Structure of the highly repeated, long interspersed DNA family (LINE or L1Rn) of the rat

The housekeeping gene (GA3PDH) and the long interspersed nuclear element (LINE) in the blood and organs of rats treated with cocaine

Housekeeping genes are necessary for maintenance of the vital activity of the cells of any phylum of organisms. Transposons or mobile genetic elements are eurysynusic in nature. Thus, the role of these and other genes in the pathogenesis of many diseases and of drug addiction in particular is being investigated. The goal of the work is to determine the influence of cocaine on the activity of GA3PDH and on a representative of the LINE family (L1Rn) in plasma, and in a pellet of blood cells, and in the organs of rats. Gene expression was evaluated by RT-PCR. The GA3PDH (452-bp fragment) was predictably found in plasma, in a pellet of blood cells, and in organs. Its quantity in plasma was greater in the experimental groups than in the control. In a pellet of blood cells and in organs, the GA3PDH activity between the different groups of animals essentially did not differ. The L1Rn fragment (319 bp) in plasma was not found. The expression of L1Rn was much higher in a pellet of blood cells and in organs of experimental animals. These experiments have shown the presence of GA3PDH in the plasma of the controls and an increase in quantity in the plasma of experimental animals. The activation of LINE in a pellet of blood cells of rats and in organs under the influence of cocaine has been demonstrated. Apparently, a recruitment phenomenon of housekeeping genes and transposons is possible in the pathogenesis of drug addiction.

Functional endogenous LINE-1 retrotransposons are expressed and mobilized in rat chloroleukemia cells

LINE-1 (L1) is a highly successful autonomous non-LTR retrotransposon and a major force shaping mammalian genomes. Although there are about 600 000 L1 copies covering 23% of the rat genome, full-length rat L1s (L1Rn) with intact open reading frames (ORFs) representing functional master copies for retrotransposition have not been identified yet. In conjunction with studies to elucidate the role of L1 retrotransposons in tumorigenesis, we isolated and characterized 10 different cDNAs from transcribed full-length L1Rn elements in rat chloroleukemia (RCL) cells, each encoding intact ORF1 proteins (ORF1p). We identified the first functional L1Rn retrotransposon from this pool of cDNAs, determined its activity in HeLa cells and in the RCL cell line the cDNAs originated from and demonstrate that it is mobilized in the tumor cell line in which it is expressed. Furthermore, we generated monoclonal antibodies directed against L1Rn ORF1 and ORF2-encoded recombinant proteins, analyzed the expression of L1-encoded proteins and found ORF1p predominantly in the nucleus. Our results support the hypothesis that the reported explosive amplification of genomic L1Rn sequences after their transcriptional activation in RCL cells is based on L1 retrotransposition. Therefore, L1 activity might be one cause for genomic instability observed during the progression of leukemia.

X accumulation of LINE-1 retrotransposons in Tokudaia osimensis, a spiny rat with the karyotype XO

The observation that LINE-1 transposable elements are enriched on the X in comparison to the autosomes led to the hypothesis that LINE-1s play a role in X chromosome inactivation. If this hypothesis is correct, loss of LINE-1 activity would be expected to result in species extinction or in an alternate pathway of dosage compensation. One such alternative pathway would be to evolve a karyotype that does not require dosage compensation between the sexes. Two of the three extant species of the Ryukyu spiny rat Tokudaia have such a karyotype; both males and females are XO. We asked whether this karyotype arose due to loss of LINE-1 activity and thus the loss of a putative component in the X inactivation pathway. Although XO Tokudaia has no need for dosage compensation, LINE-1s have been recently active in Tokudaia osimensis and show higher density on the lone X than on the autosomes.

Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents

LINE-1 transposable elements (L1s) are ubiquitous in mammals and are thought to have remained active since before the mammalian radiation. Only one L1 extinction event, in South American rodents in the genus Oryzomys, has been convincingly demonstrated. Here we examine the phylogenetic limits and evolutionary tempo of that extinction event by characterizing L1s in related rodents. Fourteen genera from five tribes within the Sigmodontinae subfamily were examined. Only the Sigmodontini, the most basal tribe in this group, demonstrate recent L1 activity. The Oryzomyini, Akodontini, Phyllotini, and Thomasomyini contain only L1s that appear to have inserted long ago; their L1s lack open reading frames, have mutations at conserved amino acid residues, and show numerous private mutations. They also lack restriction site-defined L1 subfamilies specific to any species, genus or tribe examined, and fail to form monophyletic species, genus or tribal L1 clusters. We determine here that this L1 extinction event occurred roughly 8.8 million years ago, near the divergence of Sigmodon from the remaining Sigmodontinae species. These species appear to be ideal model organisms for studying the impact of L1 inactivity on mammalian genomes.

Characterization of rat heme oxygenase-3 gene. Implication of processed pseudogenes derived from heme oxygenase-2 gene

Heme oxygenase (HO) is an enzyme responsible for the physiological degradation of heme to produce iron, CO and biliverdin. The released iron is recycled and represents the major source of this metal in heme homeostasis. A putative role as messenger in a signaling pathway is suggested for CO. Biliverdin, together with bilirubin, may function as an antioxidant. Thus far, three isoforms of HO, HO-1, HO-2 and HO-3 have been described. While HO-1 and HO-2 have been extensively investigated, HO-3 is still an elusive and poorly understood isoform. In this study, we examined the structure of the rat HO-3 gene with genomic PCR. However, we failed to isolate the reported HO-3 gene but, instead, found two HO-3-related genes, tentatively named HO-3a and HO-3b, whose sequences differed slightly from each other. Neither gene had any introns and consisted only of exon 2 through 5 of the HO-2 gene, though their sequences were not completely identical with that of HO-2. A stop codon was introduced within the coding regions of these genes due to frame-shift. The nucleotide sequence of their 5'-upstream region largely agreed with long interspersed nuclear element 3. No HO-3-related mRNAs were amplified by RT-PCR, and no HO-3-related proteins were detected in tissues by Western blot analysis. Our results suggested that there are no functional HO-3 genes in rat and that the HO-3a and HO-3b genes are processed pseudogenes derived from HO-2 transcripts.

