Alu elements creates primate specific genomic. Medical search. Frequent questions

It is obtained from analysis of many genomic loci flanked by Alu repetitive elements, which are non-autonomous retrotransposons present in high number of copies in primate genomes. (wikipedia.org)
Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. (biomedcentral.com)
A type of primate-specific transposable element , or "jumping gene," that is roughly 300 base pairs long and exists in large copy number across all chromosomes of primate genomes (over 1 million copies in the human genome). (anthropogeny.org)
Repetitive elements contribute a large part of eukaryotic genomes. (biomedcentral.com)
Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. (biomedcentral.com)
Transposable elements were initially viewed as "selfish" DNA or "parasitic" elements because of their deleterious effects on host genomes [ 7 ]. (biomedcentral.com)
Transposable elements can be considered as a source of raw material for primitive genomes, tools of genetic innovation, and ancestors of modern genes (e.g., ncRNA) [ 15 ]. (biomedcentral.com)
Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. (biomedcentral.com)
Long interspersed nuclear element-1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. (bvsalud.org)
Transposable elements, such as Long INterspersed Elements (LINEs), are DNA sequences that can replicate within genomes. (bvsalud.org)
LINE activity creates genomic structural variants in human populations and leads to somatic alterations in cancer genomes. (bvsalud.org)

In the fields of bioinformatics and computational biology, Genome survey sequences (GSS) are nucleotide sequences similar to expressed sequence tags (ESTs) that the only difference is that most of them are genomic in origin, rather than mRNA. (wikipedia.org)
Due to the staggered DNA cuts of the genome by the L1-derived endonuclease during TPRT, Alu insertions are flanked by short sequences of duplicated host DNA called target site duplications (TSDs), which can be used to identify the insertion event. (biomedcentral.com)
Our lab made several breakthroughs in the field of alternative splicing and discovered two out of three demonstrated mechanisms for the origin of alternative exons: (i) Alu exonization, i.e. the birthing process of new exons from intronic Alu sequences, and (ii) exons that changed their mode of splicing from constitutive to alternative during evolution. (tau.ac.il)
This annotation step is traditionally performed using alignment based methods, either in a de novo approach or by aligning the genome sequence to a species specific set of repetitive sequences. (biomedcentral.com)
Recently, Li (Bioinformatics 35:4408-4410, 2019) developed a novel software tool dna-brnn to annotate repetitive sequences using a recurrent neural network trained on sample annotations of repetitive elements. (biomedcentral.com)
Alphoid repeats or human alpha satellites are a human specific subclass of satellite DNA, which are long sequences of non-coding DNA appearing in tandems, i.e. the repeat instances follow each other without long gaps. (biomedcentral.com)
There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. (lookformedical.com)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)
Called Alu elements, these relatively short (approximately 300 Watson-Crick base pairs), repetitive non-coding sequences of DNA have been implicated in the rapid evolution of humans and non-human primate species. (technologynetworks.com)
The machinery 'gets confused' by the repetitive Alu sequences and responds in a way that leads to either duplication or deletion of the sequence between the Alu elements, and this can lead to disease," said Shaw, who is a statistician, a computational scientist and an associate professor of molecular and human genetics at Baylor College of Medicine, as well as senior director of bioinformatics at Baylor Genetics. (technologynetworks.com)
In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. (mdpi.com)
I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. (mdpi.com)
We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. (biomedcentral.com)
We developed a computational approach to build predictive models and identify optimal sequences and expression levels, while circumventing combinatorial explosion. (omictools.com)
Large international consortiums such as ENCODE (The Encyclopedia of DNA Elements) has shown that up to 80% of the genome is transcribed while only 1,5% of it is protein -coding sequences [ 1 ]. (biomedcentral.com)

We identified 151 novel Alu insertion loci from 11 species of tribe Cercopithecini, and used these insertions and 17 previously reported loci to infer a phylogenetic tree of the tribe Cercopithecini. (biomedcentral.com)
We detected over 30 million additional transcripts at more than 650,000 genomic loci, nearly all of which are likely nonfunctional, revealing a heretofore unappreciated amount of transcriptional noise in human cells. (biomedcentral.com)

