scholarly journals Transposons (transposable elements), discovered in maize by Barbara McClintock in 1948, are DNA sequences that can change their positions within the genome. Transposition of transposons can introduce mutations in the host genome. Actually, there was a clo

2015 ◽  
Vol 20 (8) ◽  
pp. i-i
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Host Genome ◽  
Barbara Mcclintock

scholarly journals Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Giovanni Spirito ◽  
Damiano Mangoni ◽  
Remo Sanges ◽  
Stefano Gustincich
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Cell Lines ◽  
Dna Sequences ◽  
Host Genome ◽  
Human Populations ◽  
Lymphoblastoid Cell Lines ◽  
Structural Variants ◽  
Public Data ◽  
The Impact

Abstract Background Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of primate genomes, especially from a regulatory perspective. Due to their recent activity they are also one of the primary sources of structural variants (SVs) in the human genome. By taking advantage of sequencing technologies and bioinformatics tools, recent surveys uncovered specific TE structural variants (TEVs) that gave rise to polymorphisms in human populations. When combined with RNA-seq data this information provides the opportunity to study the potential impact of TEs on gene expression in human. Results In this work, we assessed the effects of the presence of specific TEs in cis on the expression of flanking genes by producing associations between polymorphic TEs and flanking gene expression levels in human lymphoblastoid cell lines. By using public data from the 1000 Genome Project and the Geuvadis consortium, we exploited an expression quantitative trait loci (eQTL) approach integrated with additional bioinformatics data mining analyses. We uncovered human loci enriched for common, less common and rare TEVs and identified 323 significant TEV-cis-eQTL associations. SINE-R/VNTR/Alus (SVAs) resulted the TE class with the strongest effects on gene expression. We also unveiled differential functional enrichments on genes associated to TEVs, genes associated to TEV-cis-eQTLs and genes associated to the genomic regions mostly enriched in TEV-cis-eQTLs highlighting, at multiple levels, the impact of TEVs on the host genome. Finally, we also identified polymorphic TEs putatively embedded in transcriptional units, proposing a novel mechanism in which TEVs may mediate individual-specific traits. Conclusion We contributed to unveiling the effect of polymorphic TEs on transcription in lymphoblastoid cell lines.

scholarly journals Gene Expression Networks in the Drosophila Genetic Reference Panel

2019 ◽  
Author(s):  
Logan J. Everett ◽  
Wen Huang ◽  
Shanshan Zhou ◽  
Mary Anna Carbone ◽  
Richard F. Lyman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Dna Sequences ◽  
Quantitative Trait ◽  
Regulatory Networks ◽  
Target Genes ◽  
Reference Panel ◽  
Modern Biology ◽  
Specific Expression ◽  
Drosophila Genetic Reference Panel

SummaryA major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences, and mapped expression quantitative trait loci for annotated genes, novel transcribed regions (most of which are long noncoding RNAs), transposable elements and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, and genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses.

scholarly journals How Barbara McClintock discovered transposable elements in maize

2012 ◽  
Vol 10 (4) ◽  
pp. 3-13
Author(s):  
Keyword(s):  
Transposable Elements ◽  
Chromosomal Location ◽  
Chromosome Breakage ◽  
Dna Transposons ◽  
Barbara Mcclintock ◽  
Controlling Elements ◽  
Earthquake Event ◽  
Maize Kernels ◽  
The Relationship

The paper describes the early part of Barbara McClintock`s work on DNA transposons in maize, in which she discovered the Ac-Ds family of mobile "controlling elements". An account is first given of the cytology of the system that was used to generate intact chromosomes having "sticky" (broken) ends. Cytogenetical aspects of the chromatid and chromosome breakage-fusion-bridge cycles, deriving from breakage, are then described, which leads on to the way in which variegation in phenotypes of the maize kernels could be "read" in terms of chromosome breakage. The "genetic earthquake" event of 1944, triggered by introducing broken chromosomes into a zygote from both parents, lead to the discovery of Ds and Ac. Finding mobility of Ds from one chromosomal location to another was pure serendipity: the transposition showed itself while experiments were being undertaken to accurately map Ds. A similar chance observation revealed transposition of Ac as well, and then the relationship between the two elements was elucidated in terms of their autonomous and non-autonomous nature.

