Discrete and heterogeneous high molecular weight RNAs complementary to a long dispersed repeat family (a possible transposon) of human DNA

L1 expression and regulation in humans and rodents

Long interspersed elements type 1 (LINE-1s, or L1s) have impacted mammalian genomes at multiple levels. L1 transcription is mainly controlled by its 5' untranslated region (5'UTR), which differs significantly among active human and rodent L1 families. In this review, L1 expression and its regulation are examined in the context of human and rodent development. First, endogenous L1 expression patterns in three different species-human, rat, and mouse-are compared and contrasted. A detailed account of relevant experimental evidence is presented according to the source material, such as cell lines, tumors, and normal somatic and germline tissues from different developmental stages. Second, factors involved in the regulation of L1 expression at both transcriptional and posttranscriptional levels are discussed. These include transcription factors, DNA methylation, PIWI-interacting RNAs (piRNAs), RNA interference (RNAi), and posttranscriptional host factors. Similarities and differences between human and rodent L1s are highlighted. Third, recent findings from transgenic mouse models of L1 are summarized and contrasted with those from endogenous L1 studies. Finally, the challenges and opportunities for L1 mouse models are discussed.

Long interspersed nuclear elements (LINE-1): potential triggers of systemic autoimmune disease

Recent advances have identified immune complexes containing nucleic acids as stimuli for toll-like receptors and inducers of type I interferon (IFN). While a similar mechanism may serve to amplify immune system activation and production of inflammatory mediators in vivo in the context of systemic autoimmune diseases, the initial triggers of autoimmunity have not been defined. In this review, we describe a category of potential inducers of autoimmunity, the endogenous retroelements, with a particular focus on long interspersed nuclear elements (LINE-1, L1). Increased expression of L1 transcripts or decreased degradation of L1 DNA or RNA could provide potent stimuli for an innate immune response, priming of the immune system, and induction of autoimmunity and inflammation. Genomic and genetic variations among individuals, sex-related differences in L1 regulation, and environmental triggers are among the potential mechanisms that might account for increased L1 expression. Induction of type I IFN by L1-enriched nucleic acids through TLR-independent pathways could represent a first step in the complex series of events leading to systemic autoimmune disease.

Expression of transposon LINE-1 is relatively human-specific and function of the transcripts may be proliferation-essential

A new 1.7-kb LINE (L1) transcript has been discovered from the cDNA library of human small-cell lung cancer. The nucleotide sequence of 1.7-kb L1 transcript is 98.4% similar to that of open reading frame 2 (ORF2) found in consensus complete 6.5-kb L1. Although L1 DNA segments could be detected from both genomic DNAs of human and rodent cells by PCR, these L1 transcripts were not detectable from cellular RNA of rodent cells by RT-PCR and northern hybridization, implying that the expression of L1 was relatively human-specific. The functions of L1 transcripts in cells are not yet clear. This paper shows that L1 transcripts are essential for cell proliferation when determined by antisense oligonucleotides. Alternately, L1 transcripts exhibit in all human cells we have examined so far, and they map to all the human chromosomes. A sequence-similarity search in the GenBank database indicates that the major sequence of 1.7-kb L1 is integrated in human retinoblastoma (Rb), IL-2, and factor VIII genes. Since Rb and factor VIII genes have displayed high frequency of chromosomal deletions in various cancers and haemophilia A, the universal integration of long and homologous L1 segments in the genes and all chromosomes may be liable to promote abnormal DNA rearrangement.

A collection of mRNA species that are inducible in the RAW 264.7 mouse macrophage cell line by gamma interferon and other agents

To identify genes induced during macrophage activation, a cDNA library was prepared from cultures of the RAW 264.7 mouse macrophage cell line that had been treated with conditioned medium from mitogen-stimulated spleen cells, and the cDNA library was screened by differential plaque hybridization. Eleven cDNA clones, designated CRG-1 through CRG-11, corresponding to mRNA species inducible in RAW 264.7 cells by the spleen cell conditioned medium, were isolated. Inductions were not blocked by cycloheximide. All of the mRNAs were inducible by gamma interferon, and some were also inducible by alpha and beta interferons, by lipopolysaccharide, by phorbol 12-myristate 13-acetate, and by the calcium ionophore A23187. Sequencing of the cDNAs revealed that CRG-1, CRG-3, and CRG-5 are cDNAs of recently identified transcription factors IRF-1, zif/268, and LRF-1 respectively. As previously reported, CRG-2 and CRG-10 (MIG) encode new members of the platelet factor 4 family of cytokines. CRG-6 corresponds to a new member of a family of interferon-inducible genes clustered on mouse chromosome 1, CRG-9 corresponds to a prostaglandin synthase homolog, CRG-8 corresponds to beta 2-microglobulin, and CRG-4 corresponds to metallothionein II. CRG-11 contains sequences of a truncated L1Md repetitive element as well as nonrepetitive sequences. The nonrepetitive sequence of CRG-11 as well as the sequences of CRG-7 are not closely related to published sequences. The CRG genes and proteins are of interest because of their involvement in macrophage activation, because of their roles as mediators of the effects of gamma interferon and other pleiotropic agents, and because of their usefulness as tools for studying the signal pathways through which gamma interferon and other inducers exert their effects on gene and protein expression.