The limitation of genomic survey sequence is that it lacks long-range continuity because of its fragmentary nature, which makes it harder to forecast gene and marker order. (wikipedia.org)
By using special Alu sequence as target locus, specific human DNA can be obtained from clone of TAC, BAC, PAC or human-mouse cell hybrid. (wikipedia.org)
This is primarily because Alu elements do not contain coding sequence and the vast majority of insertions are highly similar to each other. (biomedcentral.com)
The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). (lookformedical.com)
DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. (lookformedical.com)
Human endogenous retroviruses (HERVs) are a family of endogenous retroviruses that comprise the ~8.93% of the human genome sequence, with a high proportion being human specific. (mdpi.com)
The way this type of repressor works, part of it binds to a specific DNA sequence and part of it binds other proteins to recruit a whole complex of proteins that creates a repressive landscape in the genome. (blogspot.com)
PCR on genomic DNA of Huh7 cells exposed to BNT162b2 amplified the DNA sequence unique to BNT162b2. (freedomontario26.ca)
We then combined the search algorithm with system-level kinetic modeling, requiring the construction and characterization of 73 variants to build a sequence-expression-activity map (SEAMAP) for a biosynthesis pathway. (omictools.com)
Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs. (omictools.com)
For example, XIST (X-inactive specific transcript), one of the first described lncRNAs has a low level of sequence conservation, but a highly conserved function across placental mammals - inactivation of the X chromosome [ 5 ]. (biomedcentral.com)

Alu repetitive element is member of Short Interspersed Elements (SINE) in mammalian genome. (wikipedia.org)
Alu elements are also called Short Interspersed Elements (SINEs) . (anthropogeny.org)
Repetitive short interspersed elements (SINEs) are ubiquitous eukaryotic retrotransposons. (biomedcentral.com)

SINEs are a class of non-autonomous mobile elements and are essentially homoplasy-free characters with known ancestral states, making them useful genetic markers for phylogenetic studies. (biomedcentral.com)

Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases. (lookformedical.com)
Given the relevance of Alu elements in human genetic diseases as well as genome evolution, the researchers wanted to find a way to predict which genes are susceptible to Alu/Alu-mediated rearrangements. (technologynetworks.com)
Binding of TFIIIC to sine elements controls the relocation of activity-dependent neuronal genes to transcription factories. (nih.gov)
A small number of lineage-specific tandem gene duplications have occurred, and these raise questions concerning how evolutionarily young homeobox genes are recruited to new regulatory roles. (blogspot.com)
According to the GENCODE project one third of all human lncRNAs genes are primate-specific [ 4 ]. (biomedcentral.com)

Transposable elements are able to affect conserved and divergent chromatin looping and contribute to cell- and species-specific gene regulation [ 11 ]. (biomedcentral.com)
Rival elements battle it out as transposable elements invade and repressors seek to shut them down. (blogspot.com)
The transposable elements are "continually evolving to escape repression," while the repressors adjust and find new ways to defeat the transposable elements. (blogspot.com)
Those astonishing levels of sophistication and subtlety in the human genome arose with the help of these invading transposable elements. (blogspot.com)
Evolution just happened to produce transposable elements, and they then became evolutionary mechanisms ? (blogspot.com)
After his PhD, Thierry focused on transposable elements and retrotransposons. (biomedcentral.com)

The function of repetitive elements has been discussed for a long time [ 3 ] and only recently has the importance of repeats in cellular processes begun to open up [ 4 ]. (biomedcentral.com)
Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. (lookformedical.com)
Unfortunately, these repeats also cause genomic structural variation that can lead to disease. (technologynetworks.com)

GSS with low coverage can generate abundant information of gene content and putative regulatory elements of comparative species. (wikipedia.org)
The disease results from a mutation in the IKBKAP gene, which leads to exon 20 skipping in a tissue-specific manner and the consequent reduction of wildtype IKBKAP protein levels. (tau.ac.il)
To cause structural variations, pairs of elements (Alu/Alu) mediate genomic rearrangements that result in either gene copy number gains or losses, and these changes can have profound consequences for an individual's health. (technologynetworks.com)
In maize, a miniature inverted-repeat transposable element (MITE) inserted into the promoter of the NAC gene ( ZmNAC111 ) has been found to enhance drought tolerance at the seedling stage [ 20 ]. (biomedcentral.com)
Notably, circRNAs display cell-type, tissue-type and developmental-stage specific expression patterns in eukaryotic transcriptome, which reveals their significant regulatory functions in gene expression. (ijbs.com)
We detected high levels of BNT162b2 in Huh7 cells and changes in gene expression of long interspersed nuclear element-1 (LINE-1), which is an endogenous reverse transcriptase. (freedomontario26.ca)

This combines the basic concepts of Li (Bioinformatics 35:4408-4410, 2019) with current techniques developed for neural machine translation, the attention mechanism, for the task of nucleotide-level annotation of repetitive elements. (biomedcentral.com)
A recent overview of functions and the evolution of repetitive elements can be found in [ 9 ]. (biomedcentral.com)
While [ 11 ] mainly describes structural properties of two of the four repetitive element classes, we additionally highlight the biological importance and, if possible, function of specific repetitive elements. (biomedcentral.com)

