Our genome consists of about two percent genes, while around 60 to 70 percent are made up of hundreds of thousands of copies of very similar DNA sequences. These repeats have accumulated over time due to specific genetic elements called transposons.

Transposons are often referred to as ‘jumping genes’, as they can move within the genome and thereby create 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. To do so, it is first transcribed into RNA – the molecules that help to make proteins – and then converted back into identical DNA sequences.

In a never-ending battle, our cells have been fighting to keep LINE-1 and its ancestors from replicating, and so evolved various defense mechanisms. Yet, LINE-1 has learned to circumvent these barriers, and continues to replicate and cause disease. Our understanding of these defenses and of how LINE-1 evades them is limited.

Previous research has shown that the LINE-1 RNA and its two encoded proteins, called ORF1p and ORF2p, interact with a series of other proteins, with which they can form different types of complexes. Now, Taylor, Altukhov, Molloy et al. used human embryonic kidney cells grown in the laboratory with different LINE-1 mutations to identify how they affect the bound proteins and RNAs. The results showed that LINE-1 can form at least two different sets of complexes with other proteins.

The complex containing ORF1p and ORF2p and several other proteins was located in the cytoplasm, the fluid that fills the cells. However, the experiments also revealed a new complex in the cell nucleus, which contained ORF2p and proteins involved in DNA replication and repair, but not ORF1p. The results suggest ORF1p delivers RNPs to the nucleus around the time the cell divides. Another group of researchers has looked more closely at what happens during cell division.

A next step will be to study how exactly LINE-1 contributes to cancer. In the future, overactive LINE-1 proteins could be targeted to kill cancer cells, to identify cancer early, or to see if the cancer has come back. LINE-1 may also provide clues on how the genome has evolved.

Sequences resulting from retrotransposition constitute more than half of the human genome and are considered to be major change agents in eukaryotic genome evolution (Kazazian, 2004). L1 retrotransposons have been particularly active in mammals (Furano et al., 2004), comprising ~20% of the human genome (Lander et al., 2001); somatic retrotransposition has been widely implicated in cancer progression (Lee et al., 2012; Tubio et al., 2014) and may even play a role in neural development (Muotri et al., 2005). Despite the magnitude of their contributions to mammalian genomes, L1 genes are modest in size. A full-length L1 transcript is ~6 knt long and functions as a bicistronic mRNA that encodes two polypeptides, ORF1p and ORF2p (Ostertag and Kazazian, 2001), which respectively comprise a homotrimeric RNA binding protein with nucleic acid chaperone activity (Martin and Bushman, 2001) and a multifunctional protein with endonuclease and reverse transcriptase activities (Mathias et al., 1991; Feng et al., 1996). Recently, a putative primate-specific third ORF, named ORF0, has been identified on the Crick strand of the L1 gene; this ORF encodes a 71 amino acid peptide and may generate insertion-site-dependent ORFs via splicing (Denli et al., 2015). ORF1p and ORF2p are thought to interact preferentially with the L1 RNA from which they were translated (in cis), forming a ribonucleoprotein (RNP) (Kulpa and Moran, 2006; Taylor et al., 2013) considered to be the canonical direct intermediate of retrotransposition (Hohjoh and Singer, 1996; Kulpa and Moran, 2005; Martin, 1991; Kulpa and Moran, 2006; Doucet et al., 2010). L1 RNPs also require host factors to complete their lifecycle (Suzuki et al., 2009; Peddigari et al., 2013; Dai et al., 2012; Taylor et al., 2013) and, consistent with a fundamentally parasitic relationship (Beauregard et al., 2008), the host has responded by evolving mechanisms that suppress retrotransposition (Goodier et al., 2013; Arjan-Odedra et al., 2012; Goodier et al., 2012; Niewiadomska et al., 2007). It follows that as the host and the parasite compete, L1 expression is likely to produce a multiplicity of RNP forms engaged in discrete stages of retrotransposition, suppression, or degradation.

Although L1 DNA sequences are modestly sized compared to typical human genes, L1 intermediates are nevertheless RNPs with a substantially sized RNA component; e.g. larger than the ~5 knt 28S rRNA (Gonzalez et al., 1985) and approximately three to four times the size of a ‘typical’ mRNA transcript (Lander et al., 2001; Sommer and Cohen, 1980). Therefore, it is likely that many proteins within L1 RNPs form interactions influenced directly and indirectly by physical contacts with the L1 RNA. We previously reported that L1 RNA comprised an estimated ~25% of mapped RNA sequencing reads in ORF2p-3xFLAG affinity captured fractions (Taylor et al., 2013). We also observed that the retention of ORF1p and UPF1 within affinity captured L1 RNPs was reduced by treatment with RNases (Taylor et al., 2013). In the same study we observed that two populations of ORF2p-associated proteins could be separated by split-tandem affinity capture (ORF2p followed by ORF1p), a two-dimensional affinity enrichment procedure (Caspary et al., 1999; Taylor et al., 2013). Initial characterization of these two L1 populations by western blotting suggested that discrete L1 populations were likely primed for function in different stages of the lifecycle. We therefore expected additional uncharacterized complexity in the spectrum of L1-associated complexes present in our affinity enriched fractions.

