Transposable elements and chromosomal rearrangements in cancer — a possible link

Nature ◽  
1979 ◽  
Vol 282 (5738) ◽  
pp. 447-448 ◽  
Author(s):  
Ruth Sager
Keyword(s):  
Transposable Elements ◽  
Chromosomal Rearrangements

scholarly journals Transposable Elements and Teleost Migratory Behaviour

2021 ◽  
Vol 22 (2) ◽  
pp. 602
Author(s):  
Elisa Carotti ◽  
Federica Carducci ◽  
Adriana Canapa ◽  
Marco Barucca ◽  
Samuele Greco ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Environmental Changes ◽  
Chromosomal Rearrangements ◽  
Quantitative Difference ◽  
Regulatory Elements ◽  
Phylogenetic Position ◽  
Migratory Behaviour ◽  
Relative Contribution ◽  
Migratory Routes ◽  
Eukaryotic Genomes

Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and freshwater for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadromous and catadromous species, independently from their phylogenetic position. This aspect is likely due to the substantial environmental changes faced by diadromous species during their migratory routes.

scholarly journals Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis

2021 ◽  
Vol 22 (4) ◽  
pp. 1614
Author(s):  
María Esther Rodríguez ◽  
Ismael Cross ◽  
Alberto Arias-Pérez ◽  
Silvia Portela-Bens ◽  
Manuel Alejandro Merlo ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Fish Species ◽  
Gasterosteus Aculeatus ◽  
Sparus Aurata ◽  
Chromosomal Rearrangements ◽  
Scophthalmus Maximus ◽  
Cynoglossus Semilaevis ◽  
Solea Senegalensis ◽  
Reference Species ◽  
Artificial Chromosomes

Cytogenomics, the integration of cytogenetic and genomic data, has been used here to reconstruct the evolution of chromosomes 2 and 4 of Solea senegalensis. S. senegalensis is a flat fish with a karyotype comprising 2n = 42 chromosomes: 6 metacentric + 4 submetacentric + 8 subtelocentric + 24 telocentric. The Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (FISH-BAC) technique was applied to locate BACs in these chromosomes (11 and 10 BACs in chromosomes 2 and 4, respectively) and to generate integrated maps. Synteny analysis, taking eight reference fish species (Cynoglossus semilaevis, Scophthalmus maximus, Sparus aurata, Gasterosteus aculeatus, Xiphophorus maculatus, Oryzias latipes, Danio rerio, and Lepisosteus oculatus) for comparison, showed that the BACs of these two chromosomes of S. senegalensis were mainly distributed in two principal chromosomes in the reference species. Transposable Elements (TE) analysis showed significant differences between the two chromosomes, in terms of number of loci per Mb and coverage, and the class of TE (I or II) present. Analysis of TE divergence in chromosomes 2 and 4 compared to their syntenic regions in four reference fish species (C. semilaevis, S. maximus, O. latipes, and D. rerio) revealed differences in their age of activity compared with those species but less notable differences between the two chromosomes. Differences were also observed in peaks of divergence and coverage of TE families for all reference species even in those close to S. senegalensis, like S. maximus and C. semilaevis. Considered together, chromosomes 2 and 4 have evolved by Robertsonian fusions, pericentric inversions, and other chromosomal rearrangements mediated by TEs.

Accumulation of Transposable Elements in Autosomes and Giant Sex Chromosomes of Omophoita (Chrysomelidae: Alticinae)

2018 ◽  
Vol 156 (4) ◽  
pp. 215-222 ◽  
Author(s):  
Lucas A.M. Rosolen ◽  
Marcelo R. Vicari ◽  
Mara C. Almeida
Keyword(s):  
Transposable Elements ◽  
Sex Chromosomes ◽  
Chromosomal Rearrangements ◽  
Dna Double Strand Breaks ◽  
Sequencing Data ◽  
High Accumulation ◽  
Strand Breaks ◽  
Cytogenetic Studies

Coleoptera is the most diverse order among insects, and comparative molecular cytogenetic studies in this group are lacking. The species of Omophoita (Oedionychina) possess a karyotype of 2n = 22 = 10II+X+Y. They are interesting models for evolutionary cytogenetic studies due to giant sex chromosomes which are asynaptic during meiosis. Transposable elements (TEs) confer plasticity and mobility to genomes and are considered hotspots for DNA double-strand breaks and chromosomal rearrangements. The objective of the present study was to verify the role of TEs in the karyotype and in the size expansion of the giant sex chromosomes in Omophoita. Thus, different TEs were characterized in the Omophoita genome and localized in the chromosomes by fluorescence in situ hybridization (FISH). The DNA sequencing data revealed identity with TE families Tc1/Mariner and RTE/L1-56_XT. FISH showed signals of all TEs in the karyotypes and a high accumulation in the sex chromosomes of the 3 Omophoita species analyzed. These data suggest that the genome size expansion and the origin of the giant sex chromosomes of Omophoita are due to an intensive genomic invasion of TEs, as those characterized here as Tc1/Mariner-Ooc and RTE-Ooc. Differences in the chromosomal location of the TEs among the 3 species indicate that they have participated in the karyotype differentiation in Omophoita.

