Transposable elements contain sequences. Medical search. Frequent questions

Depending upon the similarity of their terminal inverted repeats and target site duplications, most of the MITEs in plant genomes are divided into two major groups: Tourist-like MITEs (derived from PIF) and Stowaway-like MITEs (derived from Tc1/mariner).Stowaway and Tourist elements differ remarkably in their sequences. (wikipedia.org)
Yet there is a more insidious reason, Meissner explains: "Most genomes - including those of humans and mice - contain thousands of virus-derived sequences that have embedded themselves in the genomes of their hosts over the last few million years. (bionity.com)
Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. (mdpi.com)
Within species, genomes vary in both gene content (e.g., tandem duplicated genes, CNVs dispersed throughout the genome, and PAVs of genes) and repetitive portions of the genome (e.g., transposable elements, knob repeats, centromere repeats). (biomedcentral.com)
The second one shows that the mutation rate from direct sequencing of the genomes of parents and children agrees pretty much with the biochemical estimate. (blogspot.com)
Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. (biomedcentral.com)
LTR retrotransposons and endogenous retroviruses (ERVs) are transposable elements in eukaryotic genomes well suited for computational identification. (uni-hamburg.de)
As they reported in Cell , the researchers sequenced the genomes of more than two dozen rat strains. (genomeweb.com)
In this study, using over 200 whole-genome sequences that the Bird 10,000 Genomes Project produced over the past decade, the researchers investigated the length of orthologous microsatellites, transposable elements, and DNA deletions. (eurekalert.org)
In a series of experiments examining the T cells and B cells of multiple generations of Agouti Viable Yellow mice, the researchers screened the animals' genomes searching for transposable elements that were methylated similarly to the one that sits next to the Agouti gene. (the-scientist.com)
In the end, building such an accurate model can be used to design and evaluate artificial genetic circuits, to predict outcomes of clinically important mutations in RNA-binding proteins or RNA sequences, to develop possible solutions to reverse those outcomes, to treat genetic diseases and to understand how different cellular strategies against transposons/viruses might have shaped our genes and genomes over the course of our evolution. (mpg.de)
During my time in SOKENDAI I've been studying ancient human genomes as well single-cell RNA-sequencing in zebrafish. (soken.ac.jp)
Data for this research includes hundreds of re-sequenced genomes from three endangered species, complemented by chromosome-level assemblies, offering a robust foundation for comprehensive genomic analyses. (lu.se)

In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1. (researchsquare.com)
Advances in whole-genome sequencing technologies have enabled numerous key discoveries. (researchsquare.com)
An international team led by investigators in Belgium and France did whole-genome sequencing on the bdelloid rotifer Adineta vaga , a tiny, asexual aquatic organism that reproduces through the division of unfertilized eggs. (genomeweb.com)
Researchers at Princeton University, Harvard University, and elsewhere performed whole-genome and whole-population sequencing on 14 large and 26 small yeast populations started from replicate, haploid S. cerevisiae cells. (genomeweb.com)
Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing. (cdc.gov)

Jumping genes" (more formally known as transposable elements or transposons) are DNA sequences that can move from one location of the genome to another. (bigthink.com)
The sequence contained a lower-than-usual representation of transposable elements, the group noted, along with expansions to gene families involved in defense against transposons and oxidation. (genomeweb.com)

Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared with Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. (nih.gov)
Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. (nature.com)
This protocol describes methods to design, assemble, and validate tools for targeted activation or repression of single-copy and multi-copy genes, including repetitive and transposable elements. (springer.com)
The virus has been named Phoenix and was constructed through comparison of DNA sequences from the human endogenous retrovirus K family (HERV-K). 2 HERV-K is proposed to be a fairly young (less than 5 million years) family, as it still contains a complete set of genes (albeit with mutations) necessary for a retrovirus to produce infectious viruses. (answersingenesis.org)
Only about 10,000 of these genes have been annotated by the sea urchin sequencing team. (blogspot.com)
and a Tetrahymena transposable element (Tlr1), the virus "evolutionary tree" appears as a network of swapped genes. (sciencedaily.com)
have analyzed the tef-1α sequences of F. equiseti , as well as the toxin-related genes PKS13 , PKS4, and TRI5 [26], and Kari has successfully cloned a protease gene [27]. (researchsquare.com)
As early as 1993, Martin and Palumbi found that smaller animals, both endotherms and ectotherms, harbor more changes in the DNA sequences of certain genes than do larger animals. (eurekalert.org)
The screen identified dozens of these transposable elements but revealed that only rarely do they work as promoters to control the expression of adjacent genes. (the-scientist.com)
I was exploring if a special class of DNA capable of jumping between genes called "mobile DNA" or "transposable elements" have been partially responsible for these changes. (soken.ac.jp)
This study can be one of the first attempt to understand how transposable DNA switches on and off critical genes required for future ocean conditions. (soken.ac.jp)
Transposable elements have the unique ability to move within our DNA, causing or reversing mutations, altering genes, and even affecting the size of our genome. (lu.se)
These elements appear to influence the expression of both protein-coding genes and non-coding transcripts in the human brain through various mechanisms," says Raquel Garza. (lu.se)