In this study, we have used quantitative mass spectrometry (MS) to investigate the proteomic characteristics of endogenously assembled ectopic L1-derived macromolecules present in an assortment of affinity-enriched fractions. We revisited RNase treatment and split-tandem affinity capture approaches and complemented them with RNA sequencing, enzymatic analysis, and in-cell localization of ORF proteins by immunofluorescence microscopy (see also the companion manuscript by Mita et al., 2018). We additionally explored proteomes associated with catalytically-inactivated ORF2p point mutants and monitored the rates of protein exchange from L1 macromolecules in vitro. Taken together, our data support the existence of a variety of putative L1-related protein complexes.

Affinity proteomic experiments conducted in this study use quantitative MS based upon metabolic labeling (Oda et al., 1999). Two main experimental designs (and modifications thereof) facilitating quantitative cross-sample comparisons have been used: SILAC (Ong et al., 2002; Wang and Huang, 2008) and I-DIRT (Tackett et al., 2005; Taylor et al., 2013). In these approaches, cells are grown for several doublings in media containing amino acids composed either of naturally-occurring ‘light' isotopes or biologically identical 'heavy' isotopes (e.g. ¹³C, ¹⁵N lysine and arginine), such that the proteomes are thoroughly labeled. Protein fractions derived from the differently labeled cell populations, obtained e.g. before and after experimental manipulations are applied, are mixed and the relative differences in proteins contributed by each fraction are precisely measured by mass spectrometry. In addition to the above cited studies, these approaches have been adapted to numerous biological questions using a variety of analytical frameworks e.g. (Byrum et al., 2011; Luo et al., 2016; Trinkle-Mulcahy et al., 2008; Ohta et al., 2010; Kaake et al., 2010; Geiger et al., 2011). Because it is challenging to speculate on the potential physiological roles of protein interactions that form after extraction from the cell, we often use I-DIRT, which allows the discrimination of protein-protein interactions formed in-cell from those occurring post-extraction. Our prior affinity proteomic study, based on I-DIRT, identified 37 putative in vivo interactors (Taylor et al., 2013), described in Table 1. In this study we primarily analyze the behaviors of these ‘I-DIRT significant’ L1 interactors, in order to determine their molecular associations and ascertain the variety of distinctive macromolecular complexes formed in-cell that copurify with affinity-tagged ORF2p. The complete lists of proteins detected in each experiment are presented in the supplementary information (see Supplementary file 1). We have represented any ambiguous protein group, which occurs when the same peptides identify a group of homologous protein sequences, with a single, consistently applied gene symbol and a superscript 'a' in all figures. Supplementary file 1 contains the references to other proteins explaining the presence of the same peptides. For example, RPS27A, (ubiquitin) UBB, UBC, and (ribosomal Protein L40) UBA52 can be explained by common ubiquitin peptides shared by these genes. RPS27A-specific peptides were not identified in this study, but we retained the nomenclature for consistency with our previous work; HSPA1A is reported in this study, but cannot be distinguished from the essentially identical protein product of HSPA1B.

Except where noted otherwise, the presented experiments were conducted in suspension-cultured HEK-293T_LD cells, using a synthetic L1 construct - ORFeus-HS - driving the expression 3xFLAG-tagged L1 (ORF1; ORF2::3xFLAG; 3’-UTR) from a tetracycline inducible minimal-CMV promoter, harbored on a mammalian episome (pLD401 (Taylor et al., 2013; An et al., 2011; Dai et al., 2012)). All L1-related macromolecules described in this study were obtained by affinity capture of ORF2p-3xFLAG before further experimental manipulations were applied. We consider macromolecules containing L1 RNA (L1 RNPs, discussed throughout) and/or an L1 cDNA (i.e. L1 coding potential) to be L1s, as are their ectopic plasmid-borne and endogenous gDNA counterparts, reflecting the complexity and diversity of L1 forms arising from its lifecycle. In an effort to characterize this complexity, we have carried out RNA sequencing and enzymatic activity analyses on several affinity captured fractions, complementing the proteomic analyses.