scholarly journals Chromosomal distribution of the retroelements Rex 1, Rex 3 and Rex 6 in species of the genus Harttia and Hypostomus (Siluriformes: Loricariidae)

2019 ◽  
Vol 17 (2) ◽  
Author(s):  
Josiane B. Traldi ◽  
Roberto L. Lui ◽  
Juliana de F. Martinez ◽  
Marcelo R. Vicari ◽  
Viviane Nogaroto ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Physical Mapping ◽  
Genome Organization ◽  
Chromosomal Rearrangements ◽  
Chromosome Mapping ◽  
Chromosomal Evolution ◽  
Chromosomal Distribution ◽  
Chromosome Markers ◽  
Molecular Domestication

ABSTRACT The transposable elements (TE) have been widely applied as physical chromosome markers. However, in Loricariidae there are few physical mapping analyses of these elements. Considering the importance of transposable elements for chromosomal evolution and genome organization, this study conducted the physical chromosome mapping of retroelements (RTEs) Rex1, Rex3 and Rex6 in seven species of the genus Harttia and four species of the genus Hypostomus, aiming to better understand the organization and dynamics of genomes of Loricariidae species. The results showed an intense accumulation of RTEs Rex1, Rex3 and Rex6 and dispersed distribution in heterochromatic and euchromatic regions in the genomes of the species studied here. The presence of retroelements in some chromosomal regions suggests their participation in various chromosomal rearrangements. In addition, the intense accumulation of three retroelements in all species of Harttia and Hypostomus, especially in euchromatic regions, can indicate the participation of these elements in the diversification and evolution of these species through the molecular domestication by genomes of hosts, with these sequences being a co-option for new functions.

scholarly journals Genome stability is in the eye of the beholder: recent retrotransposon activity varies significantly across avian diversity

2021 ◽  
Author(s):  
James D. Galbraith ◽  
R. Daniel Kortschak ◽  
Alexander Suh ◽  
David L. Adelson
Keyword(s):  
Transposable Elements ◽  
Zebra Finch ◽  
Dna Sequences ◽  
Genome Stability ◽  
Chromosomal Rearrangements ◽  
Genome Structure ◽  
Past Research ◽  
Dominant Group ◽  
Avian Genome ◽  
Retrotransposon Activity

AbstractSince the sequencing of the zebra finch genome it has become clear the avian genome, while largely stable in terms of chromosome number and gene synteny, is more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element content have been noted across the avian tree. Transposable elements (TEs) are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through non-allelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, CR1 retrotransposons, either focusing on their expansion within single orders, or comparing passerines to non-passerines. Here we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and with orders. We describe high levels of TE expansion in genera which have speciated in the last 10 million years including kiwis, geese and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals.Author SummaryTransposable elements (TEs) are mobile, self replicating DNA sequences within a species’ genome, and are ubiquitous sources of mutation. The dominant group of TEs within birds are chicken repeat 1 (CR1) retrotransposons, making up 7-10% of the typical avian genome. Because past research has examined the recent inactivity of CR1s within model birds such as the chicken and the zebra finch, this has fostered an erroneous view that all birds have low or no TE activity on recent timescales. Our analysis of numerous high quality avian genomes across multiple orders identified both similarities and significant differences in how CR1s expanded. Our results challenge the established view that TEs in birds are largely inactive and instead suggest that their variation in recent activity may contribute to lineage-specific changes in genome structure. Many of the patterns we identify in birds have previously been seen in mammals, highlighting parallels between the evolution of birds and mammals.

scholarly journals Chromosomal rearrangements but no change of genes and transposable elements repertoires in an invasive forest-pathogenic fungus

2021 ◽  
Author(s):  
Arthur Demené ◽  
Benoît Laurent ◽  
Sandrine Cros-Arteil ◽  
Christophe Boury ◽  
Cyril Dutech
Keyword(s):  
Transposable Elements ◽  
Fungal Pathogen ◽  
De Novo ◽  
Pathogenic Fungus ◽  
Chromosomal Rearrangements ◽  
Low Complexity ◽  
Cryphonectria Parasitica ◽  
Genome Comparison ◽  
Structural Variations ◽  
High Quality

AbstractChromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments.Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in details for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity.We present a new de-novo whole-genome assembly obtained from a high quality DNA extraction and long reads sequencing Nanopore technology obtained from an isolate sampled in the native Japanese area of the species. The comparison with a recently published reference genome showed no significant variations in gene and transposable elements (TEs) repertoires. We also showed that theC. parasiticagenome is lowly compartmentalized, with a poor association between TEs and some specific genes, such as those potentially involved in host interactions (i.e. genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations on the invasive success of this fungal pathogen species.