Here we report that H3K9me3 is preferentially transferred onto the leading strands of replication forks, which occurs predominantly at long interspersed nuclear element (LINE) retrotransposons (also known as LINE-1s or L1s) that are theoretically transcribed in the head-on direction with replication fork movement. (bvsalud.org)

There are about 300 to 500 thousand copies of Alu repetitive element in human genome, which means one Alu element exists in 4 to 6 kb averagely. (wikipedia.org)
Although the autonomous features of L1 are straightforward, the identification of Alu element insertions that retain the ability to propagate copies of themselves has remained somewhat elusive. (biomedcentral.com)
Proliferation is initiated via recognition of promoter boxes residing in the tRNA-related region of the genomic "master-copy" by host-derived RNA polymerase III and eventually results in novel retrotransposed copies [ 6 ]. (biomedcentral.com)

The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. (lookformedical.com)
SINEs are "non-autonomous" such that amplification and integration is dependent on enzymes derived from the host genome and long interspersed nuclear elements (LINEs) [ 5 ]. (biomedcentral.com)

We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. (biomedcentral.com)
We have shown that in humans most new exons have originated from the primate-specific Alu retrotransposon. (tau.ac.il)
This resulted in primates and ultimately humans. (blogspot.com)

Detection of these variants will enhance our understanding of the complexity of the human genome and provide disease-specific and prognostic biomarkers. (tau.ac.il)
A large portion of human variation, including both variants associated and not associated with disease, is driven by small scale Alu/Alu-mediated events. (technologynetworks.com)
Scientists have estimated that Alu/Alu-associated copy number variants cause approximately 0.3 percent of human genetic diseases. (technologynetworks.com)

Family of the suborder HAPLORHINI (Anthropoidea) comprising bipedal primate MAMMALS. (lookformedical.com)

Our group has made seminal contributions to our understanding of the complexity of genomic expression through alternative mRNA splicing and the involvement of this process in genetic disorders and cancer. (tau.ac.il)
The mRNA vaccine has the advantages of being flexible and efficient in immunogen design and manufacturing, and currently, numerous vaccine candidates are in various stages of development and application. (freedomontario26.ca)

Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. (biomedcentral.com)
In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, Alu Ye5b5_ Pongo . (biomedcentral.com)
In the Homininae lineage (human, chimpanzee and gorilla), this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion. (biomedcentral.com)
This seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion. (biomedcentral.com)

This means that the ancestral state at any locus is the absence of the element and, conversely, that the presence of a shared element with matching TSDs at a given locus indicates a common ancestor. (biomedcentral.com)

With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition. (biomedcentral.com)
This rare finding is due in part to the large landscape of hundreds of relatively young elements with limited knowledge about what characteristics make them retrotransposition competent. (biomedcentral.com)
He then decided to devise a system that could detect retrotransposition of any element whose mobilization includes a reverse transcription step, no matter where the reverse transcribed, transposed element would target and integrate. (biomedcentral.com)

Among other things, his lab and the findings from other labs pointed at Alu element-mediated variation as the cause of a significant portion of some pediatric genetic diseases. (technologynetworks.com)
The question he asked at that time was simple: how to be able to monitor the transposition of these mobile elements in a mammal where genetic approaches to detect transposition were both poorly efficient and time consuming. (biomedcentral.com)

Generally, lncRNA has a lower expression level, their expression is more tissue-specific, and the majority of lncRNA has nuclear localization. (biomedcentral.com)

Approximately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but only 10% are found in LINE-1 insertions, which compose 17% of the genome. (biomedcentral.com)

In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain. (bvsalud.org)
However, it has been proven that more than 62% of genomic DNA serves as a template for transcription, which indicates that there are abundant non-coding RNAs (ncRNAs) in human transcriptome [ 2 , 3 ]. (ijbs.com)

Years later, other similarly severe medical conditions were linked to Alu/Alu-mediated structural variations, such as spastic paraplegia 4 and Fanconi anemia. (technologynetworks.com)

The Alu elements we are talking about are thought to be completely inert, they are not actively producing proteins, but problems arise when the machinery that repairs broken DNA incorrectly replicates a genomic segment flanked by a pair of repetitive Alu elements. (technologynetworks.com)

Many Type D cells senesce and become Type E cells which make the corresponding organs shrivel and be susceptible to cancers and other disease processes. (anti-agingfirewalls.com)

L1s generate hundreds of developmentally regulated and cell type-specific transcripts, many that are co-opted as chimeric transcripts or regulatory RNAs. (bvsalud.org)

