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J Virol. 2009 December; 83(23): 12643–12650.
Published online 2009 September 9. doi:  10.1128/JVI.00858-09
PMCID: PMC2786743

Human Endogenous Retroviral Long Terminal Repeat Sequences as Cell Type-Specific Promoters in Retroviral Vectors [down-pointing small open triangle]

Abstract

The human genome contains more than half a million human endogenous retrovirus (HERV) long terminal repeats (LTRs) that can be regarded as mobile regulatory modules. Many of these HERV LTRs have been recruited during evolution as transcriptional control elements for cellular gene expression. We have cloned LTR sequences from two HERV families, HERV-H and HERV-L, differing widely in their activity and tissue specificity into a murine leukemia virus (MLV)-based promoter conversion vector (ProCon). Various human cell lines were infected with the HERV-MLV hybrid vectors, and cell type-specific expression of the reporter gene was compared with the promoter specificity of the corresponding HERV LTRs in transient-transfection assays. Transcription start site analysis of HERV-MLV hybrid vectors revealed preferential use of the HERV promoter initiation site. Our data show that HERV LTRs function in the context of retroviral vectors in certain cell types and have the potential to be useful as cell type-specific promoters in vector construction.

About 8 to 9% of the human genome consists of human endogenous retroviruses (HERVs) and long terminal repeat (LTR) retroelements (22, 24). These sequences are thought to be relicts of germ line infections that became genetically fixed during primate evolution (for a review, see references 13, 26, and 44). Since then, they have amplified and spread throughout the primate genome by reinfection and/or retrotransposition.

In contrast to HERV protein coding sequences, which accumulated numerous inactivating mutations or deletions, HERV LTRs have preserved their promoter activity and still contain active regulatory elements, such as enhancer sequences, transcription factor binding sites, or polyadenylation signals. We have analyzed more than 100 arbitrarily isolated HERV LTR sequences, including 5′, 3′, and solitary LTRs, in a transient-transfection assay and found that about one-third of these LTRs are still active and may drive gene expression (2, 36; S. Weinhardt et al., unpublished data). Thus, HERVs and other LTR retrotransposons represent mobile regulatory modules that may contribute to the transcriptional regulation of cellular genes (5, 18, 28, 33, 47). There are a number of bona fide examples for the recruitment of HERV LTRs as transcriptional control elements for cellular genes (for a review, see references 16, 23, and 28), among them LTRs belonging to the multicopy families HERV-H (21, 41) and HERV-L (8, 10). In many cases, LTRs are used as alternative promoters/enhancers that confer differential tissue specificities to genes, thus increasing their transcriptional potential. One of the best-studied examples for HERV LTR-mediated tissue-specific regulation is the insertion of a HERV-E element upstream of an ancestral amylase gene that acts as a parotid gland-specific enhancer (35, 46). Interestingly, human genes initiated within HERV LTRs appear to have greater tissue specificity than genes lacking HERV promoters (5). Currently, about 5.8% of human genes are thought to be controlled by HERV promoters (5, 33).

In general, HERV LTRs appear to be active in a tissue-specific manner. Using a retrovirus-specific microarray, we have established a comprehensive HERV expression profile of 19 different human tissues (12, 38, 39). Some HERVs are ubiquitously expressed, whereas others are highly specific and transcriptionally active only in a few tissues. In addition, we and others have shown that isolated HERV LTRs maintain their promoter specificity in transient-transfection assays, suggesting that cell type specificity is mediated by the presence of transcription factor binding sites within the LTR and the availability of corresponding transcription factors in the cell and does not depend on additional cellular sequences located upstream or downstream of the LTR. For example, cloned HERV-H LTRs show a similar promoter activity in various human cell lines in transient-transfection assays as suggested by the endogenous transcription patterns of HERV-H proviruses in human tissues and cell lines (11, 14, 36, 38). To further test this assumption and to investigate the effect of reintegration on the cell type specificity of HERV promoters, we cloned three LTR sequences from two different HERV families into a modified Moloney murine leukemia virus (MLV)-based retroviral vector (pLXSNEGFP), which contains the enhanced green fluorescent protein (EGFP) gene under the transcriptional control of the retroviral LTR and the neomycin resistance gene under the control of the simian virus 40 promoter (19). pLXSNEGFP belongs to the family of ProCon vectors that allow cloning of promoter sequences by replacing the U3 region of the MLV 3′LTR (Fig. (Fig.1A).1A). After reverse transcription, the promoter sequences are duplicated and transferred to the 5′ LTR, thus driving the transcription of the transgene in the infected cells (31, 34).