Sequence analysis of a cloned 5.5-kb DNA fragment obtained from 1 of the imipenem-resistant E. asburiae isolates identified an upstream LysR-type regulator gene that explained inducibility of IMI-2 expression. (cdc.gov)
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)
The following EMC8-9 gene cDNA ORF clone sequences were retrieved from the NCBI Reference Sequence Database (RefSeq). (genscript.com)
High frequencies of sequence duplications and transposable element insertions contributed to the degeneration of the MSY resulting in low gene density. (usda.gov)
We are looking for a bioinformatician or candidates with experience in computational biology interested to work in the field of genomics to understand gene regulatory mechanisms using next-generation sequencing datasets. (helsinki.fi)
All of the mutant mice have a gene, Agouti , that influences coat color, and an adjacent transposable element-a DNA sequence that can move about the genome, creating or reversing mutations-that promotes the gene's expression. (the-scientist.com)
To dig into the problem experimentally, Ferguson-Smith and her colleagues decided to rigorously test the idea that transposable elements act generally as gene promoters and that the methylation marks on these elements could be passed from one generation to the next. (the-scientist.com)
The screen did identify one transposable element that, like the element abutting the Agouti gene, displayed a bit of memory, Ferguson-Smith says, "but our data suggested that memory is not being conferred by DNA methylation. (the-scientist.com)
Thus, any consistent gene-theory should take emergence, evolution, distribution, expression and suppression of transposable elements into account. (mpg.de)
My future plan is to study in more details the mobile DNA elements that can possibly change gene expression and help fish adapting to new environment. (soken.ac.jp)
16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome. (cdc.gov)
The project will explore the hypothesis that duplicated sequences offer genetic redundancy, potentially crucial for survival post-bottleneck, by providing backup gene copies for essential functions or evolving new ones. (lu.se)

Capture-based enrichment method reveals extremely high genome-wide sequence diversity in Theileria parva , an intracellular pathogen of host lymphocytes. (umaryland.edu)
In particular, I am involved in the data analysis of next-generation Illumina sequencing datasets of genome-wide transcription factor binding, epigenetic modifications and chromatin accessibility. (helsinki.fi)

Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae pv. (wikipedia.org)
StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees. (cdc.gov)

Illumina single nucleotide polymorphism (SNP) chips, kompetitive allele-specific PCR (KASP) assays, genotyping-by-sequencing (GBS)) and sequencing (e.g. (biomedcentral.com)

B) The 'absence' detection approach looks for reads matching on both sides of the TE insertion, i.e. , the ancestral genomic sequence prior the TE insertion . (stanford.edu)
T-lex uses the outputs of the 'absence' detection to recover the ancestral genomic sequence prior the TE insertion and detects the Target Site Duplication (TSD) , traces of the mechanism of TE insertion. (stanford.edu)
The complete genomic sequence of Pseudomonas syringae pv. (nih.gov)
This record is derived from an annotated genomic sequence (NT_033778). (genscript.com)
In this study, the complete genomic sequence of Fusarium equiseti D25-1 was determined using multiple sequencing platforms. (researchsquare.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)

