Transposable element orientation bias in the Drosophila melanogaster genome

Identification and Characterization of the HERV-K (HML-8) Group of Human Endogenous Retroviruses in the Genome

Human endogenous retroviruses (HERVs) can be vertically transmitted in a Mendelian fashion, are stably maintained in the human genome, and are estimated to constitute ∼8% of the genome. HERVs affect human physiology and pathology through their provirus-encoded protein or long terminal repeat (LTR) element effect. Characterization of the genomic distribution is an essential step to understanding the relationships between endogenous retrovirus expression and diseases. However, the poor characterization of human MMTV-like (HML)-8 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome. In light of this, the definition of an accurate and updated HERV-K HML-8 genomic map is urgently needed. In this study, we report the results of a comprehensive analysis of HERV-K HML-8 sequence presence and distribution within the human genome and hominoids, with a detailed description of the different structural and phylogenetic aspects characterizing the group. A total of 40 proviruses and 5 solo LTR elements for human were characterized, which included a detailed description of provirus structure, integration time, potentially regulated genes, transcription factor-binding sites, and primer-binding site features. Besides, 9 chimpanzee sequences, 8 gorilla sequences, and 10 orangutan sequences belonging to the HML-8 subgroup were identified. The integration time results showed that the HML-8 elements were integrated into the primate lineage around 35 and 42 million years ago (mya), during primates evolutionary speciation. Overall, the results clarified the composition of the HML-8 groups, providing an exhaustive background for subsequent functional studies.

Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

Background

Human endogenous retroviruses (HERVs) result from ancestral infections caused by exogenous retroviruses that became incorporated into the germline DNA and evolutionarily fixed in the human genome. HERVs can be transmitted vertically in a Mendelian fashion and be stably maintained in the human genome, of which they are estimated to comprise approximately 8%. HERV-K (HML1-10) transcription has been confirmed to be associated with a variety of diseases, such as breast cancer, lung cancer, prostate cancer, melanoma, rheumatoid arthritis, and amyotrophic lateral sclerosis. However, the poor characterization of HML-9 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome. In light of this, a precise and updated HERV-K HML-9 genomic map is urgently needed to better evaluate the role of these elements in human health.

Results

We report a comprehensive analysis of the presence and distribution of HERV-K HML-9 elements within the human genome, with a detailed characterization of the structural and phylogenetic properties of the group. A total of 23 proviruses and 47 solo LTR elements were characterized, with a detailed description of the provirus structure, integration time, potential regulated genes, transcription factor binding sites (TFBS), and primer binding site (PBS) features. The integration time results showed that the HML-9 elements found in the human genome integrated into the primate lineage between 17.5 and 48.5 million years ago (mya).

Conclusion

The results provide a clear characterization of HML-9 and a comprehensive background for subsequent functional studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12977-022-00596-2.

The Happy Hopping of Transposons: The Origins of V(D)J Recombination in Adaptive Immunity

Nearly 50% of the human genome is derived from transposable elements (TEs). Though dysregulated transposons are deleterious to humans and can lead to diseases, co-opted transposons play an important role in generating alternative or new DNA sequence combinations to perform novel cellular functions. The appearance of an adaptive immune system in jawed vertebrates, wherein the somatic rearrangement of T and B cells generates a repertoire of antibodies and receptors, is underpinned by Class II TEs. This review follows the evolution of recombination activation genes (RAGs), components of adaptive immunity, from TEs, focusing on the structural and mechanistic similarities between RAG recombinases and DNA transposases. As evolution occurred from a transposon precursor, DNA transposases developed a more targeted and constrained mechanism of mobilization. As DNA repair is integral to transposition and recombination, we note key similarities and differences in the choice of DNA repair pathways following these processes. Understanding the regulation of V(D)J recombination from its evolutionary origins may help future research to specifically target RAG proteins to rectify diseases associated with immune dysregulation.

On the Base Composition of Transposable Elements

Transposable elements exhibit a base composition that is often different from the genomic average and from hosts’ genes. The most common compositional bias is towards Adenosine and Thymine, although this bias is not universal, and elements with drastically different base composition can coexist within the same genome. The AT-richness of transposable elements is apparently maladaptive because it results in poor transcription and sub-optimal translation of proteins encoded by the elements. The cause(s) of this unusual base composition remain unclear and have yet to be investigated. Here, I review what is known about the nucleotide content of transposable elements and how this content can affect the genome of their host as well as their own replication. The compositional bias of transposable elements could result from several non-exclusive processes including horizontal transfer, mutational bias, and selection. It appears that mutation alone cannot explain the high AT-content of transposons and that selection plays a major role in the evolution of the compositional bias. The reason why selection would favor a maladaptive nucleotide content remains however unexplained and is an area of investigation that clearly deserves attention.