FIG. 1.FIG. 1.
Transcriptional activity of HERV promoters in different cell lines. (A) HERV-MLV hybrid vector constructs. HERV U3 or U3-R sequences were inserted into the 3′ LTR of the MLV-based promoter conversion vector pLXSNEGFP to replace the MLV U3 region. ...

For HERV LTRs, we selected members of the class I family HERV-H, which are transcribed in many different tissues (11, 14, 36, 38, 49), and members of the class III family HERV-L, which are expressed only in skin, thyroid gland, and reproductive organs (38). Both HERV families represent a huge reservoir of regulatory sequences for gene expression. The HERV-H family, which is distantly related to gammaretroviruses including MLV, comprises more than 1,000 proviral copies per haploid human genome and a similar number of solitary LTRs (17, 26). The foamy virus-related HERV-L family (3, 6) consists of about 200 full-length elements and 6,000 solitary LTRs (26). To identify LTR sequences as appropriate promoters, the U3-R region of a number of HERV-H and HERV-L LTRs was cloned into the firefly luciferase expressing vector pBL and tested in various human cell lines using the Dual-Luciferase reporter assay (Promega) as described previously (36).

HERV-H-MC16 and HERV-H-CL1 proved to be the most active, representing type I and type Ia subgroups of HERV-H LTRs, respectively. The HERV-H-CL1 LTR was found to be active in all cell lines tested so far, with the highest transcriptional activity in LC5-HeLa cells and astrocytes (U373) and lower activities in pancreatic cells (MIA PaCa-2), epidermal keratinocytes (HaCaT), and breast cancer cells (MCF7) as shown in Fig. Fig.1B1B and described previously (36). The HERV-H-MC16 LTR displays almost consistent transcription levels in MIA PaCa-2, HeLa, LC5-HeLa, HaCaT, and U373 cells. In addition, we selected the 5′ LTR of the HERV-L provirus identified by Cordonnier et al. (6) because of its high specificity for keratinocytes (Fig. (Fig.1B)1B) (S. Weinhardt, unpublished data). To further examine the tissue specificity of the selected LTRs, transgenic mice were established carrying the HERV-H-CL1 and the HERV-L-Cord U3-R region with the luciferase or EGFP gene as a reporter gene. Preliminary data suggest that the HERV-H-CL1 LTR initiates transcripts only in testes but not in other organs, whereas the HERV-L LTR is not active in any murine tissue (37; Weinhardt, unpublished), confirming previous data indicating that the activity of various HERV-H LTRs is restricted in murine cell lines compared to human cells (11). Thus, the promoter activity of these HERV LTRs appears to be primarily limited to human cells.

For construction of HERV-MLV hybrid vectors, the HERV LTR sequences were amplified by PCR and inserted into the 3′ U3-deleted MLV vector (Fig. (Fig.1A).1A). Plasmids pLXSN-HERV-H-CL1 and pLXSN-HERV-H-MC16 contain the 327-bp U3 region of HERV-H-CL1 and the 255-bp U3 region of HERV-H-MC16, respectively. To compare the infectivity and expression efficiency of constructs with and without a HERV R region, we also inserted a 323-bp fragment comprising the U3 and R regions of HERV-H-MC16 (pLXSN-HERV-H-MC16R). A 397-bp fragment containing the complete U3-R region of HERV-L was used for construction of pLXSN-HERV-L-CordR, since the exact border between U3 and R has not yet been determined.

The HERV-MLV hybrid constructs and the original MLV-derived pLXSNEGFP vector, as well as pLXSN-MMTV containing the inducible mouse mammary tumor virus (MMTV) promoter instead of the MLV U3 region in the 3′ LTR (34), were transfected into the amphotropic murine packaging cell line PA317. Virus titers were determined by infection of the feline kidney epithelial cell line CRFK. Human cell lines previously used for analysis of HERV promoter activity in transient luciferase assays were infected with supernatants obtained from vector-producing PA317 cells as described previously (30). Infected cells were cloned by neomycin selection. To verify the promoter conversion, DNA was analyzed by PCR using primers specific for the HERV U3, MLV U3 and MLV R regions in combination with a primer complementary to a sequence in the EGFP gene. Sequence analysis of the amplification products revealed that the HERV promoter was present in the correct configuration within the 5′ LTR of the vector provirus in all cell lines investigated (data not shown).