Mouse euchromatin specific "genome-painting" with a LINE probe: a rapid method for identification and mapping of human chromosomes in mouse-human microcell hybrids by two-color FISH

We describe the use of a long interspersed repetitive sequence (mCPE1.51) for mouse euchromatin specific "genome-painting". In fluorescence in situ hybridization (FISH) experiments, this probe was suitable for identification of the mouse genome and disclosure of translocations of mouse chromosome segments to chromosomes of different species without suppression hybridization. The euchromatin specificity of the probe allowed the discrimination between euchromatin and heterochromatin of mouse chromosomes. Simultaneous hybridization of the biotinylated mouse specific genome-painting probe and a digoxigenin-labeled human chromosome 3-specific cosmid probe to metaphase spreads of mouse-human microcell hybrid carrying a single deleted human chromosome 3 on a mouse fibrosarcoma background, allowed rapid identification and mapping of human chromosome 3.

Differentially expressed genes in the liver of thioacetamide treated rats

Thioacetamide is a hepatotoxic and hepatocarcinogenic compound that affects liver metabolism, inhibits mRNA transport and induces enlargement of the nucleolus. To investigate the effect of thioacetamide at the molecular level, differential display RT-PCR was conducted. Analysis of nineteen differentially expressed genes demonstrated that ten cDNAs have their expression inhibited while the other nine were positively affected by thioacetamide. Two of the cDNAs were homologous to known genes-TAP and ankyrin-binding glycoprotein-1, two corresponded to repetitive sequences and seven were homologous to expressed sequence tags. The differential expression of some of the isolated cDNAs was confirmed by northern hybridization. It is proposed that since the product of TAP is involved in mRNA transport, thioacetamide inhibition of TAP expression might, at least partially, explain the thioacetamide-induced swelling of the nucleolus.

Genomic structure of the rat and mouse histamine N-methyltransferase gene

Northern blotting analysis revealed different tissue distribution patterns of HMT mRNA between mice and rats. In the mouse, mRNA expression was detected in the brain, kidney and liver. In the rat, there was an extremely high mRNA signal only in the kidney. We isolated and characterized the rat and mouse histamine N-methyltransferase (HMT) genes from genomic DNA libraries. The rat HMT gene consists of 6 exons and 5 introns. The mouse HMT gene structure was similar to that of the rat, but had one additional exon 5' upstream from the exon containing a start codon, resulting in seven exons. Several long interspersed repetitive elements were located in the 5' flanking region of the rat and mouse HMT gene. Despite high sequence conservation of the regions around exon 6 and the 3' flanking region, the 5' flanking region had little similarity between the rat and mouse. Marked sequence similarities between rat and mouse introns were present near splice sites and outside the junction residues, suggesting the evolutionary relationship between the structural features of the rat and mouse HMT genes. This observation may explain the species difference of the tissue expression pattern of HMT mRNA.

L1 (LINE-1) retrotransposon evolution and amplification in recent human history

L1 (LINE-1) elements constitute a large family of mammalian retrotransposons that have been replicating and evolving in mammals for more than 100 Myr and now compose 20% or more of the DNA of some mammals. Here, we investigated the evolutionary dynamics of the active human Ta L1 family and found that it arose approximately 4 MYA and subsequently differentiated into two major subfamilies, Ta-0 and Ta-1, each of which contain additional subsets. Ta-1, which has not heretofore been described, is younger than Ta-0 and now accounts for at least 50% of the Ta family. Although Ta-0 contains some active elements, the Ta-1 subfamily has replaced it as the replicatively dominant subfamily in humans; 69% of the loci that contain Ta-1 inserts are polymorphic for the presence or absence of the insert in human populations, as compared with 29% of the loci that contain Ta-0 inserts. This value is 90% for loci that contain Ta-1d inserts, which are the youngest subset of Ta-1 and now account for about two thirds of the Ta-1 subfamily. The successive emergence and amplification of distinct Ta L1 subfamilies shows that L1 evolution has been as active in recent human history as it has been found to be for rodent L1 families. In addition, Ta-1 elements have been accumulating in humans at about the same rate per generation as recently evolved active rodent L1 subfamilies.

The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons

Mammalian LINE-1 (L1) elements belong to the superfamily of autonomously replicating retrotransposable elements that lack the long terminal repeated (LTR) sequences typical of retroviruses and retroviral-like retrotransposons. The non-LTR superfamily is very ancient and L1-like elements are ubiquitous in nature, having been found in plants, fungi, invertebrates, and various vertebrate classes from fish to mammals. L1 elements have been replicating and evolving in mammals for at least the past 100 million years and now constitute 20% or more of some mammalian genomes. Therefore, L1 elements presumably have had a profound, perhaps defining, effect on the evolution, structure, and function of mammalian genomes. L1 elements contain regulatory signals and encode two proteins: one is an RNA-binding protein and the second one presumably functions as an integrase-replicase, because it has both endonuclease and reverse transcriptase activities. This work reviews the structure and biological properties of L1 elements, including their regulation, replication, evolution, and interaction with their mammalian hosts. Although each of these processes is incompletely understood, what is known indicates that they represent challenging and fascinating biological phenomena, the resolution of which will be essential for fully understanding the biology of mammals.

