Transposition Of Transposable Elements Research Articles

Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis.

Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals-tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, revealing that chemically-induced epigenome changes can have long-term consequences on imprinted gene expression.

Long-read sequencing of extrachromosomal circular DNA and genome assembly of a Solanum lycopersicum breeding line revealed active LTR retrotransposons originating from S. Peruvianum L. introgressions

Transposable elements (TEs) are a major force in the evolution of plant genomes. Differences in the transposition activities and landscapes of TEs can vary substantially, even in closely related species. Interspecific hybridization, a widely employed technique in tomato breeding, results in the creation of novel combinations of TEs from distinct species. The implications of this process for TE transposition activity have not been studied in modern cultivars. In this study, we used nanopore sequencing of extrachromosomal circular DNA (eccDNA) and identified two highly active Ty1/Copia LTR retrotransposon families of tomato (Solanum lycopersicum), called Salsa and Ketchup. Elements of these families produce thousands of eccDNAs under controlled conditions and epigenetic stress. EccDNA sequence analysis revealed that the major parts of eccDNA produced by Ketchup and Salsa exhibited low similarity to the S. lycopersicum genomic sequence. To trace the origin of these TEs, whole-genome nanopore sequencing and de novo genome assembly were performed. We found that these TEs occurred in a tomato breeding line via interspecific introgression from S. peruvianum. Our findings collectively show that interspecific introgressions can contribute to both genetic and phenotypic diversity not only by introducing novel genetic variants, but also by importing active transposable elements from other species.

Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding

Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.

Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

BackgroundDetection of newly transposed events by transposable elements (TEs) from next generation sequence (NGS) data is difficult, due to their multiple distribution sites over the genome containing older TEs. The previously reported Transposon Insertion Finder (TIF) detects TE transpositions on the reference genome from NGS short reads using end sequences of target TE. TIF requires the sequence of target TE and is not able to detect transpositions for TEs with an unknown sequence.ResultThe new algorithm Transposable Element Finder (TEF) enables the detection of TE transpositions, even for TEs with an unknown sequence. TEF is a finding tool of transposed TEs, in contrast to TIF as a detection tool of transposed sites for TEs with a known sequence. The transposition event is often accompanied with a target site duplication (TSD). Focusing on TSD, two algorithms to detect both ends of TE, TSDs and target sites are reported here. One is based on the grouping with TSDs and direct comparison of k-mers from NGS without similarity search. The other is based on the junction mapping of TE end sequence candidates. Both methods succeed to detect both ends and TSDs of known active TEs in several tests with rice, Arabidopsis and Drosophila data and discover several new TEs in new locations. PCR confirmed the detected transpositions of TEs in several test cases in rice.ConclusionsTEF detects transposed TEs with TSDs as a result of TE transposition, sequences of both ends and their inserted positions of transposed TEs by direct comparison of NGS data between two samples. Genotypes of transpositions are verified by counting of junctions of head and tail, and non-insertion sequences in NGS reads. TEF is easy to run and independent of any TE library, which makes it useful to detect insertions from unknown TEs bypassed by common TE annotation pipelines.

Somatic Mobilization: High Somatic Insertion Rate of mariner Transposable Element in Drosophila simulans.

Simple SummaryTransposable elements are capable of promoting somatic mobilization, and this may potentially have biological consequences. However, the rate of somatic mobilization is poorly known. The mariner element causes somatic mobilization in Drosophila simulans. We used an assay based on sequencing of the flanking mariner region and developed a pipeline to identify new mariner insertions in D. simulans. We found that flies carrying two mariner copies (one autonomous and one non-autonomous) had approximately 300 new somatic insertions during fly development (eggs to adult). We show that the rate of somatic insertion of the mariner element in D. simulans is high.Although transposable elements (TEs) are usually silent in somatic tissues, they are sometimes mobilized in the soma and can potentially have biological consequences. The mariner element is one of the TEs involved in somatic mobilization (SM) in Drosophila and has a high rate of somatic excision. It is also known that temperature is an important factor in the increase of the mariner element SM in the fly. However, it is important to emphasize that excision is only one step of TE transposition, and the final step in this process is insertion. In the present study, we used an assay based on sequencing of the mariner flanking region and developed a pipeline to identify novel mariner insertions in Drosophila simulans at 20 and 28 °C. We found that flies carrying two mariner copies (one autonomous and one non-autonomous) had an average of 236.4 (±99.3) to 279 (±107.7) new somatic insertions at 20 °C and an average of 172.7 (±95.3) to 252.6 (±67.3) at 28 °C. In addition, we detected fragments containing mariner and others without mariner in the same regions with low-coverage long-read sequencing, indicating the process of excision and insertion. In conclusion, a low number of autonomous copies of the mariner transposon can promote a high rate of new somatic insertions during the developmental stages of Drosophila. Additionally, the developed method seems to be sensitive and adequate for the verification and estimation of somatic insertion.