Fluorescence-activated cell sorting (FACS) analysis was performed to determine the promoter activity of the HERV-MLV constructs and the proportion of cells expressing EGFP (Fig. 1C to F). For comparability, only cell clones harboring a single integrated provirus were used. As expected from the results of transient-transfection assays, HERV-H promoters were active in all cell lines investigated so far but showed slightly differential EGFP expression depending on the cell type. In contrast, the HERV-L promoter displayed a high degree of cell type specificity and was active only in HaCaT and HeLa cells. The original MLV-based vector LXSNEGFP showed nearly the same activity in all cell lines (shown in Fig. Fig.1G1G for CRFK cells), which was about threefold higher than the highest activity found for a HERV-MLV hybrid vector, i.e., LXSN-HERV-H-CL1 in LC5-HeLa cells (Fig. (Fig.1C).1C). A MMTV promoter containing hybrid vector derived from LXSNEGFP (Fig. (Fig.1G)1G) was not active in CRFK cells but could be stimulated by the glucocorticoid dexamethasone (20, 34), giving EGFP expression levels comparable to those of LXSN-HERV-H-MC16 and LXSN-HERV-H-MC16R in MIA PaCa-2 cells (Fig. 1D and E). The activity of the HERV promoters was not influenced by dexamethasone (data not shown). In summary, these data suggest a slightly reduced promoter activity of heterologous retroviral promoters compared to the primary MLV U3 region irrespective whether they are of murine or human origin.

Interestingly, the activities of LXSN-HERV-H-CL1 and LXSN-HERV-H-MC16 nearly exactly reflect the expression activity and cell specificity patterns of the corresponding pBL clones containing HERV-H LTR in transient luciferase assays (Fig. (Fig.1B).1B). No essential differences between HERV-H-MLV hybrid vectors containing or lacking the HERV R region were found. Only in HeLa-LC5 cells, a slightly higher activity (about twofold) of LXSN-HERV-H-MC16R compared to LXSN-HERV-H-MC16 was observed (Fig. (Fig.1E).1E). An enhancing effect of the R region on HERV promoters has been described previously for some class II HERVs, HERV-K(HML-4) and HERV-K(HML-2), and may be due to additional transcription factor binding sites within the R region or posttranscriptional events, such as stabilizing effects on the mRNA (2). Furthermore, the use of an additional transcription initiation site within the HERV R region or the differences in spacing between promoter and transcription start site generated by a second R region may play a role.

As expected, LXSN-HERV-LCordR containing the HERV-L promoter shows similar EGFP expression levels but a higher cell type specificity than those of the HERV-H-MLV hybrid vectors. LXSN-HERV-L is inactive in the pancreas cell line MIA PaCa-2 but highly active in HeLa and HaCaT cells. Compared with pBL plasmids containing the luciferase gene under the control of HERV-L LTR sequences, LXSN-HERV-LCordR displays the same cell type specificity (Fig. 1B and F). Remarkably, little or no activity was observed for LXSN-HERV-LCordR- and HERV-L LTR-containing pBL plasmids in the HeLa subclone LC5-HeLa, although both were highly active in the original HeLa cells. LC5-HeLa cells represent a subclone from L132 cells (29), a cell line that was originally thought to be derived from embryonic lung tissue but was subsequently found to have been established via HeLa cell contamination (CCL-5 cells [American Type Culture Collection]). Although expressing keratin, LC5-HeLa cells have lost some features typical for HeLa cells and show instead fibroblast-like characteristics (29). The endogenous HERV transcription profile of LC5-HeLa cells as established by microarray analysis does not show HERV-L expression, which is typical for the cervix (38) as well as HeLa cells (data not shown). Accordingly, transfection with three different HERV-L LTRs cloned in the luciferase-containing pBL vector did not result in expression of the reporter gene in LC5-HeLa cells, but HERV-L LTR promoter activity could be induced by treatment with phorbol ester (O. Diem, unpublished data). Thus, slight alterations of a cell type, possibly caused by selection of a certain karyotype and/or long-term cultivation, may lead to differential HERV activities in those cells.