RNase-sensitivity exhibited by components of affinity captured L1 RNPs

Figure 1 (panels A-C) illustrates the approach and displays the findings of our assay designed to reveal which proteins depend upon the presence of intact L1 RNA for retention within the obtained L1 RNPs. Briefly, metabolically-labeled affinity captured L1s were treated either with a mixture of RNases A and T1 — thus releasing proteins that require intact RNA to remain linked to ORF2p and the affinity medium — or BSA, as an inert control. After removing the fractions released by the RNase or BSA treatments, the proteins remaining on the affinity media were eluted with lithium dodecyl sulfate (LDS), mixed together, and then analyzed by MS. Proteins released, and so depleted, by RNase treatment were thus found to be more abundant in the BSA-treated control. The results obtained corroborate and extend our previous findings: ORF1p and UPF1 exhibited RNase-sensitivity (Taylor et al., 2013). We also observed that ZCCHC3 and MOV10 exhibited RNase-sensitivity to a level similar to ORF1p. The remaining I-DIRT significant proteins were RNase-resistant in this assay. With the exception of the PABPC1/4 proteins (and ORF2p itself, see Discussion), the I-DIRT significant proteins (colored nodes, Figure 1C) that were resistant to RNase treatment (nearest the origin of the graph) classify ontologically as nuclear proteins (GO:0005634, p ≈ 3 × 10⁻⁴, see Materials and methods). These same proteins were previously observed as specific L1 interactors in I-DIRT experiments targeting ORF2p but not in those targeting ORF1p; in contrast, the proteins that demonstrated RNase-sensitivity: ORF1, MOV10, ZCCHC3, and UPF1 were observed in both ORF1p and ORF2p I-DIRT experiments (Table 1). Stated another way, the proteins released upon treating an affinity captured ORF2p fraction with RNases are among those that can also be obtained when affinity capturing ORF1p directly, while those that are RNase-resistant are not ORF1p interactors (Taylor et al., 2013). The ORF1p-linked, I-DIRT significant, RNase-sensitive proteins were too few to obtain a high confidence assessment of ontological enrichment; but, when combined with the remaining proteins exhibiting sensitivity to RNase treatment (black nodes, Figure 1C), they together classified as 'RNA binding' (GO:0003723, p ≈ 1 × 10⁻¹¹). This analysis also revealed a statistically significant overrepresentation of genes associated with the exon junction complex (EJC, GO: 0035145, p ≈ 1 × 10⁻⁶, discussed below). Hence, the overlapping portion of the ORF1p- and ORF2p-associated interactomes appeared to depend upon intact L1 RNA. Host-encoded proteins segregated into groups that responded differentially to RNase treatment, with a substantial population of RNase-resistant interactors linked to both ORF2p and the nucleus. This observation led to the hypothesis that our ORF2p-3xFLAG affinity captured L1s constitute a composite purification of at least, but not limited to, (1) a population of L1-RNA-dependent, ORF1p/ORF2p-containing L1 RNPs, and (2) an ORF1p-independent nuclear population associated with ORF2p.

Figure 1

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While effects of PABPC1, MOV10, and UPF1 on L1 activity have been described (Arjan-Odedra et al., 2012; Taylor et al., 2013; Dai et al., 2012), effects of ZCCHC3 on L1 remained uncharacterized. ZCCHC3 is an RNA-binding protein associated with poly(A)+ RNAs (Castello et al., 2012) but otherwise little is known concerning its functions. Notably, in a genome-wide screen, small interfering (si)RNA knockdown of ZCCHC3 was observed to increase the infectivity of the Hepatitis C, a positive sense RNA virus (Li et al., 2009); and ZCCHC3 was observed to copurify with affinity captured HIV, a retrovirus, at a very high SILAC ratio (>10), supporting the specificity of this interaction (Engeland et al., 2014). We therefore explored the effects on L1 mobility both of over-expression and siRNA knockdown of ZCCHC3. Over-expression of ZCCHC3 reduced L1 retrotransposition to ~10% that observed in the control, consistent with a negative regulatory role for ZCCHC3 in the L1 lifecycle; small interfering RNA (siRNA) knockdown of ZCCHC3 induced a modest increase in retrotransposition compared to a scrambled control siRNA (~1.9x ± 0.1; Supplementary file 2). Moreover, although not among our I-DIRT hits (see Discussion), the presence of EJC components (MAGOH, RBM8A, EIF4A3, UPF1) among the RNase-sensitive fraction of proteins intrigued us, given that L1 genes are intronless. We speculated that L1s may use EJCs to enhance nuclear export, evade degradation by host defenses, and/or aggregate with mRNPs within cytoplasmic granules. For this reason we carried out a series of siRNA knockdowns of these EJC components and other physically or functionally related proteins found in the affinity captured fraction (listed in Supplementary file 2). siRNA knockdowns of RBM8A and EIF4A3 caused inviability of the cell line. We found that knocking-down MAGOH or the EJC-linked protein IGF2BP1 (Jønson et al., 2007) reduced retrotransposition by ~50%, consistent with a role in L1 proliferation; although these knockdowns also caused a reduction in viability of the cell line (see Discussion).