Interactions between Transposable Elements and the Host Genome

Mobile DNA II ◽  
2002 ◽  
pp. 1008-1023 ◽  
Author(s):  
Mariano Labrador ◽  
Victor G. Corces
Keyword(s):  
Transposable Elements ◽  
Host Genome

scholarly journals What is the impact of transposable elements on host genome variability?

1999 ◽  
Vol 266 (1429) ◽  
pp. 1677-1683 ◽  
Author(s):  
P. T. J. Emery ◽  
T. E. Robinson ◽  
R. Duddington ◽  
J. F. Y. Brookfield
Keyword(s):  
Transposable Elements ◽  
Host Genome ◽  
Genome Variability ◽  
The Impact

scholarly journals Retroviral DNA Integration

1999 ◽  
Vol 63 (4) ◽  
pp. 836-843 ◽  
Author(s):  
Patrick Hindmarsh ◽  
Jonathan Leis
Keyword(s):  
Dna Sequences ◽  
Host Genome ◽  
Single Site ◽  
Enzyme Complex ◽  
Enzymatic Process ◽  
Long Terminal Repeats ◽  
Host Proteins ◽  
Viral Dna ◽  
Dna Integration ◽  
Terminal Repeats

SUMMARY DNA integration is a unique enzymatic process shared by all retroviruses and retrotransposons. During integration, double-stranded linear viral DNA is inserted into the host genome in a process catalyzed by the virus-encoded integrase (IN). The mechanism involves a series of nucleophillic attacks, the first of which removes the terminal 2 bases from the 3′ ends of the long terminal repeats and of the second which inserts the viral DNA into the host genome. IN specifically recognizes the DNA sequences at the termini of the viral DNA, juxtaposing both ends in an enzyme complex that inserts the viral DNA into a single site in a concerted manner. Small duplications of the host DNA, characteristic of the viral IN, are found at the sites of insertion. At least two host proteins, HMG-I(Y) and BAF, have been shown to increase the efficiency of the integration reaction.

scholarly journals Isolation of Recombinant Adeno-Associated Virus Vector-Cellular DNA Junctions from Mouse Liver

1999 ◽  
Vol 73 (7) ◽  
pp. 5438-5447 ◽  
Author(s):  
Hiroyuki Nakai ◽  
Yuichi Iwaki ◽  
Mark A. Kay ◽  
Linda B. Couto
Keyword(s):  
Portal Vein ◽  
Dna Sequences ◽  
Mouse Liver ◽  
Host Genome ◽  
Vector System ◽  
Rrna Gene ◽  
Raav Vector ◽  
Adeno Associated Virus ◽  
Dna Junctions ◽  
Cellular Dna

ABSTRACT Recombinant adeno-associated virus (rAAV) vectors allow for sustained expression of transgene products from mouse liver following a single portal vein administration. Here a rAAV vector expressing human coagulation factor F.IX (hF.IX), AAV-EF1α-F.IX (hF.IX expression was controlled by the human elongation factor 1α [EF1α] enhancer-promoter) was injected into mice via the portal vein or tail vein, or directly into the liver parenchyma, and the forms of rAAV vector DNA extracted from the liver were analyzed. Southern blot analyses suggested that rAAV vector integrated into the host genome, forming mainly head-to-tail concatemers with occasional deletions of the inverted terminal repeats (ITRs) and their flanking sequences. To further confirm vector integration, we developed a shuttle vector system and isolated and sequenced rAAV vector-cellular DNA junctions from transduced mouse livers. Analysis of 18 junctions revealed various rearrangements, including ITR deletions and amplifications of the vector and cellular DNA sequences. The breakpoints of the vector were mostly located within the ITRs, and cellular DNA sequences were recombined with the vector genome in a nonhomologous manner. Two rAAV-targeted DNA sequences were identified as the mouse rRNA gene and the α1 collagen gene. These observations serve as direct evidence of rAAV integration into the host genome of mouse liver and allow us to begin to elucidate the mechanisms involved in rAAV integration into tissues in vivo.

