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 Small gene family encoding an eggshell (chorion) protein of the human parasite Schistosoma mansoni.

1988 ◽  
Vol 8 (8) ◽  
pp. 3008-3016 ◽  
Author(s):  
L A Bobek ◽  
D M Rekosh ◽  
P T LoVerde
Keyword(s):  
Schistosoma Mansoni ◽  
Dna Sequences ◽  
Genomic Library ◽  
Regulatory Element ◽  
Gene Promoter ◽  
Transcription Unit ◽  
Human Parasite ◽  
Intergenic Dna ◽  
Eggshell Proteins ◽  
Silkmoth Chorion

We have isolated six independent genomic clones encoding schistosome chorion or eggshell proteins from a Schistosoma mansoni genomic library. A linkage may of five of the clones spanning 35 kilobase pair (kbp) of the S. mansoni genome was constructed. The region contained two eggshell protein genes closely linked, separated by 7.5 kbp of intergenic DNA. The two genes of the cluster were arranged in the same orientation, that is, they were transcribed from the same strand. The sixth clone probably represents a third copy of the eggshell gene that is not contained within the 35-kbp region. The 5' end of the mRNA transcribed from these genes was defined by primer extension directly off the RNA. The ATCAT cap site sequence was homologous to a silkmoth chorion PuTCATT cap site sequence, where Pu indicates any purine. DNA sequence analysis showed that there were no introns in these genes. The DNA sequences of the three genes were very homologous to each other and to a cDNA clone, pSMf61-46, differing only in three or four nucleotides. A multiple TATA box was located at positions -23 to -31, and a CAAAT sequence was located at -52 upstream of the eggshell transcription unit. Comparison of sequences in regions further upstream with silkmoth and Drosophila sequences revealed several very short elements that were shared. One such element, TCACGT, recently shown to be an essential cis-regulatory element for silkmoth chorion gene promoter function, was found at a similar position in all three organisms.

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 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.

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.

scholarly journals Multiple Links between HD-Zip Proteins and Hormone Networks

2018 ◽  
Vol 19 (12) ◽  
pp. 4047 ◽  
Author(s):  
Giovanna Sessa ◽  
Monica Carabelli ◽  
Marco Possenti ◽  
Giorgio Morelli ◽  
Ida Ruberti
Keyword(s):  
Leucine Zipper ◽  
Developmental Pathways ◽  
Leucine Zipper Motif ◽  
Plant Growth And Development ◽  
Wide Range ◽  
Relevant Role ◽  
Duplication Events ◽  
Environmental Responses ◽  
Zip Genes

HD-Zip proteins are unique to plants, and contain a homeodomain closely linked to a leucine zipper motif, which are involved in dimerization and DNA binding. Based on homology in the HD-Zip domain, gene structure and the presence of additional motifs, HD-Zips are divided into four families, HD-Zip I–IV. Phylogenetic analysis of HD-Zip genes using transcriptomic and genomic datasets from a wide range of plant species indicate that the HD-Zip protein class was already present in green algae. Later, HD-Zips experienced multiple duplication events that promoted neo- and sub-functionalizations. HD-Zip proteins are known to control key developmental and environmental responses, and a growing body of evidence indicates a strict link between members of the HD-Zip II and III families and the auxin machineries. Interactions of HD-Zip proteins with other hormones such as brassinolide and cytokinin have also been described. More recent data indicate that members of different HD-Zip families are directly involved in the regulation of abscisic acid (ABA) homeostasis and signaling. Considering the fundamental role of specific HD-Zip proteins in the control of key developmental pathways and in the cross-talk between auxin and cytokinin, a relevant role of these factors in adjusting plant growth and development to changing environment is emerging.

scholarly journals Molecular Regulation of Cell Fate in Cerebral Ischemia: Role of the Inflammasome and Connected Pathways

2014 ◽  
Vol 34 (12) ◽  
pp. 1857-1867 ◽  
Author(s):  
George Trendelenburg
Keyword(s):  
Cell Fate ◽  
Current Knowledge ◽  
Protein Complexes ◽  
Sterile Inflammation ◽  
Inflammasome Activation ◽  
Stroke Incidence ◽  
Multifactorial Diseases ◽  
Relevant Role ◽  
Metabolic Conditions

Analogous to Toll-like receptors, NOD-like receptors represent a class of pattern recognition receptors, which are cytosolic and constitute part of different inflammasomes. These large protein complexes are activated not only by different pathogens, but also by sterile inflammation or by specific metabolic conditions. Mutations can cause hereditary autoinflammatory systemic diseases, and inflammasome activation has been linked to many multifactorial diseases, such as diabetes or cardiovascular diseases. Increasing data also support an important role in different central nervous diseases such as stroke. Thus, the current knowledge of the functional role of this intracellular ‘master switch’ of inflammation is discussed with a focus on its role in ischemic stroke, neurodegeneration, and also with regard to the recent data which argues for a relevant role in other organs or biologic systems which influence stroke incidence or prognosis.

