Restricting retrotransposons: a review

Mouse germ line mutations due to retrotransposon insertions

Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans.

The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection

L1 retrotransposons are transposable elements and major contributors of genetic variation in humans. Where L1 integrates into the genome can directly impact human evolution and disease. Here, we experimentally induced L1 retrotransposition in cells and mapped integration sites at nucleotide resolution. At local scales, L1 integration is mostly restricted by genome sequence biases and the specificity of the L1 machinery. At regional scales, L1 shows a broad capacity for integration into all chromatin states, in contrast to other known mobile genetic elements. However, integration is influenced by the replication timing of target regions, suggesting a link to host DNA replication. The distribution of new L1 integrations differs from those of preexisting L1 copies, which are significantly reshaped by natural selection. Our findings reveal that the L1 machinery has evolved to efficiently target all genomic regions and underline a predominant role for post-integrative processes on the distribution of endogenous L1 elements.

Oxidative stress and LINE-1 reactivation in bladder cancer are epigenetically linked through active chromatin formation

Oxidative stress and reactivation of long interspersed element-1 (LINE-1) are coincidently observed in bladder cancer (BlCa), but the mechanistic connection between these two oncogenic phenomena is unknown. Previously, we reported increases in oxidative stress and LINE-1 protein (ORF1p) expression in human BlCa tissues. In this study, we measured 5-methylcytosine (5mC), 8-hydroxydeoxyguanosine (8-OHdG), 8-oxoguanosine DNA glycosylase-1 (OGG1), H3K9me3 and HP1α in bladder tissues obtained from BlCa patients. Reactivation of LINE-1 by reactive oxygen species (ROS) through chromatin remodeling was investigated in seven BlCa cell lines. We found that 5mC was decreased, but 8-OHdG, H3K9me3 and HP1α levels were increased in BlCa tissues relative to the adjacent non-cancerous tissues. OGG1, H3K9me3 and HP1α expression in BlCa tissues were positively correlated with 8-OHdG levels. Following H₂O₂ treatment, LINE-1 transcript expression was increased in VM-CUB-1 and TCCSUP, whereas AluYa5 and AluYb8 transcripts were increased in BFTC905 cells. Basal expression of LINE-1 ORF1p varied among BlCa cell lines from none to very high. H₂O₂ treatment clearly increased expression of ORF1p in VM-CUB-1, TCCSUP and BFTC905. Chromatin immunoprecipitation experiments revealed that 5'-LINE-1 promoters became further enriched in H3K4me3 and H3K18ac in VM-CUB-1 and BFTC905 cells treated with H₂O₂. In contrast, 5'-LINE-1 promoters became more enriched in H3K9me3 and H3K27me3 in UM-UC-3 treated with H₂O₂. In summary, decreased 5mC, but increased 8-OHdG, H3K9me3 and HP1α expression were demonstrated in human BlCa tissues, indicating global DNA hypomethylation, increased oxidative stress and altered histone methylation in BlCa. Chromatin structures were profoundly changed in BlCa cells exposed to ROS, but expression of LINE-1 transcript and protein were at most modestly increased. ROS enhanced expression of full-length LINE-1 elements only in cell lines with pre-existing activation, which was paralleled by increased formation of active chromatin at LINE-1 promoter loci.

Retrotransposon-induced mosaicism in the neural genome

Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions.

Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation

The retrotransposon LINE-1 (L1) is a significant source of endogenous mutagenesis in humans. In each individual genome, a few retrotransposition-competent L1s (RC-L1s) can generate new heritable L1 insertions in the early embryo, primordial germ line, and germ cells. L1 retrotransposition can also occur in the neuronal lineage and cause somatic mosaicism. Although DNA methylation mediates L1 promoter repression, the temporal pattern of methylation applied to individual RC-L1s during neurogenesis is unclear. Here, we identified a de novo L1 insertion in a human induced pluripotent stem cell (hiPSC) line via retrotransposon capture sequencing (RC-seq). The L1 insertion was full-length and carried 5' and 3' transductions. The corresponding donor RC-L1 was part of a large and recently active L1 transduction family and was highly mobile in a cultured-cell L1 retrotransposition reporter assay. Notably, we observed distinct and dynamic DNA methylation profiles for the de novo L1 and members of its extended transduction family during neuronal differentiation. These experiments reveal how a de novo L1 insertion in a pluripotent stem cell is rapidly recognized and repressed, albeit incompletely, by the host genome during neurodifferentiation, while retaining potential for further retrotransposition.

Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys

Background

Endogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate taxa remains unclear. The aim of this study was to identify and classify the ERV sequences in the genomes of the golden snub-nosed monkey (Rhinopithecus roxellana) and the black and white snub-nosed monkey (Rhinopithecus bieti), two endangered primate species that exploit high altitude (2,500–4,500 m) temperate forests in southern and central China.

Methods

We used a TBLASTN program to search the ERV sequences of golden snub-nosed monkey genome and the black and white snub-nosed monkey genome. We retrieved all complete accession sequences from the homology search and then used the program, RetroTector, to check and identify the ERV sequences.

Results

We identified 284 and 263 endogenous retrovirus sequences in R. roxellana and R. bieti respectively. The proportion of full-length sequences of all ERV was 30% in R. roxellana and 21% in R. bieti and they were described as class I and class II or gamma-retrovirus and beta-retrovirus genera. The truncation pattern distribution in the two species was virtually identical. By analyzing and comparing ERV orthologues among 6 primate species, we identified the co-evolution of ERVs with their host. We also examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti. Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host.

Conclusions

Our results indicate that ERV sequences are widely distributed in snub-nosed monkeys, and their phylogenetic history can mirror that of their hosts over long evolutionary time scales. In addition, ERV sequences appear to have an important influence on the evolution of host pathology.