Galectin-3 and L1 retrotransposons in human breast carcinomas

Galectin-3 is a galactoside binding protein found at elevated levels in a wide variety of neoplastic cells and thought to be involved in cognitive cellular interactions during transformation and metastasis. Previously, we have shown that introduction of human galectin-3 (Mr 31,000) cDNA into the human breast cancer cells BT-549 which are galectin-3 null and non-tumorigenic in nude mice resulted in the establishment of four galectin-3 expressing clones. Three of them acquired tumorigenicity when inoculated in the mammary fat pad of nude mice. Here, we questioned what is the molecular difference between the nude mouse tumorigenic and non-tumorigenic galectin-3 expressing BT-549 cell clones. Differential display analysis and Northern blotting revealed that, unlike the tumorigenic clones, neither the parental cells nor the non-tumorigenic clone expressed a 6.5 Kb transcript. A 607 bp PCR (polymerase chain reaction) product from the differentially displayed mRNA revealed a 93% sequence homology with the human L1 retrotransposon previously suggested to play a role in the pathobiology of some breast cancers. In addition, we show that the two gene products, i.e., galectin-3 and L1, are co-expressed in breast carcinoma specimens and in other nude mouse tumorigenic cell lines.

Rapid evolution of a young L1 (LINE-1) clade in recently speciated Rattus taxa

L1 elements are retrotransposons that have been replicating and evolving in mammalian genomes since before the mammalian radiation. Rattus norvegicus shares the young L1mlvi2 clade only with its sister taxon, Rattus cf moluccarius. Here we compared the L1mlvi2 clade in these recently diverged species and found that it evolved rapidly into closely related but distinct clades: the L1mlvi2-rm clade (or subfamily), characterized here from R. cf moluccarius, and the L1mlvi2-rn clade, originally described in R. norvegicus. In addition to other differences, these clades are distinguished by a cluster of amino acid replacement substitutions in ORF I. Both rat species contain the L1mlvi2-rm clade, but the L1mlvi2-rn clade is restricted to R. norvegicus. Therefore, the L1mlvi2-rm clade arose prior to the divergence of R. norvegicus and R. cf moluccarius, and the L1mlvi2-rn clade amplified after their divergence. The total number of L1mlvi2-rm elements in R. cf moluccarius is about the same as the sum of the L1mlvi2-rm and L1mlvi2-rn elements in R. norvegicus. The possibility that L1 amplification is in some way limited so that the two clades compete for replicative supremacy as well as the implications of the other distinguishing characteristic of the L1mlvi2-rn and L1mlvi2-rm clades are discussed.

Isolation and characterization of a cDNA from the rat brain that encodes hemoprotein heme oxygenase-3

Two isozymes of heme oxygenase (HO), HO-1 or HSP32 and the constitutive form HO-2, have been characterized to date. We report the discovery of a third protein species and refer to it as HO-3. HO-3 is the product of a single transcript of approximately 2.4 kb and can encode a protein of approximately 33 kDa. The HO-3 transcript is found in the spleen, liver, thymus, prostate, heart, kidney, brain and testis and is the product of a single-copy gene. The predicted amino acid structure of HO-3 differs from both HO-1 (HSP32) and HO-2 but is closely related to HO-2 (approximately 90%). Escherichia coli expressed and purified HO-3 protein does not cross react with polyclonal antibodies to either rat HO-1 or HO-2, is a poor heme catalyst, and displays hemoprotein spectral characteristics. The predicted protein has two heme regulatory motifs that may be involved in heme binding. These motifs and the hemoprotein nature of HO-3 suggest a potential regulatory role for the protein in cellular processes which are heme-dependent.

Cloning and characterization of the promoter region of a gene encoding a 67-kDa glycoprotein

A rat genomic library constructed in lambda-EMBL3 (SP6/T7) vector () was screened using 32P-labeled rat p67 cDNA. A clone containing a segment of 5'-upstream region of p67 genomic DNA was obtained. The DNA (about 1.7 kilobase pairs) was isolated and characterized. Sequence analysis of this DNA fragment showed that the 898 base pairs at the 5'-end of the upstream region was identical to several long interspersed nucleotide sequences. One hundred forty-eight base pairs at the 3'-end contained the beginning of the first exon including the ATG initiator codon. The remaining 652 base pairs in between contained two AT-rich regions and several regulatory sequences. The mRNA initiation site was identified at 89 base pairs upstream from the translation start codon. The DNA fragment was also analyzed by transient transfection. When linked to a firefly luciferase reporter gene, this fragment enhanced transcription in a rat hepatoma cell line (KRC-7). Using a series of deletions in the DNA, the minimum essential promoter region (from -177 to -60) was identified. The promoter activity was also enhanced by treatment with phorbol 13-myristate 12-acetate (PMA). This enhancement required an AP-1 sequence (-298 to -292; 5'-TGACTCA-3') and a similar sequence (-97 to -88; 5'-ATGACATCAT-3'). Deletion of either of these sequences significantly reduced PMA enhancement. Deletion of both of these sequences almost completely eliminated PMA enhancement.

Linkage map and congenic strains to localize blood pressure QTL on rat chromosome 10

Our purposes were to develop a linkage map for rat Chromosome (Chr) 10, using chromosome-sorted DNA, and to construct congenic strains to localize blood pressure quantitative trait loci (QTL) on Chr 10 with the map. The linkage mapping panel consisted of three F2 populations totaling 418 rats. Thirty-two new and 29 known microsatellite markers were placed on the map, which spanned 88.9 centiMorgans (cM). The average distance between markers was 1.46 cM. No markers were separated by more than 6.8 cM. Four congenic strains were constructed by introgressing various segments of Chr 10 from the Milan normotensive strain (MNS) onto the background of the Dahl salt-sensitive (S) strain. A blood pressure QTL with a strong effect on blood pressure (35-42 mm Hg) when expressed on the S background was localized to a 31-cM region between D10Mco6 and D10Mcol. The region does not include the locus for inducible nitric oxide synthase (Nos2), which had been considered to be a candidate locus for the QTL.