A collection of mRNA species that are inducible in the RAW 264.7 mouse macrophage cell line by gamma interferon and other agents

To identify genes induced during macrophage activation, a cDNA library was prepared from cultures of the RAW 264.7 mouse macrophage cell line that had been treated with conditioned medium from mitogen-stimulated spleen cells, and the cDNA library was screened by differential plaque hybridization. Eleven cDNA clones, designated CRG-1 through CRG-11, corresponding to mRNA species inducible in RAW 264.7 cells by the spleen cell conditioned medium, were isolated. Inductions were not blocked by cycloheximide. All of the mRNAs were inducible by gamma interferon, and some were also inducible by alpha and beta interferons, by lipopolysaccharide, by phorbol 12-myristate 13-acetate, and by the calcium ionophore A23187. Sequencing of the cDNAs revealed that CRG-1, CRG-3, and CRG-5 are cDNAs of recently identified transcription factors IRF-1, zif/268, and LRF-1 respectively. As previously reported, CRG-2 and CRG-10 (MIG) encode new members of the platelet factor 4 family of cytokines. CRG-6 corresponds to a new member of a family of interferon-inducible genes clustered on mouse chromosome 1, CRG-9 corresponds to a prostaglandin synthase homolog, CRG-8 corresponds to beta 2-microglobulin, and CRG-4 corresponds to metallothionein II. CRG-11 contains sequences of a truncated L1Md repetitive element as well as nonrepetitive sequences. The nonrepetitive sequence of CRG-11 as well as the sequences of CRG-7 are not closely related to published sequences. The CRG genes and proteins are of interest because of their involvement in macrophage activation, because of their roles as mediators of the effects of gamma interferon and other pleiotropic agents, and because of their usefulness as tools for studying the signal pathways through which gamma interferon and other inducers exert their effects on gene and protein expression.

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.

Wilms tumor locus on 11p13 defined by multiple CpG island-associated transcripts

Wilms tumor is an embryonal kidney tumor involving complex pathology and genetics. The Wilms tumor locus on chromosome 11p13 is defined by the region of overlap of constitutional and tumor-associated deletions. Chromosome walking and yeast artificial chromosome (YAC) cloning were used to clone and map 850 kilobases of DNA. Nine CpG islands, constituting a "CpG island archipelago," were identified, including three islands that were not apparent by conventional pulsed-field mapping, and thus were at least partially methylated. Three distinct transcriptional units were found closely associated with a CpG island within the boundaries of a homozygous DNA deletion in a Wilms tumor.

Characterization of a nondeleterious L1 insertion in an intron of the human factor VIII gene and further evidence of open reading frames in functional L1 elements

We have characterized an insertional event in IVS-10 of the factor VIII gene in a pedigree containing a hemophilia A patient (JH-25). The inserted DNA is a 5' truncated L1 element that is 681 bp long followed by a 3'66-bp poly(A) tract. The L1 element is inserted 154 bp 5' to the start of exon 11 and is flanked by a 13- to 17-bp target site duplication. The L1 insertion is present in four generations of the patient's family. The maternal grandfather who carries the insertion does not have hemophilia A, indicating that the insertion is not the cause of hemophilia A in the patient. We have sequenced this insertion and two previously reported de novo L1 insertions in the factor VIII gene in patients JH-27 (3785 bp) and JH-28 (2132 bp). The three nucleotide sequences differ by 0.2-0.8%. All three of these L1 insertions have open reading frames (ORFs) (1192, 642, and 157 aa) and the three derived amino acid sequences are 98-99% identical. The previously reported sequence similarity between L1 3' ORFs and the polymerase domain of reverse transcriptases is maintained in the ORFs of the JH-27 and JH-28 L1 insertions. The presence of open reading frames and the close sequence similarity of these recently inserted L1 elements provide indirect evidence for the existence of a set of functional L1 elements that encode one or more proteins necessary for their retrotransposition.

