Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. (lookformedical.com)
The retroelement long interspersed element-1 ( LINE-1 or L1) comprises about 17% of the human genome. (researchsquare.com)
Many polymorphisms are located in the estimated 98% ofthe human genome that does not encode protein.This experiment examines a polymorphism in the human genome that iscaused by the insertion of an Alu transposon, or transposable element.Alu is a member of the family of short interspersed elements (SINEs) andis approximately 300 nucleotides in length. (e-dokumen.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)
Amino acids are encoded by the genome as different three nucleotide codes. (anthropogeny.org)
Nucleotide sequence divergence in each TE copy was calculated as the Kimura distance between the annotated TE copies in the genome and the consensus sequence of each TE family C ultrametric timetree depicting the position of Tr. (pensoft.net)
The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)
Should continue long after the initial genome sequences have been completed. (slidetodoc.com)
Prior studies paid at best lip service to the role of the environment, a perspective reified in the paradigm of gene-by-environment (G x E) interactions and its modern variants, such as genome-wide association studies, quantitative trait nucleotides, and whole-genome sequencing. (huffpost.com)
We performed deep genomic DNA sequencing of CD-1 mice and used the data to identify genome-wide SNPs, indels, and germline transposable elements relative to the mm10 reference genome. (biomedcentral.com)
However, the prior study only examined single nucleotide polymorphisms (SNPs) previously identified in other mouse strains, and to date, a full, genome-wide identification of genetic variants that exist between CD-1 mice has not been done. (biomedcentral.com)
We used the whole-genome shotgun sequencing strategy and constructed the subsequent short-insert libraries (170, 250, 500 and 800 bp) and long-insert libraries (2, 5, and 10 kb) using the standard protocol provided by Illumina (San Diego, USA). (biomedcentral.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)
Retrotransposable elements are important and peculiar genetic components derived from ancient retrovirus insertion inside plantsgenome. (sisef.it)
The analysis demonstrated the presence of multiple copies of retrotransposable elements inside the genome of beech, in accordance with the viral quasi-species theory of retrotransposon evolution. (sisef.it)
The identification of retrotransposable elements in forest trees represents an important step toward the understanding of mechanisms of genome evolution. (sisef.it)
Transposable elements (TEs) are ancient (retro)-virus insertions inside a host genome and are peculiar mobile genetic elements accounting for a large proportion of repetitive DNA regions ( [29] ). (sisef.it)
The observed differences in genome size in plants are accompanied by variations in the content of LTR retrotransposons, demonstrating that such elements might be important players in the evolution of plant genomes, along with polyploidy ( [11] ). (sisef.it)
Loss of silencing of the repeat elements leads to genome instability and human diseases, including cancer and ageing1-3. (bvsalud.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)
TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. (lookformedical.com)
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. (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)
SINE sequences are approximately 70-700 base pairs (bp) averaging about 250 bp [ 1 ] with most organized into an RNA gene-derived region, a di-nucleotide repeat region and terminating in a poly A or poly A/T tail [ 2 - 4 ]. (biomedcentral.com)
Transposable elements, such as Long INterspersed Elements (LINEs), are DNA sequences that can replicate within genomes. (bvsalud.org)
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)
While most pachytene piRNAs lack obvious targets, neither the copy numbers nor nucleotide sequences of pachytene piRNA loci are conserved 5 , 6 , 7 , and many of them are not found in syntenic regions even in closely related mammals 8 , 9 . (gokcumenlab.org)
SINEs7
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)
Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats). (lookformedical.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)
Repetitive short interspersed elements (SINEs) are ubiquitous eukaryotic retrotransposons. (biomedcentral.com)
Both LINEs and SINEs elements, despite the differences in structure and transposition mechanisms ( [44] ), are ubiquitous components of eukaryotic genomes, playing a major role in their evolution. (sisef.it)
There are 250000 copies of LINE elements in Lilium ( [21] ) and SINEs are represented, for example, by 50000 copies in tobacco ( [46] ). (sisef.it)
Repeats5
They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). (lookformedical.com)
Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. (lookformedical.com)
Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date. (biomedcentral.com)
Interspersed repeats and other mementos of transposable elements in mammalian genomes. (nih.gov)
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)
Genes2
Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases. (lookformedical.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)
Genomes5
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. (lu.se)
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)
It is therefore clear that retrotransposable elements build large parts of eukaryotic genomes ( [40] ). (sisef.it)