scholarly journals Centromere Repeats: Hidden Gems of the Genome

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 223 ◽  
Author(s):  
Gabrielle Hartley ◽  
Rachel O’Neill
Keyword(s):  
Transposable Elements ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Repetitive Sequences ◽  
Chromosomal Evolution ◽  
Satellite Dnas ◽  
Integral Role ◽  
Chromosomal Breakpoints ◽  
Karyotypic Variation ◽  
Species Specific

Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’.

scholarly journals Chromosome breakage by pairs of closely linked transposable elements of the Ac-Ds family in maize.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 855-862 ◽  
Author(s):  
H K Dooner ◽  
A Belachew
Keyword(s):  
Transposable Elements ◽  
Chromosomal Rearrangements ◽  
Chromosome Breakage ◽  
Endosperm Development ◽  
Strong Tendency ◽  
Chromosome Breaks ◽  
Chromosome Breaking ◽  
Ac Transposition

Abstract Chromosome breaks and hence chromosomal rearrangements often occur in maize stocks harboring transposable elements (TEs), yet it is not clear what types of TE structures promote breakage. We have shown previously that chromosomes containing a complex transposon structure consisting of an Ac (Activator) element closely linked in direct orientation to a terminally deleted or fractured Ac (fAc) element have a strong tendency to break during endosperm development. Here we show that pairs of closely linked transposons with intact ends, either two Ac elements--a common product of Ac transposition--or an Ac and a Ds (Dissociation) element, can constitute chromosome-breaking structures, and that the frequency of breakage is inversely related to intertransposon distance. Similar structures may also be implicated in chromosome breaks in other eukaryotic TE systems known to produce chromosomal rearrangements. The present findings are discussed in light of a model of chromosome breakage that is based on the transposition of a partially replicated macrotransposon delimited by the outside ends of the two linked TEs.

Chromosomal changes associated with changes in development

Development ◽  
1984 ◽  
Vol 83 (Supplement) ◽  
pp. 7-30
Author(s):  
Christopher J. Bostock
Keyword(s):  
T Lymphocytes ◽  
Transposable Elements ◽  
Gene Amplification ◽  
Structural Changes ◽  
Normal Development ◽  
Chromosomal Rearrangements ◽  
The Past ◽  
Chromosomal Changes ◽  
Normal Differentiation ◽  
B And T Lymphocytes

In the past there has been a tendency to dwell on aspects of chromosomes which stress constancy of structure, number and content; even to the extent of dismissing exceptions as ‘aberrations’ or ‘oddities’. It is now becoming clear that genomes can be quite plastic, and that structural changes to chromosomes are an important and often necessary part of normal differentiation and development. Elimination of whole chromosome sets or defined portions of genomes is not uncommon and selective gene amplification has been shown to be part of normal development in both protozoa and higher organisms. Chromosomal rearrangements are now a well-documented feature of normal development of, for example, B- and T- lymphocytes and trypanosomes. Transposable elements, whose mobility may not be part of normal developmental processes, can have marked effects on development if their transposition takes them to developmentally important genes. This article reviews some of the structural changes that occur during normal development, and discusses some of the consequences for development when the mechanisms which bring about these rearrangements go wrong.

Electron Microscopy and image analysis of nucleo-protein complexes

1994 ◽  
Vol 52 ◽  
pp. 88-89
Author(s):  
E. H. Egelman ◽  
X. Yu
Keyword(s):  
Electron Microscopy ◽  
Image Analysis ◽  
Normal Cell ◽  
Genetic Recombination ◽  
Protein Complexes ◽  
Chromosomal Rearrangements ◽  
Reca Protein ◽  
E Coli ◽  
Helical Polymer ◽  
Specific Protease

The RecA protein of E. coli has been shown to mediate genetic recombination, regulate its own synthesis, control the expression of other genes, act as a specific protease, form a helical polymer and have an ATPase activity, among other observed properties. The unusual filament formed by the RecA protein on DNA has not previously been shown to exist outside of bacteria. Within this filament, the 36 Å pitch of B-form DNA is extended to about 95 Å, the pitch of the RecA helix. We have now establishedthat similar nucleo-protein complexes are formed by bacteriophage and yeast proteins, and availableevidence suggests that this structure is universal across all of biology, including humans. Thus, understanding the function of the RecA protein will reveal basic mechanisms, in existence inall organisms, that are at the foundation of general genetic recombination and repair.Recombination at this moment is assuming an importance far greater than just pure biology. The association between chromosomal rearrangements and neoplasms has become stronger and stronger, and these rearrangements are most likely products of the recombinatory apparatus of the normal cell. Further, damage to DNA appears to be a major cause of cancer.

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