Nucleotide sequences of murine intracisternal A-particle gene LTRs have extensive variability within the R region

A 192 bp ERV fragment insertion in the first intron of porcine TLR6 may act as an enhancer associated with the increased expressions of TLR6 and TLR1

Background

Toll-like receptors (TLRs) play important roles in building innate immune and inducing adaptive immune responses. Associations of the TLR genes polymorphisms with disease susceptibility, which are the basis of molecular breeding for disease resistant animals, have been reported extensively. Retrotransposon insertion polymorphisms (RIPs), as a new type of molecular markers developed recently, have great potential in population genetics and quantitative trait locus mapping. In this study, bioinformatic prediction combined with PCR-based amplification was employed to screen for RIPs in porcine TLR genes. Their population distribution was examined, and for one RIP the impact on gene activity and phenotype was further evaluated.

Results

Five RIPs, located at the 3' flank of TLR3, 5' flank of TLR5, intron 1 of TLR6, intron 1 of TLR7, and 3' flank of TLR8 respectively, were identified. These RIPs were detected in different breeds with an uneven distribution among them. By using the dual luciferase activity assay a 192 bp endogenous retrovirus (ERV) in the intron 1 of TLR6 was shown to act as an enhancer increasing the activities of TLR6 putative promoter and two mini-promoters. Furthermore, real-time quantitative polymerase chain reaction (qPCR) analysis revealed significant association (p < 0.05) of the ERV insertion with increased mRNA expression of TLR6, the neighboring gene TLR1, and genes downstream in the TLR signaling pathway such as MyD88 (Myeloid differentiation factor 88), Rac1 (Rac family small GTPase 1), TIRAP (TIR domain containing adaptor protein), Tollip (Toll interacting protein) as well as the inflammatory factors IL6 (Interleukin 6), IL8 (Interleukin 8), and TNFα (Tumor necrosis factor alpha) in tissues of 30 day-old piglet. In addition, serum IL6 and TNFα concentrations were also significantly upregulated by the ERV insertion (p < 0.05).

Conclusions

A total of five RIPs were identified in five different TLR loci. The 192 bp ERV insertion in the first intron of TLR6 was associated with higher expression of TLR6, TLR1, and several genes downstream in the signaling cascade. Thus, the ERV insertion may act as an enhancer affecting regulation of the TLR signaling pathways, and can be potentially applied in breeding of disease resistant animals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13100-021-00248-w.

Gestational arsenic exposure induces site-specific DNA hypomethylation in active retrotransposon subfamilies in offspring sperm in mice

Background

Environmental impacts on a fetus can disrupt germ cell development leading to epimutations in mature germ cells. Paternal inheritance of adverse health effects through sperm epigenomes, including DNA methylomes, has been recognized in human and animal studies. However, the impacts of gestational exposure to a variety of environmental factors on the germ cell epigenomes are not fully investigated. Arsenic, a naturally occurring contaminant, is one of the most concerning environmental chemicals, that is causing serious health problems, including an increase in cancer, in highly contaminated areas worldwide. We previously showed that gestational arsenic exposure of pregnant C3H mice paternally induces hepatic tumor increase in the second generation (F2). In the present study, we have investigated the F1 sperm DNA methylomes genome-widely by one-base resolution analysis using a reduced representation bisulfite sequencing (RRBS) method.

Results

We have clarified that gestational arsenic exposure increases hypomethylated cytosines in all the chromosomes and they are significantly overrepresented in the retrotransposon LINEs and LTRs, predominantly in the intergenic regions. Closer analyses of detailed annotated DNA sequences showed that hypomethylated cytosines are especially accumulated in the promoter regions of the active full-length L1MdA subfamily in LINEs, and 5′LTRs of the active IAPE subfamily in LTRs. This is the first report that has identified the specific positions of methylomes altered in the retrotransposon elements by environmental exposure, by genome-wide methylome analysis.

Conclusion

Lowered DNA methylation potentially enhances L1MdA retrotransposition and cryptic promoter activity of 5′LTR for coding genes and non-coding RNAs. The present study has illuminated the environmental impacts on sperm DNA methylome establishment that can lead to augmented retrotransposon activities in germ cells and can cause harmful effects in the following generation.

Ectopic expression of the Stabilin2 gene triggered by an intracisternal A particle (IAP) element in DBA/2J strain of mice

Stabilin2 (Stab2) encodes a large transmembrane protein which is predominantly expressed in the liver sinusoidal endothelial cells (LSECs) and functions as a scavenger receptor for various macromolecules including hyaluronans (HA). In DBA/2J mice, plasma HA concentration is ten times higher than in 129S6 or C57BL/6J mice, and this phenotype is genetically linked to the Stab2 locus. Stab2 mRNA in the LSECs was significantly lower in DBA/2J than in 129S6, leading to reduced STAB2 proteins in the DBA/2J LSECs. We found a retrovirus-derived transposable element, intracisternal A particle (IAP), in the promoter region of Stab2^DBA which likely interferes with normal expression in the LSECs. In contrast, in other tissues of DBA/2J mice, the IAP drives high ectopic Stab2^DBA transcription starting within the 5′ long terminal repeat of IAP in a reverse orientation and continuing through the downstream Stab2^DBA. Ectopic transcription requires the Stab2-IAP element but is dominantly suppressed by the presence of loci on 59.7–73.0 Mb of chromosome (Chr) 13 from C57BL/6J, while the same region in 129S6 requires additional loci for complete suppression. Chr13:59.9–73 Mb contains a large number of genes encoding Krüppel-associated box-domain zinc-finger proteins that target transposable elements-derived sequences and repress their expression. Despite the high amount of ectopic Stab2^DBA transcript in tissues other than liver, STAB2 protein was undetectable and unlikely to contribute to the plasma HA levels of DBA/2J mice. Nevertheless, the IAP insertion and its effects on the transcription of the downstream Stab2^DBA exemplify that stochastic evolutional events could significantly influence susceptibility to complex but common diseases.

Locus-specific hypomethylation of the mouse IAP retrotransposon is associated with transcription factor-binding sites

Background

Intracisternal A particle (IAP) is one of the most transpositionally active retrotransposons in the mouse genome, but its expression varies between cell types. This variation is believed to arise from differences in the epigenetic state (e.g., DNA methylation) of the 5′ long terminal repeat (LTR), where transcription starts. However, owing to the high copy number and high sequence similarity between copies, it is difficult to analyze the epigenetic states of individual IAP LTRs in a comprehensive manner.

Results

We have developed a method called Target Enrichment after Post-Bisulfite Adaptor Tagging (TEPBAT) to analyze the DNA methylation states of a large number of individual retrotransposon copies at once. Using this method, we determined the DNA methylation levels of >8500 copies of genomic IAP LTRs (almost all copies that we aimed to target by the PCR primers) in the sperm and tail. This revealed that the vast majority of the LTRs were heavily methylated in both sperm and tail; however, hypomethylated copies were more frequently found in the sperm than in the tail. Interestingly, most of these hypomethylated LTRs were solo-type, belonged to specific IAP subfamilies, and carried binding sites for transcription factors (TFs) that are active in male germ cells.