One L1-derived long noncoding RNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. (bvsalud.org)

The clumping of cells due to the interaction of antibodies (or other proteins ) and specific molecules on the surface of cells. (anthropogeny.org)
Alu elements were considered to be a part of what has been called "junk DNA" because they do not code for the production of proteins, however they may serve some yet unknown function and definitely contribute to genomic plasticity, evolution, and disease. (anthropogeny.org)
Organic compounds that are the building blocks of proteins and participate in a number of processes such as neurotransmitter transport and biosynthesis. (anthropogeny.org)

Alu elements are distributed widely in mammalian genome, and repeatability is one of the characteristics, that is why it is called Alu repetitive element. (wikipedia.org)

Alu/Alu-mediated rearrangements had resulted in the small deletion of the LDL receptor in this patient, rendering it unfit to capture LDL-cholesterol particles and remove them from the blood. (technologynetworks.com)

Loss of silencing of the repeat elements leads to genome instability and human diseases, including cancer and ageing1-3. (bvsalud.org)

Therefore, I rapidly looked for laboratories dedicated to biology that had a special interest in these aspects of science, and I was very happy to find a very open-minded scientist, who was able both to think about receptor-ligand interactions at the molecular level and to build models for neuronal networks and integrated thinking processes, in the person of Jean-Pierre Changeux, at the Pasteur Institute. (biomedcentral.com)

Tumor specific expression, expression at the earliest stages of tumor development, and direct exposure to blood, suggest that TVMs are ideal biomarkers for both ovarian cancer diagnosis and targeted immunotherapy. (nih.gov)

The jockey elements of Drosophila are LINEs. (lookformedical.com)

Both CarD and RbpA bind near the upstream edge of the −10 element where they likely facilitate DNA bending and impede transcription bubble collapse. (regenerativemedicine.net)

Initially, I was thinking about astrophysics, but I rapidly became interested in the multiple attempts, that at that time were already very popular, to make a link between these domains of science and that of biology, and more precisely with neurobiology and the science of complex neuronal networks. (biomedcentral.com)

Yesterday James Tour, who in 2009 was ranked one of the top 10 chemists in the world, explained that evolutionists do not understand how evolution could have created life. (blogspot.com)
In other words, evolution created evolution. (blogspot.com)
It is needed to make sense of the data, because evolution doesn't. (blogspot.com)

CRISPR interference silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. (bvsalud.org)

We have also revealed that GC content architecture, specific histone modifications, and DNA methylation differ between exons and introns, and have been able to identify several mechanisms by which these affect the splicing process (Nat. (tau.ac.il)

Alternative splicing can be specific to tissue type, environment, or developmental stage. (tau.ac.il)

They lack the ability to copy and paste themselves directly, but are able to "hitchhike" via the activity of Long Interspersed Elements (LINEs) that have retained the ability to copy and paste. (anthropogeny.org)

Single-pass sequencing with lower fidelity can be used on the rapid accumulation of genomic data but with a lower accuracy. (wikipedia.org)
We've updated our Privacy Policy to make it clearer how we use your personal data. (technologynetworks.com)
Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. (philpapers.org)
existing databases, building data entry forms, and enabling interoperability between knowledge resources. (philpapers.org)

Guenons (tribe Cercopithecini) are a species-rich group of primates that have attracted considerable attention from both primatologists and evolutionary biologists. (biomedcentral.com)

Life depends on constant replenishment of human body cells with new cells created by differentiation of adult stem cells. (anti-agingfirewalls.com)

These elements may be found in both promoter and enhancer regions. (lookformedical.com)

Anatomy3

Organisms14

Diseases4

Chemicals and Drugs15

Analytical, Diagnostic and Therapeutic Techniques and Equipment14

Phenomena and Processes56

Disciplines and Occupations2

Technology, Industry, Agriculture1

Information Science4

Genomes11

Sequences16

Loci2

Sequence11

Short Interspersed Elements3

Essentially homoplasy-free characters1

Genes5

Transposable elements6

Repeats3

Gene6

Repetitive elements3

Retrotransposons1

Copies3

SINEs2

Humans3

Variants3

MAMMALS1

MRNA2

Insertion4

Locus1

Retrotransposition3

Genetic2

Tissue-specific1

Insertions1

Transcriptome2

Structural variations1

Machinery1

Susceptible1

Transcripts1

Transcript1

Proteins3

Mammalian1

Rearrangements1

Diseases1

Molecular1

Expression1

Drosophila1

Transcription1

Biology1

Evolution3

Human-specific1

Methylation1

Developmental stage1

Long1

Data4

Evolutionary1

Differentiation1

Promoter1