scholarly journals Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards

2016 ◽  
Vol 283 (1840) ◽  
pp. 20161555 ◽  
Author(s):  
Nathalie Feiner
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Adaptive Radiation ◽  
Genome Structure ◽  
Gene Clusters ◽  
Genomic Region ◽  
High Rate ◽  
Morphological Adaptations ◽  
Genomic Regions

Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region ( Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis , TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards.

Wingless signaling in the Drosophila embryo: zygotic requirements and the role of the frizzled genes

Development ◽  
1999 ◽  
Vol 126 (3) ◽  
pp. 577-586 ◽  
Author(s):  
H. Muller ◽  
R. Samanta ◽  
E. Wieschaus
Keyword(s):  
Genomic Region ◽  
Drosophila Embryo ◽  
Surface Molecules ◽  
New Genes ◽  
Wingless Signaling ◽  
Frizzled Receptors ◽  
Signaling Receptors ◽  
Genomic Regions ◽  
High Degree

Wingless signaling plays a central role during epidermal patterning in Drosophila. We have analyzed zygotic requirements for Wingless signaling in the embryonic ectoderm by generating synthetic deficiencies that uncover more than 99% of the genome. We found no genes required for initial wingless expression, other than previously identified segmentation genes. In contrast, maintenance of wingless expression shows a high degree of zygotic transcriptional requirements. Besides known genes, we have identified at least two additional genomic regions containing new genes involved in Wingless maintenance. We also assayed for the zygotic requirements for Wingless response and found that no single genomic region was required for the cytoplasmic accumulation of Armadillo in the receiving cells. Surprisingly, embryos homozygously deleted for the candidate Wingless receptor, Dfrizzled2, showed a normal Wingless response. However, the Armadillo response to Wingless was strongly reduced in double mutants of both known members of the frizzled family in Drosophila, frizzled and Dfrizzled2. Based on their expression pattern during embryogenesis, different Frizzled receptors may play unique but overlapping roles in development. In particular, we suggest that Frizzled and Dfrizzled2 are both required for Wingless autoregulation, but might be dispensable for late Engrailed maintenance. While Wingless signaling in embryos mutant for frizzled and Dfrizzled2 is affected, Wingless protein is still internalized into cells adjacent to wingless-expressing cells. Incorporation of Wingless protein may therefore involve cell surface molecules in addition to the genetically defined signaling receptors of the frizzled family.

scholarly journals Critical Role of Dispensable Genes in Mycoplasma agalactiae Interaction with Mammalian Cells

2010 ◽  
Vol 78 (4) ◽  
pp. 1542-1551 ◽  
Author(s):  
Eric Baranowski ◽  
Sébastien Guiral ◽  
Eveline Sagné ◽  
Agnès Skapski ◽  
Christine Citti
Keyword(s):  
Hela Cells ◽  
Mammalian Cells ◽  
Critical Role ◽  
Genomic Region ◽  
Mycoplasma Agalactiae ◽  
Transposon Insertion ◽  
Mammalian Cell Lines ◽  
Fold Reduction ◽  
Genomic Regions

ABSTRACT Mycoplasmas are minimal bacteria whose genomes barely exceed the smallest amount of information required to sustain autonomous life. Despite this apparent simplicity, several mycoplasmas are successful pathogens of humans and animals, in which they establish intimate interactions with epithelial cells at mucosal surfaces. To identify biological functions mediating mycoplasma interactions with mammalian cells, we produced a library of transposon knockout mutants in the ruminant pathogen Mycoplasma agalactiae and used this library to identify mutants displaying a growth-deficient pheonotype in cell culture. M. agalactiae mutants displaying a 3-fold reduction in CFU titers to nearly complete extinction in coculture with HeLa cells were identified. Mapping of transposon insertion sites revealed 18 genomic regions putatively involved in the interaction of M. agalactiae with HeLa cells. Several of these regions encode proteins with features of membrane lipoproteins and/or were involved in horizontal gene transfer with phylogenetically distant pathogenic mycoplasmas of ruminants. Two mutants with the most extreme phenotype carry a transposon in a genomic region designated the NIF locus which encodes homologues of SufS and SufU, two proteins presumably involved in [Fe-S] cluster biosynthesis in Gram-positive bacteria. Complementation studies confirmed the conditional essentiality of the NIF locus, which was found to be critical for proliferation in the presence of HeLa cells and several other mammalian cell lines but dispensable for axenic growth. While our results raised questions regarding essential functions in mycoplasmas, they also provide a means for studying the role of mycoplasmas as minimal pathogens.