Conclusions

The current study revealed subfamily- and locus-specific hypomethylation of IAP LTRs, and suggests that binding of TFs is involved in the protection from DNA methylation, whereas the IAP internal sequence enhances methylation. Furthermore, the study demonstrated that TEPBAT offers a cost-effective method for a variety of DNA methylome studies that focus on retrotransposon sequences.

Electronic supplementary material

The online version of this article (10.1186/s13100-017-0105-0) contains supplementary material, which is available to authorized users.

Biological functions of DNA methyltransferase 1 require its methyltransferase activity

DNA methyltransferase 1 (DNMT1) has been reported to interact with a wide variety of factors and to contain intrinsic transcriptional repressor activity. When a conservative point mutation was introduced at the key catalytic residue, mutant DNMT1 failed to rescue any of the phenotypes of Dnmt1-null embryonic stem (ES) cells, which indicated that the biological functions of DNMT1 are exerted through the methylation of DNA. ES cells that expressed the mutant protein did not survive differentiation. Intracisternal A-particle family retrotransposons were no longer methylated and were transcribed at high levels. The proper localization of DNMT1 depended on normal genomic methylation, and we discuss the implications of this finding for epigenetic dysregulation in cancer.

Intracisternal A-particle element in the 3' noncoding region of the mu-opioid receptor gene in CXBK mice: a new genetic mechanism underlying differences in opioid sensitivity

OBJECTIVES

CXBK mice, recombinant inbred mice derived from C57BL/6By and BALB/cBy progenitors, display reduced morphine-induced analgesia. Earlier we reported that CXBK mice expressed a reduced amount of the major transcript, MOR-1 mRNA, of the mu-opioid receptor gene. The CXBK MOR-1 mRNA contains a normal coding region and an abnormally long untranslated region.

METHODS AND RESULTS

To identify the nucleotide-sequence difference between the CXBK MOR-1 mRNA and that of the progenitors, we first characterized the 3' untranslated region of the MOR-1 mRNA, which was largely unknown. A 3' rapid amplification of cDNA ends-PCR analysis revealed that the 3' untranslated region of the C57BL/6By MOR-1 mRNA was 10 181 nucleotides transcribed from an exon. Next, we compared the MOR-1 genes in C57BL/6By, CXBK, and BALB/cBy mice, and found a 5293 nucleotide insertion only in CXBK mice. The inserted sequence was a variant of the intracisternal A-particle elements that exist in the mouse genome at approximately 1000 sites. Reverse transcription-PCR analyses revealed that the intracisternal A-particle element was transcribed as a part of the CXBK MOR-1 mRNA. No other differences were found in the MOR-1 mRNA between CXBK and BALB/cBy mice, whereas 100 nucleotides differed between C57BL/6By and CXBK mice aside from the intracisternal A-particle insertion. Finally, CXBK mice displayed reduced morphine responses compared with BALB/cBy mice.

CONCLUSIONS

Our data suggest that differences in the MOR-1 3' untranslated region appear to cause the CXBK phenotype. This genetic mechanism underlying the CXBK phenotype may provide good insight into the possible genetic mechanisms underlying individual differences in opioid sensitivity in humans.

Local mutagenic impact of insertions of LTR retrotransposons on the mouse genome

Solitary LTR loci are the predominant form of LTR retrotransposons in most eukaryotic genomes. They originate from recombination between the two LTRs of an ancestral retrovirus and are therefore incapable of transposition. Despite this inactivity, they appear to have a substantial impact on the host genome. Here we use the murine RMER10 LTR family as an example to describe how such elements can reshape regions of the genome through multiple mutations on an evolutionary time scale. Specifically, we use phylogenetic analysis of multiple copies of RMER10 in rodent species, as well as comparisons of orthologous pairs in mouse and rat, to argue that insertions of members of this family have locally induced the emergence of tandem repeat loci as well as many indels. Analysis of structural aspects of these sequences (secondary structures and transcription factors signals) may explain why RMER10 can become endogenous "mutagenic" factors through induction of replication fork blockages and/or error-prone repair of aberrant DNA structures. This hypothesis is also consistent with features of other interspersed repeated elements.

Molecular characterization and genomic distribution of Isis: a new retrotransposon of Drosophila buzzatii

A new transposable element, Isis, is identified as a LTR retrotransposon in Drosophila buzzatii. DNA sequence analysis shows that Isis contains three long ORFs similar to gag, pol and env genes of retroviruses. The ORF1 exhibits sequence homology to matrix, capsid and nucleocapsid gag proteins and ORF2 encodes a putative protease (PR), a reverse transcriptase (RT), an Rnase H (RH) and an integrase (IN) region. The analysis of a putative env product, encoded by the env ORF3, shows a degenerated protein containing several stop codons. The molecular study of the putative proteins coded by this new element shows striking similarities to both Ulysses and Osvaldo elements, two LTR retrotransposons, present in D. virilis and D. buzzatii, respectively. Comparisons of the predicted Isis RT to several known retrotransposons show strong phylogenetic relationships to gypsy-like elements, particulary to Ulysses retrotransposon. Studies of Isis chromosomal distribution show a strong hybridization signal in centromeric and pericentromeric regions, and a scattered distribution along all chromosomal arms. The existence of insertional polymorphisms between different strains and high molecular weight bands by Southern blot suggests the existence of full-sized copies that have been active recently. The presence of euchromatic insertion sites coincident between Isis and Osvaldo could indicate preferential insertion sites of Osvaldo element into Isis sequence or vice versa. Moreover, the presence of Isis in different species of the buzzatii complex indicates the ancient origin of this element.

Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse

Genome-wide epigenetic reprogramming by demethylation occurs in early mouse embryos and primordial germ cells. In early embryos many single-copy sequences become demethylated both by active and passive demethylation, whereas imprinted gene methylation remains unaffected. In primordial germ cells single-copy and imprinted sequences are demethylated, presumably by active demethylation. Here we investigated systematically by bisulphite sequencing the methylation profiles of IAP and Line1 repeated sequence families during preimplantation and primordial germ cell development. Whereas Line1 elements were substantially demethylated during both developmental periods, IAP elements were largely resistant to demethylation, particularly during preimplantation development. This may be desirable in order to prevent IAP retrotransposition, which could cause mutations. In turn, this can result in the transgenerational inheritance of epigenetic states of IAPs, which could lead to heritable epimutations of neighbouring genes through influencing their transcriptional states.

Capture of DNA sequences at double-strand breaks in mammalian chromosomes

To study double-strand break (DSB)-induced mutations in mammalian chromosomes, we transfected thymidine kinase (tk)-deficient mouse fibroblasts with a DNA substrate containing a recognition site for yeast endonuclease I-SceI embedded within a functional tk gene. To introduce a genomic DSB, cells were electroporated with a plasmid expressing endonuclease I-SceI, and clones that had lost tk function were selected. Among 253 clones analyzed, 78% displayed small deletions or insertions of several nucleotides at the DSB site. Surprisingly, approximately 8% of recovered mutations involved the capture of one or more DNA fragments. Among 21 clones that had captured DNA, 10 harbored a specific segment of the I-SceI expression plasmid mapping between two replication origins on the plasmid. Four clones had captured a long terminal repeat sequence from an intracisternal A particle (an endogenous retrovirus-like sequence) and one had captured what appears to be a cDNA copy of a moderately repetitive B2 sequence. Additional clones displayed segments of the tk gene and/or microsatellite sequences copied into the DSB. This first systematic study of DNA capture at DSBs in a mammalian genome suggests that DSB repair may play a considerable role in the evolution of eukaryotic genomes.