To overcome that, T-lex identifies the TE insertions nested or in high-repeat density regions (see 'TE flanking sequence analysis' part), and detects putatively mis-annotated TE insertions (see 'Mis-annotated TE detection' part). (stanford.edu)
De novo identification tools such as LTRharvest determine the position of potential LTR retrotransposon or ERV insertions in genomic sequences. (uni-hamburg.de)
High-Throughput Sequencing of Transposable Element Insertions Suggests Adaptive Evolution of the Invasive Asian Tiger Mosquito Towards Temperate Environments. (cdc.gov)

Differences between the reference and the reads are indicative either of polymorphisms, or of sequencing errors. (stanford.edu)

What would be a way to access curated annotation of all kinds of transposable elements (SINE, Alu seq. (stackexchange.com)
Combined evidence annotation of transposable elements in genome sequences. (genscript.com)
It accepts sequence data in a variety of formats and a basic LTR annotation in GFF3format as input. (uni-hamburg.de)

Johan Jakobsson, a professor at Lund University and research group leader at MultiPark and Lund Stem Cell Center, explains, "LINE-1 retrotransposons are a rich source of genetic sequences that we suspect have shaped the evolution of the human brain, and we now have the tools to explore their role in brain development. (lu.se)
Transposable elements (TEs) are mobile genetic sequences that comprise around 50% of our genomic DNA. (lu.se)

To try to answer this question a research team including Eugene Koonin from the NIH and Didier Raoult from URMITE compared the genetic material from virophages, such as the Mavirus, Sputnik, or OLV (which was isolated from an Antarctic organic lake), to eukaryotic self replicating transposable elements known as Polintons or Mavericks. (sciencedaily.com)

Comparative sequence analysis of pPATH pathogenicity plasmids in Pantoea agglomerans gall-forming bacteria. (tau.ac.il)

Since transposable elements and DNA deletions also drive the expansion and contraction of genome size, the researchers also studied the relationship between these two genomic traits and variation in genome size. (eurekalert.org)
The contribution of DNA deletions to genome size evolution is similar to that of transposable elements, according to Prof. LEI. (eurekalert.org)

T-lex is a computational pipeline that detects presence and/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data. (stanford.edu)
T-lex starts by extracting the TE junction sequences and the NGS data are converted into binary formats (bfa and bfq, respectively). (stanford.edu)
Indeed, for now we have sequencing data, but given our analyses we're willing to use them 'as is' as they have also been already aligned. (stackexchange.com)
This sequence was derived from sequence data generated by Human Genome Sequencing Center at Baylor College: Bovine Genome Project. (girinst.org)
I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. (mdpi.com)
Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). (researchgate.net)
To better understand the karyotype organization in Melipona and the relationship among the subgenera, we mapped repetitive sequences and analyzed previously reported cytogenetic data with the aim to identify cytogenetic markers to be used for investigating the phylogenetic relationships and chromosome evolution in the genus. (karger.com)
In addition, the sequence data and the accompanying commentaries will be automatically reprinted in Repbase, also known as Repbase Update, and distributed worldwide. (girinst.org)
Repbase will continue to compile sequence information available through public domain but will no longer accept original data. (girinst.org)
The entire communication in RR should not exceed one printed page per new element (excluding the sequence data). (girinst.org)
A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
Rather our data suggests that Maviruses have evolved from a fusion between a Politon/Maverick-like transposable element and an unknown virus. (sciencedaily.com)
I am also analyzing long-read nanopore sequencing data for improved mapping of repetitive elements in cancer cells. (helsinki.fi)
With advances in genome sequencing technology and rich long-term data accumulated about the life history traits of birds, scientists are now able to tackle this issue from a slightly different genomic perspective. (eurekalert.org)
De Novo Generation and Characterization of New Zika Virus Isolate Using Sequence Data from a Microcephaly Case. (cdc.gov)

Gregory TR (2005) Synergy between sequence and size in large-scale genomics. (springer.com)
The Web site "www.artichokegenome.unito.it" hosts all the available genomic sequences, together with their structural/functional annotations and project information are presented to users via the open-source tool JBrowse, allowing the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for Cynara cardunculus genomics. (researchgate.net)
Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. (biomedcentral.com)

Hidden within our DNA are repetitive sequences known as transposable elements. (lu.se)
This approach helped us to address these highly repetitive sequences, usually masked in standard bioinformatics pipelines, allowing us to accurately measure LINE-1 expression in each cell type found in our samples," explains Raquel Garza, co-first author of the study. (lu.se)