L1 RNA and LEAP activity in affinity captured fractions

Because the L1 RNA is an integral component of proliferating L1s, and because we observed that interactions between ORF2p, ORF1p, and some host proteins were sensitive to treatment with RNases, we sought to characterize the RNAs present in our samples. We extracted RNAs from each of the three fractions produced by split-tandem affinity capture (Figure 1D) and carried out RNA sequencing; Figure 2A displays the sequence coverage observed across the entirety of our synthetic L1 construct in each fraction, revealing a normalized ~2 fold difference in abundance between the elution and supernatant fractions. Synthetic L1s constituted ~60% of the mapped, annotated sequence reads in the fractions eluted from the α-FLAG and α-ORF1p affinity media, and ~30% of the reads in the ORF1p-depleted supernatant fraction; sequencing reads mapping to protein coding genes made up the majority of the remaining annotated population in all fractions. We observed that a substantial number of reads mapped to unannotated regions of the human genome, in particular in the supernatant fraction, enriched for putative nuclear L1 complexes; the breakdown of mapped and annotated sequencing reads is summarized in Figure 2B and expanded in Supplementary file 4.

Figure 2

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Retrotransposition-competent L1 RNPs form in cis, with ORF proteins binding to the L1 RNA that encoded them (‘cis preference’), presumably at the site of translation in the cytoplasm (Kulpa and Moran, 2006; Wei et al., 2001). Given that ORF1/2p partitioned to the split-tandem elution fraction (cytoplasmic) along with the greater fraction of L1 RNA, yet only ORF2p and a lesser portion of the L1 RNA were observed in the supernatant (nuclear), an important consideration regarding these fractions is: to what extent they contain L1 macromolecules capable of proliferation. To address this question, we performed the LINE-1 element amplification protocol (LEAP) on split-tandem affinity captured fractions (Figure 2C; Supplementary file 4), including a ΔORF1 construct (pLD561) as a control (Taylor et al., 2013). LEAP is currently the best biochemical assay for functional co-assembly of L1 RNA and proteins (Kulpa and Moran, 2006); it measures the ability of ORF2p to amplify its associated L1 RNA by reverse transcription. To execute LEAP on the α-ORF1p affinity captured fraction, we developed a competitive di-peptide elution reagent based on the linear peptide sequence used to generate the α-ORF1p 4H1 monoclonal antibody: residues 35–44 in ORF1p ([Khazina et al., 2011; Taylor et al., 2013]; see Materials and methods). We were thus able to assay the partitioning of enzymatic activity within the different populations of copurifying proteins in a split-tandem affinity capture experiment. Our data showed robust LEAP activity in both nuclear and cytoplasmic split-tandem supernatant and elution fractions. We note that our 3xFLAG eluted fractions have been shown to possess ~70 fold higher specific activity than L1 RNPs obtained by sucrose cushion velocity sedimentation (Taylor et al., 2013), hence the activity levels detected far exceed those obtained by sedimentation.

ORF1p/ORF2p immunofluorescence protein localization

Although our proteomic and biochemical analyses supported the existence of distinctive nuclear and cytoplasmic L1 populations, our prior immunofluorescence (IF) analyses did not reveal an apparent nuclear population, leading us to revisit IF studies. Previously, IF of ORF1p and ORF2p in HeLa and HEK-293T cells yielded two striking observations: (i) ORF2 expression was seemingly stochastic, with ORF2p observed in ~30% of cells; and (ii) while ORF1p and ORF2p co-localized in cells that exhibited both, we did not observe an apparent nuclear population of either protein (Taylor et al., 2013). Subsequently, we noted an absence of mitotic cells from these preparations. Reasoning that these cells were lost due to selective adherence on glass slides, and noting that cell division has been reported to promote L1 transposition (Xie et al., 2013; Shi et al., 2007), we repeated the assays using puromycin-selected Tet-on HeLa cells grown on fibronectin coated coverslips. The results are shown in Figure 3.

Figure 3

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Figure 3—source data 1

Source data used in the analysis of ORF2p+ inter nuclear distance analysis: Figure 3 and Supplementary file 5.

https://doi.org/10.7554/eLife.30094.007

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The modified IF assay corroborated our prior results in that nearly all the cells exhibited cytoplasmic ORF1p and a minority subset of ~1/3^rd also exhibited co-localized cytoplasmic ORF2p (Figure 3A, top row). We also observed an uncommon and previously unrecognized subpopulation of cells, consisting of pairs exhibiting nuclear localized ORF2p (Figure 3A, middle row); because these cells occurred in proximal pairs, we presumed them to have recently gone through mitosis. Statistical analysis of microscopy images displaying cells with nuclear localized ORF2p confirmed their proximities to be significantly closer than those of randomly selected cells (Figure 3B; Supplementary file 5). Expression of ORF2 in the absence of ORF1 (ΔORF1; pLD561) resulted in the majority of cells exhibiting cytoplasmic ORF2p, consistent with our previous work (Taylor et al., 2013). We did not observe instances of nuclear ORF2p using the ΔORF1 construct (Figure 3A, bottom row), suggesting that ORF1p is required for ORF2p nuclear localization (see Discussion). In a separate study, including more detailed analyses of ORF protein localization, Mita et al., 2018 observed that both ORF proteins enter the nucleus of HeLa cells during mitosis, however, nuclear ORF1p does not seem to be physically associated with nuclear ORF2p (see Discussion). Taken together, the data obtained from the modified IF experiments aligned well with our proteomic and biochemical data; L1 expression resulted in at least two distinct populations: cytoplasmic complexes containing both ORF1p and ORF2p, and nuclear complexes containing ORF2p while potentially lacking ORF1p.