Differential expression of intracisternal A-particle transcripts in immunogenic versus tumorigenic S49 murine lymphoma cells

Tumorigenic S49 mouse lymphoma cells (T-25) were compared to their nontumorigenic (immunogenic) substrate-adherent descendants (T-25-Adh), using the differential display technique. A 784-bp fragment with 92% sequence homology to the intracisternal A-particle (IAP) element family was isolated from the latter cells. IAP sequences are endogenous, noninfectious retroviral elements that can undergo transpositions and act as mutagens. Expression of IAP transcripts (as detected by the isolated fragment) was 5- to 10-fold higher in T-25-Adh cells than in T-25 cells. IAP RT-PCR cDNA clones derived from the immunogenic T-25-Adh cells, but not from T-25 cells, contain two distinctive motifs: (i) a motif characteristic of IAP elements expressed in lymphoid cells (lymphocyte specific, LS); (ii) a nonapeptide sequence known to stimulate cytotoxic T lymphocytes in a leukemia cell line expressing IAP sequences. In addition, expression of transcripts containing these motifs is enhanced in the immunogenic cells as opposed to the tumorigenic cells. Furthermore, one of the IAP elements (belonging to the LS1 subfamily) is specifically hypomethylated in the DNA of the immunogenic cells. The above-mentioned relationship was strengthened when tumorigenic revertants derived from T-25-Adh cells, as well as independently selected tumorigenic and immunogenic S49 sublines, were studied. In all cases, enhanced immunogenicity was linked to the up-regulation of specific IAP elements. No transpositions of LS1 elements were observed among the different sublines studied. These findings suggest that, in the S49 lymphoma, selectively expressed IAP retroviral elements may function in a tumor suppressive capacity by affecting the immunogenic potential of these cells.

Increased expression of intracisternal A-particle RNA in regenerated myeloid cells after X irradiation in C3H/He inbred mice

Myeloid Cells after X Irradiation in C3H/He Inbred Mice. Myeloid leukemia cells were derived from regenerated hematopoietic cells damaged by sublethal doses of X radiation in C3H/He inbred mice. We previously found that within the genome of the myeloid leukemia cells, a retrotransposon, the intracisternal A-particle (IAP) element, is integrated. Levels of IAP RNA, the source of cDNA for the integration, were analyzed quantitatively in C3H mice. Higher levels of IAP transcripts were observed in normal cells, particularly in hematopoietic cells, from C3H/He mice, than in those from C57BL/6J and STS/A mice. In the C3H/He mice, an approximately twofold increase in IAP RNA was found in the regenerated spleen and bone marrow cells at 5 days and from 12 to 90 days after whole-body X irradiation. In addition, an increased level of IAP RNA was observed in all the myeloid leukemia cells derived from C3H/He mice. This suggests that the elevated levels of IAP RNA in the regenerated hematopoietic cells after irradiation contribute to the increase in retrotransposition of IAP found in myeloid leukemia cells from C3H/He mice.

Analysis of the promoter from an expanding mouse retrotransposon subfamily

The mouse genome contains several subfamilies of the retrotransposon L1. One subfamily, TF, contains 4000-5000 full-length members and is expanding due to retrotransposition of a large number of active elements. Here we studied the TF 5' untranslated region (UTR), which contains promoter activity required for subfamily expression. Using reporter assays, we show that promoter activity is derived from TF-specific monomer sequences and is proportional to the number of monomers in the 5' UTR. These data suggest that nearly all full-length TF elements in the mouse genome are currently competent for expression. We aligned the sequences of 53 monomers to generate a consensus TF monomer and determined that most TF elements are truncated near a potential binding site for a transcription initiation factor. We also determined that much of the sequence variation among TF monomers results from transition mutations at CpG dinucleotides, suggesting that genomic TF 5' UTRs are methylated at CpGs.

Structure and evolution of Cyclops: a novel giant retrotransposon of the Ty3/Gypsy family highly amplified in pea and other legume species

We characterized a novel giant Gypsy-like retrotransposon, Cyclops, present in about 5000 copies in the genome of Pisum sativum. The individual element Cyclops-2 measures 12 314 bp including long terminal repeats (LTRs) of 1504 bp and 1594 bp, respectively, showing 4.1% sequence divergence between one another. Cyclops-2 carries a polypurine tract (PPT) and an unusual primer binding site (PBS) complementary to tRNA-Glu. The element is bounded by 5 bp target site duplications and harbors three successive internal regions with homology to retroviral genes gag (424 codons) and pol (1382 codons) and an additional open reading frame (423 codons) of unknown function indicating the element's potential capacity for gene transduction. The pol region contains sequence motifs related to the enzymes protease, reverse transcriptase, RNAse H and integrase in the same typical order (5'-PR-RT-RH-IN-3') known for retroviruses and Gypsy-like retrotransposons. The reading frame of the pol region is disrupted by several mutations suggesting that Cyclops-2 does not encode functional enzymes. A phylogenetic analysis of the reverse transcriptase domain confirms our differential genetic assessment that Cyclops from pea is a novel element with no specific relationship to the previously described Gypsy-like elements from plants. Genomic Southern hybridizations show that Cyclops is abundant not only in pea but also in common bean, mung bean, broad bean, soybean and the pea nut suggesting that Cyclops may be an useful genetic tool for analyzing the genomes of agronomically important legumes.

Detection and cloning of unique integration sites of retrotransposon, intracisternal A-particle element in the genome of acute myeloid leukemia cells in mice

We previously found retrotransposition of the intracisternal A-particle (IAP) element in the genome of acute myeloid leukemia (AML) cells induced by X-irradiation of C3H/He mice (FEBS 16333). To analyze the occurrence of the IAP-mediated retrotransposition in AML cells, we compared integration sites of the IAP element by polymerase chain reaction (PCR) in the genomes of five AML strains derived from different C3H mice. Unique PCR products were found in all of the above independent leukemia cells, whereas no such products were detected in normal cells. Results of cloning, sequencing and Southern analyses showed that the PCR products were derived from novel integration sites of the IAP element in the genome. The data suggest that IAP-mediated retrotransposition occurs frequently in radiation-induced AML cells from C3H/He mice.