The impact of transposable element activity on therapeutically relevant human stem cells

Human stem cells harbor significant potential for basic and clinical translational research as well as regenerative medicine. Currently ~ 3000 adult and ~ 30 pluripotent stem cell-based, interventional clinical trials are ongoing worldwide, and numbers are increasing continuously. Although stem cells are promising cell sources to treat a wide range of human diseases, there are also concerns regarding potential risks associated with their clinical use, including genomic instability and tumorigenesis concerns. Thus, a deeper understanding of the factors and molecular mechanisms contributing to stem cell genome stability are a prerequisite to harnessing their therapeutic potential for degenerative diseases. Chemical and physical factors are known to influence the stability of stem cell genomes, together with random mutations and Copy Number Variants (CNVs) that accumulated in cultured human stem cells. Here we review the activity of endogenous transposable elements (TEs) in human multipotent and pluripotent stem cells, and the consequences of their mobility for genomic integrity and host gene expression. We describe transcriptional and post-transcriptional mechanisms antagonizing the spread of TEs in the human genome, and highlight those that are more prevalent in multipotent and pluripotent stem cells. Notably, TEs do not only represent a source of mutations/CNVs in genomes, but are also often harnessed as tools to engineer the stem cell genome; thus, we also describe and discuss the most widely applied transposon-based tools and highlight the most relevant areas of their biomedical applications in stem cells. Taken together, this review will contribute to the assessment of the risk that endogenous TE activity and the application of genetically engineered TEs constitute for the biosafety of stem cells to be used for substitutive and regenerative cell therapies.

Retrotransposons in the development and progression of amyotrophic lateral sclerosis

Endogenous retrotransposon sequences constitute approximately 42% of the human genome, and mobilisation of retrotransposons has resulted in rearrangements, duplications, deletions, novel transcripts and the introduction of new regulatory domains throughout the human genome. Both germline and somatic de novo retrotransposition events have been involved in a range of human diseases, and there is emerging evidence for the modulation of retrotransposon activity during the development of specific diseases. Particularly, there is unequivocal consensus that endogenous retrotransposition can occur in neuronal lineages. This review addresses our current knowledge of the different mechanisms through which retrotransposons might influence the development of and predisposition to amyotrophic lateral sclerosis.

Latent infection with Kaposi's sarcoma-associated herpesvirus enhances retrotransposition of long interspersed element-1

Kaposi's sarcoma (KS)-associated herpesvirus (KSHV), a gamma-2 herpesvirus, is the causative agent of KS, primary effusion lymphoma (PEL), and a plasma cell variant of multicentric Castleman's disease. Although KSHV latency is detected in KS-related tumors, oncogenic pathways activated by KSHV latent infection are not fully understood. Here, we found that retrotransposition of long interspersed element-1 (L1), a retrotransposon in the human genome, was enhanced in PEL cells. Among the KSHV latent genes, viral FLICE-inhibitory protein (vFLIP) enhanced L1 retrotransposition in an NF-κB-dependent manner. Intracellular cell adhesion molecule-1 (ICAM-1), an NF-κB target, regulated the vFLIP-mediated enhancement of L1 retrotransposition. Furthermore, ICAM-1 downregulated the expression of Moloney leukemia virus 10 (MOV10), an L1 restriction factor. Knockdown of ICAM-1 or overexpression of MOV10 relieved the vFLIP-mediated enhancement of L1 retrotransposition. Collectively, during KSHV latency, vFLIP upregulates ICAM-1 in an NF-κB-dependent manner, which, in turn, downregulates MOV10 expression and thereby enhances L1 retrotransposition. Because active L1 retrotransposition can lead to genomic instability, which is commonly found in KS and PEL, activation of L1 retrotransposition during KSHV latency may accelerate oncogenic processes through enhancing genomic instability. Our results suggest that L1 retrotransposition may be a novel target for impeding tumor development in KSHV-infected patients.

The Lupus Susceptibility Locus Sgp3 Encodes the Suppressor of Endogenous Retrovirus Expression SNERV

Elevated endogenous retrovirus (ERV) transcription and anti-ERV antibody reactivity are implicated in lupus pathogenesis. Overproduction of non-ecotropic ERV (NEERV) envelope glycoprotein gp70 and resultant nephritis occur in lupus-prone mice, but whether NEERV mis-expression contributes to lupus etiology is unclear. Here we identified suppressor of NEERV (Snerv) 1 and 2, Krüppel-associated box zinc-finger proteins (KRAB-ZFPs) that repressed NEERV by binding the NEERV long terminal repeat to recruit the transcriptional regulator KAP1. Germline Snerv1/Snerv2 deletion increased activating chromatin modifications, transcription, and gp70 expression from NEERV loci. F1 crosses of lupus-prone New Zealand Black (NZB) and 129 mice to Snerv1/Snerv2^-/- mice failed to restore NEERV repression, demonstrating that loss of SNERV underlies the lupus autoantigen gp70 overproduction that promotes nephritis in susceptible mice and that SNERV encodes for Sgp3 (in NZB mice) and Gv-1 loci (in 129 mice). Increased ERV expression in lupus patients inversely correlated with three putative ERV-suppressing KRAB-ZFPs, suggesting that loss of KRAB-ZFP-mediated ERV control may contribute to human lupus pathogenesis.

The Physiology of Homeoprotein Transduction

The homeoprotein family comprises ~300 transcription factors and was long seen as primarily involved in developmental programs through cell autonomous regulation. However, recent evidence reveals that many of these factors are also expressed in the adult where they exert physiological functions not yet fully deciphered. Furthermore, the DNA-binding domain of most homeoproteins contains two signal sequences allowing their secretion and internalization, thus intercellular transfer. This review focuses on this new-found signaling in cell migration, axon guidance, and cerebral cortex physiological homeostasis and speculates on how it may play important roles in early arealization of the neuroepithelium. It also describes the use of homeoproteins as therapeutic proteins in mouse models of diseases affecting the central nervous system, in particular Parkinson disease and glaucoma.

New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the study of TE population dynamics focusing on fruit flies and humans, which represent two extremes in terms of TE abundance, diversity, and activity. We review the most recent methodological approaches applied to the study of TE dynamics as well as the new knowledge on host factors involved in the regulation of TE activity. In addition to transposition rates, we also focus on TE deletion rates and on the selective forces that affect the dynamics of TEs in genomes.

Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis

BACKGROUND

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving loss of motor neurons and having no known cure and uncertain etiology. Several studies have drawn connections between altered retrotransposon expression and ALS. Certain features of the LINE-1 (L1) retrotransposon-encoded ORF1 protein (ORF1p) are analogous to those of neurodegeneration-associated RNA-binding proteins, including formation of cytoplasmic aggregates. In this study we explore these features and consider possible links between L1 expression and ALS.