The effects of retrotransposition-blocking point mutations on the interactomes of affinity captured L1 RNPs

Based on the hypothesis that our composite purifications contain bona fide nuclear intermediates, we decided to explore the effects of catalytic point mutations within the ORF2p endonuclease and reverse transcriptase domains, respectively. We reasoned that such mutants may bottleneck L1 intermediates at the catalytic steps associated with host gDNA cleavage and L1 cDNA synthesis, potentially revealing protein associations that are important for these discrete aspects of target-primed reverse transcription (TPRT), the presumed mechanism of L1 transposition (Luan et al., 1993; Feng et al., 1996; Cost et al., 2002). For this we used an H230A mutation to inactivate the endonuclease activity (EN^-/pLD567), and a D702Y mutation to inactivate the reverse transcriptase activity (RT^-/pLD624) (Taylor et al., 2013). Figure 4 illustrates the approach and displays the findings of our assay. Broadly, while we observed comparable RNA-level properties between samples (Figure 4B, Supplementary file 4), our findings revealed several classes of distinctive protein-level behaviors (Figure 4C). Two classes of behavior appeared to be particularly striking: (1) the yield of constituents of cytoplasmic L1s was reduced, relative to WT, by the EN^- mutation, yet elevated by the RT^- mutation (Figure 4C, left side); and (2) numerous constituents of nuclear L1s were elevated in yield by the EN^- mutation but reduced or nominally unchanged, relative to WT, by the RT^- mutation (Figure 4C, right side). With respect to the second group, IPO7, NAP1L4, NAP1L1, FKBP4, HSP90AA1, and HSP90AB1 were all elevated in the EN^- mutants, potentially implicating these proteins as part of an L1 complex (or complexes) immediately preceding DNA cleavage. Notably, there is a third class of proteins, including PURA/B, PCNA, TOP1, and PARP1, that all respond similarly to both EN^- and RT^- mutants compared to WT, exhibiting reduced associations with the mutant L1s; although, the RT^- mutant showed a larger effect size on the PURA/B proteins. These data suggest that cleavage of the host genomic DNA by ORF2p fosters associations between L1 and this third class of proteins, but that interactions with PURA/B may be further enhanced by L1 cDNA production. Other nuclear L1 proteins: HSPA8, HAX1, HSPA1A, TUBB, and TUBB4B were increased in both mutants. To better visualize the range of behaviors exhibited by our proteins of interest, and the population at large, we cross-referenced the relative enrichments of each protein detected in both experiments, shown in Figure 4D. We noted the same striking trend mentioned above, that two seemingly opposite behavioral classes of interactors could also be observed globally among all proteins associating with ORF2p catalytic mutants (see Figure 4C, left side and right side, and Figure 4D), creating the crisscross pattern displayed (see also Figure 4—figure supplement 1). Notably, the pattern observed appears to track with the relative behavior of ORF1p, which, along with other cytoplasmic L1 factors is elevated in RT^- mutants and reduced in EN^- mutants. We therefore speculate that the sum of observed interactomic changes include effects attributable directly to the catalytic mutations as well as potential indirect effects resulting in increased cytoplasmic RNPs (including ORF1p)in the RT^- mutant.

Figure 4 with 1 supplement see all

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Dynamics of L1 RNPs in vitro

We next decided to measure the in vitro dynamics of proteins copurifying with affinity captured L1s, reasoning that proteins with comparable profiles are likely candidates to be physically linked to one another or otherwise co-dependent for maintaining stable interactions with L1s. To achieve this, we first affinity captured heavy-labeled, affinity-tagged L1s and subsequently incubated them, while immobilized on the medium, with light-labeled, otherwise identically prepared cell extracts from cells expressing untagged L1s (Luo et al., 2016). In this scenario, heavy-labeled proteins present at the zero time point are effectively ‘infinitely diluted’ with light-labeled cell extract. The exchange of proteins, characterized by heavy-labeled proteins decaying from the immobilized L1s and being replaced by light-labeled proteins supplied by the cell extract, was monitored by quantitative MS. These experiments were conducted using constructs based on the naturally occurring L1RP sequence (Dai et al., 2014; Taylor et al., 2013; Kimberland et al., 1999). Figure 5 illustrates the approach and displays the findings of our assay. We observed three distinctive clusters of behaviors (Figure 5B,C). Notably, ORF1p, ZCCHC3, and the cytoplasmic poly(A) binding proteins clustered together, forming a relatively stable core complex. Exhibiting an intermediate level of relative in vitro dynamics, UPF1 and MOV10 clustered with TUBB, TUBB4B, and HSP90AA1. A third, and least stable, cluster consisted of only nuclear L1 interactors.