The Chironomus (Camptochironomus) tentans genome contains two non-LTR retrotransposons

A cDNA library from salivary gland cells of Chironomus tentans was screened with a probe containing the NLRCth1 non-LTR (long terminal repeat) retrotransposon from Chironomus thummi. Several positive clones were obtained and one of them, p62, was characterized by in situ hybridization and sequencing. The sequencing analysis showed that this clone contained a 4607 bp nucleotide sequence of a new transposable element that hybridized in situ to more than 100 sites over all four C. tentans chromosomes. The detailed analysis of this sequence revealed the presence of the 3'-end of open reading frame 1 (ORF1), a complete ORF2, and a 1.3-kb 3'-end untranslated region (UTR). The new element has been designated NLRCt2 (non-LTR retrotransposon 2 from C. tentans). A comparison of the nucleotide sequences of NLRCth1 and NLRCt2 showed 30% similarity in the region of ORF1 and 70% similarity in the region of ORF2. Based on the results of Southern blot analysis, two transposable elements have been found in the C. tentans genome, one of which is identical to NLRCth1 from C. thummi. This may be explained by horizontal transmission. The second element, NLRCt2, has been found in two different forms in the C. tentans genome. These can be distinguished by the presence of the 1.3-kb 3'-end UTR in one of the forms. Since the cDNA clone investigated was isolated from a tissue-specific cDNA library, the data showed that NRLCt2 is expressed in somatic cells.

Genomic organization of the rat aspartyl-tRNA synthetase gene family: a single active gene and several retropseudogenes

The genomic organization of the gene encoding rat aspartyl-tRNA synthetase (AspRS), a class II aminoacyl-tRNA synthetase (aaRS), was determined. A single active gene and several pseudogenes were isolated from a rat genomic DNA library and characterized. The active DRS1 gene encoding the rat AspRS spans approximately 60 kb and is divided into 16 exons. Exons 8-16, encoding the nt-binding domain of the synthetase, are clustered in the 3'-region of the gene, whereas exons 3, 4, and 5, encoding the anticodon-binding domain are separated by large introns (up to 15 kb) containing LINE sequences. One of the pseudogenes, psi DRS1, has a nt sequence 93% identical to that of the complete cDNA sequence of rat AspRS but several stop codons interrupt the coding sequence, thus identifying psi DRS1 to an inactive processed pseudogene. Two repetitive elements from the LINE family are inserted into psi DRS1. Calculation of nt substitution rates suggests that psi DRS1 sequences arose approximately 27 Myr ago. The other pseudogene, psi DRS2, should be more ancient. Taken together, these results clearly demonstrate that the AspRS gene family is composed of only one active gene. The availability of the gene structure of AspRS could help to clarify molecular evolution of class II aaRS.

Two persistent LINE-1 lineages in Peromyscus have unequal rates of evolution

LINE-1, the major family of long, interspersed repeats in the mammalian genome, moves via an RNA intermediate and encodes its own reverse transcriptase. Comparative sequence analysis was used to reconstruct the phylogenetic history of LINE-1 dynamics in the deer mouse, Peromyscus. As is the case in Mus and Rattus, a very small number of active templates produce the majority of LINE-1 copies in Peromyscus. However, in contrast to the single LINE-1 lineage seen in the muroid rodents, Peromyscus has at least two LINE-1 lineages whose most recent common ancestor probably existed before the peromyscine radiation. Species-specific variants of Lineage 1, and intact open reading frames in the youngest elements of both Lineages 1 and 2, suggest that both lineages have remained active within the same genome. The higher number of shared-sequence variants in Lineage 1 relative to Lineage 2 suggests that Lineage 1 has replaced its master template much more frequently than Lineage 2 or that the reverse transcriptase Lineage 1 is more error prone. The implications of the method used to acquire LINE-1 sequences for analysis are discussed.

Cytoplasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA

P40 is the protein encoded by the first open reading frame (ORF1) of the human LINE-1 (L1Hs) retrotransposon; it is 338 amino acids long, has a leucine zipper motif and has been found in human teratocarcinoma cell lines and some tumor cells. In this report, we describe properties of p40 in the human teratocarcinoma cell lines NTera2D1 and 2102Ep. The results indicate that: (i) most of p40 occurs in large multimeric cytoplasmic complexes, (ii) L1Hs RNA is associated with the p40 complexes, (iii) the complexes are dissociated by ribonuclease and (iv) p40 is a novel RNA-binding protein. Cross-linking experiments with full-length and truncated p40 produced in Escherichia coli also showed that: (i) p40 itself can form a multimeric complex larger than 250 kDa, (ii) the leucine zipper motif and the region conserved among the predicted ORF1 polypeptides of mammalian LINE-1s participate in complex formation and (iii) the amino terminal region is important for the stability of complex formation. Analysis of the amino acid sequence of p40 suggests that long segments of the molecule can assume an alpha-helical configuration including the leucine zipper and the conserved region. The evidence presented here suggests that the p40 complex is a ribonucleoprotein complex containing L1Hs RNA(s) and that protein-protein interactions in which alpha-helix structures participate, for example coiled-coils, may occur in the complex.

