References - S.C. Hardies Page

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Adey NB, Schichman SA, Hutchison CA III, and Edgell MH. 1991. Composite of A and F-type 5' terminal sequences defines a subfamily of mouse LINE-1 elements. J. Mol. Biol. 221:367-373.

Adey, N.B., Schichman, S.A., Graham, D.K., Peterson, S.N., Edgell, M.H., Hutchison, C.A. III. 1994. Rodent L1 evolution has been driven by a single dominant lineage that has repeatedly acquired new transcriptional regulatory sequences. Mol. Biol. Evol. 11:778-789.

Adey NB, Tollefsbol TO, Sparks AB, Edgell MH, Hutchison CA III. 1994. Molecular resurrection of an extinct ancestral promoter for mouse L1. Proc. Natl. Acad. Sci., USA: 91:1569-1573.

Aquadro, C.F. 1992. Why is the genome variable? Insights from Drosophila. Trends in Genetics 8:255-262.

Asch HL. Eliacin E. Fanning TG. Connolly JL. Bratthauer G. Asch BB. 1996. Comparative expression of the LINE-1 p40 protein in
human breast carcinomas and normal breast tissues. Oncology Research. 8(6):239-47.

Bellis M, Jubier-Maurin V, Dod B, Vanlerberghe F, Laurent A- M, Senglat C, Bonhomme F, and Roizes G. 1987. Distribution of two recently inserted long interspersed elements of the L1 repetitive family at the Alb and Beta-h3 loci in wild mice populations. Mol. Biol. Evol. 4:351-363.

These are the only two mouse LINE-1 inserts for which an inserted allele frequency has been determined to my knowledge. They were picked with the idea that these were young inserts, although the available resolution in time in those days was only about 0.5 Myr. The Beta-h3 insert is L1Md4. It was found in 9/114 M. m. domesticus mice and 0/140 M. m. musculus mice. The positives were geographically highly localized and all were associated with the Hbb^p haplotype, even though L1Md4 was originally found in the BALB/c inbred strain in a Hbb^d haplotype.
Now we know that L1Md4 has only 3 differences with L1reeler which is the prototype for this clade. The length is 2075, so assuming 1% divergence/Myr on each lineage the age estimate is about 70,000 years old.
The Alb L1 is also called I12 or MMLINSAA in GenBank (acc X13060). It has 2/842 differences with L1MdA2 computing to being about 120,000 years old. It was found in 8/140 M. m. musculus and 34/92 M. m. domesticus .

Benit, L., De Parseval, N., Casella, J.-F., Callebaut, I., Cordonnier, A., and Heidmann, T. 1997. Cloning of a new murine endogenous retrovirus, MuERV-L, with strong similarity to the human HERV-L element and with a gag coding sequence closely related to the Fv1 restriction gene. J. Vir. 71: 5652-5657.

Bird A. 1997. Does DNA methylation control transposition of selfish elements in the germline? Trends in Genetics 13:469- 472.

Response to Yoder et al. (1997) arguing against a role for genomic methylation as a host defense against transposons.

Boeke JD. 1997 LINEs and Alus - the polyA connection. Nature Genet. 16: 6-7.

Boissinot S. Entezam A. Furano AV. 2001. Selection against deleterious LINE-1-containing loci in the human lineage.
Molecular Biology & Evolution. 18(6):926-35.

Boissinot S. Chevret P. Furano AV. 2000. L1 (LINE-1) retrotransposon evolution and amplification in recent human history.
Molecular Biology & Evolution. 17(6):915-28.

Boissinot S. Furano AV. 2001. Adaptive evolution in LINE-1 retrotransposons. Molecular Biology & Evolution.
18(12):2186-94.

Bourset P, Din W, Anand R, Darviche D, Dod B, Von Deiming F, Talwar GP, & Bonhomme. 1996. Origin and radiation of the house mouse: mitochondrial DNA phylogeny. J. Evol. Biol. 9: 391-415.

The mitochondrial DNA phylogeny reported in this paper generally supports the story developed in Din et al., 1996, but also establishes a time frame. Origin of the house mouse complex is reported to be in northern India at about 900,000 yr BP based on the time at which the genetic diversity coalesces. Origin of the subspecies domesticus, musculus, and castaneus is reported to be at about 350,000 yr BP. Mouse mitochondrial DNA divergence is taken to be 4%/Myr as opposed to about 1%/Myr for nuclear genes.

Branciforte, D. and Martin, S.L. 1994. Developmental and cell type specificity of LINE-1 expression in mouse testis: Implications for transposition. Mol. Cell Biol. 14: 2584-2592.

Bratthauer GL. Fanning TG. 1992. Active LINE-1 retrotransposons in human testicular cancer. Oncogene.
7(3):507-10.

Bratthauer, G.L., Fanning, T.G. 1993. LINE-1 expression in pediatric germ cell tumors. Cancer 71: 2383-2386.

Bratthauer, G.L., Cardiff, R.D., and Fanning, T.G. 1994. Expression of LINE-1 retrotransposons in human breast cancer. Cancer 73: 2333-2336.

Britten RJ. 1998. DNA sequence insertion and evolutionary variation in gene regulation. Proc. Natl. of Sci. USA 93:9376-9377

Britten RJ, & Davidson EH. 1969. Science 165:349-357.

Bucheton, A., Simonilig, M., Vaury, C., and Crozatier, M. 1986. Sequences similar to the I transposable element involved in I-R hybrid dysgenesis in D. melanogaster occur in other Drosophila species. Nature 322:650-652.

