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.

[1]  A. Furano,et al.  Long interspersed repeated DNA (LINE) causes polymorphism at the rat insulin 1 locus , 1985, Molecular and cellular biology.

[2]  M F Singer,et al.  Expression of a cytoplasmic LINE-1 transcript is regulated in a human teratocarcinoma cell line. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[3]  A. C. Peacock,et al.  Two-dimensional electrophoretic display of restriction fragments from genomic DNA. , 1985, Analytical biochemistry.

[4]  L. Leinwand,et al.  Transcriptional measurements of mouse repeated DNA sequences. , 1985, Nucleic acids research.

[5]  J. Sikela,et al.  Nucleotide sequence and organization of the mouse adenine phosphoribosyltransferase gene: presence of a coding region common to animal and bacterial phosphoribosyltransferases that has a variable intron/exon arrangement. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[6]  J. Skowroński,et al.  Making sense out of LINES: long interspersed repeat sequences in mammalian genomes , 1985 .

[7]  R. Scarpulla.  Association of a truncated cytochrome c processed pseudogene with a similarly truncated member from a long interspersed repeat family of rat. , 1985, Nucleic acids research.

[8]  M. DePamphilis,et al.  The role of palindromic and non-palindromic sequences in arresting DNA synthesis in vitro and in vivo. , 1984, Journal of molecular biology.

[9]  P. Macdonald,et al.  Regulation of a new bacteriophage T4 gene, 69, that spans an origin of DNA replication. , 1984, The EMBO journal.

[10]  C. Hutchison,et al.  Dispersal process associated with the L1 family of interspersed repetitive DNA sequences. , 1984, Journal of molecular biology.

[11]  T. Osborne,et al.  HMG CoA reductase: A negatively regulated gene with unusual promoter and 5′ untranslated regions , 1984, Cell.

[12]  G. Grimaldi,et al.  Defining the beginning and end of KpnI family segments. , 1984, The EMBO journal.

[13]  R. Schimke.  Gene amplification in cultured animal cells , 1984, Cell.

[14]  A. Tramontano,et al.  Statistical evaluation of the coding capacity of complementary DNA strands. , 1984, Nucleic acids research.

[15]  S. Henikoff.  Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. , 1984, Gene.

[16]  D. Tautz,et al.  Simple sequences are ubiquitous repetitive components of eukaryotic genomes. , 1984, Nucleic acids research.

[17]  C. Hutchison,et al.  A large interspersed repeat found in mouse DNA contains a long open reading frame that evolves as if it encodes a protein. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[18]  L. Leinwand,et al.  Organization and expression of non-Alu family interspersed repetitive DNA sequences in the mouse genome. , 1984, Journal of molecular biology.

[19]  W. C. Barker,et al.  Nucleotide sequences of the retroviral long terminal repeats and their adjacent regions. , 1984, Nucleic acids research.

[20]  A. F. Scott,et al.  Transcripts homologous to a long repeated DNA element in the human genome. , 1984, The Journal of biological chemistry.

[21]  A. Furano,et al.  The spread of sequence variants in Rattus satellite DNAs. , 1984, Nucleic acids research.

[22]  C. Hutchison,et al.  The L1Md long interspersed repeat family in the mouse: almost all examples are truncated at one end. , 1983, Nucleic acids research.

[23]  J. Messing,et al.  Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. , 1983, Gene.

[24]  R. E. Thayer,et al.  Homology between the KpnI primate and BamH1 (M1F-1) rodent families of long interspersed repeated sequences. , 1983, Nucleic acids research.

[25]  J. Maio,et al.  Transcription of the KpnI families of long interspersed DNAs in human cells , 1983, Nature.

[26]  R. E. Thayer,et al.  Kpn I family of long interspersed repeated DNA sequences in primates: polymorphism of family members and evidence for transcription. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[27]  W. Jelinek,et al.  Discrete and heterogeneous high molecular weight RNAs complementary to a long dispersed repeat family (a possible transposon) of human DNA. , 1983, Journal of molecular biology.