Figure 5

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Multidataset integration

Having observed coordinated and distinctive behaviors exhibited by groups of L1 interacting proteins across several distinctive biochemical assays, we then integrated the data and calculated the behavioral similarity of the I-DIRT-significant interactors, producing a dendrogram; Figure 6 displays their relative similarities. A cluster containing the putative cytoplasmic L1 components (MOV10, UPF1, ZCCHC3, PABC1/4, ORF1p) was observed, as was a cluster containing PURA/B, PCNA, TOP1, PARP1, aligning with our assessments of the separated datasets (Figures 1, 4 and 5). In addition to these, we also observed three distinctive clusters derived from the nuclear L1 interactome. We believe that this is likely to reflect the presence of a collection of distinctive macromolecules.

Figure 6

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In this study we have characterized biochemical, interatomic, enzymatic, and cellular localization properties of ectopically expressed L1s. Through the assays explored, we observed discrete and coordinated behaviors, permitting us to refine our model of L1 intermediates, diagrammed in Figure 7. We propose a cytoplasmic L1, composed of ORF1/2 p, L1 RNA, PABPC1/4, MOV10, UPF1, and ZCCHC3, that constitutes an abundant, canonical RNP intermediate often referred to in the literature. MOV10, UPF1, and ZCCHC3 are apparently substoichiometric to ORF2p in our preparations, therefore it may be that only a subset of cytoplasmic intermediates engages these host restriction factors. On the other hand, this apparent relative abundance may simply reflect a lower in vitro stability of UPF1 and MOV10 within this complex (Figure 5). Although ORF1p is apparently required for efficient ORF2p nuclear entry, we also propose a second more complicated population, lacking (or with significantly less) ORF1p, that constitutes nuclear or pre- dominantly nuclear L1 macromolecules. We note that Alu elements exhibit ORF2p-dependent mobilization that does not require ORF1p, but appears to be enhanced by ORF1p in some contexts (Dewannieux et al., 2003; Wallace et al., 2008); this is not true for L1 or processed pseudogenes, and we conclude Alu RNPs likely exploit an alternate mechanism of nuclear entry. The nuclear L1 population is enriched for factors linked to DNA replication and repair, including PURA, PURB, PCNA, TOP1, and PARP1; we propose that these proteins, along with ORF2p, form part of a direct intermediate of TPRT, although these components may not all act in synergy. Our proposals are broadly supported by the findings of Mita et al., 2018, who present data to support the hypothesis that PCNA-associated ORF2p is not appreciably associated with ORF1p, and also identified TOP1 and PARP1 in complex with ORF2p/PCNA.

Figure 7

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Although the protein purification approach was the similar, we observed an apparently larger proportion of L1 RNA in our recent preparations than in our previous study. We reported that L1 constituted ~25% of mapped reads previously (Taylor et al., 2013); a comparable result was obtained when we reanalyzed that data using the pipeline described here (see Materials and methods): ~93% of reads in our reanalyzed 2013 dataset mapped to the human genome, and L1 constituted ~20% of reads mapped to annotated features (‘annotated reads’) in 3xFLAG eluates. In this study we report that ~60% of annotated reads mapped to synthetic L1 in 3xFLAG eluates (Figure 2A). The higher proportion of L1 recovered may be due to the combination of higher fidelity RNA preparative methods and advanced sequencing technology used here; we observed ~10x more total reads mapping to L1 and comparatively improved, more uniform coverage across the entire L1 sequence, likely explaining the discrepancy. We also noted that the number of normalized reads mapped to L1 in our initial 3xFLAG elutions (‘input’) and subsequent tandem-purified α-ORF1p elutions were comparable, and yet ~1/2 as many were seen in the α-ORF1p supernatant fraction (Figure 2A,B). We suspect that this is due to saturation in library preparations or sequencing steps for the ‘input’ and ‘elution’ fractions, but conclude that more L1 RNA is in the ‘cytoplasmic’ elution fraction than the ‘nuclear’ supernatant.

We observed substantial and comparable LEAP activity in both our tandem-purified ORF1p+ (‘elution’) and ORF1p– (immuno-depleted ‘supernatant’) populations (Figure 2C, Supplementary file 4). To our knowledge, these represent the simplest and purest endogenously assembled L1 RNPs yet reported that exhibit robust signal in the LEAP assay. We note that, our results demonstrating robust activity in the nuclear-enriched supernatant fraction (depleted of ORF1p) may contrast with previous reports of reduced LEAP activity in constructs where ORF1p RNA binding was compromised (Kulpa and Moran, 2006), but our fractions merit further study and comparisons on the basis of ORF2p and RNA levels to determine specific activity.