Unit-length line-1 transcripts in human teratocarcinoma cells

We have characterized the approximately 6.5-kilobase cytoplasmic poly(A)+ Line-1 (L1) RNA present in a human teratocarcinoma cell line, NTera2D1, by primer extension and by analysis of cloned cDNAs. The bulk of the RNA begins (5' end) at the residue previously identified as the 5' terminus of the longest known primate genomic L1 elements, presumed to represent "unit" length. Several of the cDNA clones are close to 6 kilobase pairs, that is, close to full length. The partial sequences of 18 cDNA clones and full sequence of one (5,975 base pairs) indicate that many different genomic L1 elements contribute transcripts to the 6.5-kilobase cytoplasmic poly(A)+ RNA in NTera2D1 cells because no 2 of the 19 cDNAs analyzed had identical sequences. The transcribed elements appear to represent a subset of the total genomic L1s, a subset that has a characteristic consensus sequence in the 3' noncoding region and a high degree of sequence conservation throughout. Two open reading frames (ORFs) of 1,122 (ORF1) and 3,852 (ORF2) bases, flanked by about 800 and 200 bases of sequence at the 5' and 3' ends, respectively, can be identified in the cDNAs. Both ORFs are in the same frame, and they are separated by 33 bases bracketed by two conserved in-frame stop codons. ORF 2 is interrupted by at least one randomly positioned stop codon in the majority of the cDNAs. The data support proposals suggesting that the human L1 family includes one or more functional genes as well as an extraordinarily large number of pseudogenes whose ORFs are broken by stop codons. The cDNA structures suggest that both genes and pseudogenes are transcribed. At least one of the cDNAs (cD11), which was sequenced in its entirety, could, in principle, represent an mRNA for production of the ORF1 polypeptide. The similarity of mammalian L1s to several recently described invertebrate movable elements defines a new widely distributed class of elements which we term class II retrotransposons.

Unit-length line-1 transcripts in human teratocarcinoma cells

We have characterized the approximately 6.5-kilobase cytoplasmic poly(A)+ Line-1 (L1) RNA present in a human teratocarcinoma cell line, NTera2D1, by primer extension and by analysis of cloned cDNAs. The bulk of the RNA begins (5' end) at the residue previously identified as the 5' terminus of the longest known primate genomic L1 elements, presumed to represent "unit" length. Several of the cDNA clones are close to 6 kilobase pairs, that is, close to full length. The partial sequences of 18 cDNA clones and full sequence of one (5,975 base pairs) indicate that many different genomic L1 elements contribute transcripts to the 6.5-kilobase cytoplasmic poly(A)+ RNA in NTera2D1 cells because no 2 of the 19 cDNAs analyzed had identical sequences. The transcribed elements appear to represent a subset of the total genomic L1s, a subset that has a characteristic consensus sequence in the 3' noncoding region and a high degree of sequence conservation throughout. Two open reading frames (ORFs) of 1,122 (ORF1) and 3,852 (ORF2) bases, flanked by about 800 and 200 bases of sequence at the 5' and 3' ends, respectively, can be identified in the cDNAs. Both ORFs are in the same frame, and they are separated by 33 bases bracketed by two conserved in-frame stop codons. ORF 2 is interrupted by at least one randomly positioned stop codon in the majority of the cDNAs. The data support proposals suggesting that the human L1 family includes one or more functional genes as well as an extraordinarily large number of pseudogenes whose ORFs are broken by stop codons. The cDNA structures suggest that both genes and pseudogenes are transcribed. At least one of the cDNAs (cD11), which was sequenced in its entirety, could, in principle, represent an mRNA for production of the ORF1 polypeptide. The similarity of mammalian L1s to several recently described invertebrate movable elements defines a new widely distributed class of elements which we term class II retrotransposons.

The F-type 5' motif of mouse L1 elements: a major class of L1 termini similar to the A-type in organization but unrelated in sequence

It has previously been shown that the L1 family in the mouse (L1Md) contains two alternative 5' ends called the A- and F-type sequences (1,2). We show here that the F-type element is a major class of murine L1 elements and report on the details of organization of the 5' motif of these F-type elements. Although the A- and F-type 5' sequences share no detectable sequence homology the organization of an F-type 5' end is strikingly similar to that of an A-type. That is, the F-type 5' sequences consist of a tandem array of a small number of 206 bp monomers while the A-type 5' motif consists of a tandem array of 208 bp monomers. All of the A-type elements characterized to date have a truncated monomer at the 5' end of the array. Many of the F-type elements are also terminated at the 5' end by a truncated copy but unlike the A-type elements some F-type elements terminate with a monomer which is within a few nucleotides of being complete. In addition the F-type consensus sequence, in contrast to the A-type sequence, shows homology (70%) to the body of the L1Md starting at the position where the monomer joins the rest of the L1 element.

Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence

A consensus sequence for the human long interspersed repeated DNA element, L1Hs (LINE or KpnI sequence), is presented. The sequence contains two open reading frames (ORFs) which are homologous to ORFs in corresponding regions of L1 elements in other species. The L1Hs ORFs are separated by a small evolutionarily nonconserved region. The 5' end of the consensus contains frequent terminators in all three reading frames and has a relatively high GC content with numerous stretches of weak homology with AluI repeats. The 5' ORF extends for a minimum of 723 bp (241 codons). The 3' ORF is 3843 bp (1281 codons) and predicts a protein of 149 kD which has regions of weak homology to the polymerase domain of various reverse transcriptases. The 3' end of the consensus has a 208-bp nonconserved region followed by an adenine-rich end. The organization of the L1Hs consensus sequence resembles the structure of eukaryotic mRNAs except for the noncoding region between ORFs. However, due to base substitutions or truncation most elements appear incapable of producing mRNA that can be translated. Our observation that individual elements cluster into subfamilies on the basis of the presence or absence of blocks of sequence, or by the linkage of alternative bases at multiple positions, suggests that most L1 sequences were derived from a small number of structural genes. An estimate of the mammalian L1 substitution rate was derived and used to predict the age of individual human elements. From this it follows that the majority of human L1 sequences have been generated within the last 30 million years. The human elements studied here differ from each other, yet overall the L1Hs sequences demonstrate a pattern of species-specificity when compared to the L1 families of other mammals. Possible mechanisms that may account for the origin and evolution of the L1 family are discussed. These include pseudogene formation (retroposition), transposition, gene conversion, and RNA recombination.