A genetic linkage map of the laboratory rat, Rattus norvegicus

We report the construction of the first complete genetic linkage map of the laboratory rat. By testing 1171 simple sequence length polymorphisms (SSLPs), we have identified 432 markers that show polymorphisms between the SHR and BN rat strains and mapped them in a single (SHR x BN) F2 intercross. The loci define 21 large linkage groups corresponding to the 21 rat chromosomes, together with a pair of nearby markers on chromosome 9 that are not linked to the rest of the map. Because 99.5% of the markers fall into one of the 21 large linkage groups, the maps appear to cover the vast majority of the rat genome. The availability of the map should facilitate whole genome scans for genes underlying qualitative and quantitative traits relevant to mammalian physiology and pathobiology.

Rat liver cytochrome P450 2B3: structure of the CYP2B3 gene and immunological identification of a constitutive P450 2B3-like protein in rat liver

The cytochrome P450 2B subfamily in the rat contains an estimated eight to eleven members at the genomic level. Synthesis in the liver of the prototypic forms P450 2B1 and P450 2B2 is dramatically induced by phenobarbital. The 1.9-kb mRNA for P450 2B3, a third member of the P450 2B subfamily, is constitutively present in rat liver but is not inducible by phenobarbital. We have now cloned and sequenced exonic sequences corresponding to the entire 2B3 mRNA and determined their exon-intron structure, which is identical to that of CYP2B1/CYP2B2 and other CYP2B genes. A putative CYP2B3 transcription start site was identified and CYP2B3 5'- and 3'-flanking sequences were compared to those of CYP2B1 and CYP2B2. CYP2B3, like CYP2B1 and CYP2B2, has a modified TATA box preceding the transcription start site and lacks the canonical polyadenylation signal preceding the poly(A) site. A 2B3 expression vector, pMT2-2B3, directed the synthesis in COS-1 cells of an approximately 50-kD protein detectable on Western blots with a polyclonal antibody and with one of four monoclonal antibodies raised against 2B1 but not with a polyclonal antibody raised against P450 PB6. The 2B3 protein migrated with a slightly higher electrophoretic mobility than 2B1 and comigrated with a protein detected by anti-2B1 antibodies in liver microsomes from untreated rats. The results indicate that a 2B3-like protein is present in rat liver and that it is distinct from P450 PB6 and other known constitutive rat hepatic P450s.

Amplification of the ancient murine Lx family of long interspersed repeated DNA occurred during the murine radiation

We identified and characterized the relics of an ancient rodent L1 family, referred to as Lx, which was extensively amplified at the time of the murine radiation about 12 million years ago, and which we showed was ancestral to the modern L1 families in rat and mouse. Here we have extended our analysis of the Lx amplification by examining more murine and nonmurine species for Lx sequences using both blot hybridization and the polymerase chain reaction for a total of 36 species. In addition we have determined the relative copy number and sequence divergence, or age, of Lx elements in representative murine genera. Our results show that while Lx sequences are confined to murine genera, the extent of the amplification was different in the different murine lineages, indicating that the amplification of Lx did not precede, but was coincident with, the murine radiation. The implications of our findings for the evolutionary dynamics of L1 families and the utility of ancestral amplification events for systematics are discussed.

Multiple L1 progenitors in prosimian primates: phylogenetic evidence from ORF1 sequences

One of the uncertainties regarding the evolution of L1 elements is whether there are numerous progenitor genes. We present phylogenetic evidence from ORF1 sequences of slow loris (Nycticebus coucang) and galago (Galago crassicaudatus) that there were at least two distinct progenitors, active at the same time, in the ancestor of this family of prosimian primates. A maximum parsimony analysis that included representative L1s from human, rabbit, and rodents, along with the prosimian sequences, revealed that one of the galago L1s (Gc11) grouped very strongly with the slow loris sequences. The remaining galago elements formed their own unique and strongly supported clade. An analysis of replacement and silent site changes for each link of the most parsimonious tree indicated that during the descent of the Gc11 sequence approximately two times more synonymous than nonsynonymous substitutions had occurred, implying that the Gc11 founder was functional for some time after the split of galago and slow loris. Strong purifying selection was also evident on the galago branch of the tree. These data indicate that there were two distinct and contemporaneous L1 progenitors in the lorisoid ancestor, evolving under purifying selection, that were retained as functional L1s in the galago lineage (and presumably also in the slow loris). The prosimian ORF1 sequences could be further subdivided into subfamilies. ORF1 sequences from both the galago and slow loris have a premature termination codon near the 3' end, not shared by the other mammalian sequences, that shortens the open reading frame by 288 bp. An analysis of synonymous and nonsynonymous substitutions for the 5' and 3' portions, that included intra- and inter-subfamily comparisons, as well as comparisons among the other mammalian sequences, suggested that this premature stop codon is a prosimian acquisition that has rendered the 3' portion of ORF1 in these primates noncoding.

Characterization and genetic organization of full-length copies of a LINE retroposon family dispersed in the genome of Culex pipiens mosquitoes

Many full-length copies of a long interspersed repetitive element family, designated Juan-C, are reiterated in the genome of Culex pipiens mosquitoes. The complete Juan-C elements have a length of 4.48 kb. They are terminated at one end with an adenosine-rich sequence preceded with an AATAAA polyadenylation signal, lack terminal repeats and cause duplication of the host DNA at the site of their integration. Full-length Juan-C copies display two long open reading frames potentially encoding two proteins. The first one includes a domain typical of nucleic-acid-binding proteins, while the second resembles reverse transcriptases. Therefore, Juan-C elements are similar to LINE retroposons in their overall genetic organization and can probably be transposed by reverse transcription of an RNA intermediate. Juan-C elements are most similar in their sequence and coding potential to the Juan-A elements which are reiterated in mosquito species belonging to the genus Aedes. They also display homologies with some Drosophila LINEs such as Jockey, suggesting that all these elements have arisen from a common precursor. Nearly identical full-length Juan-C copies are amplified in C. pipiens strains from different continents. This finding that Juan-C retroposons reiterated in different strains form an homogeneous family is interpreted to indicate that these elements have spread recently in the C. pipiens species.

