Retroviral Elements and Their Hosts: Insertional Mutagenesis in the Mouse Germ Line

The inbred mouse is an invaluable model for human biology and disease. Nevertheless, when considering genetic mechanisms of variation and disease, it is important to appreciate the significant differences in the spectra of spontaneous mutations that distinguish these species. While insertions of transposable elements are responsible for only ~0.1% of de novo mutations in humans, the figure is 100-fold higher in the laboratory mouse. This striking difference is largely due to the ongoing activity of mouse endogenous retroviral elements. Here we briefly review mouse endogenous retroviruses (ERVs) and their influence on gene expression, analyze mechanisms of interaction between ERVs and the host cell, and summarize the variety of mutations caused by ERV insertions. The prevalence of mouse ERV activity indicates that the genome of the laboratory mouse is presently behind in the “arms race” against invasion

A Novel Protein Isoform of the Multicopy Human NAIP Gene Derives from Intragenic Alu SINE Promoters

The human neuronal apoptosis inhibitory protein (NAIP) gene is no longer principally considered a member of the Inhibitor of Apoptosis Protein (IAP) family, as its domain structure and functions in innate immunity also warrant inclusion in the Nod-Like Receptor (NLR) superfamily. NAIP is located in a region of copy number variation, with one full length and four partly deleted copies in the reference human genome. We demonstrate that several of the NAIP paralogues are expressed, and that novel transcripts arise from both internal and upstream transcription start sites. Remarkably, two internal start sites initiate within Alu short interspersed element (SINE) retrotransposons, and a third novel transcription start site exists within the final intron of the GUSBP1 gene, upstream of only two NAIP copies. One Alu functions alone as a promoter in transient assays, while the other likely combines with upstream L1 sequences to form a composite promoter. The novel transcripts encode shortened open reading frames and we show that corresponding proteins are translated in a number of cell lines and primary tissues, in some cases above the level of full length NAIP. Interestingly, some NAIP isoforms lack their caspase-sequestering motifs, suggesting that they have novel functions. Moreover, given that human and mouse NAIP have previously been shown to employ endogenous retroviral long terminal repeats as promoters, exaptation of Alu repeats as additional promoters provides a fascinating illustration of regulatory innovations adopted by a single gene

Distributions of transposable elements reveal hazardous zones in mammalian introns.

Comprising nearly half of the human and mouse genomes, transposable elements (TEs) are found within most genes. Although the vast majority of TEs in introns are fixed in the species and presumably exert no significant effects on the enclosing gene, some markedly perturb transcription and result in disease or a mutated phenotype. Factors determining the likelihood that an intronic TE will affect transcription are not clear. In this study, we examined intronic TE distributions in both human and mouse and found several factors that likely contribute to whether a particular TE can influence gene transcription. Specifically, we observed that TEs near exons are greatly underrepresented compared to random distributions, but the size of these "underrepresentation zones" differs between TE classes. Compared to elsewhere in introns, TEs within these zones are shorter on average and show stronger orientation biases. Moreover, TEs in extremely close proximity (<20 bp) to exons show a strong bias to be near splice-donor sites. Interestingly, disease-causing intronic TE insertions show the opposite distributional trends, and by examining expressed sequence tag (EST) databases, we found that the proportion of TEs contributing to chimeric TE-gene transcripts is significantly higher within their underrepresentation zones. In addition, an analysis of predicted splice sites within human long terminal repeat (LTR) elements showed a significantly lower total number and weaker strength for intronic LTRs near exons. Based on these factors, we selectively examined a list of polymorphic mouse LTR elements in introns and showed clear evidence of transcriptional disruption by LTR element insertions in the Trpc6 and Kcnh6 genes. Taken together, these studies lend insight into the potential selective forces that have shaped intronic TE distributions and enable identification of TEs most likely to exert transcriptional effects on genes

Transposable elements: an abundant and natural source of regulatory sequences for host genes

International audienceThe fact that transposable elements (TEs) can influence host gene expression was first recognized more than 50 years ago. However, since that time, TEs have been widely regarded as harmful genetic parasites-selfish elements that are rarely co-opted by the genome to serve a beneficial role. Here, we survey recent findings that relate to TE impact on host genes and remind the reader that TEs, in contrast to other noncoding parts of the genome, are uniquely suited to gene regulatory functions. We review recent studies that demonstrate the role of TEs in establishing and rewiring gene regulatory networks and discuss the overall ubiquity of exaptation. We suggest that although individuals within a population can be harmed by the deleterious effects of new TE insertions, the presence of TE sequences in a genome is of overall benefit to the population

Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution.