Mouse pale ear (ep) is homologous to human Hermansky-Pudlak syndrome and contains a rare 'AT-AC' intron

Hermansky-Pudlak syndrome (HPS) is a rare, often fatal, autosomal recessive disorder in which albinism, bleeding and lysosomal storage are associated with defects of diverse cytoplasmic organelles, including melanosomes, platelet dense granules and lysosomes. Similar multi-organellar defects occur in the Chediak-Higashi syndrome (CHS), as well as in a large number of different mouse mutants. The HPS gene is located in 10q23, and two genetically distinct mouse loci, pale ear (ep) and ruby-eye (ru), both with mutant phenotypes similar to human HPS, map close together in the homologous region of murine chromosome 19, suggesting that one of these loci might be homologous to human HPS. We recently identified the human HPS gene, which encodes a novel ubiquitously-expressed transmembrane protein of unknown function. Here, we describe characterization of the mouse Hps cDNA and genomic locus, and identification of pathologic Hps gene mutations in ep but not in ru mice, establishing mouse pale ear as an animal model for human HPS. The phenotype of homozygous ep mutant mice encompasses those of both HPS and CHS, suggesting that these disorders may be closely related. In addition, the mouse and human HPS genes both contain a rare 'AT-AC' intron, and comparison of the sequences of this intron in the mouse and human genes identified conserved sequences that suggest a possible role for pre-mRNA secondary structure in excision of this rare class of introns.

Unusual long target duplication by insertion of intracisternal A-particle element in radiation-induced acute myeloid leukemia cells in mouse

Retrotransmission into the IL-3/GM-CSF gene locus by the retrotransposon intracisternal A-particle (IAP) had been observed in distinct tumor cell lines. We analyzed the locus in genomes from 7 different myeloid leukemia cell strains which were originally generated by whole-body X-irradiation of the inbred C3H/He mice at a dose of 3 Gy and maintained by in vivo passage. In one leukemia cell strain out of 7 such cases, RFLP of an allele of the interleukin-3 gene was found. Sequence analysis after cloning from the genomic library showed that a type I delta 2 IAP element was inserted in the region upstream of the IL-3 gene in the head-to-head orientation. This suggests that the locus in myeloid cells is sensitive for integration of IAP elements. Additionally, an unusual long target duplication of 82 bp, 14-fold larger than normal one, was found at the junction of the element. This suggests the possibility of a radiation-induced integration mechanism which is distinct from normal retrotransmission.

A novel non-mouse mammary tumor virus activation of the Int-3 gene in a spontaneous mouse mammary tumor

In a mouse mammary tumor model system in which carcinogenic progression can be investigated, we have found a unique mutation of Int-3 associated with progression from premalignant lobular hyperplasia to tumor. Sequence analysis of the rearranged fragment revealed an insertion of an intracisternal type A particle (IAP) within the Int-3 gene. Int-3 is mutated frequently in mouse mammary tumor virus (MMTV)-induced mammary tumors by insertion of MMTV proviral DNA into this intragenic region. In these mutations, the insertion produces a chimeric Int-3 transcript encoding the cytoplasmic portion of the Int-3 protein driven by the MMTV long terminal repeat promoter. In this case, the IAP DNA was inserted in the opposite transcriptional orientation relative to Int-3; nevertheless, a similar chimeric RNA transcript driven by a cryptic promoter in the oppositely oriented 5' IAP long terminal repeat was generated. This is the first demonstration that an insertional mutation unrelated to MMTV activates an Int gene commonly associated with mammary tumorigenesis.

Intracisternal A-type particle elements as genetic markers: detection by repeat element viral element amplified locus-PCR

We describe a novel, PCR-based technique termed REVEAL-PCR for examining the inheritance of intracisternal A-type particles (IAP). Amplifications use an unlabeled primer to SINE repeats and a radiolabeled primer to the IAP long terminal repeat; labeled products, which can be resolved on sequencing gels, are formed when IAPs lie in proximity to SINEs. With this technique we have identified a total of 124 polymorphisms in the BXH and CXS recombinant inbred strains. We suggest that this method will be equally applicable for examining other gene families present at around a thousand copies per genome.

Neomorphic agouti mutations in obese yellow mice

Several dominant mutations of the mouse agouti coat colour gene have pleiotropic effects that include obesity and a yellow coat. The Ay allele is caused by a large deletion that affects the expression of several contiguous genes. We show that three other obesity-associated agouti mutations, Aiy, Asy and Avy, are due to different molecular alterations that result in ubiquitous expression of a chimaeric RNA that encodes a normal agouti protein. The Aiy and Avy alleles are caused by insertion of an intracisternal A particle element 1 kb or 100 kb, respectively, upstream of agouti coding sequences. These results provide a model for other genes that show allele-specific imprinting, and demonstrate that molecular mechanisms typically responsible for activation of proto-oncogenes can also lead to other disease phenotypes.

Selection of DNA clones with enhancer sequences

A method is described for selection of DNA clones that contain enhancer sequences that activate gene expression. An Escherichia coli-rodent cell shuttle vector, pPyE0, was used that contains polyoma viral DNA without the polyoma enhancer region. Replication of pPyE0 DNA in mouse cells is markedly reduced due to deletion of the polyoma enhancer region. Insertion of mouse genomic DNA fragments that contain putative enhancer sequences into pPyE0 adjacent to the polyoma origin of replication restored, to varying extents, the ability of the recombinant plasmid DNA to replicate in mouse cells. Recombinant plasmids that replicate well in mouse cells, therefore, are amplified selectively. Transfection of mouse neuroblastoma or fibroblast cells that constitutively synthesize polyoma large tumor antigen with a library of mouse genomic DNA fragments inserted in pPyE0 yielded many recombinant plasmids. DNA inserts from each of the 16 clones that were examined stimulated the expression of an enhancerless chloramphenicol acetyltransferase reporter gene. The DNA inserts from 4 clones that were studied resulted in 4- to 13-fold increases in chloramphenicol acetyltransferase mRNA in transfected mouse cells. Nucleotide sequence analysis led to the identification of 5 genomic DNA clones that were obtained by selection. All of the homologies found were to regions of DNA that are thought to be involved in the regulation of gene expression.

Selective expression of intracisternal A-particle genes in established mouse plasmacytomas

Mouse plasmacytomas generally express higher levels of RNA transcripts from endogenous intracisternal A-particle (IAP) proviral elements than do lipopolysaccharide-stimulated normal lymphocytes. Lymphocytes express a limited and highly characteristic set of IAP elements (lymphocyte-specific [LS] elements). In this study, we examined whether LS elements are expressed at higher levels after transformation of the cells and/or whether new IAP elements are activated. The IAP elements expressed in plasmacytoma MPC11 were characterized by sequence analysis of 22 cDNA clones. The long terminal repeats (LTRs) of the tumor cDNAs proved to be highly related in sequence. None of the clones was of the LS cDNA type. The MPC11 LTRs were five- to sixfold more active than an LS cDNA LTR when tested for promoter activity by transfection into plasmacytoma cells. The LTRs of the tumor-derived cDNAs contained a canonical ATF core sequence (ATF-PC), while the LS cDNAs contained an altered sequence (ATF-LS). An ATF-PC oligonucleotide probe detected multiple IAP transcripts on Northern (RNA) blots of RNA from several plasmacytoma but gave no reaction with RNA from stimulated B lymphocytes. In contrast, an ATF-LS probe detected higher levels of RNA in lymphocyte than in tumor RNAs. Thus, expression of IAP elements in transformed B cells is selective for a different set of regulatory sequence variants than those expressed in normal B cells. Other oligonucleotide probes representing LS- and PC-specific sequence variants detected multiple common hypomethylated IAP proviral loci in three independently derived plasmacytomas. Overall, the results show that established plasmacytomas exhibit a characteristic pattern of IAP proviral hypomethylation and regulatory sequence selection.