Characterization of the L1NH repeat family of Novikoff hepatoma

Long interspersed repeated sequences of the Novikoff hepatoma rat tumour cell genome were cloned and studied. No basic differences were found when the genomic organization of the Novikoff hepatoma was compared with that of other mammalian L1 families. The nucleotide sequence of the central approximately 4 kb (1 kb = 10(3) bases) part of the Novikoff hepatoma LINE (L1NH) appeared to be more highly conserved than the sequences found at the 5' and 3' ends. Moreover, the central approximately 4 kb core fragments were not always associated with the same end sequences. Thus, the occurrence of the more-conserved and more-abundant central portion in L1NH suggest that: (1) besides reverse transcription, other DNA- and/or RNA-mediated mechanisms might be involved in the dispersal of LINE families; and that (2) L1 sequences can sometimes consist of a compound unit made up of members of different L1 subunits and sequences with different genomic copy numbers.

Cloned extrachromosomal circular DNA copies of the human transposable element THE-1 are related predominantly to a single type of family member

The 2300 base-pair transposon-like human element, THE-1, has been identified in the extrachromosomal circular DNA of the established human cell line HeLa as a relatively homogeneous population of covalently closed 1900 base-pair molecules. THE-1, which has been classified tentatively as a retroviral-like transposable element (a retrotransposon), is present in the extrachromosomal circular DNA of African green monkey (BSC-1) and human lymphoblastoid (Jurkat) cell lines. The 1900 base-pair extrachromosomal elements isolated and cloned from HeLa cells (1) appear to contain only THE-1-specific nucleotide sequences, (2) are circularized versions of the linear chromosomal sequence, and (3) are related predominantly to a single, or single type of, family member.

Discrete high molecular weight RNA transcribed from the long interspersed repetitive element L1Md

The repetitive element LINE (L1) previously has been shown to contain two long open reading frames which are overlapping and out-of-frame similar to those found in retroviruses (1). In rodents and in human cells, these repeats appear to be transcribed into a heterogeneous population of RNAs in most cell types (2,3,4). No discrete transcript has been reported which is likely to be a mRNA for the open reading frames in rodent cells. In this paper, a discrete RNA species of approximately 8 kb has been identified in most murine lymphoid cells examined. This RNA is cytoplasmic and binds to oligo (dT) cellulose columns. Hybridization with labeled probes indicates that the transcript is of the same strandedness as the open reading frames. These results are consistent with proposals that L1Md is a retroposon with protein-encoding function.

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

We present the DNA sequence of a 6.7-kilobase member of the rat long interspersed repeated DNA family (LINE or L1Rn). This member (LINE 3) is flanked by a perfect 14-base-pair (bp) direct repeat and is a full-length, or close-to-full-length, member of this family. LINE 3 contains an approximately 100-bp A-rich right end, a number of long (greater than 400-bp) open reading frames, and a ca. 200-bp G + C-rich (ca. 60%) cluster near each terminus. Comparison of the LINE 3 sequence with the sequence of about one-half of another member, which we also present, as well as restriction enzyme analysis of the genomic copies of this family, indicates that in length and overall structure LINE 3 is quite typical of the 40,000 or so other genomic members of this family which would account for as much as 10% of the rat genome. Therefore, the rat LINE family is relatively homogeneous, which contrasts with the heterogeneous LINE families in primates and mice. Transcripts corresponding to the entire LINE sequence are abundant in the nuclear RNA of rat liver. The characteristics of the rat LINE family are discussed with respect to the possible function and evolution of this family of DNA sequences.

Characterization of a member of the highly repeated long interspersed rat DNA family with long open reading frames

A highly repetitive long interspersed sequence from rat DNA has been isolated and partly characterized. This sequence comprises at least a 1300 base-pair and a 2400 base-pair EcoRI fragment and probably additional elements. The 2400 base-pair segment has been analyzed in detail. It appears to be part of the chromosomal DNA in rat cells. The 2400 base-pair repeat is likely to be distributed over several regions in the rat genome. The 2400 base-pair segment has been cloned, mapped for restriction sites, and part of its nucleotide sequence has been determined. The 2400 base-pair sequence is a member of a typical highly repetitive long interspersed sequence with high copy number and restriction site polymorphism. There are sequence homologies to mouse and human DNA. A striking homology has been detected to the flanking sequences of a repetitive mouse DNA sequence that has been described to be located adjacent to one of the kappa-immunoglobulin variable genes. Elements in the 2400 base-pair rat repeat are transcribed in cells from most rat organs and from several continuous rat cell lines. This RNA from rat cell lines was found polyadenylated or not polyadenylated. The nucleotide sequence of parts of the 2400 base-pair DNA segment revealed open reading frames for polypeptide sequences. Such open reading frames have been detected in two different segments of the 2400 base-pair DNA repeat. Open reading frames exist in the two complementary strands in the same DNA segment. The hypothetical polypeptide whose sequence has been determined in toto has a length of 190 amino acid residues and is enriched in hydrophobic amino acids, reminiscent of the amino acid composition in membrane proteins. Hence, it is conceivable that the 2400 base-pair repeat sequence from rat DNA, at least in part, encodes messenger RNAs that might be translated into functional proteins.