Onset of chromatin fragmentation in chloroma cell apoptosis is highly sensitive to UV and begins at non-B DNA conformation

UV irradiation induces programmed death, or apoptosis, in rat chloroleukaemia cells, a process characterized by typical cell morphology, fragmentation of chromatin into units of single and multiple nucleosomes, and transcriptional activation of LINE. Our study shows that this process is initiated by very low UV doses: exposure to one minimal erythema dose (MED, about 200 J/m2), at defined wavelengths ranging from 270 to 330 nm, is sufficient. By sequencing 100 randomly selected blunt-end chromatin fragments (single and multiple nucleosomes) we observed that at an early stage of apoptosis the fragmented DNA contains a four-fold excess of both long and short interspersed nuclear retroelements (LINEs and SINEs). A distinct sequence finding was also the observation that fragmented DNA is very rich in microsatellites, (CA)n dinucleotides in particular, and in long stretches of homopurine/homopyrimidine domains. The present results thus indicate that chromatin fragmentation in UV-induced apoptosis begins at non-random locations involving non-B DNA conformation, and that the onset of the suicide process in chloroleukaemia cells is surprisingly sensitive to UV exposure.

Characterization of a LINE retroposon dispersed in the genome of three non-sibling Aedes mosquito species

A family of long interspersed repetitive elements (LINEs) dispersed in the genome of Aedes mosquitoes is described. Basically, full-length copies of the element designated Juan-A are dispersed in the genome of A. aegypti, but some elements are truncated or deleted. Complete Juan-A elements are 4.7 kb long, and their overall genetic organization is similar to that of LINEs from other species in which this class of nonviral retrotransposons has been described. Juan-A elements are terminated at the 3' end by an adenosine(A)-rich sequence and are flanked by target-site duplications. They display two long open reading frames potentially encoding two polypeptides. The first one contains Cys-rich motifs typical of nucleic-acid-binding proteins, while the other shows homology to the reverse transcriptases. These features are characteristic of LINE retroposons and indicate that Juan-A elements can be transposed by reverse transcription of an RNA intermediate. Furthermore, Juan-A retroposons display significant homologies with the Drosophila LINEs Jockey and F, suggesting that all these elements have arisen from a common precursor. The full-length Juan-A copies which are amplified in the genomes of various strains belonging to the three non-sibling species, A. aegypti, A. albopictus and A. polynesiensis, form an internally homogeneous family. These data are interpreted to indicate that active Juan-A retroposons underwent a recent amplification in the strains analyzed. Furthermore, they suggest that these elements have spread by horizontal transfer between the three non-sibling species.

The 5' ends of LINE1 repeats in rabbit DNA define subfamilies and reveal a short sequence conserved between rabbits and humans

The 5' ends of five full-length LINE1 (L1) repeats from the rabbit genome (L1Oc) were mapped and their nucleotide sequences determined. Computer-generated alignments showed that these five L1Oc repeats can be divided into subfamilies, each of which has a characteristic sequence upstream of the first open reading frame (ORF1). These five L1Ocs range in size from 6.5 to 7.3 kb, with 5' ends located 76 to 1125 bp upstream of ORF1. Two of these subfamilies appear to have diverged from a common ancestor at least 66 million years ago. Comparisons of the 5' ends of L1s from rabbit, human, mouse, and rat show no common sequence 5' to ORF1, except for a 22-bp sequence that is found near the beginning of all characterized full-length L1s from rabbit and human. A statistical analysis indicates that this 22-bp aligned block is highly significant. Part of this 22-bp sequence matches the microE1 binding site in immunoglobulin gene enhancers. This strong conservation suggests that the microE1 binding site may be part of a transcriptional regulatory element at the 5' ends of rabbit and human L1 repeats.

Strand-specific LINE-1 transcription in mouse F9 cells originates from the youngest phylogenetic subgroup of LINE-1 elements

LINE-1 (L1) is a mammalian family of highly repeated DNA sequences that are members of a class of transposable elements whose movement involves an RNA intermediate. Both structural and evolutionary data indicate that the L1 family consists of a small number of active transposable elements interspersed with a large number of L1 pseudogenes. In the mouse, the longest, characterized L1 sequences span about 7000 base-pairs and contain two long open reading frames. Two subfamilies of mouse L1 elements, A and F, have been defined on the basis of the type of putative transcriptional regulatory sequence found at the 5' end. In order to identify a transcribed subset of L1 elements in mouse F9 teratocarcinoma cells, we have examined the strand-specificity of L1 transcription by Northern analysis and compared the open reading frame-1 sequences of ten A-type cDNAs with fifteen genomic A-type L1 elements. Transcripts containing A-type sequence are far more abundant than those containing F-type sequence. Although the majority of L1 RNA in F9 cells appears to be transcribed non-specifically from both strands, our results provide evidence for a subpopulation of variable length, strand-specific transcripts arising from A-type transcriptional regulatory sequences. F9 cell cDNA sequences, which share greater than 99.5% sequence identity with one another, represent a homogeneous subset of the genomic L1 population. Examination of genomic mouse L1 sequences reveals three types of length polymorphism in a defined segment of the first open reading frame. Phylogenetic analysis shows a correlation between the type of length polymorphism in the first open reading frame and the relative age of an individual A-type genomic L1 element. Comparison of the cDNA and genomic sequences indicates that the youngest subgroup of A-type L1 elements is preferentially transcribed in F9 cells. This subgroup may be currently dominating the L1 dispersal process in mice.