The Intricate Evolutionary Balance between Transposable Elements and Their Host: Who Will Kick at Goal and Convert the Next Try?

Simple SummaryTransposable elements (TEs) are mobile DNA sequences that can jump from one genomic locus to another and that have colonized the genomes of all living organisms. While TE mobilization is an important source of genomic innovations that greatly contribute to the host species evolution, it is also a major threat to genome integrity that can lead to pathologies. In this review, we discuss how TEs successfully bypass the host silencing machineries to propagate in the host’s genome and how hosts engage in a fightback against TE invasion and propagation. We highlight how TEs and their hosts have been evolving together to achieve a fine balance between transposition activity and repression.Transposable elements (TEs) are mobile DNA sequences that can jump from one genomic locus to another and that have colonized the genomes of all living organisms. TE mobilization and accumulation are an important source of genomic innovations that greatly contribute to the host species evolution. To ensure their maintenance and amplification, TE transposition must occur in the germ cell genome. As TE transposition is also a major threat to genome integrity, the outcome of TE mobility in germ cell genomes could be highly dangerous because such mutations are inheritable. Thus, organisms have developed specialized strategies to protect the genome integrity from TE transposition, particularly in germ cells. Such effective TE silencing, together with ongoing mutations and negative selection, should result in the complete elimination of functional TEs from genomes. However, TEs have developed efficient strategies for their maintenance and spreading in populations, particularly by using horizontal transfer to invade the genome of novel species. Here, we discuss how TEs manage to bypass the host’s silencing machineries to propagate in its genome and how hosts engage in a fightback against TE invasion and propagation. This shows how TEs and their hosts have been evolving together to achieve a fine balance between transposition and repression.

Roles of transposable elements on plant genome evolution, epigenetics and adaptation

<p indent="0mm">Transposable elements (TEs) are mobile DNA sequences within the genome, and their structure and transposition mechanism are highly diverse. TEs can be divided into retrotransposons (RTs; Class I) and DNA transposons (Class II), depending on whether their transposition intermediate is RNA or DNA. RTs transpose in a “copy-and-paste” manner and are therefore considered to be an essential contributor during genome expansion. RTs can be further divided into long terminal repeat retrotransposons (LTR-RTs) and non-long terminal repeat retrotransposons (non-LTR-RTs). <italic>Copia</italic> and <italic>Gypsy</italic> are two superfamilies of LTR-RTs commonly found in plant genomes, and their structural differences lie in the <italic>INT</italic> positions in the internal sequence of the <italic>pol</italic> open reading frame (ORF). Non-LTR-RTs include long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), which lack LTRs and usually have poly(A) or simple repeats at their 3′ end. DNA transposons directly cut the DNA sequence at the original site by transposase and insert a new site, similar to “cut-and-paste”. Insertion of DNA transposons into new sites results in target site duplications (TSDs), and DNA strand breaks due to transposition are repaired by DNA repair mechanisms. DNA transposons in plants can be further divided into “cut-and-paste” transposons and <italic>Helitrons</italic> with the “rolling circle” transposition pattern. TEs play an important role in genome evolution. In the process of their insertion, deletion, and amplification, the host may alter its genome size, gene expression, and gene function. Additionally, TEs may mediate chromosomal rearrangements through homologous recombination or alternative transposition. Overall, TEs are very powerful mutagens that can affect the stability of their host genomes. In order to defend against the transposition of TEs, the host has evolved various silencing mechanisms. In plants, the silencing of TEs is mainly established through RNA-directed DNA methylation (RdDM), which can stably repress the activity of TEs across generations. Methylation not only silences TEs but may also result in DNA methylation of nearby genes and affect expression and function of host genes. Interestingly, the phenotypic differences caused by the insertion of TEs play an important role in crop domestication. Methylation does not always keep TEs silent, such as burst events in some TE families. The evidence for the interaction between TEs and the host is growing, especially under environmental stress conditions, and TEs can be re-activated to help the host survive under stressful conditions. Furthermore, the insertion of TEs is preferred in many cases, and their insertion can be tolerated. Thus, TEs may not be completely inhibited, and they and their hosts may develop a cooperative relationship under environmental stress. This review summarizes some relevant research on TEs in plant genome evolution, introduces commonly occurring TEs found in plants, and examines how TEs are involved in plant genome evolution, epigenetic regulation, and the symbiotic relationship with the host under cooperative stress.

Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns.

Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.

Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline.

Long-read data is a great tool to discover new active transposable elements (TEs). However, no ready-to-use tools were available to gather this information from low coverage ONT datasets. Here, we developed a novel pipeline, nanotei, that allows detection of TE-contained structural variants, including individual TE transpositions. We exploited this pipeline to identify TE insertion in the Arabidopsis thaliana genome. Using nanotei, we identified tens of TE copies, including ones for the well-characterized ONSEN retrotransposon family that were hidden in genome assembly gaps. The results demonstrate that some TEs are inaccessible for analysis with the current A. thaliana (TAIR10.1) genome assembly. We further explored the mobilome of the ddm1 mutant with elevated TE activity. Nanotei captured all TEs previously known to be active in ddm1 and also identified transposition of non-autonomous TEs. Of them, one non-autonomous TE derived from (AT5TE33540) belongs to TR-GAG retrotransposons with a single open reading frame (ORF) encoding the GAG protein. These results provide the first direct evidence that TR-GAGs and other non-autonomous LTR retrotransposons can transpose in the plant genome, albeit in the absence of most of the encoded proteins. In summary, nanotei is a useful tool to detect active TEs and their insertions in plant genomes using low-coverage data from Nanopore genome sequencing.

Transposable Element Dynamics and Regulation during Zygotic Genome Activation in Mammalian Embryos and Embryonic Stem Cell Model Systems.

Transposable elements (TEs) are mobile genetic sequences capable of duplicating and reintegrating at new regions within the genome. A growing body of evidence has demonstrated that these elements play important roles in host genome evolution, despite being traditionally viewed as parasitic elements. To prevent ectopic activation of TE transposition and transcription, they are epigenetically silenced in most somatic tissues. Intriguingly, a specific class of TEs—retrotransposons—is transiently expressed at discrete phases during mammalian development and has been linked to the establishment of totipotency during zygotic genome activation (ZGA). While mechanisms controlling TE regulation in somatic tissues have been extensively studied, the significance underlying the unique transcriptional reactivation of retrotransposons during ZGA is only beginning to be uncovered. In this review, we summarize the expression dynamics of key retrotransposons during ZGA, focusing on findings from in vivo totipotent embryos and in vitro totipotent-like embryonic stem cells (ESCs). We then dissect the functions of retrotransposons and discuss how their transcriptional activities are finetuned during early stages of mammalian development.

Extensively Current Activity of Transposable Elements in Natural Rice Accessions Revealed by Singleton Insertions.

Active transposable elements (TEs) have drawn more attention as they continue to create new insertions and contribute to genetic diversity of the genome. However, only a few have been discovered in rice up to now, and their activities are mostly induced by artificial treatments (e.g., tissue culture, hybridization etc.) rather than under normal growth conditions. To systematically survey the current activity of TEs in natural rice accessions and identify rice accessions carrying highly active TEs, the transposon insertion polymorphisms (TIPs) profile was used to identify singleton insertions, which were unique to a single accession and represented the new insertion of TEs in the genome. As a result, 10,924 high-confidence singletons from 251 TE families were obtained, covering all investigated TE types. The number of singletons varied substantially among different superfamilies/families, perhaps reflecting distinct current activity. Particularly, eight TE families maintained potentially higher activity in 3,000 natural rice accessions. Sixty percent of rice accessions were detected to contain singletons, indicating the extensive activity of TEs in natural rice accessions. Thirty-five TE families exhibited potentially high activity in at least one rice accession, and the majority of them showed variable activity among different rice groups/subgroups. These naturally active TEs would be ideal candidates for elucidating the molecular mechanisms underlying the transposition and activation of TEs, as well as investigating the interactions between TEs and the host genome.

Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability

The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeler DDM1 causes hundreds of genomic regions to switch from CMT2 dependency to RdDM dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). Furthermore, we found that dysfunction in both DDM1 and RdDM causes strong reactivation of TEs and a burst of TE transposition in the first generation of mutant plants, indicating that the DDM1 and RdDM pathways together are critical to maintaining TE repression and protecting genomic stability. Our findings reveal the existence of a pathway conversion-based backup mechanism to guarantee the maintenance of DNA methylation and genome integrity.