Selective expression of intracisternal A-particle genes in established mouse plasmacytomas

Mouse plasmacytomas generally express higher levels of RNA transcripts from endogenous intracisternal A-particle (IAP) proviral elements than do lipopolysaccharide-stimulated normal lymphocytes. Lymphocytes express a limited and highly characteristic set of IAP elements (lymphocyte-specific [LS] elements). In this study, we examined whether LS elements are expressed at higher levels after transformation of the cells and/or whether new IAP elements are activated. The IAP elements expressed in plasmacytoma MPC11 were characterized by sequence analysis of 22 cDNA clones. The long terminal repeats (LTRs) of the tumor cDNAs proved to be highly related in sequence. None of the clones was of the LS cDNA type. The MPC11 LTRs were five- to sixfold more active than an LS cDNA LTR when tested for promoter activity by transfection into plasmacytoma cells. The LTRs of the tumor-derived cDNAs contained a canonical ATF core sequence (ATF-PC), while the LS cDNAs contained an altered sequence (ATF-LS). An ATF-PC oligonucleotide probe detected multiple IAP transcripts on Northern (RNA) blots of RNA from several plasmacytoma but gave no reaction with RNA from stimulated B lymphocytes. In contrast, an ATF-LS probe detected higher levels of RNA in lymphocyte than in tumor RNAs. Thus, expression of IAP elements in transformed B cells is selective for a different set of regulatory sequence variants than those expressed in normal B cells. Other oligonucleotide probes representing LS- and PC-specific sequence variants detected multiple common hypomethylated IAP proviral loci in three independently derived plasmacytomas. Overall, the results show that established plasmacytomas exhibit a characteristic pattern of IAP proviral hypomethylation and regulatory sequence selection.

Pao, a highly divergent retrotransposable element from Bombyx mori containing long terminal repeats with tandem copies of the putative R region

Analysis of aberrant ribosomal DNA (rDNA) repeats of Bombyx mori resulted in the discovery of a 4.8 kilobase retrotransposable element, Pao. Approximately 40 copies of Pao are present in the genome with most located outside the rDNA units. The complete sequence of one Pao element and partial sequence of four other copies indicated that Pao encodes an 1158 amino acid open-reading frame (ORF). Located within this ORF are domains with sequence similarity to retroviral gag genes, aspartic protease and reverse transcriptase. RNase H and integrase domains were not identified suggesting that the cloned copies were not full-length elements. Pao elements contain long terminal repeats (LTRs) with a central region composed of variable numbers of 46 bp tandem repeats. The variable region appears to correspond to the R region of retroviral LTRs, the region responsible for strand transfer during reverse transcription. Based on a sequence analysis of its reverse transcriptase domain, Pao is most similar to TAS of Ascaris lumbricoides. Pao and TAS represent a subgroup of LTR retrotransposons distinct from the Copia-Ty1 and Gypsy-Ty3 subgroups.

An intracisternal A-particle DNA sequence is closely linked to the thrombomodulin gene in some strains of laboratory mice

Sequence analysis of the 5' end of the thrombomodulin (TM) gene has identified a difference in two strains of laboratory mice, BALB/cBD (maintained at the Oak Ridge National Laboratory) and the strain used for the sequence listed in the GenBank data base. An intracisternal A-particle (IAP) provirus was present in the BALB/cBD sequence but absent from the GenBank sequence. Thus, there are two different 5' regions for the TM gene in mice. Southern blot and polymerase chain reaction analyses on other mouse strains demonstrated the presence of this proviral sequence in five out of ten strains tested. Northern blot analyses demonstrated that there were differences (up to three-fold) in the steady-state levels of TM mRNA among the strains. However, TM mRNA levels did not correlate directly with the presence of the IAP DNA upstream from the TM gene. This is in contrast to other loci (the interleukin-3 gene, c-mos, and the immunoglobulin Ck gene), in which the IAP element is known to affect levels of RNA transcription. While the IAP provirus does not appear to have an effect on TM transcription under normal conditions, it is possible that transcription levels altered by factors like thrombin and tumor necrosis factor are affected by the IAP provirus.

Reverse transcriptase families and a copia-like retrotransposon, Osser, in the green alga Volvox carteri

By using the polymerase chain reaction (PCR) we have isolated and sequenced two distinct families of reverse transcriptase (RT) sequences from the genome of the colonial alga, Volvox carteri. Probing a genomic library with these RT clones revealed copia-like retrotransposons. One of these elements, named Osser, is 4,875 bp long, bordered by 197-bp identical long terminal repeats (LTRs), and shows the typical organization of retrotransposons belonging to the copia-Tyl group. This is the first complete copia-like retrotransposon sequence described in a green alga.

Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses

We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.

Sequence variations and promoter activities of long terminal repeats from rat intracisternal A-particles

Nucleotide sequences of three novel rat long terminal repeats (LTR) of intracisternal A-particles (IAP) were determined and compared with two previously published solitary rat IAP LTRs from the genomic clone H12 (Furter et al. (1989) J. Biol. Chem. 264, 18276-18279) and from the upstream region of the oncomodulin (OM) gene (Banville and Boie (1989) J. Mol. Biol. 207, 481-490). These five LTRs have a length of 286 to 370 bp and show the major variability within the U3 region. The CCAAT and the TATA boxes, the AATAAA polyadenylation signals and the CA polyadenylation sites are well conserved in sequence and position in all five LTRs, whereas several putative transcriptional factor binding sites in the U3 domain show considerable heterogeneity. The transcriptional activities of three LTRs were tested in transient gene expression assays using the human growth hormone (hGH) reporter gene in chemically transformed T14c cells which produce considerable amounts of oncomodulin. Promoter strengths of the three investigated LTRs varied considerably.

Selective activation of a discrete family of endogenous proviral elements in normal BALB/c lymphocytes

Intracisternal A-particle (IAP) proviral elements are abundant and widely dispersed in the mouse genome. IAP-related transcripts have been detected in normal mouse tissues where expression is under genetic control. In this study, we sought to determine whether IAP expression in BALB/c thymus and lipopolysaccharide-stimulated B cells was due to selective or indiscriminate activation of IAP elements. cDNA libraries were prepared from each source. A total of 86 IAP cDNA clones were isolated from both libraries, and 37 of these were sequenced over a common 0.7- to 1.0-kb region of the IAP genome that included the 3' long terminal repeat (LTR). Three highly related families of elements were found to be expressed in the two cell types examined. All of the related elements had a distinctive U3 regulatory region. Thirteen individual IAP proviral elements were distinguished on the basis of sequence differences within the R region of the LTR. Hybridization of genomic DNA with element-specific oligonucleotide probes confirmed the presence of a restricted number of proviral copies in the lymphocyte-specific family of elements. Most of these copies were found to be methylated in the lymphocyte DNA, but at least seven were hypomethylated in their 5' LTRs. This study shows that activation of IAP elements in normal normal mouse lymphocytes is highly selective. Activation is probably a function of both sequence specificity and methylation status of the proviral LTR.