Molecular functions of human endogenous retroviruses in health and disease

Human endogenous retroviruses (HERVs) and related genetic elements form 504 distinct families and occupy ~8% of human genome. Recent success of high-throughput experimental technologies facilitated understanding functional impact of HERVs for molecular machinery of human cells. HERVs encode active retroviral proteins, which may exert important physiological functions in the body, but also may be involved in the progression of cancer and numerous human autoimmune, neurological and infectious diseases. The spectrum of related malignancies includes, but not limits to, multiple sclerosis, psoriasis, lupus, schizophrenia, multiple cancer types and HIV. In addition, HERVs regulate expression of the neighboring host genes and modify genomic regulatory landscape, e.g., by providing regulatory modules like transcription factor binding sites (TFBS). Indeed, recent bioinformatic profiling identified ~110,000 regulatory active HERV elements, which formed at least ~320,000 human TFBS. These and other peculiarities of HERVs might have played an important role in human evolution and speciation. In this paper, we focus on the current progress in understanding of normal and pathological molecular niches of HERVs, on their implications in human evolution, normal physiology and disease. We also review the available databases dealing with various aspects of HERV genetics.

Visualized computational predictions of transcriptional effects by intronic endogenous retroviruses

When endogenous retroviruses (ERVs) or other transposable elements (TEs) insert into an intron, the consequence on gene transcription can range from negligible to a complete ablation of normal transcripts. With the advance of sequencing technology, more and more insertionally polymorphic or private TE insertions are being identified in humans and mice, of which some could have a significant impact on host gene expression. Nevertheless, an efficient and low cost approach to prioritize their potential effect on gene transcription has been lacking. By building a computational model based on artificial neural networks (ANN), we demonstrate the feasibility of using machine-learning approaches to predict the likelihood that intronic ERV insertions will have major effects on gene transcription, focusing on the two ERV families, namely Intracisternal A-type Particle (IAP) and Early Transposon (ETn)/MusD elements, which are responsible for the majority of ERV-induced mutations in mice. We trained the ANN model using properties associated with these ERVs known to cause germ-line mutations (positive cases) and properties associated with likely neutral ERVs of the same families (negative cases), and derived a set of prediction plots that can visualize the likelihood of affecting gene transcription by ERV insertions. Our results show a highly reliable prediction power of our model, and offer a potential approach to computationally screen for other types of TE insertions that may affect gene transcription or even cause disease.

Abundance and distribution of transposable elements in two Drosophila QTL mapping resources

Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster. The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that “burden tests” that test for the effect of TEs as a class may be more fruitful.

Gene properties and chromatin state influence the accumulation of transposable elements in genes

Transposable elements (TEs) are mobile DNA sequences found in the genomes of almost all species. By measuring the normalized coverage of TE sequences within genes, we identified sets of genes with conserved extremes of high/low TE density in the genomes of human, mouse and cow and denoted them as ‘shared upper/lower outliers (SUOs/SLOs)’. By comparing these outlier genes to the genomic background, we show that a large proportion of SUOs are involved in metabolic pathways and tend to be mammal-specific, whereas many SLOs are related to developmental processes and have more ancient origins. Furthermore, the proportions of different types of TEs within human and mouse orthologous SUOs showed high similarity, even though most detectable TEs in these two genomes inserted after their divergence. Interestingly, our computational analysis of polymerase-II (Pol-II) occupancy at gene promoters in different mouse tissues showed that 60% of tissue-specific SUOs show strong Pol-II binding only in embryonic stem cells (ESCs), a proportion significantly higher than the genomic background (37%). In addition, our analysis of histone marks such as H3K4me3 and H3K27me3 in mouse ESCs also suggest a strong association between TE-rich genes and open-chromatin at promoters. Finally, two independent whole-transcriptome datasets show a positive association between TE density and gene expression level in ESCs. While this study focuses on genes with extreme TE densities, the above results clearly show that the probability of TE accumulation/fixation in mammalian genes is not random and is likely associated with different factors/gene properties and, most importantly, an association between the TE insertion/fixation rate and gene activity status in ES cells.