I challenged the Intelligent Design Creationists to explain not only that the sequences are similar but that the degree of similarity is evidence of evolution. (blogspot.com)

A few Stowaway elements also contain cis-acting regulatory domains. (wikipedia.org)
Currently, my project focuses on understanding the non-coding regulatory genome with a special emphasis on the role of transposable elements in organ-specific cancer. (helsinki.fi)

Gerdes P, Richardson SR, Mager DL, Faulkner GJ (2016) Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. (springer.com)

Garza, R 2024, ' Transposable Elements in the Healthy and Diseased Human Brain ', Doctor, Department of Experimental Medical Science, Lund. (lu.se)
Researchers at Lund University have discovered that a specific group of genetic elements in our DNA influence the development of the human brain, their study was published in Science Advances. (lu.se)
Researchers at Lund University offer new insights in their latest study, published in Science Advances, detailing how a specific group of genetic elements have influenced the development of the human brain over time. (lu.se)
These elements are suspected to have played a key role in shaping the development of the human brain. (lu.se)
In Lund, researchers are investigating these repetitive regions of our DNA to understand the role transposable elements play in human brain development and evolution. (lu.se)

One clone ID might be correlated to multiple accession numbers, which share the same CDS sequence. (genscript.com)

My computational analysis showed that some of these mobile DNA elements are more prevalent in fish exposed to higher acidity then those that have been growing at normal water conditions. (soken.ac.jp)

I am using next-generation sequencing based methods such as massively parallel reporter assays (STARR-seq) to decode enhancer function and nascent RNA mapping for understanding their role in cancer genome reprogramming. (helsinki.fi)

However, the highly repetitive sequence content of TEs is a major source of assembly gaps. (researchgate.net)

From the resulting 218 million-base genome assembly, researchers determined that the organism has a tetraploid genome housing paired allelic sequences that are rearranged in ways that would make it impossible to separate genetic material into equal parcels during meiosis, the type of cell division that sexually reproducing organisms use to make germs cells. (genomeweb.com)
For example, instead of studying changes in base pairs of DNA sequences, the current researchers looked at a suite of genomic attributes that may represent mutations generated by different processes. (eurekalert.org)
Using statistical models, the researchers found support for a connection between generation time and the length of orthologous microsatellites and transposable elements among neoavian birds (excluding passerines). (eurekalert.org)
Researchers have postulated that transposable elements may have methylation marks resistant to reprogramming-so, in theory, these marks should be most likely to be inherited. (the-scientist.com)
The researchers could see that methylation marks on this transposable element were erased between generations, and reestablished again in a form reminiscent of what was found in the parental generation. (the-scientist.com)
Using advanced sequencing technologies and a set of specialized bioinformatics tools, created by PhD student Raquel Garza, the researchers successfully detected the activity of LINE-1 elements and were able to dig into their functions and epigenetic profiles. (lu.se)

DNA methylation, particularly 5-methylcytosine (5mC) at CpG sequences, is widely conserved in eukaryotes. (elifesciences.org)
ABOVE: Agouti Viable Yellow mice share the same DNA sequence, but have different methylation patterns. (the-scientist.com)
The methylation marks on these transposable elements are also wiped clean and reprogrammed after fertilization, the team found, meaning they can't be directly passed from generation to generation ( Cell , 175:1259-71.e13, 2018). (the-scientist.com)

2008), the single reads are then mapped on the TE junction sequences. (stanford.edu)
2011), the reads are then mapped as pairs (PE) and/or single reads on the TE concatenated sequence. (stanford.edu)
Sequenced reads were assembled into 352 scaffolds total. (researchgate.net)

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential. (umaryland.edu)

Complete genome sequence of an Israeli isolate of Xanthomonas hortorum pv. (tau.ac.il)

Our results show that patterns of sequence evolution are driven by a balance between these chance effects of hitchhiking and interference, which increase stochastic variation in evolutionary outcomes," they continued, "and the deterministic action of selection on individual mutations, which favors parallel evolutionary solutions in replicate populations. (genomeweb.com)

After 4 weeks of conversion, we performed global analyses of RNA and protein levels by RNA-sequencing and mass spectrometry. (lu.se)