Selective activation of a discrete family of endogenous proviral elements in normal BALB/c lymphocytes

Intracisternal A-particle (IAP) proviral elements are abundant and widely dispersed in the mouse genome. IAP-related transcripts have been detected in normal mouse tissues where expression is under genetic control. In this study, we sought to determine whether IAP expression in BALB/c thymus and lipopolysaccharide-stimulated B cells was due to selective or indiscriminate activation of IAP elements. cDNA libraries were prepared from each source. A total of 86 IAP cDNA clones were isolated from both libraries, and 37 of these were sequenced over a common 0.7- to 1.0-kb region of the IAP genome that included the 3' long terminal repeat (LTR). Three highly related families of elements were found to be expressed in the two cell types examined. All of the related elements had a distinctive U3 regulatory region. Thirteen individual IAP proviral elements were distinguished on the basis of sequence differences within the R region of the LTR. Hybridization of genomic DNA with element-specific oligonucleotide probes confirmed the presence of a restricted number of proviral copies in the lymphocyte-specific family of elements. Most of these copies were found to be methylated in the lymphocyte DNA, but at least seven were hypomethylated in their 5' LTRs. This study shows that activation of IAP elements in normal normal mouse lymphocytes is highly selective. Activation is probably a function of both sequence specificity and methylation status of the proviral LTR.

Intracisternal A-particle-specific oligonucleotides provide multilocus probes for genetic linkage studies in the mouse

Oligonucleotide probes representing distinct intracisternal A-particle (IAP) subfamilies were derived from the long terminal repeats (LTRs) of transcriptionally active IAP genes in normal mouse cells. These probes were used to examine the distribution of IAP proviral elements in the genomic DNA of several inbred mouse strains. Each oligonucleotide probe identified multiple polymorphisms between the different strains. The distribution of polymorphic restriction fragments among the CXB set of recombinant inbred (RI) strains demonstrates the feasibility of using these probes for chromosome mapping. These and other subset-specific IAP probes can provide a useful series of multilocus markers for genomic mapping and genetic analysis in the mouse.

Intracisternal A-type particle-mediated activations of cytokine genes in a murine myelomonocytic leukemia: generation of functional cytokine mRNAs by retroviral splicing events

Previously we have described the derivation of three distinct classes of leukemic cell clones from a single in vivo-passaged myelomonocytic leukemia, WEHI-274, that arose in a mouse infected with the Abelson leukemia virus/Moloney leukemia virus complex (K. B. Leslie and J. W. Schrader, Mol. Cell. Biol. 9:2414-2423, 1989). The three classes of cell clones were characterized by distinct patterns of growth in vitro, the production of cytokines, and the presence of cytokine gene rearrangements. However, all three classes of WEHI-274 clones bore a common rearrangement of the c-myb gene, suggesting that all were derived from the one ancestral cell and that at least three distinct and independent autostimulatory events were involved in the progression of a single myeloid leukemic disease. In this article, we demonstrate that the autocrine growth factor production by the WEHI-274 leukemic clones resulted from cytokine gene activations mediated by the insertion of an intracisternal A-type particle (IAP) sequence 5' to the interleukin-3 (IL-3) gene, in the case of the class I clone, or 5' to the gene for granulocyte-macrophage colony-stimulating factor (GM-CSF), in the case of the class II clones. IAPs are defective murine retroviruses encoded by endogenous genetic elements which may undergo transpositions and act as endogenous mutagens. The functional IL-3 and GM-CSF mRNAs were generated by mechanisms in which the splice donor apparatus of the IAP sequence has been used in IAP gag-to-IL-3 or -GM-CSF splicing events.

Intracisternal A-type particle-mediated activations of cytokine genes in a murine myelomonocytic leukemia: generation of functional cytokine mRNAs by retroviral splicing events

Previously we have described the derivation of three distinct classes of leukemic cell clones from a single in vivo-passaged myelomonocytic leukemia, WEHI-274, that arose in a mouse infected with the Abelson leukemia virus/Moloney leukemia virus complex (K. B. Leslie and J. W. Schrader, Mol. Cell. Biol. 9:2414-2423, 1989). The three classes of cell clones were characterized by distinct patterns of growth in vitro, the production of cytokines, and the presence of cytokine gene rearrangements. However, all three classes of WEHI-274 clones bore a common rearrangement of the c-myb gene, suggesting that all were derived from the one ancestral cell and that at least three distinct and independent autostimulatory events were involved in the progression of a single myeloid leukemic disease. In this article, we demonstrate that the autocrine growth factor production by the WEHI-274 leukemic clones resulted from cytokine gene activations mediated by the insertion of an intracisternal A-type particle (IAP) sequence 5' to the interleukin-3 (IL-3) gene, in the case of the class I clone, or 5' to the gene for granulocyte-macrophage colony-stimulating factor (GM-CSF), in the case of the class II clones. IAPs are defective murine retroviruses encoded by endogenous genetic elements which may undergo transpositions and act as endogenous mutagens. The functional IL-3 and GM-CSF mRNAs were generated by mechanisms in which the splice donor apparatus of the IAP sequence has been used in IAP gag-to-IL-3 or -GM-CSF splicing events.

Identification of a novel murine IAP-promoted placenta-expressed gene

We have cloned and characterized a novel cellular gene that is promoted by an intracisternal A-particle (IAP) LTR and expressed in the mouse placenta (mouse IAP promoted placental gene, MIPP). A 1067bp cDNA clone containing an IAP LTR U5 region duplicated in its 5' terminus and an ORF coding for a potential 202 amino acids protein was isolated from an 8.5 day old mouse embryo cDNA library. Sequence analysis of the 5' region of a genomic clone revealed the presence of a solo IAP LTR with the same U5 duplication, and primer extension analysis confirmed that transcription of the MIPP gene is under the control of the IAP LTR. Expression of the MIPP gene parallels that of IAP genes in normal mouse tissues with abundant transcripts present in the placenta and also in the myeloma MOPC-315. The MIPP-encoded protein is composed of four 48-amino acid repeat units and shares homology with a vaccinia virus gene product. MIPP-related sequences were also detected in higher eukaryotic genomes including human.

Retrotransposition of a mouse IAP sequence tagged with an indicator gene

We have marked a cloned mouse IAP sequence with a neomycin-containing indicator gene whose expression is conditioned by passage of the transposon through an RNA intermediate. Transposition of the marked IAP introduced into tumor cells could be detected by simple selection of the cells in G418, at a frequency of 10(-6) per cell per generation. Southern blot analysis and nucleotide sequencing after PCR amplification demonstrated "retrotransposition" of the marked element, with splicing out of an intron contained in the indicator gene, and retroviral-like reverse transcription and integration of the transposed IAPs, with 6 bp duplications of the identified target sites. Transposition was found to be mutagenic for the element, as might be expected if the identified marked and endogenous IAP transcripts were coencapsidated into IAP particles as dimers.