Unique functions of repetitive transcriptomes

Repetitive sequences occupy a huge fraction of essentially every eukaryotic genome. Repetitive sequences cover more than 50% of mammalian genomic DNAs, whereas gene exons and protein-coding sequences occupy only ~3% and 1%, respectively. Numerous genomic repeats include genes themselves. They generally encode "selfish" proteins necessary for the proliferation of transposable elements (TEs) in the host genome. The major part of evolutionary "older" TEs accumulated mutations over time and fails to encode functional proteins. However, repeats have important functions also on the RNA level. Repetitive transcripts may serve as multifunctional RNAs by participating in the antisense regulation of gene activity and by competing with the host-encoded transcripts for cellular factors. In addition, genomic repeats include regulatory sequences like promoters, enhancers, splice sites, polyadenylation signals, and insulators, which actively reshape cellular transcriptomes. TE expression is tightly controlled by the host cells, and some mechanisms of this regulation were recently decoded. Finally, capacity of TEs to proliferate in the host genome led to the development of multiple biotechnological applications.

Retroelements and their impact on genome evolution and functioning

Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a "junk DNA" or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition.

Evolution of the Caenorhabditis elegans genome

A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.

Integration target site selection by a resurrected human endogenous retrovirus

At least 8% of the human genome was formed by integration of retroviral DNA sequences. Here we analyze the forces directing the accumulation of human endogenous retroviruses (HERVs) by comparing de novo HERV integration targeting with the distribution of fixed HERV elements in the human genome. All known genomic HERVs are inactive due to mutation, but we were able to study integration targeting using a reconstituted consensus HERV-K (designated HERV-K(Con)). We found that HERV-K(Con) integrated preferentially in transcription units, in gene-rich regions, and near features associated with active transcription units and associated regulatory regions. In contrast, genomic HERV-K proviruses are found preferentially outside transcription units. The minority of genomic HERVKs present inside transcription units are in opposite transcriptional orientation relative to the host gene, the orientation predicted to be minimally disruptive to host mRNA synthesis, but de novo HERV-K(Con) integration within transcription units showed no orientation bias. We also found that the youngest HERV-K elements in the human genome showed a distribution intermediate between de novo HERV-K(Con) integration sites and older fixed HERV-Ks. These findings indicate that accumulation of HERVs in the human germline is a two-step process: integration targeting biases direct initial accumulation, then purifying selection leads to loss of proviruses disrupting gene function.

Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element

Understanding the molecular mechanisms that influence transposable element target site preferences is a fundamental challenge in functional and evolutionary genomics. Large-scale transposon insertion projects provide excellent material to study target site preferences in the absence of confounding effects of post-insertion evolutionary change. Growing evidence from a wide variety of prokaryotes and eukaryotes indicates that DNA transposons recognize staggered-cut palindromic target site motifs (TSMs). Here, we use over 10 000 accurately mapped P-element insertions in the Drosophila melanogaster genome to test predictions of the staggered-cut palindromic target site model for DNA transposon insertion. We provide evidence that the P-element targets a 14-bp palindromic motif that can be identified at the primary sequence level, which predicts the local spacing, hotspots and strand orientation of P-element insertions. Intriguingly, we find that the although P-element destroys the complete 14-bp target site upon insertion, the terminal three nucleotides of the P-element inverted repeats complement and restore the original TSM, suggesting a mechanistic link between transposon target sites and their terminal inverted repeats. Finally, we discuss how the staggered-cut palindromic target site model can be used to assess the accuracy of genome mappings for annotated P-element insertions.

Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements

Endogenous retroviral elements (ERVs) in mice are significant genomic mutagens, causing ∼10% of all reported spontaneous germ line mutations in laboratory strains. The majority of these mutations are due to insertions of two high copy ERV families, the IAP and ETn/MusD elements. This significant level of ongoing retrotranspositional activity suggests that inbred mice are highly variable in content of these two ERV groups. However, no comprehensive genome-wide studies have been performed to assess their level of polymorphism. Here we compared three test strains, for which sufficient genomic sequence is available, to each other and to the reference C57BL/6J genome and detected very high levels of insertional polymorphism for both ERV families, with an estimated false discovery rate of only 0.4%. Specifically, we found that at least 60% of IAP and 25% of ETn/MusD elements detected in any strain are absent in one or more of the other three strains. The polymorphic nature of a set of 40 ETn/MusD elements found within gene introns was confirmed using genomic PCR on DNA from a panel of mouse strains. For some cases, we detected gene-splicing abnormalities involving the ERV and obtained additional evidence for decreased gene expression in strains carrying the insertion. In total, we identified nearly 700 polymorphic IAP or ETn/MusD ERVs or solitary LTRs that reside in gene introns, providing potential candidates that may contribute to gene expression differences among strains. These extreme levels of polymorphism suggest that ERV insertions play a significant role in genetic drift of mouse lines.