Synaptonemal complexes from DNase-treated rat pachytene chromosomes contain (GT)n and LINE/SINE sequences

Purified chromosome cores (synaptonemal complexes) of rat pachytene chromosomes, from which the chromatin is removed by extensive DNase II digestion, retain a residual class of DNA, presumably the bases of chromatin loops. This synaptonemal complex-associated DNA, isolated by proteinase digestion and phenol extraction of purified DNase-treated synaptonemal complexes, and cloned in plasmid vector pEMBL18, has a length distribution of 50-500 bp. From a library of these fragments, 21 fragments were sequenced. Present in this sample are short 40-200-bp segments with greater than 80% identity to "long" and "short" interspersed repeated elements (LINE/SINEs), an excess of GT/CA tandem repeats and a number of unidentified sequences. The LINE/SINE segments may play a role in homology vs. nonhomology recognition during meiosis and the alternating purine-pyrimidine sequences have been implicated in genetic recombination. Their enrichment in synaptonemal complexes may be related to the synapsis and recombination functions of meiosis.

Evidence for a reverse transcription intermediate for a marked line transposon in tumoral rat cells

We have marked a "reconstituted" LINE element from rat with an intron-containing indicator gene, to test for its RNA-mediated transposition in tumoral rat cells in culture. Three cloned LINE promoter-containing fragments were tested by a transient transfection assay using a LacZ reporter gene, and the promoter with maximum expression was substituted--in an homologous manner--to the 5' domain of a close to full-length genomic LINE. The resulting marked LINE was stably introduced by transfection into tumoral rat cells. PCR amplification of the DNA from several transfected clones, using primers bracketting the intronic domain of the indicator gene, yielded fragments with a reduced size: their DNA sequencing, in four cases out of four, demonstrated splicing out of the intron as expected for the passage of the marked LINE through an RNA intermediate and its reverse transcription. Fractionation of cellular DNA by the Hirt procedure indicated that reverse transcribed copies are present in the "extrachromosomal" fraction. Their abundance is close to 1 copy per 10(4) cells. These results strongly suggest that rat LINEs transpose through an RNA intermediate and its reverse transcription, as previously demonstrated for the Drosophila LINE I element and, further, that reverse transcription might take place prior to integration, resulting in extrachromosomal DNA molecules as preintegrative transposition intermediates.

Molecular characterization of rat multigene family encoding proline-rich proteins

Three members of the rat proline-rich protein multigene family have been characterized. Each of these genes, RP4, RP13, and RP15, contains three exons and they are approximately 4.8, 5.7, and 5.4 kb, respectively. The DAN sequences of RP4 and RP13 are greater than 93% homologous in the 3.1-kb segment extending from the 5'-upstream region (approximately nucleotide -930) to 238 nucleotides after the second exon/intron junction; however, regions further downstream, intron II and exon III, share less than 43% identity. In contrast, exon III from RP15, RP13, and the previously sequenced mouse PRP gene MP2 are more than 73% conserved. These analyses suggest that the duplication of the ancestral genes to RP13 and RP4 occurred prior to the divergence of the rat PRP genes. The results also indicate that in the past 21.5 million years, multiple recombination events have resulted in a very high degree of divergence among intron II and exon III of RP4 and RP13. This divergence is due in part to the insertion of members of the rat long interspersed repeat DNA family at -930 bp upstream from the transcription initiation site and within intron II of RP13. Comparisons of the nucleotide sequences and organization of exon I with the genomic organization of PRP and glutamic acid/glutamine-rich protein genes in this and previous studies reveal striking resemblance among these genes. These observations are consistent with the notion that this super multigene family arose from duplication of progenitor genes via unequal crossing over events. In addition, the results suggest that concerted evolution has occurred within the tandemly repeated motif of exon II.

Rat vasopressin and oxytocin genes are linked by a long interspersed repeated DNA element (LINE): sequence and transcriptional analysis of LINE

Sequence analysis of the rat vasopressin and oxytocin gene family reveals that the two genes are linked by a long interspersed repeated DNA element (LINE) giving rise to seven long open reading frames encoding hypothetical proteins of 99 to 556 amino acid residues. Furthermore, although both DNA strands of LINEs serve as templates for transcription, transcripts initiated at the 3' end are more abundant than those started from the 5' end. The LINEs are transcribed preferentially in brain tissues as analyzed by Northern blot, in situ hybridization, and RNase protection experiments. The data show that most LINEs are transcribed at their entire length and that a major fraction of respective RNAs does not enter the cytoplasm but remains in the cell nucleus.

Molecular characteristics of the heterochromatic I elements from a reactive strain of Drosophila melanogaster

There are two categories of strains in Drosophila melanogaster with respect to the I-R system of hybrid dysgenesis. The inducer strains contain particular transposable elements named I factors. They are not present in the strains of the other category called reactive (R) strains. Defective I elements are present in the pericentromeric regions of both categories of strains. This last subfamily of I sequences has not yet been described in detail and little is known about its origin. In this paper, we report that the defective I elements display an average of 94% of sequence identity with each other and with the transposable I factor. The results suggest that they cannot be the progenitors of the present day I factors, but that each of these two subfamilies started to evolve independently several million years ago. Furthermore, the sequence comparison of these I elements with an active I factor from Drosophila teissieri provides useful information about when the deleted I elements became immobilized.