A cloned fragment of HeLa DNA containing consensus sequences of satellite II and III DNA hybridizes with the Drosophila P-element and with the 1.8 kb family of human KpnI fragments

We have cloned a repetitive EcoRI fragment from the human genome which displays weak homologies with the Drosophila melanogaster transposable P-element. This cloned DNA appeared not to be a mobile element but, instead, a divergent member of human satellite II or III DNAs. We present here the first complete nucleotide sequence of a 1.797 kilobase pair (kb) satellite-like DNA. Moreover, this EcoRI satellite monomer contains a unique sequence of 49 basepairs (bp) that is devoid of the satellite consensus repeat 5'TTCCA3'. Southern hybridization analysis revealed that the cloned insert is closely related to a highly repetitive 1.8 kb KpnI family of tandemly organized satellite DNAs. Thus, the relationships among these satellite DNA families appear to be complex and may be a factor in their copy number, position and spatial organization.

L1 family of repetitive DNA sequences in primates may be derived from a sequence encoding a reverse transcriptase-related protein

Primate and rodent genomes contain a family of highly repetitive, long interspersed sequences, designated the L1 family or LINE-1. Characteristic features of the L1 family sequences such as an A-rich stretch at the 3' end, a truncated 5' end, the existence of significantly long open reading frames (ORFs) and the presence of L1 family transcripts in various types of cells, including pluripotential embryonic cells, suggest that the L1 family is derived from a sequence encoding a protein(s) and dispersed in the genome through an RNA-mediated process. These features of the L1 family are believed to be due to reverse transcription beginning at the 3' end of the L1 transcript and terminating prematurely and to the site duplication caused by the insertion of the complementary DNA. It is likely that this type of transcript is converted to cDNA and inserted into the chromosome through a process similar to that of the formation of processed pseudogenes. The above model, however, does not necessarily explain why the L1 family should produce the extraordinarily large number of copies (more than 10(4) per haploid genome) seen during evolution. It seems likely that the progenitor of the L1 family itself carries (or carried) a function which promotes the active dispersion of the L1 family sequence. We reasoned that such a function, if present, must be conserved during evolution and may be shown by comparative analysis of L1 family sequences from evolutionarily distant species. We show here that the L1 family sequence contains an ORF possessing significant sequence homology to several RNA-dependent DNA polymerases of viral and transposable element origins.(ABSTRACT TRUNCATED AT 250 WORDS)

Conservation in the 5' region of the long interspersed mouse L1 repeat: implications of comparative sequence analysis

A clone of 7.1kb corresponding to the mouse L1 interspersed repeat family was selected for homology to a human interspersed repeat. This clone fairly represents mouse genomic members. Mapping of the clone revealed one common element at both the 5' and 3' ends in a head to tail arrangement, suggesting that at least some long L1 family members are tandemly arranged; genomic studies confirmed the unexpected tandem arrangement of a minor proportion of L1 members. A short SmaI tandem repeat appears to define the 5' end of most L1 family members. SmaI repeats may maintain, via a recursive regulatory function, the transcriptional viability of L1 members after retroposition events. A 2.5kb portion of the mouse L1 repeat that has not been previously sequenced is presented. It is 55-70% homologous to a corresponding portion of the human KpnI repeat family. Comparative sequence analysis revealed that one common open reading frame may conserve potential coding function across species. A second open reading frame bears an asymmetric distribution of codon replacements unlike both genes and pseudogenes. This latter feature could be consistent with a proposed chromosome organization function that is unrelated to peptide expression.

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

We present the DNA sequence of a 6.7-kilobase member of the rat long interspersed repeated DNA family (LINE or L1Rn). This member (LINE 3) is flanked by a perfect 14-base-pair (bp) direct repeat and is a full-length, or close-to-full-length, member of this family. LINE 3 contains an approximately 100-bp A-rich right end, a number of long (greater than 400-bp) open reading frames, and a ca. 200-bp G + C-rich (ca. 60%) cluster near each terminus. Comparison of the LINE 3 sequence with the sequence of about one-half of another member, which we also present, as well as restriction enzyme analysis of the genomic copies of this family, indicates that in length and overall structure LINE 3 is quite typical of the 40,000 or so other genomic members of this family which would account for as much as 10% of the rat genome. Therefore, the rat LINE family is relatively homogeneous, which contrasts with the heterogeneous LINE families in primates and mice. Transcripts corresponding to the entire LINE sequence are abundant in the nuclear RNA of rat liver. The characteristics of the rat LINE family are discussed with respect to the possible function and evolution of this family of DNA sequences.