RESULTS

We first considered factors that modulate aggregation and subcellular distribution of LINE-1 ORF1p, including nuclear localization. Changes to some ORF1p amino acid residues alter both retrotransposition efficiency and protein aggregation dynamics, and we found that one such polymorphism is present in endogenous L1s abundant in the human genome. We failed, however, to identify CRM1-mediated nuclear export signals in ORF1p nor strict involvement of cell cycle in endogenous ORF1p nuclear localization in human 2102Ep germline teratocarcinoma cells. Some proteins linked with ALS bind and colocalize with L1 ORF1p ribonucleoprotein particles in cytoplasmic RNA granules. Increased expression of several ALS-associated proteins, including TAR DNA Binding Protein (TDP-43), strongly limits cell culture retrotransposition, while some disease-related mutations modify these effects. Using quantitative reverse transcription PCR (RT-qPCR) of ALS tissues and reanalysis of publicly available RNA-Seq datasets, we asked if changes in expression of retrotransposons are associated with ALS. We found minimal altered expression in sporadic ALS tissues but confirmed a previous report of differential expression of many repeat subfamilies in C9orf72 gene-mutated ALS patients.

CONCLUSIONS

Here we extended understanding of the subcellular localization dynamics of the aggregation-prone LINE-1 ORF1p RNA-binding protein. However, we failed to find compelling evidence for misregulation of LINE-1 retrotransposons in sporadic ALS nor a clear effect of ALS-associated TDP-43 protein on L1 expression. In sum, our study reveals that the interplay of active retrotransposons and the molecular features of ALS are more complex than anticipated. Thus, the potential consequences of altered retrotransposon activity for ALS and other neurodegenerative disorders are worthy of continued investigation.

Ten things you should know about transposable elements

Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of genomics and large-scale functional assays has shed new light on the multi-faceted activities of TEs and implies that they should no longer be marginalized. Here, we introduce the fundamental properties of TEs and their complex interactions with their cellular environment, which are crucial to understanding their impact and manifold consequences for organismal biology. While we draw examples primarily from mammalian systems, the core concepts outlined here are relevant to a broad range of organisms.

Transposable Element Expression in Acute Myeloid Leukemia Transcriptome and Prognosis

Over half of the human genome is comprised of transposable elements (TE). Despite large-scale studies of the transcriptome in cancer, a comprehensive look at TE expression and its relationship to various mutations or prognosis has not been performed. We characterized the expression of TE in 178 adult acute myeloid leukemia (AML) patients using transcriptome data from The Cancer Genome Atlas. We characterized mutation specific dysregulation of TE expression using a multivariate linear model. We identified distinct patterns of TE expression associated with specific mutations and transcriptional networks. Genes regulating methylation was not associated with significant change in TE expression. Using an unpenalized cox regression analysis we identified a TE expression signature that predicted prognosis in AML. We identified 14 candidate prognostic TE transcripts (TEP) that classified AML as high/low-risk and this was independent of mutation-based and coding-gene expression based risk-stratification. TEP was able to predict prognosis in independent cohorts of 284 pediatric AML patients and 19 relapsed adult AML patients. This first comprehensive study of TE expression in AML demonstrates that TE expression can serve as a biomarker for prognosis in AML, and provides novel insights into the biology of AML. Studies characterizing its role in other cancers are warranted.

Somatic Mutagenesis in Mammals and Its Implications for Human Disease and Aging

DNA mutations as a consequence of errors during DNA damage repair, replication, or mitosis are the substrate for evolution. In multicellular organisms, mutations can occur in the germline and also in somatic tissues, where they are associated with cancer and other chronic diseases and possibly with aging. Recent advances in high-throughput sequencing have made it relatively easy to study germline de novo mutations, but in somatic cells, the vast majority of mutations are low-abundant and can be detected only in clonal lineages, such as tumors, or single cells. Here we review recent results on somatic mutations in normal human and animal tissues with a focus on their possible functional consequences.

Uridylation by TUT4/7 Restricts Retrotransposition of Human LINE-1s

LINE-1 retrotransposition is tightly restricted by layers of regulatory control, with epigenetic pathways being the best characterized. Looking at post-transcriptional regulation, we now show that LINE-1 mRNA 3' ends are pervasively uridylated in various human cellular models and in mouse testes. TUT4 and TUT7 uridyltransferases catalyze the modification and function in cooperation with the helicase/RNPase MOV10 to counteract the RNA chaperone activity of the L1-ORF1p retrotransposon protein. Uridylation potently restricts LINE-1 retrotransposition by a multilayer mechanism depending on differential subcellular localization of the uridyltransferases. We propose that uridine residues added by TUT7 in the cytoplasm inhibit initiation of reverse transcription of LINE-1 mRNAs once they are reimported to the nucleus, whereas uridylation by TUT4, which is enriched in cytoplasmic foci, destabilizes mRNAs. These results provide a model for the post-transcriptional restriction of LINE-1, revealing a key physiological role for TUT4/7-mediated uridylation in maintaining genome stability.

SAMHD1 deficient human monocytes autonomously trigger type I interferon

Germline mutations in the human SAMHD1 gene cause the development of Aicardi-Goutières Syndrome (AGS), with a dominant feature being increased systemic type I interferon(IFN) production. Here we tested the state of type I IFN induction and response to, in SAMHD1 knockout (KO) human monocytic cells. SAMHD1 KO cells exhibited spontaneous transcription and translation of IFN-β and subsequent interferon-stimulated genes (ISGs) as compared to parental wild-type cells. This elevation of IFN-β and ISGs was abrogated via inhibition of the TBK1-IRF3 pathway in the SAMHD1 KO cells. In agreement, we found that SAMHD1 KO cells present high levels of phosphorylated TBK1 when compared to control cells. Moreover, addition of blocking antibody against type I IFN also reversed elevation of ISGs. These experiments suggested that SAMHD1 KO cells are persistently auto-stimulating the TBK1-IRF3 pathway, leading to an enhanced production of type I IFN and subsequent self-induction of ISGs.

Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion

Endogenous retroviruses (ERVs) are proviral sequences that result from host germ-line invasion by exogenous retroviruses. The majority of ERVs are degraded. Using the koala retrovirus (KoRV) as a model system, we demonstrate that recombination with an ancient koala retroelement disables KoRV, and that recombination occurs frequently and early in the invasion process. Recombinant KoRVs (recKoRVs) are then able to proliferate in the koala germ line. This may in part explain the generally degraded nature of ERVs in vertebrate genomes and suggests that degradation via recombination is one of the earliest processes shaping retroviral genomic invasions.