scholarly journals Organization and Chromosomal Distribution of Histone Genes and Transposable Rex Elements in the Genome of Astyanax bockmanni (Teleostei, Characiformes)

2015 ◽  
Vol 146 (4) ◽  
pp. 311-318 ◽  
Author(s):  
Sandro N. Daniel ◽  
Manolo Penitente ◽  
Duílio M.Z.A. Silva ◽  
Diogo T. Hashimoto ◽  
Daniela C. Ferreira ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
B Chromosome ◽  
Gene Probe ◽  
Histone Genes ◽  
Chromosomal Distribution ◽  
Evolutionary Mechanisms ◽  
Small Sites ◽  
Eukaryotic Organisms

An important feature of eukaryotic organisms is the number of different repetitive DNA sequences in their genome, a feature not observed in prokaryotes. These sequences are considered to be important components for understanding evolutionary mechanisms and the karyotypic differentiation processes. Thus, we aimed to physically map the histone genes and transposable elements of the Rex family in 6 fish populations of Astyanax bockmanni. FISH results using a histone H1 gene probe showed fluorescent clusters in 2 chromosome pairs in all 6 samples analyzed. In contrast, FISH with a histone H3 probe showed conspicuous blocks in 4 chromosomes in 5 of the 6 populations analyzed. The sixth population revealed 7 chromosomes marked with this probe. Probes for the transposable elements Rex1 and Rex6 showed small sites dispersed on most chromosomes of the 6 populations, and the Rex3 element is located in a big block concentrated in only 1 acrocentric chromosome of 2 populations. As for the other populations, a Rex3 probe showed large blocks in more than 1 chromosome. Fish from Alambari and Campo Novo Stream have Rex3 elements dispersed along most of the chromosomes. Additionally, the conspicuous signals of Rex1, Rex3, and Rex6 were identified in the acrocentric B microchromosome of A. bockmanni found only in individuals of the Alambari River. Thus, we believe that different mechanisms drive the spread of repetitive sequences among the populations analyzed, which appear to be organized differently in the genome of A. bockmanni. The presence of transposable elements in the B chromosome also suggests that these sequences could play a role in the origin and maintenance of the supernumerary element in the genome of this species.

Mammalian genome evolution as a result of epigenetic regulation of transposable elements

2014 ◽  
Vol 5 (3) ◽  
pp. 183-194 ◽  
Author(s):  
Reuben M. Buckley ◽  
David L. Adelson
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Epigenetic Regulation ◽  
Dna Sequences ◽  
Defense Mechanisms ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Epigenetic Marks ◽  
Rna Molecules ◽  
Mammalian Genomes

AbstractTransposable elements (TEs) make up a large proportion of mammalian genomes and are a strong evolutionary force capable of rewiring regulatory networks and causing genome rearrangements. Additionally, there are many eukaryotic epigenetic defense mechanisms able to transcriptionally silence TEs. Furthermore, small RNA molecules that target TE DNA sequences often mediate these epigenetic defense mechanisms. As a result, epigenetic marks associated with TE silencing can be reestablished after epigenetic reprogramming – an event during the mammalian life cycle that results in widespread loss of parental epigenetic marks. Furthermore, targeted epigenetic marks associated with TE silencing may have an impact on nearby gene expression. Therefore, TEs may have driven species evolution via their ability to heritably alter the epigenetic regulation of gene expression in mammals.

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