Discrete size classes of monkey extrachromosomal circular DNA containing the L1 family of long interspersed nucleotide sequences are produced by a general non-sequence specific mechanism

The L1 family of long interspersed nucleotide sequences (LINES) has recently been identified and characterized in the small polydisperse circular DNA (spc-DNA) populations of monkey (1), human (2) and mouse (3) cells. In monkey spc-DNA, the L1 (also known as Kpn I) family is present in discrete size classes (ranging from 300 to 6000 base pairs (bp)) which appear to be generated by non homologous recombination events within chromosomal elements. In this communication it is shown that different regions of the consensus L1 family are present at different frequencies in monkey spc-DNA (as they are in chromosomal DNA), that all regions of the family are present in extrachromosomal DNA, and that each region appears to be represented in an identical discrete spc-DNA size distribution. This size distribution reflects a non-sequence specific mechanism that generates spc-DNA size classes by chromosomal DNA recombination events that are in some way constrained to occur between sites separated by relatively defined lengths.

DNA sequences homologous to long double-stranded RNA. Transcription of intracisternal A-particle genes and major long repeat of the mouse genome

Long double-stranded RNA (dsRNA-A) (Kramerov, D.A., Ryskov, A.P. and Georgiev, G.P. (1977) Biochim. Biophys. Acta 475, 461-475) from Ehrlich ascites carcinoma cells was used for the search for mobile dispersed genes in the mouse genome. Two kinds of genomic sequences hybridizing to dsRNA-A were cloned. They were designated A1 and A2. The A1 sequence was identified as the gene for intracisternal A particles, while the A2 sequence was found to be the major long repetitive sequence of the mouse genome. Melted dsRNA-A hybridized equally well to both DNA strands of A1 and A2 sequences while total poly(A)+ RNA bound preferentially to one of them. Thus, a partially symmetrical transcription took place in the case of A1 and A2 elements. The analysis of transcripts of A1 elements in Ehrlich carcinoma cells revealed RNAs with sizes of 9.5 kb, 6.8 kb and 6.0 kb. In plasmocytoma MOPC 21 cells, instead of the 6.0 kb RNA, two other kinds of RNA with sizes 5.3 kb and 7.8 kb were found. These transcripts poorly coincided with the four known variants of intracisternal A-particle (IAP) genes. It seemed that at least some of the described RNAs were transcribed from some minor non-identified variants of IAP genes. The A2 transcripts were practically restricted to nuclei, their sizes being heterogeneous.

Rat LINE1: the origin and evolution of a family of long interspersed middle repetitive DNA elements

We present approximately 7.0 kb of composite DNA sequence of a long interspersed middle repetitive element (LINE1) present in high copy number in the rat genome. The family of these repeats, which includes transcribing members, is the rat homologue of the mouse MIF-Bam-R and human Kpn I LINEs. Sequence alignments between specimens from these three species define the length of a putative unidentified open reading frame, and document extensive recombination events that, in conjunction with retroposition, have generated this large family of pseudogenes and pseudogene fragments. Comparative mapping of truncated elements indicates that a specific endonucleolytic activity might be involved in illegitimate (nonhomologous) recombination events. Sequence divergence analyses provide insights into the origin and molecular evolution of these elements.

L1 sequences in HeLa extrachromosomal circular DNA: evidence for circularization by homologous recombination

Subcloned probes of the L1 family of repetitive elements were used to isolate L1-carrying clones from a plasmid library of HeLa cell extrachromosomal circular DNA. One clone was analyzed in detail by restriction mapping, cross-hybridization to L1 probes, and base sequence analysis. In addition to approximately the 3' half of a full-sized L1 element, this clone carried 390 base pairs of non-L1 sequence that is single copy in the HeLa genome. A HeLa genomic clone of this unique chromosomal region was isolated and the sequence organization of the circle clone was compared with the linear chromosomal region from which it was ultimately derived. We discuss possible mechanisms of circular DNA formation and propose homologous intrachromosomal recombination between 9-base-pair direct repeats to be most likely in this case.

Extrachromosomal DNA forms of copia-like transposable elements, F elements and middle repetitive DNA sequences in Drosophila melanogaster. Variation in cultured cells and embryos

Drosophila melanogaster embryos and cells in culture were screened for the presence of unintegrated covalently closed circular DNA forms that hybridize to copia-like transposable elements, the F element and uncharacterized dispersed middle repetitive DNA elements. Our results indicate that the majority of copia-like elements (including copia, 297, 412, mdg1, mdg3 and gypsy), the F elements, and 9 of 12 middle repetitive DNA elements are present as free DNA forms in cultured cells and embryos. An 18 base-pair inverted repeat has been reported to flank the long direct repeat of mdg3, implying that mdg3 is not an orthodox copia-like element; however, we have sequenced two independently isolated mdg3 clones and shown that the inverted repeat is not part of the element. The relative abundance with which free DNA forms are found varies between the cultured cells used, and between cultured cells and embryos. This variation, which can be up to 20-fold for some elements, does not correlate well with either the amount of element-specific poly(A)+ RNA present per cell or the number of element-specific sequences integrated in the genome.

