genome must include both copies of the sex chromosomes. For example, the standard reference genome of humans consists of one copy of each of the 22 autosomes plus one X chromosome and one Y chromosome. A genome sequence

12152-826: The observed number per base pair (i.e. the frequency) of these motifs has increased rapidly in the eumetazoa for which complete genomic sequences are available. This suggests that the sequences may be under positive selection enabled by the evolution of systems capable of suppressing non-B structure formation. More recently, advanced web-based toolboxes for identifying G-quadruplex forming sequences were developed, including user-friendly and open access version of G4Hunter based on sliding window approach or G4RNA Screener based on machine learning algorithm. A number of experimental methods have been developed to identify G-quadruplexes. These methods can be broadly defined into two classes: biophysical and biochemical methods. Biochemical techniques were employed to interrogate G-quadruplex formation in

12276-460: The open duplex region. The binding of APE1 then plays an important role by stabilizing the formation of G-quadruplex structures in that region. This promotes formation of G-quadruplex structures by the folding of the stand. This looping process brings four bases in close proximity that will be held together by Hoogsteen base pairing. After this stage the APE1 gets acetylated by multiple lysine residues on

12400-537: The pilin antigenic variation system of the pathogenic Neisseria . The roles of quadruplex structure in translation control are not as well explored. The direct visualization of G-quadruplex structures in human cells as well as the co-crystal structure of an RNA helicase bound to a G-quadruplex have provided important confirmations of their relevance to cell biology. The potential positive and negative roles of quadruplexes in telomere replication and function remains controversial. T-loops and G-quadruplexes are described as

12524-464: The potential to form mutually exclusive hairpin or G-quadruplex structures depends heavily on the position of the hairpin-forming sequence. Because repair enzymes would naturally recognize ends of linear chromosomes as damaged DNA and would process them as such to harmful effect for the cell, clear signaling and tight regulation is needed at the ends of linear chromosomes. Telomeres function to provide this signaling. Telomeres, rich in guanine and with

12648-403: The presence of hypoxia to begin the process of angiogenesis . Through recent research into this specific gene pathway, the polypurine and polypyrimidine region allows for the transcription of this specific gene and the formation of an intramolecular G-quadruplex structure. However, more research is necessary to determine whether the formation of G-quadruplex regulates the expression of this gene in

12772-511: The process of angiogenesis or the formation of new blood vessels. The formation of an intramolecular G-quadruplex structure has been shown through studies on the polypurine tract of the promoter region of the VEGF gene. Through recent research on the role of G-quadruplex function in vivo, the stabilization of G-quadruplex structures was shown to regulate VEGF gene transcription, with inhibition of transcription factors in this pathway. The intramolecular G-quadruplex structures are formed mostly through

12896-492: The promoter region of PDGF-A has exhibited the ability to form intramolecular parallel G-quadruplex structures and remains suggested to play a role in transcriptional regulation of PDGF-A. However, research has also identified the presence of G-quadruplex structures within this region due to the interaction of TMPyP4 with this promoter sequence. Telomeres are generally made up of G-quadruplexes and remain important targets for therapeutic research and discoveries. These complexes have

13020-633: The promoter regions of these oncogenes tend to be parallel-stranded G-quadruplex DNA structures. Some of these oncogenes include c-KIT, PDGF-A, c-Myc and VEGF, showing the importance of this secondary structure in cancer growth and development. While the formation of G-quadruplex structure vary to some extent for the different promoter regions of oncogenes, the consistent stabilization of these structures have been found in cancer development. Current therapeutic research actively focuses on targeting this stabilization of G-quadruplex structures to arrest unregulated cell growth and division. One particular gene region,

13144-702: The propeller type, positioned to the sides of the quadruplex. If one or more of the runs of guanine bases has a 5’-3’ direction opposite to the other runs of guanine bases, the quadruplex is said to have adopted an antiparallel topology. The loops joining runs of guanine bases in intramolecular antiparallel quadruplexes are either diagonal, joining two diagonally opposite runs of guanine bases, or lateral (edgewise) type loops, joining two adjacent runs of guanine base pairs. In quadruplexes formed from double-stranded DNA, possible interstrand topologies have also been discussed . Interstrand quadruplexes contain guanines that originate from both strands of dsDNA. Following sequencing of

13268-590: The proportion of non-repetitive DNA decreases along with increasing genome size in complex eukaryotes. Noncoding sequences include introns , sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences make up 98% of the human genome. There are two categories of repetitive DNA in the genome: tandem repeats and interspersed repeats. Short, non-coding sequences that are repeated head-to-tail are called tandem repeats . Microsatellites consisting of 2–5 basepair repeats, while minisatellite repeats are 30–35 bp. Tandem repeats make up about 4% of

13392-586: The protein C9orf72 which is found throughout the brain in neuronal cytoplasm and at presynaptic terminals. Mutations of the C9orf72 gene have been linked to the development of FTD and ALS. These two diseases have a causal relationship to GGGGCC (G 4 C 2 ) repeats within the 1st intron of C9orf72 gene. Normal individuals typically have around 2 to 8 G 4 C 2 repeats, but individuals with FTD or ALS have from 500 to several thousand G 4 C 2 repeats. The transcribed RNA of these repeats have been shown to form stable G-quadruplexes, with evidence showing that

13516-439: The proteins encoded by LINEs for transposition. The Alu element is the most common SINE found in primates. It is about 350 base pairs and occupies about 11% of the human genome with around 1,500,000 copies. DNA transposons encode a transposase enzyme between inverted terminal repeats. When expressed, the transposase recognizes the terminal inverted repeats that flank the transposon and catalyzes its excision and reinsertion in