scholarly journals Transposable elements in natural populations of Drosophila melanogaster

2010 ◽  
Vol 365 (1544) ◽  
pp. 1219-1228 ◽  
Author(s):  
Yuh Chwen G. Lee ◽  
Charles H. Langley
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Copy Number ◽  
Population Genomics ◽  
Natural Populations ◽  
Crossing Over ◽  
Large Role ◽  
Essential Components ◽  
Replicative Transposition

Transposable elements (TEs) are families of small DNA sequences found in the genomes of virtually all organisms. The sequences typically encode essential components for the replicative transposition sequences of that TE family. Thus, TEs are simply genomic parasites that inflict detrimental mutations on the fitness of their hosts. Several models have been proposed for the containment of TE copy number in outbreeding host populations such as Drosophila . Surveys of the TEs in genomes from natural populations of Drosophila have played a central role in the investigation of TE dynamics. The early surveys indicated that a typical TE insertion is rare in a population, which has been interpreted as evidence that each TE is selected against. The proposed mechanisms of this natural selection are reviewed here. Subsequent and more targeted surveys identify heterogeneity among types of TEs and also highlight the large role of homologous and possibly ectopic crossing over in the dynamics of the Drosophila TEs. The recent discovery of germline-specific RNA interference via the piwi-interacting RNA pathway opens yet another interesting mechanism that may be critical in containing the copy number of TEs in natural populations of Drosophila . The expected flood of Drosophila population genomics is expected to rapidly advance understanding of the dynamics of TEs.

scholarly journals Coevolution between transposable elements and recombination

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160458 ◽  
Author(s):  
Tyler V. Kent ◽  
Jasmina Uzunović ◽  
Stephen I. Wright
Keyword(s):  
Transposable Elements ◽  
Genome Structure ◽  
Rate Variation ◽  
Species Variation ◽  
Insertion Polymorphism ◽  
Recombination Rates ◽  
Recombination Suppression ◽  
Evolutionary Forces ◽  
Genomic Regions ◽  
Recombination Rate Variation

One of the most striking patterns of genome structure is the tight, typically negative, association between transposable elements (TEs) and meiotic recombination rates. While this is a highly recurring feature of eukaryotic genomes, the mechanisms driving correlations between TEs and recombination remain poorly understood, and distinguishing cause versus effect is challenging. Here, we review the evidence for a relation between TEs and recombination, and discuss the underlying evolutionary forces. Evidence to date suggests that overall TE densities correlate negatively with recombination, but the strength of this correlation varies across element types, and the pattern can be reversed. Results suggest that heterogeneity in the strength of selection against ectopic recombination and gene disruption can drive TE accumulation in regions of low recombination, but there is also strong evidence that the regulation of TEs can influence local recombination rates. We hypothesize that TE insertion polymorphism may be important in driving within-species variation in recombination rates in surrounding genomic regions. Furthermore, the interaction between TEs and recombination may create positive feedback, whereby TE accumulation in non-recombining regions contributes to the spread of recombination suppression. Further investigation of the coevolution between recombination and TEs has important implications for our understanding of the evolution of recombination rates and genome structure. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

scholarly journals Transposable Elements in the Genome of Human Parasite Schistosoma mansoni: A Review