CpG methylation of an endogenous retroviral enhancer inhibits transcription factor binding and activity

The endogenous retrovirus, intracisternal A-particle (IAP), is expressed at unique stages during murine embryogenesis and is also activated during the in vitro differentiation of F9 cells. We have examined the DNA elements and protein factors that control IAP expression during F9 differentiation. In the present study an IAP upstream enhancer (IUE) is identified by transient transfection assays and found to be active in both undifferentiated and differentiated cells. Further analyses reveal that a ubiquitous 65 kDa protein factor, the IUE binding protein (IUEB), binds with the IUE. Site-specific methylation within the IUEB binding site strongly inhibits both IUEB binding and IUE transcriptional activity, suggesting that methylation may regulate IUE function and IAP expression.

The angiotensinogen gene of Swiss mice is closely linked to a retrovirus-like element

Angiotensinogen is cleaved by renin and angiotensin-converting enzyme to liberate the potent vasocontrictor peptide angiotensin II. We have recently identified a cis-acting genetic lesion associated with high levels of angiotensinogen mRNA in the testis and salivary gland of Swiss mice. To determine the molecular basis of this mutation, the Swiss angiotensinogen gene was cloned, and its structure was compared to that from a low-expressing strain (BALB/c). I show that a retrovirus-like element belonging to the intracisternal A-particle gene family has been inserted 9 kb upstream from the cap site of the Swiss angiotensinogen gene. This intracisternal A-particle, named IAP-Agt, segregated concordantly with angiotensinogen expression phenotypes in CXB recombinant inbred mice. However, genomic Southern analysis showed that IAP-Agt was present in some, but not all, inbred laboratory mouse strains displaying high levels of angiotensinogen gene expression. On the basis of this evolutionary evidence, it is unlikely that IAP-Agt is the cause of the angiotensinogen mutation. It is intriguing that Ren-2, the duplicated mouse renin gene, is expressed to high levels in the male salivary gland and also contains a transposed intracisternal A-particle genome.

Functional murine interleukin 6 receptor with the intracisternal A particle gene product at its cytoplasmic domain. Its possible role in plasmacytomagenesis

Two species of the cDNAs encoding murine IL-6-R (one is abnormal and the other authentic) have been cloned from a plasmacytoma cell line, P3U1, and BALB/c mouse spleen cDNA libraries. In the cDNA encoding the abnormal IL-6-R, the region corresponding to an intracytoplasmic domain was replaced with a part of the long terminal repeat of the intracisternal A particle gene (IAP-LTR). The authentic IL-6-R consists of 460 amino acids with the domain of the Ig superfamily. The overall homology between murine and human IL-6-R was 69 and 54% at DNA and protein levels, respectively. The extracellular domain after the Ig-like domain of murine IL-6-R was found to have an homology with those of murine erythropoietin R, human IL-2-R beta chain, murine IL-4-R, and human granulocyte-macrophage CSF-R, as in the case of human IL-6-R, and these receptors have been classified as members of the IL receptor family. In P3U1 cells, the expression of the mRNA encoding abnormal IL-6-R was much higher than that of the mRNA encoding authentic IL-6-R. An IL-6-dependent human T cell line, KT-3, which did not respond to murine IL-6, acquired the responsiveness to murine IL-6 when transfected with the cDNA encoding abnormal IL-6-R, indicating that abnormal IL-6-R lacking a normal cytoplasmic domain can function. Since IL-6 functions as a potent growth factor for murine plasmacytomas, over-expression of abnormal IL-6-R may function as a positive selection element for the development of certain plasmacytomas.

Potential retroviral RNAs in Creutzfeldt-Jakob disease

The molecular nature of the related infectious agents that cause Creutzfeldt-Jakob disease (CJD) and scrapie is poorly understood, and an agent-specific nucleic acid genome has not yet been identified. Several biological manifestations of these agents resemble those seen in retrovirus-induced diseases. We therefore attempted to identify an agent-specific retrovirus-like RNA transcript in CJD infectious fractions. A series of synthetic oligonucleotides complementary to known mammalian retroviral primer binding sites were used in a primer extension assay. Substrate nucleic acids isolated from partially purified hamster brain CJD infectious fractions and from parallel normal brain fractions were compared with total starting brain RNA. This sensitive exogenous strong-stop reaction revealed that CJD infectious fractions contained a series of potential retroviral RNAs including apparent transcripts of endogenous hamster IAP genes. Most transcripts selectively recovered in the fractions were substantially protected from micrococcal nuclease digestion, and at least one substrate RNA, consistent with an intracisternal A particle, was packaged in a form that had the same buoyant density as CJD infectivity. Although a completely CJD-specific transcript was not identified, the copurification of potential retroviral transcripts with CJD infectivity suggests that models of disease involving retrovirus-like nucleic acid elements deserve further consideration.

Characterization of the long terminal repeats of micropia elements microdissected from the Y-chromosomal lampbrush loops "threads" of Drosophila hydei

Four micropia elements from Drosophila melanogaster and D. hydei have been analysed by sequencing. Two elements, from D. hydei, micropia-DhMiF8 and -DhMiF2, were recovered by cloning microdissected Y-chromosomal lampbrush loops "threads". This method allows isolation of repetitive sequences from defined chromosomal positions, but recovery of large and overlapping inserts is difficult. In case of the Y-chromosomal micropia elements it was not possible to define the endpoints of their long terminal repeat sequences precisely. Comparison of these locus-defined micropia elements to complete micropia elements isolated from D. melanogaster allowed identification of micropia-DhMiF8 and micropia-DhMiF2 long terminal repeats (LTRs). LTR sequences from the two Drosophila species are not conserved except for a few short sequences found at comparable positions that are believed to have functional significance. In contrast, the Leu-tRNA primer binding site and plus strand primer binding site are conserved between D. melanogaster and D. hydei.

Activation and demethylation of the intracisternal A particle genes by 5-azacytidine

Treatment of C3H 10T1/2 mouse embryo fibroblasts with the cytidine analogues 5-azacytidine and 5-aza-2-deoxycytidine causes altered gene expression and results in the manifestation of phenotypic changes and altered cell morphology. This includes the conversion of these cells to adipocytes, chondrocytes and myotubes. The effects of these analogues on intracisternal A particle (IAP) gene expression in mouse C3H 10T1/2 cells have been examined. Treatment with either 3 microM 5-azacytidine or 0.3 microM 5-aza-2-deoxycytidine for 24 h was associated with an immediate increase in IAP gene transcription, and with the subsequent appearance of IAPs in the cisternae of the cells 24 h after removal of the drug. Control cells contained no, or very few, IAPs and IAP mRNA. Analysis of the methylation status of the IAP genes, using the restriction endonucleases HpaII, MspI and HhaI, showed that these genes were already demethylated at the end of the 24-h treatment period. IAP gene transcripts were detectable even after a 16-h drug treatment period, at which stage the genes were not yet fully demethylated. After further growth in fresh medium for 90 h, the levels of IAP RNA started to decline, but the demethylated CpG sites were not yet remethylated. These results suggest the involvement of other factors, in addition to methylation, in the regulation of IAP gene expression. These drugs were found to have no stimulatory effect on several oncogenes examined in this study.