Endogenous retroviruses (ERVs) are proviral sequences that result from colonization of the host germ line by exogenous retroviruses. The majority of ERVs represent defective retroviral copies. However, for most ERVs, endogenization occurred millions of years ago, obscuring the stages by which ERVs become defective and the changes in both virus and host important to the process. The koala retrovirus, KoRV, only recently began invading the germ line of the koala (Phascolarctos cinereus), permitting analysis of retroviral endogenization on a prospective basis. Here, we report that recombination with host genomic elements disrupts retroviruses during the earliest stages of germ-line invasion. One type of recombinant, designated recKoRV1, was formed by recombination of KoRV with an older degraded retroelement. Many genomic copies of recKoRV1 were detected across koalas. The prevalence of recKoRV1 was higher in northern than in southern Australian koalas, as is the case for KoRV, with differences in recKoRV1 prevalence, but not KoRV prevalence, between inland and coastal New South Wales. At least 15 additional different recombination events between KoRV and the older endogenous retroelement generated distinct recKoRVs with different geographic distributions. All of the identified recombinant viruses appear to have arisen independently and have highly disrupted ORFs, which suggests that recombination with existing degraded endogenous retroelements may be a means by which replication-competent ERVs that enter the germ line are degraded.

Partition of Repeat-Induced Point Mutations Reveals Structural Aspects of Homologous DNA-DNA Pairing

In some fungi, a premeiotic process known as repeat-induced point mutation (RIP) can accurately identify and mutate nearly all gene-sized DNA repeats present in the haploid germline nuclei. Studies in Neurospora crassa have suggested that RIP detects sequence homology directly between intact DNA double helices, without strand separation and without the participation of RecA-like proteins. Those studies used the aggregated number of RIP mutations as a simple quantitative measure of RIP activity. Additional structural information about homologous DNA-DNA pairing during RIP can be extracted by analyzing spatial distributions of RIP mutations converted into profiles of partitioned RIP propensity (PRP). Further analysis shows that PRP is strongly affected by the topological configuration and the relative positioning of the participating DNA segments. Most notably, pairs of closely positioned repeats produce very distinct PRP profiles depending on whether these repeats are present in the direct or the inverted orientation. Such an effect can be attributed to a topology-dependent redistribution of the supercoiling stress created by the predicted limited untwisting of the DNA segments during pairing. This and other results raise a possibility that such pairing-induced fluctuations in DNA supercoiling can modulate the overall structure and properties of repetitive DNA. Such effects can be particularly strong in the context of long tandem-repeat arrays that are typically present in the pericentromeric and centromeric regions of chromosomes in many species of plants, fungi, and animals, including humans.

Transgenic Mouse Models in Cancer Research

The use of existing mouse models in cancer research is of utmost importance as they aim to explore the casual link between candidate cancer genes and carcinogenesis as well as to provide models to develop and test new therapies. However, faster progress in translating mouse cancer model research into the clinic has been hampered due to the limitations of these models to better reflect the complexities of human tumors. Traditionally, immunocompetent and immunodeficient mice with syngeneic and xenografted tumors transplanted subcutaneously or orthotopically have been used. These models are still being widely employed for many different types of studies, in part due to their widespread availability and low cost. Other types of mouse models used in cancer research comprise transgenic mice in which oncogenes can be constitutively or conditionally expressed and tumor-suppressor genes silenced using conventional methods, such as retroviral infection, microinjection of DNA constructs, and the so-called "gene-targeted transgene" approach. These traditional transgenic models have been very important in studies of carcinogenesis and tumor pathogenesis, as well as in studies evaluating the development of resistance to therapy. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing approach has revolutionized the field of mouse cancer models and has had a profound and rapid impact on the development of more effective systems to study human cancers. The CRISPR/Cas9-based transgenic models have the capacity to engineer a wide spectrum of mutations found in human cancers and provide solutions to problems that were previously unsolvable. Recently, humanized mouse xenograft models that accept patient-derived xenografts and CD34+ cells were developed to better mimic tumor heterogeneity, the tumor microenvironment, and cross-talk between the tumor and stromal/immune cells. These features make them extremely valuable models for the evaluation of investigational cancer therapies, specifically new immunotherapies. Taken together, improvements in both the CRISPR/Cas9 system producing more valid mouse models and in the humanized mouse xenograft models resembling complex interactions between the tumor and its environment might represent one of the successful pathways to precise individualized cancer therapy, leading to improved cancer patient survival and quality of life.

Contrasting Rates of LINE-1 Amplification among New World Primates of the Atelidae Family

LINE-1 (L1) retrotransposons constitute the dominant category of transposons in mammalian genomes. L1 elements are active in the vast majority of mammals, and only a few cases of L1 extinction have been documented. The only possible case of extinction in primates was suggested for South American spider monkeys. However, these previous studies were based on a single species. We revisited this question with a larger phylogenetic sample, covering all 4 genera of Atelidae and 3 species of spider monkeys. We used an enrichment method to clone recently inserted L1 elements and performed an evolutionary analysis of the sequences. We were able to identify young L1 elements in all taxa, suggesting that L1 is probably still active in all Atelidae examined. However, we also detected considerable variations in the proportion of recent elements indicating that the rate of L1 amplification varies among Atelidae by a 3-fold factor. The extent of L1 amplification in Atelidae remains overall lower than in other New World monkeys. Multiple factors can affect the amplification of L1, such as the demography of the host and the control of transposition. These factors are discussed in the context of host life history.

Horizontal transfer of BovB and L1 retrotransposons in eukaryotes

BACKGROUND

Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events.

RESULTS

Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonised more than half of the genome sequence in today's mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms.

CONCLUSIONS

We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.

L1 retrotransposition in the soma: a field jumping ahead

Retrotransposons are transposable elements (TEs) capable of "jumping" in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses. However, the biological consequences of almost all somatic L1 insertions identified thus far remain unknown. In this review, we briefly summarize the current state-of-the-art in the field, including estimates of L1 retrotransposition rate in neurons. We bring forward the hypothesis that an extensive subset of retrotransposition-competent L1s may be de-repressed and mobile in the soma but largely inactive in the germline. We discuss recent reports of non-canonical L1-associated sequence variants in the brain and propose that the elevated L1 DNA content reported in several neurological disorders may predominantly comprise accumulated, unintegrated L1 nucleic acids, rather than somatic L1 insertions. Finally, we consider the main objectives and obstacles going forward in elucidating the biological impact of somatic retrotransposition.

Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers

Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons are normally suppressed in somatic tissues mainly due to DNA methylation and antiviral defense. However, the mechanism to suppress L1s may be disrupted in cancers, thus allowing L1s to act as insertional mutagens and cause genomic rearrangement and instability. Whereas the frequency of somatic L1 insertions varies greatly among individual tumors, much remains to be learned about underlying genetic, cellular, or environmental factors. Here, we report multiple correlates of L1 activity in stomach, colorectal, and esophageal tumors through an integrative analysis of cancer whole-genome and matched RNA-sequencing profiles. Clinical indicators of tumor progression, such as tumor grade and patient age, showed positive association. A potential L1 expression suppressor, TP53, was mutated in tumors with frequent L1 insertions. We characterized the effects of somatic L1 insertions on mRNA splicing and expression, and demonstrated an increased risk of gene disruption in retrotransposition-prone cancers. In particular, we found that a cancer-specific L1 insertion in an exon of MOV10, a key L1 suppressor, caused exon skipping and decreased expression of the affected allele due to nonsense-mediated decay in a tumor with a high L1 insertion load. Importantly, tumors with high immune activity, for example, those associated with Epstein–Barr virus infection or microsatellite instability, tended to carry a low number of L1 insertions in genomes with high expression levels of L1 suppressors such as APOBEC3s and SAMHD1. Our results indicate that cancer immunity may contribute to genome stability by suppressing L1 retrotransposition in gastrointestinal cancers.

LINE1 contributes to autoimmunity through both RIG-I- and MDA5-mediated RNA sensing pathways

Improper host immune activation leads to the development of the autoimmune disease Aicardi-Goutières syndrome (AGS), which is attributed to defined genetic mutations in such proteins as TREX1 and ADAR1. The mechanism of immune activation in AGS patients has not been thoroughly elucidated to date. In this study, we report that endogenous LINE1 components trigger IFNβ production in multiple human cell types, including those defective for cGAS/STING-mediated DNA sensing. In these cells, LINE1 DNA synthesis and retrotransposition were not required for LINE1-triggered immune activation, but RNA sensing pathways were essential. LINE1-triggered immune activation could be suppressed by diverse LINE1 inhibitors, including AGS-associated proteins targeting LINE1 RNA or proteins. However, AGS-associated ADAR1 or TREX1 mutants were defective in suppressing LINE1 retrotransposition or LINE1-triggered immune activation. Therefore, we have revealed a new function for LINE1 as an endogenous trigger of innate immune activation, which is important for understanding the molecular basis of IFN-based autoimmune diseases and may offer new intervention strategies.

Heritable L1 Retrotransposition Events During Development: Understanding Their Origins: Examination of heritable, endogenous L1 retrotransposition in mice opens up exciting new questions and research directions

The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) has played a major role in shaping the sequence composition of the mammalian genome. In our recent publication, "Heritable L1 retrotransposition in the mouse primordial germline and early embryo," we systematically assessed the rate and developmental timing of de novo, heritable endogenous L1 insertions in mice. Such heritable retrotransposition events allow L1 to exert an ongoing influence upon genome evolution. Here, we place our findings in the context of earlier studies, and highlight how our results corroborate, and depart from, previous research based on human patient samples and transgenic mouse models harboring engineered L1 reporter genes. In parallel, we outline outstanding questions regarding the stage-specificity, regulation, and functional impact of embryonic and germline L1 retrotransposition, and propose avenues for future research in this field.

Oocyte Quality Control: Causes, Mechanisms, and Consequences

Oocyte quality and number are key determinants of reproductive life span and success. These variables are shaped in part by the elimination of oocytes that experience problems during the early stages of meiosis. Meiotic prophase-I marks an extended period of genome vulnerability in which epigenetic reprogramming unleashes retroelements and hundreds of DNA double-strand breaks (DSBs) are inflicted to initiate the programmed recombination required for accurate chromosome segregation at the first meiotic division. Expression of LINE-1 retroelements perturbs several aspects of meiotic prophase and is associated with oocyte death during the early stages of meiotic prophase I. Defects in chromosome synapsis and recombination also trigger oocyte loss, but typically at a later stage, as cells transition into quiescence and form primordial follicles. Interrelated pathways that signal defects in DSB repair and chromosome synapsis mediate this late oocyte attrition. Here, I review our current understanding of early and late oocyte attrition based on studies in mouse and describe how these processes appear to be both distinct and overlapping and how they help balance the quality and size of oocyte reserves to maximize fecundity.

A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells

In mouse embryonic stem cells (mESCs), the expression of provirus and endogenous retroelements is epigenetically repressed. Although many cellular factors involved in retroelement silencing have been identified, the complete molecular mechanism remains elusive. In this study, we performed a genome-wide CRISPR screen to advance our understanding of retroelement silencing in mESCs. The Moloney murine leukemia virus (MLV)–based retroviral vector MSCV-GFP, which is repressed by the SETDB1/TRIM28 pathway in mESCs, was used as a reporter provirus, and we identified more than 80 genes involved in this process. In particular, ATF7IP and the BAF complex components are linked with the repression of most of the SETDB1 targets. We characterized two factors, MORC2A and RESF1, of which RESF1 is a novel molecule in retroelement silencing. Although both factors are recruited to repress provirus, their roles in repression are different. MORC2A appears to function dependent on repressive epigenetic modifications, while RESF1 regulates repressive epigenetic modifications associated with SETDB1. Our genome-wide CRISPR screen cataloged genes which function at different levels in silencing of SETDB1-target retroelements and provides a useful resource for further molecular studies.

Long INterspersed nuclear Elements (LINEs) in brain and non-brain tissues of the rat

Long INterspersed Element-1 (L1) is a transposable element that can insert copies of itself in new genomic locations causing genomic instability. In somatic cells, L1 retrotransposition activity is usually repressed but somatic L1 retrotransposition has recently been observed during neuronal differentiation. In this study, we evaluate whether L1 elements are differentially active in rat tissues during postnatal development. To this purpose, we quantified L1 in genomic DNA extracted from the olfactory bulb (OB), cerebellum (CE), cortex (CO) and heart (H). Each analysis was repeated on rats aged 7, 21 and 60 days. We found that L1 content in OB and CE tissue was significantly higher than H tissue, in rats of all three ages studied, suggesting that L1 activity could be modulated in postnatal development and neurogenesis.