2021 ◽  
Vol 6 (3) ◽  
pp. 126
Author(s):  
Gisele Strieder Philippsen
Keyword(s):  
Gene Duplication ◽  
Transposable Elements ◽  
Schistosoma Mansoni ◽  
Dna Sequences ◽  
Current Knowledge ◽  
Coding Sequences ◽  
Human Parasite ◽  
Relevant Role ◽  
Duplication Events

Transposable elements (TEs) are DNA sequences able to transpose within the host genome and, consequently, influence the dynamics of evolution in the species. Among the possible effects, TEs insertions may alter the expression and coding patterns of genes, leading to genomic innovations. Gene-duplication events, resulting from DNA segmental duplication induced by TEs transposition, constitute another important mechanism that contributes to the plasticity of genomes. This review aims to cover the current knowledge regarding TEs in the genome of the parasite Schistosoma mansoni, an agent of schistosomiasis—a neglected tropical disease affecting at least 250 million people worldwide. In this context, the literature concerning TEs description and TEs impact on the genomic architecture for S. mansoni was revisited, displaying evidence of TEs influence on schistosome speciation—mediated by bursts of transposition—and in gene-duplication events related to schistosome–host coevolution processes, as well several instances of TEs contribution into the coding sequences of genes. These findings indicate the relevant role of TEs in the evolution of the S. mansoni genome.

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 Distinct chromatin signatures of DNA hypomethylation in aging and cancer

2017 ◽  
Author(s):  
Raúl F. Pérez ◽  
Juan Ramón Tejedor ◽  
Gustavo F. Bayón ◽  
Agustín F. Fernández ◽  
Mario F. Fraga
Keyword(s):  
Dna Methylation ◽  
Dna Sequences ◽  
Es Cells ◽  
Gene Promoters ◽  
Dna Hypomethylation ◽  
Chromatin Signature ◽  
Unknown Gene ◽  
Genomic Regions ◽  
Nih Roadmap

AbstractBackgroundCancer is an aging-associated disease but the underlying molecular links between these processes are still largely unknown. Gene promoters that become hypermethylated in aging and cancer share a common chromatin signature in ES cells. In addition, there is also global DNA hypomethylation in both processes. However, any similarities of the regions where this loss of DNA methylation occurs is currently not well characterized, nor is it known whether such regions also share a common chromatin signature in aging and cancer.ResultsTo address this issue we analysed TCGA DNA methylation data from a total of 2,311 samples, including control and cancer cases from patients with breast, kidney, thyroid, skin, brain and lung tumors and healthy blood, and integrated the results with histone, chromatin state and transcription factor binding site data from the NIH Roadmap Epigenomics and ENCODE projects. We identified 98,857 CpG sites differentially methylated in aging, and 286,746 in cancer. Hyper- and hypomethylated changes in both processes each had a similar genomic distribution across tissues and displayed tissue-independent alterations. The identified hypermethylated regions in aging and cancer shared a similar bivalent chromatin signature. In contrast, hypomethylated DNA sequences occurred in very different chromatin contexts. DNA hypomethylated sequences were enriched at genomic regions marked with the activating histone posttranslational modification H3K4me1 in aging, whilst in cancer, loss of DNA methylation was primarily associated with the repressive H3K9me3 mark.ConclusionsOur results suggest that the role of DNA methylation as a molecular link between aging and cancer is more complex than previously thought.

scholarly journals The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2952
Author(s):  
Melody Nicolau ◽  
Nathalie Picault ◽  
Guillaume Moissiard
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Dna Sequences ◽  
Current Knowledge ◽  
Genome Structure ◽  
Host Cells ◽  
Dna Elements ◽  
Potential Benefits ◽  
Jumping Genes ◽  
Silencing Pathways

Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.