Taken together, these data suggest that cell type specificity of HERV promoters may be conferred on retroviral vectors. Interestingly, our results are also in good agreement with previous findings obtained with a retrovirus-specific microarray used to investigate the endogenous expression patterns and tissue specificities of different HERVs (38). The data confirm the high specificity of HERV-L elements, the expression of which is restricted essentially to skin, thyroid gland, and tissues involved in reproduction, such as uterus, cervix, placenta, and testes, in contrast to the ubiquitous expression of HERV-H elements (11, 14, 36, 38). Therefore, we conclude that reintegration does not alter cell type specificity in principle, even though expression levels should also be influenced by the genomic context.

To investigate whether adaptive evolution of the HERV LTR sequences may have occurred during infection and selection of infected cell lines, the sequences of five LXSN-HERV-H-CL1-infected cell clones, five LXSN-HERV-H-MC16-infected cell clones, three LXSN-HERV-H-MC16R-infected cell clones, and five LXSN-HERV-L-CordR-infected cell clones were compared with the original HERV LTR sequences of the vectors. No sequence variations could be detected, suggesting that mutations must be a rare event at least in nonreplicative vectors.

In our experiments, infected cell clones have been selected by neomycin resistance. Therefore, only integrations within active chromosomal regions have been investigated, so the HERV promoter, like the internal simian virus 40 promoter driving neomycin resistance gene expression, is unlikely to be silenced by methylation or inactivated chromatin. Our data should therefore particularly reflect the availability of transcription factors and their interaction with the HERV promoter in a given cell type. The longer U3 regions of HERVs compared to MLV, especially of HERV-L, may contain more potential binding sites for transcription modulating factors that confine activity in certain cells and thus may increase cell type specificity. The interaction of HERV-H and HERV-L LTRs with cellular factors was investigated previously, and some potential transcription factor binding sites were identified (1, 7, 9, 10, 32, 42). Binding sites for the transcription factor Sp1 have been detected in HERV-H and HERV-L LTRs but appear to act in a different context. HERV-H type Ia LTRs (represented by HERV-H-CL1) contain three Sp1 binding sites that probably act synergistically (32, 42). In several active HERV-L LTRs (including HERV-L-Cord), at least one Sp1 binding site was identified within the U3 region, although at different locations in LTRs with diverse cell type specificities (9, 10; Weinhardt, unpublished). Sp1 is ubiquitously expressed in many different cells, and Sp1 binding sites are commonly present in LTRs. However, several alternatively spliced transcripts encoding different isoforms of Sp1 are known, which are associated with different cell types or stages (45). The differential tissue specificities of HERV-L and HERV-H LTRs may be due to binding of different Sp1 variants or additional, as-yet-unknown, interacting cellular factors, e.g., cell type-dependent repressors.

To determine transcription initiation sites of HERV-H- and HERV-L-MLV hybrid vectors (Fig. (Fig.1A),1A), rapid amplification of 5′ cDNA ends (5′RACE) of vector constructs integrated in HeLa, LC5-HeLa, or HaCaT cells was performed as described previously (27). Nested PCR was carried out with forward primers specific for the 5′RACE adapter. Both reverse primers were located within the EGFP gene to avoid amplification of endogenous HERV-H or HERV-L elements. Several independent clones derived from each PCR product were sequenced.

Generally, the transcription start of HERV-H promoter-containing vectors was found to be more precisely defined than that of LXSN-HERV-LCordR. In six of eight cases, LXSN-HERV-H-CL1 used exactly the predicted initiation site at the transition between the HERV-H U3 region and the MLV R region in infected HeLa and LC5-HeLa cells (Fig. (Fig.2A2A).

FIG. 2.
Mapping of transcription start sites in different HERV-MLV hybrid LTRs by 5′RACE. Total RNA was extracted from HeLa and LC5-HeLa cells infected with LXSN-HERV-H-CL1, LXSN-HERV-H-MC16, or LXSN-HERV-H-MC16R, as well as two different HaCaT cell clones ...

The transcription initiation sites of LXSN-HERV-H-MC16 in LC5-HeLa cells are mainly located in two regions (Fig. (Fig.2B),2B), one around the beginning of the MLV R region and a second exactly at the first A of the MLV polyadenylation signal. The use of the latter as an additional transcription start site was also observed in LXSN-HERV-L-CordR-infected cells (Fig. (Fig.2D).2D). Further potential transcription start sites within the MLV R region of LXSN-HERV-H-CL1 and LXSN-HERV-H-MC16 did not appear several times in independent experiments and might therefore be due to failure during the RACE procedure.