The laboratory mouse is the most widely used mammal for biological research. Hundreds of inbred mouse strains have been developed that vary in characteristics such as susceptibility to cancer or other diseases. There is much interest in uncovering differences between strains that result in different traits and, to aid this effort, millions of single nucleotide differences or polymorphisms between strains have been cataloged. To date, there has been less emphasis placed on other sources of genetic variation. In this study, we have conducted a genome-wide analysis to examine the level of polymorphism of mouse endogenous retroviral sequences (ERVs). ERVs are derived from infectious retroviruses that now exist in the genome and are inherited as part of chromosomes. Unlike in humans, genomic insertions of ERVs cause many new mutations in mice but their extent of variation between strains has been difficult to study because of their high copy numbers. By comparing genomic sequences of four common mouse strains, we found very high levels of polymorphism for two large active families of ERVs. Moreover, we documented nearly 700 polymorphic ERVs located within gene introns and found evidence that some of these affect gene transcript levels. This study demonstrates that ERV polymorphisms are a major source of genetic variability among mouse strains and likely contribute to strain-specific traits.

Retrotransposons influence the mouse transcriptome: implication for the divergence of genetic traits

Massive accumulation of retrotransposons, comprising >40% of human and mouse genomes, is one of the major events in the evolution of the genome. However, most retrotransposons have lost retrotransposition competency, which makes studying their role in genome evolution elusive. Intracisternal A-particle (IAP) elements are long terminal repeat (LTR)-type mouse retrotransposons consisting of full-length and internally deleted types. Some are retrotransposition competent and their upregulated activity has been reported in mutant mice deficient in genome defense systems, suggesting that IAP elements provide a unique platform for studying the interaction between retrotransposons and mammalian genomes. Using the IAP element as a model case, here we show that mobilization of retrotransposons alters the mouse transcriptome. Retrotransposition assay in cultured cells demonstrated that a subset of internally deleted IAP elements, called IDelta1 type, retrotranspose efficiently when supplied with functional IAP proteins. Furthermore, the IDelta1 type IAP element exhibited substantial transcription-inducing activity in the flanking region. Genomewide transcript analysis of embryonic stem (ES) cells identified IAP-induced transcripts, including fusion transcripts between IAP sequence and endogenous genes. Unexpectedly, nearly half of these IAP elements obtained from ES cells derived from 129 mouse strain were absent in the C57BL/6 genome, suggesting that IAP-driven transcription contributes to the unique trait of the individual mouse strain. On the basis of these data, we propose that retrotransposons are one of the drivers that shape the mammalian transcriptome.

Multiple effects govern endogenous retrovirus survival patterns in human gene introns

BACKGROUND

Endogenous retroviruses (ERVs) and solitary long terminal repeats (LTRs) have a significant antisense bias when located in gene introns, suggesting strong negative selective pressure on such elements oriented in the same transcriptional direction as the enclosing gene. It has been assumed that this bias reflects the presence of strong transcriptional regulatory signals within LTRs but little work has been done to investigate this phenomenon further.

RESULTS

In the analysis reported here, we found significant differences between individual human ERV families in their prevalence within genes and degree of antisense bias and show that, regardless of orientation, ERVs of most families are less likely to be found in introns than in intergenic regions. Examination of density profiles of ERVs across transcriptional units and the transcription signals present in the consensus ERVs suggests the importance of splice acceptor sites, in conjunction with splice donor and polyadenylation signals, as the major targets for selection against most families of ERVs/LTRs. Furthermore, analysis of annotated human mRNA splicing events involving ERV sequence revealed that the relatively young human ERVs (HERVs), HERV9 and HERV-K (HML-2), are involved in no human mRNA splicing events at all when oriented antisense to gene transcription, while elements in the sense direction in transcribed regions show considerable bias for use of strong splice sites.

CONCLUSION

Our observations suggest suppression of splicing among young intronic ERVs oriented antisense to gene transcription, which may account for their reduced mutagenicity and higher fixation rate in gene introns.