Neuronal apoptosis inhibitory protein (NAIP, also known as BIRC1) is a member of the conserved inhibitor of apoptosis protein (IAP) family. Lineage-specific rearrangements and expansions of this locus have yielded different copy numbers among primates and rodents, with human retaining a single functional copy and mouse possessing several copies, depending on the strain. Roles for this gene in disease have been documented, but little is known about transcriptional regulation of NAIP. We show here that NAIP has multiple promoters sharing no similarity between human and rodents. Moreover, we demonstrate that multiple, domesticated long terminal repeats (LTRs) of endogenous retroviral elements provide NAIP promoter function in human, mouse, and rat. In human, an LTR serves as a tissue-specific promoter, active primarily in testis. However, in rodents, our evidence indicates that an ancestral LTR common to all rodent genes is the major, constitutive promoter for these genes, and that a second LTR found in two of the mouse genes is a minor promoter. Thus, independently acquired LTRs have assumed regulatory roles for orthologous genes, a remarkable evolutionary scenario. We also demonstrate that 5' flanking regions of IAP family genes as a group, in both human and mouse are enriched for LTR insertions compared to average genes. We propose several potential explanations for these findings, including a hypothesis that recruitment of LTRs near NAIP or other IAP genes may represent a host-cell adaptation to modulate apoptotic responses

Promoter Activity of the <i>mNaip</i> LTRs

<p>The ORR1E LTRs for each copy were cloned into a modified pGL3B vector and tested for luciferase activity in the MS1 cell line. pGL3B and pGL3P, containing a SV40 promoter, were used as negative and positive controls, respectively. Luciferase activity was normalized relative to the cotransfected <i>Renilla</i> luciferase control and then to pGL3B to demonstrate fold activation. Each bar represents the mean of at least four independent transfections ± SEM.</p

Contribution of LTR Promoters to Mouse and Rat <i>Naip</i> Transcription and a Summary of 5′ RACE Results

<div><p>(A) Representation of 5′ region of rodent <i>Naip</i> genes. Transcription initiates at arrows situated above the underlying genomic DNA, with representative RNAs pictured above. Gray shaded boxes represent the solitary LTR insertions, and black boxes represent exons in DNA and RNA forms. Mouse and rat <i>Naip</i> transcription predominately initiates in ORR1E LTRs. <i>mNaipe</i> and <i>mNaipf</i> have an MTC LTR (dashed gray box) and ∼3 kb of L1_Mus1 LINE1 sequence has integrated into the ORR1E LTRs associated with these two genes, shown by a dashed white box. The <i>rNaip2</i> ORR1E LTR has also been interrupted by an independent insertion of 300 bp of Lx2A1 LINE1, shown by solid white box.</p><p>(B) Partial alignment of the rodent ORR1E LTRs associated with <i>Naip</i> transcription. The 5′ end of the sequences shown corresponds to the following coordinates in the mouse (mm8) and rat (rn4) draft sequences. (<i>mNaipa</i> = Chromosome 13: 101,553,198; <i>mNaipb</i> = Chromosome 13: 101,302,420; <i>mNaipe</i> = Chromosome 13: 101,347,641; <i>mNaipf</i> = Chromosome 13: 101,418,005; <i>rNaip1</i> = Chromosome 2: 31,268,656; <i>rNaip2</i> = Chromosome 2: 31,204,793). Numbers above boldfaced nucleotides indicate sites of transcription initiation and the number of 5′ RACE clones obtained that align to each TSS. A few <i>mNaipe</i> clones aligned beyond the boundaries of the ORR1E sequence shown. Underlines indicate putative initiator elements and boxed sequence represents putative TATA boxes. Asterisks denote sites of transcription that are supported by >1 CAGE tag [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030010#pgen-0030010-b027" target="_blank">27</a>].</p><p>(C) Partial alignment of the <i>mNaipe/f</i> MTC alternative promoters. (<i>mNaipe</i> = Chromosome 13: 101,346,591; <i>mNaipf</i> = Chromosome 13: 101,416,943).</p><p>(D) Genomic sequence surrounding the <i>mNaipb</i> non-LTR promoter (<i>mNaipb</i> = Chromosome 13: 101,289,682). Full characterization of mouse UTRs can be found in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030010#pgen-0030010-sg002" target="_blank">Figure S2</a>.</p></div

Comparison of Genomic Sequence Surrounding the Rodent <i>Naip</i> ORR1E LTRs

<p>3 kb of sequence centered around the ORR1Es was analyzed by dot plots; diagonal lines represent regions of homology between compared sequences. Light gray, dark gray, white, and black boxes represent LTR elements, SINEs, LINEs, and simple repeats, respectively.</p

Common Effects of ETn and IAP Insertions on Gene Expression

<div><p>(A) ETn effects on gene transcript processing. The most common patterns of aberrant transcript processing caused by ETns in gene introns are shown. The natural LTR polyadenylation (polyA) site and a second cryptic polyadenylation site in the internal region, along with four cryptic splice acceptors (SA) and a donor site (SD), are involved in most cases. The number of such cases is an underestimate, since several reports lack sufficient detail of aberrant transcripts. In some cases, several aberrant forms have been found. Boxes denote gene exons, thin lines denote introns, and thick lines denote spliced mRNAs, with direction of transcription from left to right. For clarity, cryptic splice acceptor sites in the 3' LTR are not shown since no documented splicing events involving these sites were found. Intronic mutagenic ETns and the affected gene are most often found in the same orientation (15 of 16 cases).</p><p>(B) IAP promoter effects on gene transcription. Ectopic gene expression driven by an antisense promoter in the 5' LTR of an IAP has been reported in eight cases. In some cases, the IAP is located a significant distance upstream of the gene.</p></div