To investigate the influence of an additional HERV R region upstream of the MLV R region on the selection of transcription initiation sites, we performed 5′RACE of LXSN-HERV-H-MC16R and LXSN-HERV-LCordR containing two R regions derived from HERV and MLV sequences. All transcription start sites of LXSN-HERV-H-MC16R in HeLa and LC5-HeLa cells were found to cluster around the boundary between the HERV U3 and HERV R regions (Fig. (Fig.2C).2C). The transcription initiation sites of the MLV R region were not used by LXSN-HERV-H-MC16R.

For LXSN-HERV-LCordR, two different clones of infected HaCaT cells were analyzed. In contrast to HERV-H-MLV hybrid vectors, LXSN-HERV-LCordR appears to possess multiple transcription initiation sites in a region spanning about 300 bp of HERV and MLV sequences (Fig. (Fig.2D).2D). The transition between the HERV-L U3 and R regions in HERV-L elements has not yet been defined. In one of the two analyzed clones of infected HaCaT cells, the majority of transcription start sites of LXSN-HERV-LCordR cluster within 7 bp of the HERV-L sequence, suggesting that this might be the natural U3/R boundary of HERV-L elements. In both clones, the transcription start site located at the border between the HERV-L R region and the MLV R region is also used, as well as the minor initiation site starting with the first A of the polyadenylation signal. As sequence variations between the LTRs could be excluded, the differential use of transcription start sites in different clones of the same cell line infected with the same vector suggests a possible influence of vector integration sites on initiation of transcription. Notably, the promoter activity of the HERV-L LTR was significantly lower in cells in which only the MLV start site was used than in the cells preferentially initiating at the HERV start site (data not shown).

In contrast to exogenous retroviruses, which mostly have a strong TATA box and a single major transcription start site, multiple initiation sites have been found in several endogenous retroviruses and retroviral elements (15, 27, 43). Multiple transcription initiation sites are thought to be characteristic for promoters with a weak TATA box but several Sp1 binding sites. The majority of human genes possess highly variable transcription start sites, reflecting the dynamic nature of transcription (48). This led to the assumption that endogenous retroviruses residing in the genome gradually approximate cellular genes and assume more flexibility in transcriptional control than their exogenous counterparts (27). Thus, HERV LTRs probably resemble cellular transcription units more than they resemble promoters of exogenous retroviruses.

Cell type-specific promoters and enhancers are a prerequisite for the construction of targeted retroviral expression vectors and their controlled use in gene therapy. HERV LTRs represent a huge reservoir of regulatory sequences in the human genome that are easy to isolate and characterize. They have a number of features that make them advantageous for the construction of therapeutic vectors. They have adapted themselves to their hosts over millions of years, and thus, pathogenic sequences have largely been eliminated during evolution. Recombination of HERV elements with HERV-derived vectors will not create completely new types of retroviruses, as would be the case with vectors based on animal retroviruses or human exogenous retroviruses, such as lentiviruses. On the other hand, homologous recombination of HERV sequences with HERV-based vectors might be utilized for targeted gene transfer. In contrast to cellular promoters, which often depend on additional signal structures located at some distance upstream or downstream, the regulatory elements of retroviruses are concentrated in a small and clearly defined region to maintain transcriptional independence regardless of the integration site in the host genome. Furthermore, many HERV LTRs are characterized by multiple Sp1 binding sites that may protect against inactivation by de novo methylation (4, 40).

In our study, all of the HERV-H hybrid vectors are replication defective. Replication-competent retroviral vectors, however, could be used for example for selection of cell type-specific and efficient HERV promoters, when the original MLV promoter is replaced by a mixture of arbitrarily amplified HERV LTR sequences. The HERV promoter sequence, which replicates most efficiently in a certain cell type, could then be isolated after several replication cycles. Recently, synthetic promoters have been inserted in place of the MLV promoter in replication-competent retroviral vectors (25, 30), and such viruses have been shown to be replication competent for a number of replication cycles before losing the heterologous promoter. HERV LTRs may prove to be even more stable in the context of replicating vectors, since they are of retroviral origin and yet can still restrict expression in a cell type-specific manner. Considering that a multitude of HERV LTRs have already been recruited during evolution as control elements for gene expression, HERV LTRs should be a valuable source of new cell type-specific regulatory sequences and represent promising candidates for the construction of retroviral vectors for use in human gene therapy.

Acknowledgments

This work was supported in part by a grant from the Bayerische Forschungsstiftung, Forschungsverbund FORGEN 2.

Footnotes

[down-pointing small open triangle]Published ahead of print on 9 September 2009.

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