The preparation of L1 RNPs was carried out essentially as previously described (Taylor et al., 2013, Taylor et al., 2016), with modifications described here. Briefly, HEK-293T_LD cells (Dai et al., 2012) transfected with L1 expression vectors were cultured as previously described or using a modified suspension-growth SILAC strategy described below. L1 expression was induced with with 1 μg/ml doxycycline for 24 hr, and the cells were harvested and extruded into liquid nitrogen. In all cases the cells were then cryogenically milled (LaCava et al., 2016) and used in affinity capture experiments and downstream assays. Custom computer code written in the R programming language was used in the analysis of mass spectrometry and RNA sequencing data; it has been published on https://bitbucket.org (Altukhov, 2017); a copy is archived at https://github.com/elifesciences-publications/altukhov-line-1.

All normalized affinity values, derived from H/(H + L) and L/(H + L) isotopic ratios, can be found in Supplementary file 1 on the appropriate sheet; pre-normalization values are located on the sheets named ‘Integration’ and ‘Raw.’

Modified SILAC strategy

Appendix 1—figure 1

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RNase sensitivity affinity capture

Data normalization

The RNase sensitivity data were rescaled and normalized such that proteins that did not change upon treatment with RNases were centered at the origin and those that were completely sensitive would give a value of 1.0. In a perfect experiment, unchanging proteins would yield a ratio of 0.5 when comparing the fraction of each protein present in the BSA-treated sample to the sum of both the BSA- and RNase-treated samples; i.e. 1 / (1 + 1). However, our data show some variability (below, left and also Supplementary file 1), with one replicate centering on ~0.4 (red) and another ~0.6 (blue). Therefore, we normalized the data such that the peaks at ~0.4 and~0.6 were both re-centered at 0.5. From this set, 0.5 was subtracted from the data (centering insensitive proteins at the origin, and completely sensitive proteins at 0.5), followed by multiplication by two to expand the data to cover the range from 0 (insensitive) to 1 (completely sensitive); depicted below, right. These latter two transformations are encompassed by the functions: g(x)=x + b [where b = −0.5] and f(g(x))=a(x + b) [where a = 2].

Appendix 1—figure 2

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RNase normality test The distances from the (0,0) point to protein coordinates were calculated. Proteins with distance less than two median distances were selected. The Shapiro-Wilk normality test (the null-hypothesis of this test is that the population is normally distributed) was applied for the distances (p-value=0.29). The distribution of the distances was plotted as a histogram displaying the frequency (y-axis) versus RNase sensitivity (x-axis) of a simulation of normally distributed data (shown in black) and the actual data (Supplementary file 1) shown in blue. A Q-Q plot was also drawn.

Appendix 1—figure 3

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Split-tandem affinity capture

Data normalization The data were treated as follows: a and b coefficients were calculated as solutions of equation 1; the normalized values were calculated using the equation 2.

(1) ${\displaystyle \left(\begin{array}{c}\mathrm{a}\\ \mathrm{b}\end{array}\right)\left(\begin{array}{cc}\mathrm{m}\mathrm{e}\mathrm{d}\mathrm{i}\mathrm{a}\mathrm{n}& 1\\ \mathrm{O}\mathrm{R}\mathrm{F}1& 1\end{array}\right)=\left(\begin{array}{c}\mathrm{m}\mathrm{e}\mathrm{d}\mathrm{i}\mathrm{a}\mathrm{n}\\ 1\end{array}\right)}$

(2) ${\displaystyle {\displaystyle {\mathrm{x}}_{{\displaystyle \mathrm{n}\mathrm{o}\mathrm{r}\mathrm{m}\mathrm{a}\mathrm{l}\mathrm{i}\mathrm{z}\mathrm{e}\mathrm{d}}}={\displaystyle ({\mathrm{a}}^{\ast }{\mathrm{x}}_{{\displaystyle \mathrm{i}\mathrm{n}\mathrm{i}\mathrm{t}\mathrm{i}\mathrm{a}\mathrm{l}}})+\mathrm{b}}}}$

Appendix 1—figure 4

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Calculate the distances between node pairs

Distance between two points A and B with coordinates (A_x, A_y) and (B_x, B_y) was calculated as: $\sqrt{{({\mathit{A}}_{\mathit{x}}-{\mathit{B}}_{\mathit{x}})}^2+\mathit{}{({\mathit{A}}_{\mathit{y}}-{\mathit{B}}_{\mathit{y}})}^2}$

For each three points, the mean paired distance was calculated. The distributions of mean values are presented in the histograms below.

Appendix 1—figure 5

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Appendix 1—figure 6

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Associated likelihoods of selected clusters

Here, likelihood is defined as the frequency with which the same mean distance or less is observed within the distribution of clusters with the same number of nodes (above).