scholarly journals Atlas of transcriptionally active transposable elements in human adult tissues

2019 ◽  
Author(s):  
Gireesh K. Bogu ◽  
Ferran Reverter ◽  
Marc A. Marti-Renom ◽  
Michael P. Snyder ◽  
Roderic Guigó
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Regulation Of Gene Expression ◽  
Regulation Of Expression ◽  
Protein Coding ◽  
Potential Implication ◽  
Human Adult ◽  
Adult Tissues ◽  
Early Human Development

AbstractApproximately half of the human genome consists of mobile repetitive DNA sequences known as transposable elements (TEs). They are usually silenced by epigenetic mechanisms, but a few are known to escape silencing at embryonic stages, affecting early human development by regulating nearby protein-coding genes. To investigate transcriptional activity in human adult tissues we systematically investigate the expression landscape of about 4.2 million non-coding TEs in 8,051 RNA-Seq datasets from up to 49 adult tissues and 540 individuals. We show that approximately 79,558 individual TEs (2%). belonging to 856 subfamilies escape epigenetic silencing in adult tissues and become transcriptionally active, often in a very tissue-specific manner. Supporting a role for TEs in the regulation of expression of nearby genes, we found the expression of TEs often correlated with the expression of nearby genes, and significantly stronger when the TEs include eQTLs for the genes. We identified thousands of tissue-elevated, sex-associated TEs in the breast, ethnicity-associated in the skin and age-associated in the tibial artery, where we found a potential implication of two TE subfamilies in atherosclerosis. Our results suggest a functional role of TEs in the regulation of gene expression, support their implication in human phenotypes, and also serve as a comprehensive resource of transcriptionally active TEs in human adult tissues.

An 82 bp tandem repeat family typical of 3' non-coding end of Gypsy/TAT LTR retrotransposons is conserved in Coffea spp. pericentromeres

Genome ◽  
2021 ◽  
Author(s):  
Leonardo Adabo Cintra ◽  
Thaissa Boldieri de Souza ◽  
Letícia Maria Parteka ◽  
Lucas Mesquita Barreto ◽  
Luiz Filipe Protasio Pereira ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Repetitive Dna ◽  
Tandem Repeat ◽  
Dna Sequences ◽  
Ltr Retrotransposons ◽  
Non Coding Rna ◽  
Functional Aspects ◽  
Good Coverage ◽  
Short Tandem

Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around centromeres. However, proximal regions of Coffea chromosomes remain poorly understood, especially on the nature and organisation of the sequences. Taking advantage of genome sequences of C. arabica (2n = 44), C. canephora, and C. eugenioides (C. arabica progenitors with 2n = 22) and good coverage genome sequencing of dozens of other wild Coffea spp., repetitive DNA sequences were identified, and the genomes were compared to decipher particularities of pericentromeric structures. The searches revealed a short tandem repeat (82 bp length) typical of Gypsy/TAT LTR retrotransposons, named Coffea_sat11. This repeat organises clusters with fragments of other transposable elements, comprising regions of non-coding RNA production. Cytogenomic analyses showed that Coffea_sat11 extend from pericentromeres towards the middle of the chromosomal arms. This arrangement was observed in the allotetraploid C. arabica chromosomes, as well as in its progenitors. This study improve our understanding of the role of Gypsy/TAT LTR retrotransposon lineage in the organization of Coffea pericentromeres, as well as the conservation of Coffea_sat11 within the genus. The relationships with fragments of other transposable elements and the functional aspects of these sequences on the pericentromere chromatin were also evaluated.

scholarly journals Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks

2019 ◽  
Author(s):  
Agnès Baud ◽  
Mariène Wan ◽  
Danielle Nouaud ◽  
Nicolas Francillonne ◽  
Dominique Anxolabéhère ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Dark Matter ◽  
Transposable Elements ◽  
Dna Sequences ◽  
Binding Sites ◽  
Functional Role ◽  
Gene Network ◽  
Significant Proportion ◽  
Coding Sequences ◽  
Gene Regulation Networks

1AbstractTransposable elements (TEs) are mobile, repetitive DNA sequences that make the largest contribution to genome bulk. They thus contribute to the so-called “dark matter of the genome”, the part of the genome in which nothing is immediately recognizable as biologically functional.We developed a new method, based on k-mers, to identify degenerate TE sequences. With this new algorithm, we detect up to 10% of the A. thaliana genome as derived from as yet unidentified TEs, bringing the proportion of the genome known to be derived from TEs up to 50%. A significant proportion of these sequences overlapped conserved non-coding sequences identified in crucifers and rosids, and transcription factor binding sites. They are overrepresented in some gene regulation networks, such as the flowering gene network, suggesting a functional role for these sequences that have been conserved for more than 100 million years, since the spread of flowering plants in the Cretaceous.

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