2 (HERVs throughout the genome have presumably accumulated different mutations, and through comparison a consensus sequence can be determined. (answersingenesis.org)
RR will publishes consensus sequences of Transposable Elements and other repetitive DNA, unreported anywhere else. (girinst.org)
Consensus sequences of new repetitive families and subfamilies as well as short descriptions of these sequences and adequate references. (girinst.org)
Extended and improved consensus sequences of known repetitive families accompanied by new biological information. (girinst.org)

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. (nature.com)

We report a papaya primitive Y chromosome with a small male-specific region, the MSY, that is about 10% of the chromosome showing severe suppression of recombination and degeneration of DNA sequences. (usda.gov)

The location of integration sites of transposable elements are used to determine evolutionary relationships: "A specific retroviral integration site shared by two species is indicative of a common ancestor because the likelihood of independent integrations at exactly the same locus (insertional homoplasy) is negligible. (answersingenesis.org)
In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. (mdpi.com)
The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. (researchgate.net)
NEW YORK (GenomeWeb News) - A genome sequencing study in Nature offered hints about genetic strategies organisms may use to maintain species diversity, even in the absence of sexual reproduction. (genomeweb.com)
Our project seeks to unravel these mysteries by examining how genetic redundancy through duplicated sequences, like orthologs, and the role of non-coding elements such as transposable elements (TEs), contribute to species resilience during and after population bottlenecks. (lu.se)

Transposable elements (TE) play critical roles in shaping genome evolution. (researchgate.net)
This makes it difficult to decipher the impact of these elements on the dynamics of genome evolution. (researchgate.net)
Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. (biomedcentral.com)
Also in Nature , a look at the evolution of genome sequences in populations of Saccharomyces cerevisiae. (genomeweb.com)

Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. (nature.com)
The work presented in this thesis focuses on the bioinformatic methods for a TE-centric analysis of next- and third-generation sequencing technologies. (lu.se)

These sequences represent the protein coding region of the EMC8-9 cDNA ORF which is encoded by the open reading frame (ORF) sequence. (genscript.com)
GenScript guarantees 100% sequence accuracy of all synthetic DNA constructs we deliver, but we do not guarantee protein expression in your experimental system. (genscript.com)
The grey blocks at the end of the element represent the LTRs, while the coloured elements in the middle represent protein domain hits. (uni-hamburg.de)

2001). Every single transposable element (TE) insertion to our genome is a massive burden: each element is copied trillions of times in a single organism (there are ~37 trillion cells in a human body). (mpg.de)

The increased capacity of long-read sequencing technologies to span highly repeti. (researchgate.net)

Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA. (blogspot.com)
These elements, once considered "Junk DNA", are now providing important clues as to how our brain has evolved to differ from that of our closest living relative, the chimpanzee. (lu.se)

I need to annotate human genome with different types of information, amongst them: transposable elements. (stackexchange.com)
We used LTRdigest to annotate the chromosome 4 sequence of Mus musculus (Results). (uni-hamburg.de)

The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns. (tau.ac.il)
One article stated, "Genomic rearrangements caused by scattered homologous proviral sequences gave rise to countless genetic variations on which the evolutionary powers of selection and adaptation could work. (answersingenesis.org)
Last month I explained how the difference in DNA sequence between chimps and humans corresponds to what we would predict from evolutionary theory. (blogspot.com)
The complex network of evolutionary relationships the authors describe suggests that viruses evolved from non-viral mobile genetic elements and vice versa, on more than one occasion. (sciencedaily.com)

The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. (mdpi.com)

Stowaway elements possess target site specificity, have small size and conserved terminal inverted repeat. (wikipedia.org)

We found that male mimicry originated in an ancestrally sexually dimorphic lineage in association with multiple structural changes, probably driven by transposable element activity. (lu.se)

Sequence finishing and mapping of Drosophila melanogaster heterochromatin. (genscript.com)

Minimizing Next-Generation Sequencing Errors for HIV Drug Resistance Testing. (cdc.gov)

Anatomy20

Organisms44

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Chemicals and Drugs49

Analytical, Diagnostic and Therapeutic Techniques and Equipment26

Phenomena and Processes131

Disciplines and Occupations4

Technology, Industry, Agriculture6

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Transposons2

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Insertions3

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20161

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