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) is a continuing source of germline and somatic mutagenesis in mammals. Deregulated L1 activity is a hallmark of cancer, and L1 mutagenesis has been described in numerous human malignancies. We previously employed retrotransposon capture sequencing (RC-seq) to analyze hepatocellular carcinoma (HCC) samples from patients infected with hepatitis B or hepatitis C virus and identified L1 variants responsible for activating oncogenic pathways. Here, we have applied RC-seq and whole-genome sequencing (WGS) to an Abcb4 (Mdr2)-/- mouse model of hepatic carcinogenesis and demonstrated for the first time that L1 mobilization occurs in murine tumors. In 12 HCC nodules obtained from 10 animals, we validated four somatic L1 insertions by PCR and capillary sequencing, including TF subfamily elements, and one GF subfamily example. One of the TF insertions carried a 3' transduction, allowing us to identify its donor L1 and to demonstrate that this full-length TF element retained retrotransposition capacity in cultured cancer cells. Using RC-seq, we also identified eight tumor-specific L1 insertions from 25 HCC patients with a history of alcohol abuse. Finally, we used RC-seq and WGS to identify three tumor-specific L1 insertions among 10 intra-hepatic cholangiocarcinoma (ICC) patients, including one insertion traced to a donor L1 on Chromosome 22 known to be highly active in other cancers. This study reveals L1 mobilization as a common feature of hepatocarcinogenesis in mammals, demonstrating that the phenomenon is not restricted to human viral HCC etiologies and is encountered in murine liver tumors.

Overlooked: Extrachromosomal DNA and Their Possible Impact on Whole Genome Sequencing

Extrachromosomal (ec) DNA in eukaryotic cells has been known for decades. The structures described range from linear double stranded (ds) DNA to circular dsDNA, distinct from mitochondrial (mt) DNA. The sizes of circular forms are described from some hundred base pairs (bp) up to more than 150 kbp. The number of molecules per cell ranges from several hundred to a thousand. Semi-quantitative determinations of circular dsDNA show proportions as high as several percentages of the total DNA per cell. These ecDNA fractions harbor sequences that are known to be present in chromosomal DNA (chrDNA) too. Sequencing projects on, for example the human genome, have to take into account the ecDNA sequences which are simultaneously ascertained; corrections cannot be performed retrospectively. Concerning the results of sequencings derived from extracted whole DNA: if the ecDNA fractions contained therein are not taken into account, erroneous conclusions at the chromosomal level may result.

A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing

Subsets of endogenous retroviruses (ERVs) are derepressed in mouse embryonic stem cells (mESCs) deficient for Setdb1, which catalyzes histone H3 lysine 9 trimethylation (H3K9me3). Most of those ERVs, including IAPs, remain silent if Setdb1 is deleted in differentiated embryonic cells; however they are derepressed when deficient for Dnmt1, suggesting that Setdb1 is dispensable for ERV silencing in somatic cells. However, H3K9me3 enrichment on ERVs is maintained in differentiated cells and is mostly diminished in mouse embryonic fibroblasts (MEFs) lacking Setdb1. Here we find that distinctive sets of ERVs are reactivated in different types of Setdb1-deficient somatic cells, including the VL30-class of ERVs in MEFs, whose derepression is dependent on cell-type-specific transcription factors (TFs). These data suggest a more general role for Setdb1 in ERV silencing, which provides an additional layer of epigenetic silencing through the H3K9me3 modification.

Previous studies suggest that DNA methylation is the main mechanism to silence endogenous retroviruses (ERVs) in somatic cells. Here the authors provide evidence that distinctive sets of ERVs are silenced by Setdb1 in different types of somatic cells, suggesting a general function in ERV silencing.

Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction

Background

LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros. This mammalian order offers an excellent model to study the extinction of L1 since the rhinoceros is one of the few mammalian species to have lost active L1.

Results

We found that multiple L1 lineages, carrying different 5’UTRs, have been simultaneously active during the evolution of perissodactyls. We also found that L1 has continuously amplified and diversified in horse. In rhinoceros, L1 was very prolific early on. Two successful families were simultaneously active until ~20my ago but became extinct suddenly at exactly the same time.

Conclusions

The general pattern of L1 evolution in perissodactyls is very similar to what was previously described in mouse and human, suggesting some commonalities in the way mammalian genomes interact with L1. We confirmed the extinction of L1 in rhinoceros and we discuss several possible mechanisms.

Electronic supplementary material

The online version of this article (10.1186/s13100-018-0117-4) contains supplementary material, which is available to authorized users.

Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p

LINE-1 (L1) is an autonomous retrotransposon, which acted throughout mammalian evolution and keeps contributing to human genotypic diversity, genetic disease and cancer. L1 encodes two essential proteins: L1ORF1p, a unique RNA-binding protein, and L1ORF2p, an endonuclease and reverse transcriptase. L1ORF1p contains an essential, but rapidly evolving N-terminal portion, homo-trimerizes via a coiled coil and packages L1RNA into large assemblies. Here, we determined crystal structures of the entire coiled coil domain of human L1ORF1p. We show that retrotransposition requires a non-ideal and metastable coiled coil structure, and a strongly basic L1ORF1p amino terminus. Human L1ORF1p therefore emerges as a highly calibrated molecular machine, sensitive to mutation but functional in different hosts. Our analysis rationalizes the locally rapid L1ORF1p sequence evolution and reveals striking mechanistic parallels to coiled coil-containing membrane fusion proteins. It also suggests how trimeric L1ORF1p could form larger meshworks and indicates critical novel steps in L1 retrotransposition.

Almost half of the human genome consists of DNA strings that have been copied and pasted from one part of the genome to another many thousands of times. These strings of DNA are called mobile genetic elements. Mobile elements can disrupt important genes, causing disease and cancer, but they can also drive evolution.

Presently, only one type of mobile element, called LINE-1, is active in the human genome and able to multiply without help from other mobile elements. LINE-1 DNA is ‘transcribed’ to form molecules of LINE-1 RNA, which can then be ‘translated’ into two distinct proteins. These bind to LINE-1 RNA, which then gets back-transcribed into DNA and inserted as a new LINE-1 element in a new region of the genome. One of the two proteins, called L1ORF1p, forms complexes where three copies of the protein come together. These ‘trimers’ cover and protect LINE-1 RNA and are required for LINE-1 mobility.

Different versions of L1ORF1p are found in different animals. Part of the protein is the same across all mammals, and this ‘conserved’ part controls the ability of L1ORF1p to bind to RNA. The non-conserved part of L1ORF1p differs even between humans and their closest animal relatives and little was known about its structure or role. However, this rapidly evolving part of L1ORF1p is essential for LINE-1 mobility.