Sensing Non-sense in Animal Sex From Perspective of Transposable Elements

2021 ◽  
Vol 1 (2) ◽  
pp. 1-9
Author(s):  
Ayan Mukherjee
Keyword(s):  
Transposable Elements ◽  
Sex Determination ◽  
Sex Chromosomes ◽  
Chromosomal Rearrangement ◽  
Repetitive Sequences ◽  
Regulatory Elements ◽  
Vertebrate Species ◽  
Temperature Dependent ◽  
Genomic Regions

Evolution of vertebrate species took shape through millions of years, where sex played an important role in maintenance of a lineage, genetic diversifications and reproductive isolation. On due course of sexual evolution, sex determination strategies have been proposed to flow from temperature dependent sex determination to genetic sex determination, which has been demonstrated as XY system in mammals and ZW system in birds. In contrary to this established conception, different lineages showed to have overlapping sex determining strategies. While searching possible reasons for these phenomenons, researchers observed that gene content of sex chromosomes is highly variable as far as their location and prevalence is concerned, which otherwise suggested autosomal origin of sex chromosomes. Although the exact mechanisms of gene transfer and thereby origin of sex chromosomes are yet to be unveiled, but chromosomal rearrangement and introgression has been hypothesized to be the possible effector. Transposable elements (TEs) are long been considered to be ‘Selfish’ or ‘Junk’ DNA material as most of the non-coding genomic regions are comprised by TEs, which did not make any sense to be a part of species genome. But recently, TEs are being considered to be a nature’s tool for biological innovation by creating new regulatory elements, new coding sequences, genetic disruption and chromosomal remodelling. So, this has been postulated that TEs could facilitate rearrangement and introgression, which ultimately lead to evolution of sex chromosomes and sex determining genes through positive selection. Prevalence of highly repetitive sequences in sex chromosomes, particularly in Y, makes it a hot bed for TEs mediated rearrangement and introgression. In this review, I tried to discuss whether it makes any sense to focus on the role of TEs in sexual evolution of animals.

scholarly journals Smc5/6-mediated regulation of replication progression contributes to chromosome assembly during mitosis in human cells

2014 ◽  
Vol 25 (2) ◽  
pp. 302-317 ◽  
Author(s):  
Lina Marcela Gallego-Paez ◽  
Hiroshi Tanaka ◽  
Masashige Bando ◽  
Motoko Takahashi ◽  
Naohito Nozaki ◽  
...  
Keyword(s):  
Dna Replication ◽  
Mammalian Cells ◽  
Genome Structure ◽  
Dna Breaks ◽  
Damage Response ◽  
Chromatin Fractionation ◽  
And Function ◽  
Genomic Regions ◽  
Structural Maintenance Of Chromosomes

The structural maintenance of chromosomes (SMC) proteins constitute the core of critical complexes involved in structural organization of chromosomes. In yeast, the Smc5/6 complex is known to mediate repair of DNA breaks and replication of repetitive genomic regions, including ribosomal DNA loci and telomeres. In mammalian cells, which have diverse genome structure and scale from yeast, the Smc5/6 complex has also been implicated in DNA damage response, but its further function in unchallenged conditions remains elusive. In this study, we addressed the behavior and function of Smc5/6 during the cell cycle. Chromatin fractionation, immunofluorescence, and live-cell imaging analyses indicated that Smc5/6 associates with chromatin during interphase but largely dissociates from chromosomes when they condense in mitosis. Depletion of Smc5 and Smc6 resulted in aberrant mitotic chromosome phenotypes that were accompanied by the abnormal distribution of topoisomerase IIα (topo IIα) and condensins and by chromosome segregation errors. Importantly, interphase chromatin structure indicated by the premature chromosome condensation assay suggested that Smc5/6 is required for the on-time progression of DNA replication and subsequent binding of topo IIα on replicated chromatids. These results indicate an essential role of the Smc5/6 complex in processing DNA replication, which becomes indispensable for proper sister chromatid assembly in mitosis.

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