PURA/PURB/PCNA: Likelihood = 3.2 × 10⁻⁷

PABPC1/PABPC4: Likelihood = 0.0008388427

HSPA8/HSPA1A: Likelihood = 0.0001991309

NAP1L1/IPO7: Likelihood = 0.0075885198

Efficacy elution from α-ORF1 4H1 affinity medium using ORF1p peptides

Appendix 1—figure 7

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ORF1p-FLAG was purified from 25 mg of cryo-milled HEK-293T_LD expressing pLD288 using α-ORF1 affinity medium, essentially as previously described (Taylor et al., 2013), and then eluted either eluted directly with 15 μl of 1x LDS, 70°C for 5 min (Ctrl LDS), with 2 mM monomeric ORF1 peptide (Mono pep), or 2 mM dimeric ORF1 peptide (Di pep) (in both cases for 15 min at room temperature). After elution with peptide, the affinity medium was further eluted with 1x LDS at 70°C for 5 min (Mono and Di LDS, respectively).

Retrotransposition mutants affinity capture

The distributions of normalized affinities for the two sets of experiments are shown below.

Appendix 1—figure 8

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Protein in vitro exchange

The distributions of H/(H + L) values present at each time point are shown.

Appendix 1—figure 9

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Author details

1. Martin S Taylor

   Department of Pathology, Massachusetts General Hospital, Boston, United States

   Contribution

   Conceptualization, Investigation, Visualization, Methodology, Writing—original draft, Writing—review and editing

   Contributed equally with

   Ilya Altukhov and Kelly R Molloy

   For correspondence

   MSTAYLOR@PARTNERS.ORG

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-5824-142X

2. Ilya Altukhov

   Moscow Institute of Physics and Technology, Dolgoprudny, Russia

   Contribution

   Data curation, Software, Formal analysis, Visualization, Methodology

   Contributed equally with

   Martin S Taylor and Kelly R Molloy

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-9821-1890

3. Kelly R Molloy

   Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States

   Contribution

   Data curation, Investigation, Methodology

   Contributed equally with

   Martin S Taylor and Ilya Altukhov

   For correspondence

   kmolloy@rockefeller.edu

   Competing interests

   No competing interests declared

4. Paolo Mita

   Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States

   Contribution

   Investigation, Writing—review and editing

   For correspondence

   paolo.mita@nyumc.org

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-2093-4906

5. Hua Jiang

   Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States

   Contribution

   Investigation

   For correspondence

   hjiang01@rockefeller.edu

   Competing interests

   No competing interests declared

6. Emily M Adney

   1. Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States
   2. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States

   Contribution

   Investigation

   For correspondence

   eadney@gmail.com

   Competing interests

   No competing interests declared

7. Aleksandra Wudzinska

   McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States

   Contribution

   Investigation

   For correspondence

   aleksandra.wudzinska@nyumc.org

   Competing interests

   No competing interests declared

8. Sana Badri

   Department of Pathology, NYU Langone Health, New York, United States

   Contribution

   Software, Formal analysis

   For correspondence

   Sana.Badri@nyumc.org

   Competing interests

   No competing interests declared

9. Dmitry Ischenko

   Moscow Institute of Physics and Technology, Dolgoprudny, Russia

   Contribution

   Formal analysis

   For correspondence

   ischenko.dmitry@gmail.com

   Competing interests

   No competing interests declared

10. George Eng

    Department of Pathology, Massachusetts General Hospital, Boston, United States

    Contribution

    Software

    For correspondence

    george_eng@mgh.harvard.edu

    Competing interests

    No competing interests declared

11. Kathleen H Burns

    1. Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
    2. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States

    Contribution

    Resources, Funding acquisition, Writing—review and editing

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0003-1620-3761

12. David Fenyö

    Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States

    Contribution

    Resources, Formal analysis

    For correspondence

    david@fenyolab.org

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0001-5049-3825

13. Brian T Chait

    Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States

    Contribution

    Resources, Funding acquisition

    For correspondence

    chait@mail.rockefeller.edu

    Competing interests

    No competing interests declared

14. Dmitry Alexeev

    Novosibirsk State University, Novosibirsk, Russia

    Contribution

    Resources, Data curation, Formal analysis, Supervision, Funding acquisition

    For correspondence

    exappeal@gmail.com

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0003-0783-1176

15. Michael P Rout

    Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States

    Contribution

    Resources, Funding acquisition, Writing—review and editing

    For correspondence

    Michael.Rout@rockefeller.edu

    Competing interests

    No competing interests declared

16. Jef D Boeke

    Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States

    Contribution

    Conceptualization, Resources, Funding acquisition, Writing—review and editing

    For correspondence

    jef.boeke@nyumc.org

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0001-5322-4946

17. John LaCava

    1. Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States
    2. Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States

    Contribution

    Conceptualization, Data curation, Supervision, Investigation, Visualization, Methodology, Writing—original draft, Project administration, Funding Acquisition, Writing—review and editing

    For correspondence

    jlacava@rockefeller.edu

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0002-6307-7713

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