Using X-ray crystallography, Khazina and Weichenrieder obtained a molecular snapshot of the part of L1ORF1p that interacts with other copies of the protein to form trimers. Combined with earlier snapshots of L1ORF1p’s conserved part, this generated a complete structural model of the L1ORF1p trimer. Additional biophysical characterizations suggest that L1ORF1p trimers form a semi-stable structure that can partially open up, indicating how trimers could form larger assemblies of L1ORF1p on LINE-1 RNA. Indeed, the need to maintain a semi-stable structure could explain why L1ORF1p is evolving so rapidly. A second important finding is that the beginning of L1ORF1p needs to be positively charged – a requirement that warrants further exploration.

The structural and mechanistic insight into L1ORF1p points to critical new steps in LINE-1 mobilization. It will help to design inhibitor molecules with the goal to halt the mobilization process at various points and to dissect such steps in great detail. Understanding how to control LINE-1 mobility could help to improve stem cell therapies and reproduction assistance techniques, due to the fact that LINE-1 mobility is a potential source of mutation in stem cells, egg and sperm cells, and newly formed embryos.

Characterization of breakpoint regions of large structural autosomal mosaic events

Recent studies have reported a higher than anticipated frequency of large clonal autosomal mosaic events >2 Mb in size in the aging population. Mosaic events are detected from analyses of intensity parameters of linear stretches with deviations in heterozygous probes of single nucleotide polymorphism microarrays. The non-random distribution of detected mosaic events throughout the genome suggests common mechanisms could influence the formation of mosaic events. Here we use publicly available data tracks from the University of California Santa Cruz Genome Browser to investigate the genomic characteristics of the regions at the terminal ends of two frequent types of large structural mosaic events: telomeric neutral events and interstitial losses. We observed breakpoints are more likely to occur in regions enriched for open chromatin, increased gene density, elevated meiotic recombination rates and in the proximity of repetitive elements. These observations suggest that detected mosaic event breakpoints are preferentially recovered in genomic regions that are observed to be active and thus more accessible to environmental exposures and events related to gene transcription. We propose that errors in DNA repair pathways, such as non-homologous end joining and homologous recombination, may be important cellular mechanisms that lead to the formation of large structural mosaic events such as interstitial losses and copy neutral events that include telomeres. Further studies using next generation sequencing technologies should be instrumental in mapping the specific junctions of mosaic events to the nucleotide and provide insights into the molecular mechanisms responsible for clonal somatic structural events.

Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease

Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigenetic regulation of biochemical processes throughout the central nervous system (CNS), and thus are hypothesized to have contributed to the origin of human cognition. Despite the benefits that Alus provide, deleterious Alu activity is associated with a number of neurological and neurodegenerative disorders. In particular, neurological networks are potentially vulnerable to the epigenetic dysregulation of Alu elements operating across the suite of nuclear-encoded mitochondrial genes that are critical for both mitochondrial and CNS function. Here, we highlight the beneficial neurological aspects of Alu elements as well as their potential to cause disease by disrupting key cellular processes across the CNS. We identify at least 37 neurological and neurodegenerative disorders wherein deleterious Alu activity has been implicated as a contributing factor for the manifestation of disease, and for many of these disorders, this activity is operating on genes that are essential for proper mitochondrial function. We conclude that the epigenetic dysregulation of Alu elements can ultimately disrupt mitochondrial homeostasis within the CNS. This mechanism is a plausible source for the incipient neuronal stress that is consistently observed across a spectrum of sporadic neurological and neurodegenerative disorders.

Reading the tea leaves: Dead transposon copies reveal novel host and transposon biology

Transposable elements comprise a huge portion of most animal genomes. Unlike many pathogens, these elements leave a mark of their impact via their insertion into host genomes. With proper teasing, these sequences can relay information about the evolutionary history of transposons and their hosts. In a new publication, Larson and colleagues describe a previously unappreciated density of long interspersed element-1 (LINE-1) sequences that have been spliced (LINE-1 and other reverse transcribing elements are necessarily intronless). They provide data to suggest that the retention of these potentially deleterious splice sites in LINE-1 results from the sites' overlap with an important transcription factor binding site. These spliced LINE-1s (i.e., spliced integrated retrotransposed elements [SpiREs]) lose their ability to replicate, suggesting they are evolutionary dead ends. However, the lethality of this splicing could be an efficient means of blocking continued replication of LINE-1. In this way, the record of inactive LINE-1 sequences in the human genome revealed a new, though infrequent, event in the LINE-1 replication cycle and motivates future studies to test whether splicing might be another weapon in the anti-LINE-1 arsenal of host genomes.

On the move

The mechanisms by which a retrotransposon called LINE-1 duplicates itself and spreads through the human genome are becoming clearer.

Genome-wide hypomethylation of LINE-1 and Alu retroelements in cell-free DNA of blood is an epigenetic biomarker of human aging

Aging associated DNA hypomethylation of LINE-1 and Alu retroelements may be a crucial determinant of loss of genomic integrity, deterioration and cancer. In peripheral blood LINE-1 hypomethylation has been reported to increase during aging, but other studies did not observe significant changes. We hypothesized that these apparently inconsistent reports might relate to differences between cellular and cell-free DNA. Using the technique of idiolocal normalization of real-time methylation-specific PCR (IDLN-MSP) for genetic imbalanced DNA specimens we obtained evidence that LINE-1 hypomethylation in cell-free DNA, but not cellular DNA from peripheral blood is an epigenetic biomarker for human aging. Furthermore, hypomethylation of cell-free DNA is more extensive in smokers, suggesting that it might be used as a surrogate marker for monitoring the improvement of smoking-induced adverse effects after cancelling smoking.

Post-transcriptional regulation of LINE-1 retrotransposition by AID/APOBEC and ADAR deaminases

Long interspersed element-1 (LINE-1 or L1) retrotransposons represent the only functional family of autonomous transposable elements in humans and formed 17% of our genome. Even though most of the human L1 sequences are inactive, a limited number of copies per individual retain the ability to mobilize by a process termed retrotransposition. The ongoing L1 retrotransposition may result in insertional mutagenesis that could lead to negative consequences such as genetic disease and cancer. For this reason, cells have evolved several mechanisms of defense to restrict L1 activity. Among them, a critical role for cellular deaminases [activation-induced deaminase (AID)/apolipoprotein B mRNA-editing catalytic polypeptide-like (APOBEC) and adenosine deaminases that act on RNA (ADAR) enzymes] has emerged. The majority of the AID/APOBEC family of proteins are responsible for the deamination of cytosine to uracil (C-to-U editing) within DNA and RNA targets. The ADARs convert adenosine bases to inosines (A-to-I editing) within double-stranded RNA (dsRNA) targets. This review will discuss the current understanding of the regulation of LINE-1 retrotransposition mediated by these enzymes.