Micropia: a retrotransposon of Drosophila combining structural features of DNA viruses, retroviruses and non-viral transposable elements

The retrotransposon micropia was first described from Y-chromosomal fertility genes of Drosophila hydei. Screening a Drosophila melanogaster genomic library yielded several clones representing micropia elements in D. melanogaster. The DNA sequences of two elements from D. hydei (micropia-DhMiF2 and micropia-DhMiF8) and two elements from D. melanogaster (micropia-Dm2 and micropia-Dm11) permitted a detailed analysis of the spatial organization of micropia constituents. Micropia represents the typical gene organization represented by "core"-protein domains followed by a protease, reverse transcriptase, RNase and integrase domain. New features of the micropia family compared with other retrotransposons are: (1) a region of similarity to class I major histocompatibility complex antigens of mammals; (2) only one main open reading frame of about 4000 bases length; (3) a non-protein-coding region of about 500 base-pairs length between the 3' end of the open reading frame and the 5' start of the 3' long terminal repeat. This region includes 32 base-pair tandem repeats; (4) within the long terminal repeats, 82 base-pair tandem repeats with four potential ecdysteroid receptor binding sites. Because micropia combines many evolutionary features of different viruses, non-viral transposable elements, chromosomal genes and repetitive sequence organizations, this retrotransposon may be seen as a "minigenome" reflecting evolutionary principles of the construction of genomic components.

Multiple protein-binding sites in an intracisternal A particle long terminal repeat

The long terminal repeats (LTRs) of cloned intracisternal A particles (IAPs) can function as effective promoters in heterologous and homologous cell types (K. K. Lueders, J. W. Fewell, E. L. Kuff, and T. Koch, Mol. Cell. Biol. 4:2128-2135, 1984) and respond to transcriptional factors induced by various nuclear oncogene products (S. Luria and M. Horowitz, J. Virol. 57:998-1003, 1986). Using the first 139 base pairs of the U3 region of a cloned mouse IAP LTR as probe, we demonstrated multiple exonuclease III stop sites which appeared specifically in the presence of nuclear extract protein. Various extracts gave similar footprints, but the amount of nuclear protein required varied up to 10-fold. Cell lines transformed with known nuclear oncogenes, such as adenovirus E1a and E1b (293 cells), simian virus 40 large T antigen (COS7 cells), and c-myc (MOPC-315 cells) had more and/or higher-affinity factors for the IAP LTR than extracts from HeLa, CV1, and NIH 3T3 cells did. DNase I footprinting revealed at least five distinct protein-binding domains within the 139-base-pair region. These domains correspond to segments of highly conserved nucleotide sequence among a number of IAP LTRs. Gel retardation studies with oligonucleotides encompassing the DNase I footprint sites showed that the nuclear factors are present in different proportions and different absolute levels in extracts from different cell types. Moreover, the oligonucleotide probes indicate that individual motifs can be occupied independently of one another. Three of the DNase I footprints include a sequence with homology to the simian virus 40 core enhancer and sequence motifs that closely resemble the binding sites for transcription factors SP1 and AP-1. The other two binding sites are not obviously related to previously recognized motifs. The multiple protein-binding sites in close proximity indicate the complex regulatory mechanism for IAP transcription.

Identification of genes involved in growth autonomy of hematopoietic cells by analysis of factor-independent mutants

The factor-dependent myeloid precursor cell line D35 mutates spontaneously at a frequency greater than 2.4 x 10(-7) to growth factor autonomy. This frequency could be increased at least 20-fold by retrovirus insertional mutagenesis. The isolation and characterization of factor-independent mutants allowed the identification of genes involved in growth autonomy. Mutants could be subdivided into two sets: those that secreted a stimulating factor (10/11) and those that did not (1/11). In one case, the factor released was distinct from previously characterized growth factors. In most mutants (6/9), the activation of a growth factor gene was associated with rearrangement that could be attributed to the insertion of a transposable-like element either 5' or 3' of the factor coding region in all cases examined, excluding oncogene involvement. All factor-independent mutants were tumorigenic, consistent with the hypothesis that growth-factor independence initiated by aberrant growth factor gene activation is an important and early step in tumorigenesis.

Functional analysis of the long terminal repeats of intracisternal A-particle genes: sequences within the U3 region determine both the efficiency and direction of promoter activity

The transcriptional activity of five intracisternal A-particle (IAP) long terminal repeats (LTRs) in mouse embryonal carcinoma PCC3-A/1 cells and in Ltk- cells was determined. We tested the promoter activity of the LTRs by coupling them to the reporter gene chloramphenicol acetyltransferase (CAT) or guanosine-xanthine phosphoribosyltransferase (gpt). Each LTR was tested for promoter function in both the sense (5' to 3') and antisense (3' to 5') orientation preceding the reporter gene. The transcriptional activity of individual IAP gene LTRs varied considerably, and the LTR from IAP81 possessed promoter activity in both directions. The bidirectional activity of the IAP81 LTR confirmed by monitoring Ecogpt expression in stably transfected Ltk- cells, with the initiation sites for sense and antisense transcription being localized to within the IAP81 LTR by S1 nuclease mapping. Deletions of LTR81 show that for normal 5'-to-3' gene transcription (sense direction), the 3'U3/R region determines the basal level of transcription, whereas sequences within the 5'U3 region enhance transcription four- to fivefold. Deletion mapping for antisense transcription indicates that a 64-base-pair region (nucleotides 47 to 110) within the U3 region is essential for activity. These data indicate that the U3 region contains all the regulatory elements for bidirectional transcription in IAP LTRs.

Functional analysis of the long terminal repeats of intracisternal A-particle genes: sequences within the U3 region determine both the efficiency and direction of promoter activity

The transcriptional activity of five intracisternal A-particle (IAP) long terminal repeats (LTRs) in mouse embryonal carcinoma PCC3-A/1 cells and in Ltk- cells was determined. We tested the promoter activity of the LTRs by coupling them to the reporter gene chloramphenicol acetyltransferase (CAT) or guanosine-xanthine phosphoribosyltransferase (gpt). Each LTR was tested for promoter function in both the sense (5' to 3') and antisense (3' to 5') orientation preceding the reporter gene. The transcriptional activity of individual IAP gene LTRs varied considerably, and the LTR from IAP81 possessed promoter activity in both directions. The bidirectional activity of the IAP81 LTR confirmed by monitoring Ecogpt expression in stably transfected Ltk- cells, with the initiation sites for sense and antisense transcription being localized to within the IAP81 LTR by S1 nuclease mapping. Deletions of LTR81 show that for normal 5'-to-3' gene transcription (sense direction), the 3'U3/R region determines the basal level of transcription, whereas sequences within the 5'U3 region enhance transcription four- to fivefold. Deletion mapping for antisense transcription indicates that a 64-base-pair region (nucleotides 47 to 110) within the U3 region is essential for activity. These data indicate that the U3 region contains all the regulatory elements for bidirectional transcription in IAP LTRs.