The KpnI family of long interspersed nucleotide sequences is present on discrete sizes of circular DNA in monkey (BSC-1) cells

Discretely sized molecules of small circular DNAs in African green monkey kidney (BSC-1) cells contain nucleotide sequences homologous to the KpnI family of long interspersed repetitive nucleotide sequences. The size distribution of these KpnI family-containing circular DNAs differs markedly from those of BSC-1 cell circular DNAs containing either the Alu family of short interspersed nucleotide sequences or the alpha-satellite family of tandemly repeated sequences. The structures of several cloned, apparently whole, KpnI family-related circular DNAs of varying sizes were analyzed and compared with a compilation of chromosomal KpnI sequences. In general, it was found that the cloned DNAs all contained only KpnI sequences, and that the recombination events given rise to them did not involve any noticeable gain of nucleotides.

Chromosomal and nuclear distribution of the HindIII 1.9-kb human DNA repeat segment

A human interspersed repetitive DNA cloned in pBR322, the HindIII 1.9-kb (kilobase pair) sequence, was labeled with biotinylated dUTP and hybridized to acid-fixed chromosomes and paraformaldehyde-fixed whole cells in situ. Using our most sensitive detection techniques this probe highlighted on the order of 200 discrete loci, in punctate or banded arrays, that resembled a Giemsa-dark band pattern on chromosome arms. Interphase cells also displayed many discrete punctate spots of hybridization along chromosome fibers. The ubiquitous Alu sequence repeat also appeared to be concentrated in specific regions of the chromosome and predominantly highlighted Giemsa-light bands. Centromeric or ribosomal spacer DNA repeats used as controls in all studies gave the expected hybridization profiles and showed no non-specific labeling of chromosome arms. Cohesive groups of centromeric DNA arrays and rDNA clusters were observed in interphase nuclei. Refinements in methods for detecting biotin-labeled probes in situ were developed during these studies and calculations indicated that about 20 kb or more of the 1.9-kb repeat were present at each hybridization site. The chromosomal distribution of the 1.9-kb repeat suggests that this sequence may reflect, or participate in defining, ordered structural domains along the chromosome.

Transcription of a long, interspersed, highly repeated DNA element in Xenopus laevis

We have analyzed the transcription of 1723, a long, repeated DNA element that is interspersed in the genome of Xenopus laevis (B. K. Kay and I. B. Dawid (1983) J. Mol. Biol. 170, 583-596). We have detected RNA homologous to 1723 in total cellular RNA from ovaries, embryos, liver, and cultured kidney cells. Transcripts from both strands of the element are present at similar concentrations in these different RNA preparations. In oocytes, approximately 100 pairs of lampbrush chromosome loops are active in the transcription of 1723 elements. The abundance of 1723 RNA increases during embryogenesis, with the highest level reached at the tadpole stage. From cellular fractionation studies, we conclude that 1723 transcripts are largely limited to the nucleus.

Non-Alu family interspersed repeats in human DNA and their transcriptional activity

Randomly selected human genomic clones have been surveyed for the presence of non-Alu family interspersed repeats. Four such families of repeats have been isolated and characterized with respect to repetition frequency, interspersion, base sequence, sequence divergence, in vitro RNA polymerase III transcription, elongation of transcripts in isolated nuclei, and in vivo transcription. The two most abundant of the four families of repeats correspond to previously reported families of repeats, namely the kpn I family and poly (CA). We conclude that most of the highly repetitive (greater than 50,000 copies) human interspersed repeats have already been identified. Two lower abundance repeats families are also described here. The abundance with which each of these families is represented in nuclear RNA qualitatively corresponds to their genomic reiteration frequencies. Further, the complementary strands of each repeat family are approximately symmetrically transcribed. The abundance of these repeats in cytoplasmic RNA is qualitatively less than in nuclear RNA. The bulk of the in vivo transcriptional activity of these repeats thus appears to be nonspecific read through from other promoters.

A large interspersed repeat found in mouse DNA contains a long open reading frame that evolves as if it encodes a protein

DNA sequence analysis of a region contained within a large, interspersed repetitive family of mice reveals a long open reading frame. This sequence extends 978 base pairs between two stop codons, creating a reading frame that is open for 326 amino acids. The DNA sequence in this region is conserved between three distantly related Mus species, as well as between mouse and monkey, in a manner that is characteristic of regions undergoing selection for protein function.