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

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.

Epigenetics drive the evolution of sex chromosomes in animals and plants.

We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

Asexual Experimental Evolution of Yeast Does Not Curtail Transposable Elements.

Compared with asexual reproduction, sex facilitates the transmission of transposable elements (TEs) from one genome to another, but boosts the efficacy of selection against deleterious TEs. Thus, theoretically, it is unclear whether sex has a positive net effect on TE’s proliferation. An empirical study concluded that sex is at the root of TE’s evolutionary success because the yeast TE load was found to decrease rapidly in approximately 1,000 generations of asexual but not sexual experimental evolution. However, this finding contradicts the maintenance of TEs in natural yeast populations where sexual reproduction occurs extremely infrequently. Here, we show that the purported TE load reduction during asexual experimental evolution is likely an artifact of low genomic sequencing coverages. We observe stable TE loads in both sexual and asexual experimental evolution from multiple yeast data sets with sufficient coverages. To understand the evolutionary dynamics of yeast TEs, we turn to asexual mutation accumulation lines that have been under virtually no selection. We find that both TE transposition and excision rates per generation, but not their difference, tend to be higher in environments where yeast grows more slowly. However, the transposition rate is not significantly higher than the excision rate and the variance of the TE number among natural strains is close to its neutral expectation, suggesting that selection against TEs is at best weak in yeast. We conclude that the yeast TE load is maintained largely by a transposition–excision balance and that the influence of sex remains unclear.

Toxin-Antitoxin Gene Pairs Found in Tn3 Family Transposons Appear To Be an Integral Part of the Transposition Module.

Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tns). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase and transposase. We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial persistence. At least six different TA gene pairs are associated with various Tn3 members. Our data suggest that several independent acquisition events have occurred. In contrast to most Tn3 family passenger genes, which are generally located away from the transposition module, the TA gene pairs abut the res site upstream of the resolvase genes. Although their role when part of Tn3 family transposons is unclear, this finding suggests a potential role for the embedded TA in stabilizing the associated transposon with the possibility that TA expression is coupled to expression of transposase and resolvase during the transposition process itself.IMPORTANCE Transposable elements (TEs) are important in genetic diversification due to their recombination properties and their ability to promote horizontal gene transfer. Over the last decades, much effort has been made to understand TE transposition mechanisms and their impact on prokaryotic genomes. For example, the Tn3 family is ubiquitous in bacteria, molding their host genomes by the paste-and-copy mechanism. In addition to the transposition module, Tn3 members often carry additional passenger genes (e.g., conferring antibiotic or heavy metal resistance and virulence), and three were previously known to carry a toxin-antitoxin (TA) system often associated with plasmid maintenance; however, the role of TA systems within the Tn3 family is unknown. The genetic context of TA systems in Tn3 members suggests that they may play a regulatory role in ensuring stable invasion of these Tns during transposition.

Targeted deletion of rice retrotransposon Tos17 via CRISPR/Cas9.

A successful example of transposon deletion via CRISPR/Cas9-mediated genome editing suggests a novel alternative approach to plant breeding. Transposition of transposable elements (TEs) can affect adjacent genes, leading to changes in genetic traits. Expression levels and patterns, splicing and epigenetic status, and function of genes located in, or near, the inserted/excised locus can be affected. Artificial modification of loci adjacent to TEs, or TEs themselves, by genome editing could mimic the translocation of TEs that occurs in nature, suggesting that it might be possible to produce novel plants by modification of TEs via genome editing. To our knowledge, there are no reports thus far of modification of TEs by genome editing in plants. In this study, we performed targeted deletion of the Tos17 retrotransposon, which is flanked at both ends by long terminal repeat (LTR) sequences, via genome editing in rice. We succeeded in targeted mutagenesis of the LTR, and targeted deletion between LTRs, in calli transformed with CRISPR/Cas9 vectors for the Tos17 LTR. Moreover, we also successfully obtained regenerated plants derived from transformed calli and plants homozygous for lacking Tos17 in the next generation. Taken together, our results demonstrate successful deletion of the Tos17 retrotransposon from the rice genome by targeted mutagenesis using CRISPR/Cas9. We believe that this strategy could be applied to other TEs in many plant species, providing a rapid breeding technology as an alternative means to re-activate expression of agronomically important genes that have been inactivated by TE insertion, especially in plants such as fruit trees, in which it is difficult to maintain parental agronomical traits by cross-breeding due to high heterozygosity.