Nuclease sensitivity of estradiol-charged estrogen receptor binding sites in nuclei isolated from normal and neoplastic rat mammary tissues

The interaction of partially purified calf uterine estradiol-charged estrogen receptor ([3H]ER) with rat nuclei was studied in vitro. We previously observed a significantly greater number of [3H]ER binding sites (at saturation) in nuclei of R3230AC mammary tumors from intact vs ovariectomized (ovex) rats with no difference in the affinity of [3H]ER binding for these nuclei. We now report on the nuclease sensitivity of [3H]ER binding sites in nuclei from these tumors and from normal rat tissues. Digestion of tumor nuclei with deoxyribonuclease I (DNase I) prior to incubation with [3H]ER in vitro resulted in a progressive loss of [3H]ER binding capacity, which was not accompanied by alterations in the affinity of [3H]ER for the nuclei (Kd = 1-3 nM). A significantly lower concentration (P less than 0.005) of DNase I eliminated 50% of the [3H]ER binding sites in nuclei of tumors from intact hosts (8 unit.min/ml) compared to tumors from ovex hosts (22 unit.min/ml). These results indicate that DNA regions capable of binding ER are more susceptible to DNase I digestion in tumors from intact rats than those from ovex hosts, suggesting that the endogenous hormonal milieu is responsible, at least in part, for maintenance of nuclease-sensitive DNA conformations in this hormone-responsive mammary tumor. The amount of DNase I required to eliminate 50% of [3H]ER binding to nuclei from lactating mammary gland, liver, and kidney ranged from 14 to 56 unit.min/ml. Therefore, accessibility of [3H]ER binding sites to nuclease digestion in normal rat tissue is generally less than that of R3230AC tumors.

UV light and ionizing radiations cause programmed death of rat chloroleukaemia cells by inducing retropositions of a mobile DNA element (L1Rn)

The long interspersed repetitive DNA, L1 or LINE, is a class of mobile genetic elements which can amplify in the cell genome by retroposition, i.e. by a mechanism similar to that of retroviruses. We have shown before that in rat chloroleukaemia cells, maintained in suspension culture in vitro, this element is spontaneously transcriptionally activated at about half of the maximal population density. About 24 h later an explosive amplification of the L1 element is seen in DNA: about 300,000 copies are inserted into apparently random locations in the cell genome, thus creating an outburst of lethal mutations. Dead cells display morphological features typical to programmed death. The present results show that UV light and ionizing radiation induce rapid, premature activation of the L1Rn element during the fast exponential growth of chloroleukaemia cells, and that also this exogenously induced activation is followed by programmed cell death. Transcriptional activation of the L1Rn element can be very strong after the UV exposure: at least 70-fold. Severe hyperthermia, lethal to the cells, does not lead to L1Rn activation (actually a marked suppression is seen) and the mode of phenomic death is necrosis. Some biological implications of the results are discussed.

The transcription control region of the rat alpha-fetoprotein gene. DNA sequence and homology studies

The alpha-fetoprotein (AFP) gene, an important system for studying developmental and tissue-specific gene expression, is regulated mostly through the control of transcription. The promoter and cis-acting DNA elements which regulate the rat gene lie within a 7 kbp region upstream of the cap site. We have determined the sequence of this entire region. It contains several repetitive elements and a species-specific distribution of DNA methylation sites. We aligned our rat AFP sequence with fragmentary mouse and human AFP sequences to define blocks of highly conserved sequence, which we then analyzed for homology to known transcription regulatory sequences. Our analysis demonstrates that the regulatory region of the rat AFP gene is unusually complex.

Two LINE 1 repeats in rat

One LINE 1 repeat has been located 661 bp downstream from the last albumin exon and another approx. 10 kbp downstream from the last alpha-fetoprotein exon in the rat genomic DNA. The LINE 1 repeat following the albumin gene is truncated at its 5' end and is 1204 nucleotides long. The 5' end of the longer repeat downstream from the alpha-fetoprotein gene has not been determined. The two repeats have 95% homology with each other, with the exception of a short diverse 3' end sequence just preceding the putative polyadenylation signal.

I elements of Drosophila melanogaster generate specific chromosomal rearrangements during transposition

We report a detailed molecular analysis of three chromosomal rearrangements, which have been produced during I-R hybrid dysgenesis in Drosophila melanogaster. They all disrupt the yellow gene. One of them is a deletion; the other two are inversions, which may be interpreted as the results of recombination events between I elements inserted at their break points. These events appear to occur at the time of transposition and involve integrating rather than resident I elements. They are produced by a mechanism very similar to homologous ectopic recombination.

Composite transposable elements in the Xenopus laevis genome

Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit.

Full length L1 retroposons contain tRNA-like sequences near the 5' termini--hypothesis on the replication mechanism of retroposons

Retrotransposons replicate via a complex mechanism which depends on, among other things, the presence of long terminal repeats (LTRs) and a tRNA binding site just 3' of the 5' LTR. The LINES 1 (L1) family of sequences, which similar to retrotransposons in many other properties, represents a new class of retroposon which does not possess LTRs. However, we show here that the repetitive 5' motif associated with murine L1 elements contains a tRNA-like sequence in a location analogous to the position of the retro-transposon tRNA binding site. Although the repetition of such a 5' motif has only been found associated with murine L1 elements, we have found an analogous tRNA-like sequence near the 5' ends of the L1 elements from each of the other analyzed species for which the L1 family has been characterized, that is rat (L1Rr), human (L1Hs), drosophila (I element) and trypanosome (INGI). The conservation of this tRNA-like sequence near the 5' terminus of L1 elements from such diverse species suggests that it plays a functional role in the life of the L1 class of retroposon.