Some extrachromosomal circular DNAs containing the Alu family of dispersed repetitive sequences may be reverse transcripts

A 300 base-pair (bp) size class of small polydisperse circular DNA (spcDNA) isolated from the BSC-1 line of African Green monkey kidney cells was cleaved with the restriction endonuclease Sau3A, and the resulting fragments (100 to 200 bp) were cloned in bacteriophage M13 mp7. The nucleotide sequence of each of 24 clones containing DNA sequences homologous to the Alu family of mobile, dispersed, repetitive elements was then determined. Analysis of these sequences revealed that many, and perhaps all, of the 300 bp Alu-containing spcDNAs had regions in which the 5' and 3' ends of the normal Alu element were juxtaposed and covalently joined. Although more than one model can explain the generation of such circular molecules, the most attractive one at this time involves their generation from reverse transcripts of Alu-specific RNAs.

Rearranged sequences of a human Kpn I element

The complete nucleotide sequence of a human Kpn I element inserted into alpha-satellite DNA is presented. This sequence reveals several features of interest. First, a large block of DNA normally associated with Kpn I elements has been deleted. Second, the order of the remaining sequences is permuted in a manner that cannot be accounted for by simple inversion. Third, a significant open reading frame of 675 bases is detected.

An abundant family of methylated repetitive sequences dominates the genome of Physarum polycephalum

A significant portion (20%) of the Physarum genome can be isolated as a HpaII-resistant, methylated fraction. Cloned DNA probes containing highly-repeated sequences derived from this fraction were used to define the pattern of structural organisation of homologous repeats in Physarum genomic DNA. It is shown that the probes detect an abundant, methylated family of sequences with an estimated genomic repetition frequency greater than 2100, derived from a large repeated element whose length exceeds 5.8kb. Sequences comprising the long repetitive element dominate the HpaII-resistant compartment and account for between 4-20% of the Physarum genome. Detailed restriction/hybridisation analysis of cloned DNA segments derived from this compartment shows that HpaII/MspI restriction sites within some copies of the long repeated sequence are probably deleted by mutation. Additionally, segments of the repeat are often found in different organisational patterns that represent scrambled versions of its basic structure, and which are presumed to have arisen as a result of recombinational rearrangement in situ in the Physarum genome. Preliminary experiments indicate that the sequences are transcribed and that the structural properties of the repeat bear some resemblance to those of transposable genetic elements defined in other eukaryotic species.

Kpn I family of long-dispersed repeated DNA sequences of man: evidence for entry into genomic DNA of DNA copies of poly(A)-terminated Kpn I RNAs

We have isolated eight cDNA clones complementary to the human Kpn I repeat and determined the base sequence of three. We have also determined a portion of the base sequences of three human Kpn I family members. The three cDNA sequences are extensively homologous with the 3' ends of the three genomic Kpn I family members and with a simian Kpn I family member recently described [Thayer, R. E. & Singer, M. F. (1983) Mol. Cell. Biol. 6, 967-973]. The genomic repeats terminate in regions of sequence rich in dAMP residues close to sequences at the 3' ends of the cDNA clones; a precise 3'-terminal nucleotide cannot be distinguished. These structural features are consistent with the dispersal of at least some Kpn I family members by entry into genomic DNA of copies of Kpn I RNA transcripts. Each cDNA contains a long poly(dAMP) homopolymer at its 3' end and either one or two A-A-T-A-A-A polyadenylylation signal sequences upstream from it, suggesting that Kpn I family members may be transcribed by RNA polymerase II.

Some KpnI family members are associated with the Alu family in the human genome

The structures of the termini and their flanking regions of two human KpnI family members were investigated. The two differed in length, but the starting sequence at one terminal (defined as the 5' terminal) was found to be common to both members. The Alu family sequence was found in the 5' flanking regions. The KpnI family sequence started several base-pairs downstream from the 3' end of the Alu family sequence. In both cases, the Alu family sequence was not flanked by the direct repeat sequence common to the Alu family. These two members showed no sequence homology in 3' terminal regions. Interestingly, the Alu family plus the KpnI family unit was found to be flanked by a direct repeat sequence of several base-pair length. Based on these findings, relationship between the Alu family and KpnI family is discussed.

Homology between the KpnI primate and BamH1 (M1F-1) rodent families of long interspersed repeated sequences

The KpnI and BamH1 (or M1F-1) families are the predominant sets of long interspersed repeated DNA sequences (LINEs) in primates and rodents, respectively. Recently, the sequences of several cloned subsegments from each family were determined in different laboratories. These sequences have now been compared and found to be homologous over at least 1400 bp. The data suggest that the two LINE families had a common progenitor and have been conserved in similar abundance although in divergent forms in the two mammalian orders.

A precise termination site in the mouse beta major-globin transcription unit

Nascent labeled RNA from induced, globin-producing mouse erythroleukemia cells was hybridized to cloned regions of the beta major-globin gene. Transcription ceases about 1,000 bases downstream from the poly(A) site as indicated by protection from nuclease digestion of a discrete-sized RNA fragment that it shorter than the protecting cloned DNA fragment. This defines an apparently unique termination site for a protein-coding gene that is transcribed by RNA polymerase II.