Transposable elements, placental development, and oocyte activation: Cellular stress and AMPK links jumping genes with the creation of human life

Transposable elements (TEs), also known as “jumping genes”, are DNA sequences first described by Nobel laureate Barbara McClintock that comprise nearly half of the human genome and are able to transpose or move from one genomic location to another. As McClintock also noted that a genome “shock” or stress may induce TE activation and transposition, accumulating evidence suggests that cellular stress (e.g. mediated by increases in intracellular reactive oxygen species [ROS] and calcium [Ca2+], etc.) induces TE mobilization in several model organisms and L1s (a member of the retrotransposon class of TEs) are active and capable of retrotransposition in human oocytes, human sperm, and in human neural progenitor cells. Cellular stress also plays a critical role in human placental development, with cytotrophoblast (CTB) differentiation leading to the formation of the syncytiotrophoblast (STB), a cellular layer that facilitates nutrient and gas exchange between the mother and the fetus. Syncytin-1, a protein that promotes fusion of CTB cells and is necessary for STB formation, and its receptor is found in human sperm and human oocytes, respectively, and increases in ROS and Ca2+ promote trophoblast differentiation and syncytin-1 expression. Cellular stress is also essential in promoting human oocyte maturation and activation which, similar to TE mobilization, can be induced by compounds that increase intracellular Ca2+ and ROS levels. AMPK is a master metabolic regulator activated by increases in ROS, Ca2+, and/or an AMP(ADP)/ATP ratio increase, etc. as well as compounds that induce L1 mobilization in human cells. AMPK knockdown inhibits trophoblast differentiation and AMPK-activating compounds that promote L1 mobility also enhance trophoblast differentiation. Cellular stressors that induce TE mobilization (e.g. heat shock) also promote oocyte maturation in an AMPK-dependent manner and the antibiotic ionomycin activates AMPK, promotes TE activation, and induces human oocyte activation, producing normal, healthy children. Metformin promotes AMPK-dependent telomerase activation (critical for telomere maintenance) and induces activation of the endonuclease RAG1 (promotes DNA cleavage and transposition) via AMPK. Both RAG1 and telomerase are derived from TEs. It is our hypothesis that cellular stress and AMPK links TE activation and transposition with placental development and oocyte activation, facilitating both human genome evolution and the creation of all human life. We also propose the novel observation that various cellular stress-inducing compounds (e.g. metformin, resveratrol, etc.) may facilitate beneficial TE activation and transposition and enhance fertilization and embryological development through a common mechanism of AMPK activation.

Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids.

The merging of two divergent genomes in a hybrid is believed to trigger a “genomic shock”, disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. Although our study did not examine TE transposition activity in hybrids, the examination of the transcriptome shows that TE expression is globally robust to hybridization. The term “genomic shock” is perhaps not appropriate to describe transcriptional modification in a viable hybrid merging divergent genomes.

The Effect of Hobo Transposon Excision on DNA repair in Drosophila melanogaster

As the repository of genetic information, it is critical to organisms that DNA damage is repaired quickly and with high fidelity. When DNA damage is improperly repaired, it may cause diseases such as cancer and severe combined immunodeficiency. DNA can be mutated by numerous agents both external and internal. One internal source of DNA damage is from the transposition of transposable elements, including the P and hobo elements. Transposable elements “jump” out from one section of the DNA and reinsert into another, leaving double strand DNA breaks at the excision site. Hobo excisions are preferentially repaired by nonhomologous end‐joining, NHEJ. DNA repair and transposable elements themselves can be studied in Drosophila melanogaster. This study looked at the hobo on P, or HOP, element. The P element is located inside of the Hobo element; HOP8 is nonautonomous and needs hobo transposase to be supplied in trans. Curly winged, glazed eye female flies that have an inducible source of hobo transposase were crossed with HOP8 male flies and heat shocked to trigger transposition, leaving a double strand DNA break requiring repair behind. The resulting mosaic eyed male flies were then crossed with wild type female flies because mosaic eyes mark meiotic recombination in the P element. Female flies with white eyes indicating that hobo transposition occurred, were collected and stored in a freezer. Experiments are underway to determine the original location and new insertion sites of hobo using inverse PCR to further understand DNA repair.Support or Funding InformationAlbion College Foundation for Undergraduate Research, Scholarship, and Creative Activity (FURSCA)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.