Two retrotransposons, belonging to the two major classes of LTR and non-LTR elements, were characterized trough a SCAR (Sequence Characterized Amplified Region) strategy. (sisef.it)
The cloning and sequencing of amplification products and a Cleaved Amplified Polymorphisms (CAPs) approach on the identified retrotransposons, showed a high level of diversity among the multiple copies of both elements. (sisef.it)
Non-LTR retrotransposons can be divided in several subclasses, such as LINE (Long INterspersed Elements) and SINE (Short INterspersed Elements - [44] ). (sisef.it)
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)
Repetitive elements4
There are two classes of interspersed repetitive elements. (edu.au)
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)
Copies3
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)
the gypsy LTR element is present in 20000 copies in maize. (sisef.it)
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)
Retroelements1
Notably, the L1 element can retrotranspose itself as well as other retroelements, such as Alu and SVA (SINE-VNTR-Alu: short interspersed element-variable number tandem repeat-Alu). (researchsquare.com)
Transcripts4
These transcripts are almost evenly divided between those arising from enhancer-associated (elncRNA) or promoter-associated (plncRNA) elements. (biomedcentral.com)
Long-read RNA sequencing technologies, including Oxford Nanopore and PacBio, can directly sequence relatively long transcripts, thus providing the opportunity to examine full-length LINE transcripts. (bvsalud.org)
In our pipeline, we utilized RepeatMasker to identify LINE-1 (L1) transcripts from long-read transcriptome data and incorporated several criteria, such as transcript start position, divergence, and length, to remove likely false positives. (bvsalud.org)
However, treating Trp53 mutant MEF's with DNA demethylating agent caused a huge increase in the level of transcripts encoding short interspersed nuclear elements and other species of noncoding RNAs that generated a strong type 1 IFN response. (codondex.com)
Gene4
We are entering the third epoch, what might be called the epigenetic synthesis, which combines elements of the previous iterations and incorporates environmental modulation of temporal and spatial control of gene expression without altering the underlying DNA sequence. (huffpost.com)
Transposable elements are able to affect conserved and divergent chromatin looping and contribute to cell- and species-specific gene regulation [ 11 ]. (biomedcentral.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)
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)
Evolution3
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)
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)
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Retrotransposition2
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)
SNPs1
We performed deep genomic DNA (gDNA) sequencing in order to map both the uniform and non-uniform variants of CD-1, including SNPs, insertions and deletions (indels), and germline transposable elements (TEs). (biomedcentral.com)
Methylation1
We find that most sequence elements, including most classes of transposable elements, acquire methylation at similar rates overall. (biomedcentral.com)
Insertions1
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)
Transcriptome1
By employing bioinformatics methodologies on long-read transcriptome data, this study demonstrates the landscape of L1 expression in tissues and cell lines. (bvsalud.org)
RNAs1
Mammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). (biomedcentral.com)
Genetics1
COVID-19 - Coronavirus In the field of genetics I study 'transposable elements', which are tiny fragments of inactive, viral DNA. (codondex.com)
Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. (biomedcentral.com)
Brain1
Garza, R 2024, ' Transposable Elements in the Healthy and Diseased Human Brain ', Doctor, Department of Experimental Medical Science, Lund. (lu.se)
Species1
Retrotransposable elements are well characterized in model or crop species like Arabidopsis thaliana and Oryza sativa , but are poorly known in forest tree species. (sisef.it)
Noncoding RNA1
One L1-derived long noncoding RNA, LINC01876, is a human-specific transcript expressed exclusively. (lu.se)
Base pairs1
The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. (biomedcentral.com)
Human1
For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. (cshl.edu)
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)
Variation1
Here we report the construction of 12 BAC/BES framework physical maps derived from these libraries and an analysis of the BESs in terms of transposable element, simple sequence repeat (SSR), microRNA (miRNA), and single nucleotide variation (SNV) content. (biomedcentral.com)
Single1
Equations describing renaturation Let C = concentration of single-stranded DNA at time t (expressed as moles of nucleotides per liter). (slidetodoc.com)
Autonomous1
Fig. 1 - Schematic representation of the general structure of class I RNA mediated LTR TE (A), class I RNA mediated non-LTR elements (B) and class II DNA mediated elements (C) in their autonomous and non autonomous configurations. (sisef.it)
We thought long and hard about signals and interactions between proteins as they move over each nucleotide. (codondex.com)
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They are 24-35 nt long, have 2´- O -methyl-modified 3´ termini, and associate with PIWI proteins, a specialized family of Argonaute proteins expressed in germ cells. (gokcumenlab.org)