13640-429: The quadruplex which has stacked quartets and the loops of nucleic acids holding it together.  When bound, MM41's central chromophore is situated on top of the 3’ terminal G-quartet and the side chains of the ligand associate to the loops of the quadruplex. The quartet and the chromophore are bound with a π-π bond while the side chains and loops are not bound but are in close proximity. What makes this binding strong

13764-619: The repair process to be more efficient. Deacetylation of AcAPE1 is the driving force behind the loading of these TFs, where APE1 dissociates from the G-quadruplex structures. When a study downregulated the presence of APE1 and AcAPE1 in the cell, the formation of G-quadruplex structures was inhibited, which proves the importance of APE1 for the formation of these structures. However, not all G-quadruplex structures require APE1 for formation, in fact some of them formed greater G-quadruplex structures in its absence. Therefore, we can conclude that APE1 has two important roles in genome regulation- Stabilizing

13888-413: The rule effectively identifies sites of G-quadruplex formation, it also identifies a subset of the imperfect homopurine mirror repeats capable of triplex formation and C-strand i-motif formation. Moreover, these sequences also have the capacity to form slipped and foldback structures that are implicit intermediates in the formation of both quadruplex and triplex DNA structures. In one study, it was found that

14012-449: The sequences. This is more common in PQS sequences which form oxidized structures, such as 8-oxoguanine . Once the cell is aware of oxidative stress and damage, it recruits OGG1 to the site, whose main function is to initiate the BER pathway. OGG1 does so by cleaving the oxidized base and thus creating an AP site, primarily through the process of negative superhelicity. This AP site then signals cells to engage APE1 binding, which binds to

14136-423: The shortest 45 000 000 nucleotides in length and the longest 248 000 000 nucleotides, each contained in a different chromosome. There is no clear and consistent correlation between morphological complexity and genome size in either prokaryotes or lower eukaryotes . Genome size is largely a function of the expansion and contraction of repetitive DNA elements. Since genomes are very complex, one research strategy

14260-448: The small-molecule ligands to stack on the planar terminal tetrads within the G-quadruplex regions. A disadvantage of using small-molecule ligands as a therapeutic technique is that specificity is difficult to manage due to the variability of G-quadruplexes in their primary sequences, orientation, thermodynamic stability, and nucleic acid strand stoichiometry. As of now, no single small-molecule ligand has been able to be perfectly specific for

14384-469: The statement, “If G-quadruplexes form so readily in vitro , Nature will have found a way of using them in vivo ” - Aaron Klug , Nobel Prize Winner in Chemistry (1982). Interest in in vivo function of G-quadruplexes surged after large scale genome-wide analysis showed the prevalence of potential G-quadruplex (pG4)-forming sequences within gene promoters of human, chimpanzee, mouse, and rat - presented in

14508-546: The telomeric regions of DNA strands. Current research consists of identifying the biological function of these G-Quadruplex structures for specific oncogenes and discovering effective therapeutic treatments for cancer based on interactions with G-quadruplexes. Early evidence for the formation of G-quadruplexes in vivo in cells was established by isolating them from cells, and later by the observation that specific DNA helicases could be identified where small molecules specific for these DNA structures accumulated in cells. The length of

14632-457: The two tertiary DNA structures that protect telomere ends and regulate telomere length. Many of the genome regulatory processes have been linked to the formation of G-quadruplex structures, attributable to the huge role it plays in DNA repair of apurinic/apyrimidinic sites also known as AP sites. A new technique to map AP sites has been developed known as AP-seq which utilizes a biotin-labeled aldehyde-reactive probe (ARP) to tag certain regions of

14756-447: The unique structural features of the G-quadruplex. The strategy involves designing synthetic oligonucleotides that mimic the G-quadruplex structure and compete with the endogenous G-quadruplexes for binding to transcription factors. These decoys are typically composed of a G-rich sequence that can form a stable G-quadruplex structure and a short linker region that can be modified to optimize their properties. When introduced to cancer cells

14880-541: The virus), pol (reverse transcriptase and integrase), pro (protease), and in some cases env (envelope) genes. These genes are flanked by long repeats at both 5' and 3' ends. It has been reported that LTRs consist of the largest fraction in most plant genome and might account for the huge variation in genome size. Non-long terminal repeats (Non-LTRs) are classified as long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and Penelope-like elements (PLEs). In Dictyostelium discoideum , there

15004-509: Was also more prevalent in certain regions of the genome that contain specific active promoter and enhancer markers, some of which were linked to regions responsible for lung adenocarcinoma and colon cancer. AP site damage was found to be predominant in PQS regions of the genome, where formation of G-quadruplex structures is regulated and promoted by the DNA repair process, base excision repair (BER). Base excision repair processes in cells have been proved to be reduced with aging as its components in

15128-405: Was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave . New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine . A major step toward that goal was the completion in 2007 of the full genome of James D. Watson , one of

15252-566: Was reported to interact with G-quadruplex in the promoter of the human telomerase (hTERT) gene and regulate hTERT expression In 2019, the telomere-binding-factor-2 (TRF2 or TERF2) was shown to bind to thousands of non-telomeric G-quadruplexes in the human genome by TRF2 ChIP-seq. There are many studies that implicate quadruplexes in both positive and negative transcriptional regulation, including epigenetic regulation of genes like hTERT. Function of G-quadruplexes have also been reported in allowing programmed recombination of immunologlobin heavy genes and

15376-475: Was started in October 1990, and then reported the sequence of the human genome in April 2003, although the initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences. With advancements in technology that could handle sequencing of the many repetitive sequences found in human DNA that were not fully uncovered by the original Human Genome Project study, scientists reported

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