[28]  P. Gruss,et al.  Multiple point mutations affecting the simian virus 40 enhancer. , 1983, Science.

[29]  D. Lipman,et al.  Rapid similarity searches of nucleic acid and protein data banks. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[30]  G. Grimaldi,et al.  Members of the KpnI family of long interspersed repeated sequences join and interrupt alpha-satellite in the monkey genome. , 1983, Nucleic acids research.

[31]  A. Furano,et al.  The independent evolution of two closely related satellite DNA elements in rats (Rattus). , 1983, Nucleic acids research.

[32]  R. Ivarie,et al.  Asymmetrical distribution of CpG in an 'average' mammalian gene. , 1982, Nucleic acids research.

[33]  K. Skryabin,et al.  Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing. , 1982, Nucleic acids research.

[34]  Alfred Nordheim,et al.  Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding , 1982, Cell.

[35]  J. Maio,et al.  KpnI families of long, interspersed repetitive DNAs associated with the human beta-globin gene cluster. , 1982, Gene.

[36]  J. Fickett.  Recognition of protein coding regions in DNA sequences. , 1982, Nucleic acids research.

[37]  W. Jelinek,et al.  The Alu family of dispersed repetitive sequences. , 1982, Science.

[38]  L. Manuelidis.  Nucleotide sequence definition of a major human repeated DNA, the Hind III 1.9 kb family. , 1982, Nucleic acids research.

[39]  Douglas L. Brutlag,et al.  SEQ: a nucleotide sequence analysis and recombination system , 1982, Nucleic Acids Res..

[40]  Robert G. Martin,et al.  The remarkable instability of replication loops provides a general method for the isolation of origins of DNA replication , 1981, Cell.

[41]  G. Dover,et al.  Organization and evolutionary progress of a dispersed repetitive family of sequences in widely separated rodent genomes. , 1981, Journal of molecular biology.

[42]  W. Ansorge,et al.  Improvements of DNA sequencing gels. , 1981, Analytical biochemistry.

[43]  Manolo Gouy,et al.  Codon catalog usage is a genome strategy modulated for gene expressivity , 1981, Nucleic Acids Res..

[44]  A. Nienhuis,et al.  A family of long reiterated DNA sequences, one copy of which is next to the human beta globin gene. , 1980, Nucleic acids research.

[45]  T. Jukes.  Silent nucleotide substitutions and the molecular evolutionary clock. , 1980, Science.

[46]  C. Schildkraut,et al.  A family of moderately repetitive sequences in mouse DNA. , 1980, Nucleic acids research.

[47]  L. Manuelidis.  Novel classes of mouse repeated DNAs. , 1980, Nucleic acids research.

[48]  F C Kafatos,et al.  Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. , 1979, Nucleic acids research.

[49]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[50]  R. Britten,et al.  Repeated Sequences in DNA , 1968 .

[51]  J. Rogers,et al.  The origin and evolution of retroposons. , 1985, International review of cytology.

[52]  G. Bernardi,et al.  The Bam repeats of the mouse genome belong in several superfamilies the longest of which is over 9 kb in size. , 1984, Nucleic acids research.

[53]  H. Manor,et al.  "Onion skin" replication of integrated polyoma virus DNA and flanking sequences in polyoma-transformed rat cells: termination within a specific cellular DNA segment. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[54]  P. Gruss,et al.  Enhancer elements , 1983, Cell.

[55]  M. Singer.  Highly repeated sequences in mammalian genomes. , 1982, International review of cytology.

[56]  G. Bernardi,et al.  Sequence organization and genomic distribution of the major family of interspersed repeats of mouse DNA. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[57]  P Chambon,et al.  Organization and expression of eucaryotic split genes coding for proteins. , 1981, Annual review of biochemistry.

[58]  M. Botchan,et al.  Studies on simian virus 40 excision from cellular chromosomes. , 1979, Cold Spring Harbor symposia on quantitative biology.

[59]  S. Falkow,et al.  Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. , 1977, Gene.

[60]  H. Zachau,et al.  Nucleic Acids Research Nucleotide sequence of a highly repetitive component of rat DNA , 2022 .