Mammalian transposable elements and their impacts on genome evolution

Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs. Second, most mammalian genomes are dominated by LINE and SINE retrotransposons, more limited LTR retrotransposons, and minimal DNA transposon accumulation. Third, most mammal genome contains at least one family of actively accumulating retrotransposon. Finally, horizontal transfer of TEs among lineages is rare. TE exaptation events are being recognized with increasing frequency. Despite these beneficial aspects of TE content and activity, the majority of TE insertions are neutral or deleterious. To limit the deleterious effects of TE proliferation, the genome has evolved several defense mechanisms that act at the epigenetic, transcriptional, and post-transcriptional levels. The interaction between TEs and these defense mechanisms has led to an evolutionary arms race where TEs are suppressed, evolve to escape suppression, then are suppressed again as the defense mechanisms undergo compensatory change. The result is complex and constantly evolving interactions between TEs and host genomes.

De Novo characterization of transcriptomes from two North American Papaipema stem-borers (Lepidoptera: Noctuidae)

Stem-borers in the genus Papaipema (Lepidoptera: Noctuidae) range from highly polyphagous agricultural pests to specialists on more than 20 families of flowering plants, many of them highly toxic. Papaipema is the largest genus of noctuids endemic to North America and provides an excellent study system for the evolution of noctuid host plant use. To improve the availability of genomic resources for such investigations, we performed de novo transcriptome sequencing and assembly for two specialist Papaipema with unusual larval hosts: P. speciosissima, which is associated with ferns, and the undescribed P. “sp. 4,” which is associated with bamboo. The resulting transcriptomes were similar in terms of completeness, gene count, and gene identity, but we identified some 8,000 genes (~17% of each transcriptome) not shared between the two species. While some of these have identifiable orthologs in other Lepidoptera, ~5% of each transcriptome consists of species-specific genes. We examine the function of these genes and find that almost half have retrotransposon-related functional domains. The potential role of species-specific genes is discussed, and the expansion of certain retrotransposon families in Papaipema is examined.

Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients

Significant transcriptome alterations are detected in the brain of patients with amyotrophic lateral sclerosis (ALS), including carriers of the C9orf72 repeat expansion and C9orf72-negative sporadic cases. Recently, the expression of repetitive element transcripts has been associated with toxicity and, while increased repetitive element expression has been observed in several neurodegenerative diseases, little is known about their contribution to ALS. To assess whether aberrant expression of repetitive element sequences are observed in ALS, we analysed RNA sequencing data from C9orf72-positive and sporadic ALS cases, as well as healthy controls. Transcripts from multiple classes and subclasses of repetitive elements (LINEs, endogenous retroviruses, DNA transposons, simple repeats, etc.) were significantly increased in the frontal cortex of C9orf72 ALS patients. A large collection of patient samples, representing both C9orf72 positive and negative ALS, ALS/FTLD, and FTLD cases, was used to validate the levels of several repetitive element transcripts. These analyses confirmed that repetitive element expression was significantly increased in C9orf72-positive compared to C9orf72-negative or control cases. While previous studies suggest an important link between TDP-43 and repetitive element biology, our data indicate that TDP-43 pathology alone is insufficient to account for the observed changes in repetitive elements in ALS/FTLD. Instead, we found that repetitive element expression positively correlated with RNA polymerase II activity in postmortem brain, and pharmacologic modulation of RNA polymerase II activity altered repetitive element expression in vitro. We conclude that increased RNA polymerase II activity in ALS/FTLD may lead to increased repetitive element transcript expression, a novel pathological feature of ALS/FTLD.

LINE-1 protein localization and functional dynamics during the cell cycle

LINE-1/L1 retrotransposon sequences comprise 17% of the human genome. Among the many classes of mobile genetic elements, L1 is the only autonomous retrotransposon that still drives human genomic plasticity today. Through its co-evolution with the human genome, L1 has intertwined itself with host cell biology. However, a clear understanding of L1’s lifecycle and the processes involved in restricting its insertion and intragenomic spread remains elusive. Here we identify modes of L1 proteins’ entrance into the nucleus, a necessary step for L1 proliferation. Using functional, biochemical, and imaging approaches, we also show a clear cell cycle bias for L1 retrotransposition that peaks during the S phase. Our observations provide a basis for novel interpretations about the nature of nuclear and cytoplasmic L1 ribonucleoproteins (RNPs) and the potential role of DNA replication in L1 retrotransposition.

Only two percent of our genetic material or genome are occupied by genes, while between 60-70 percent are made up of hundreds of thousands of copies of very similar DNA sequences. These repetitive sequences evolved from genetic elements called transposons.

Transposons are often referred to as ‘jumping genes’, as they can randomly move within the genome and thereby create dangerous mutations that may lead to cancer or other genetic diseases. LINE-1 is the only remaining active transposon in humans, and it expands by copying and pasting itself to new locations via a process called 'retrotransposition'. To do so, it is first transcribed into RNA – the molecules that help to make proteins – and then converted back into identical DNA sequences.

Previous research has shown that LINE-1 can form complexes with a series of proteins, including the two encoded by LINE-1 RNA itself: ORF1p and ORF2p. The LINE-1 complexes can enter the nucleus of the cell and insert a new copy of LINE-1 into the genome. However, until now it was not known how they do this. To investigate this further, Mita et al. used human cancer cells grown in the lab and tracked LINE-1 during the different stages of the cell cycle.

The results showed that LINE-1 enters the nucleus as the cell starts to divide and the membrane of the nucleus breaks down. The LINE-1 complexes are then retained in the nucleus while the membrane of the nucleus reforms. Later, as the cell duplicates its genetic material, LINE-1 starts to copy and paste itself. Mita et al., together with another group of researchers, also found that during this process, only LINE-1 RNA and ORF2p were found in the nucleus.

This shows that the cell cycle dictates both where the LINE-1 complexes gather and when LINE-1 is active. A next step will be to further investigate how the ‘copy and paste’ mechanisms of LINE-1 and the two LINE-1 proteins are regulated during the cell cycle. In future, this may help to identify LINE-1’s role in processes like aging or in diseases such as cancer.