Brookfield JFY, Badge RM. 1997. Population genetics models of transposable elements. Genetica 100:281-294.

Discusses how passage of a host population through a population bottleneck could reduce restraints on transposon copy number.

Burke, W.D., Eickbush, D.G., Xiong, Y., Jakubczak, J., and Eickbush, T.H. 1993. Sequence relationship of retrotransposable elements R1 and R2 within and between divergent insect species. Mol. Biol. Evol 10: 163-185.

Cabot EL, Angeletti B, Usdin K, Furano AV. 1997. Rapid evolution of a young L1 (LINE-1) clade in recently speciated Rattus taxa. J. Mol. Evol. 45:412-423.

Capy P, Bazin C, Higuet D, Langin T. 1998. Dynamics and Evolution of Transposable Elements. Molecular Biology Intelligence Unit. Chapman & Hall, New York.

An excellent compendium of information about all manner of transposons, focusing on classification by structure, sequence, and behavior.
A good source of references to locate literature about specific transposons.
Has a section emphasizing the ambiguities attendant to concluding that an element has transferred horizontally.

Casavant, N.C., Sherman, A.N., and Wichman, H.A. 1996. Two persistent LINE-1 lineages in Peromyscus have unequal rates of evolution. Genetics 142:1289-1298.

Casavant NC, Lee RN, Sherman AN, and Wichman HA. 1998. Molecular evolution of two lineages of L1 (LINE-1) retrotransposons in the California mouse, Peromyscus californicus. Genetics 150:345-357.

Cavalli-Sforza,L. Luca, Paolo Menozzi, Alberto Piazza "The History and Geography of Human Genes" (1994) Princeton Univ. Press, Princeton, N.J.

Chao L, Vargas C, Spear BB, Cox EC. 1983. Transposable elements as mutator genes in evolution. Nature 303: 633-35.

Charlesworth B, & Charlesworth D. 1983. The population dynamics of transposable elements. Genet. Res. 42: 1-27.

A distribution function is described for Drosophila transposons that leads to an equilibrium condition. Charlesworth & Langley, 1989, gives a more explanatory account.

Charlesworth B. 1985. The population genetics of transposable elements. In Population Genetics and Molecular Evolution ed. T. Ohta, K. Aoki, pp. 213-32. Springer Verlag.

Charlesworth B, and Langley CH. 1986. The evolution of self- regulated transposition of transposable elements. Genetics 112:359- 383.

Charlesworth B, and Langley CH. 1989. The population genetics of Drosophila transposable elements. Ann. Rev. Genet. 23:251-287.

A thorough review of the equilibrium model for Drosophila transposons. Equilibrium is described with a constant copy number per family of about 10/genome, a transposition frequency per element (assumed to be a constant) of 10^-4 to 10^-5, an excision frequency per element of 10^-5 to 10^-6, very low allele frequency, and selection coefficients on the order of 10^-5 against individual inserts.

DeBerardinis RJ, and Kazazian HH Jr. 1998. Full-length L1 elements have arisen recently in the same 1-kb region of the gorilla and human genomes. J. Mol. Evol. 47:292-301.

DeBerardinis RJ, Goodier JL, Ostertag EM, Kazazian HH Jr. 1998. Rapid amplification of a retrotransposon subfamily is evolving the mouse genome. Nat.Genetics 20:288-290.

11 full length domesticus TF sequences characterized.
7 found to be competent to transpose in culture
An A-type element named L1Md-A101 found to transpose in culture.
Strain distribution of 7 TF inserts given
Estimated copy number of full length TF elements as 4800/diploid genome.

DeBerardinis RJ, Kazazian HH Jr. (1999) Analysis of the promoter from an expanding mouse retrotransposon subfamily. Genomics 56: 317-323.

Does in vitro transcription on TF promoter array, and components.
Discusses the density of CGs and substitutions at CGs in the TF promoter arrays.

Deininger PL, Batzer MA, Hutchison CA III, and Edgell MH. 1992. Master genes in mammalian repetitive DNA apmlification. Trends Genet. 8: 307-311.

Din W, Anand R, Bourset P, Darviche D, Dod B, Jouvin-Marche E, Orth A, Talwar GP, Cazenave P-A, & Bonhomme F. 1996. Origin and radiation of the house mouse: clues from nuclear genes. J. Evol. biol. 9: 529-539.

This paper indicates that the house mouse originated in the northern part of the Indian subcontinent. The populations with the greatest genetic variation exist in this region, including the population known as M. m. bactrianus . M. m. domesticus, M. m. musculus, and M. m. castaneus are less diverse populations that moved out in three different directions from this central population. A timescale for these events is established in Bourset et al, 1996.

Dombroski BA, Mathias SL, Nanthakumar E, Scott AF, and Kazazian HH Jr. 1991. Isolation of an active human transposable element. Science 254:1805-1807.

Dombroski, B.A., Feng, Q.F., Mathias, S.L., Sassaman, D.M., Scott, A.F., Kazazian, H.H. Jr., and Boeke, J.D. 1994. An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 14: 4485-4492. Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601.

Doolittle WF, Kirkwood TBL, and Dempster MAH. 1984. Selfish DNAs with self-restraint. Nature 307:601-603.

Doolittle, R.F., Feng, D.-F., Johnson, M.S., and McClure, M.A. 1989. Origins and evolutionary relationships of retroviruses. Quant. Rev. Biol. 64: 1-30.

Edgell, M.H., Hardies, S.C., Loeb, D.D., Shehee, W.R., Padgett, R.W., Burton, F.H. Comer, M.B., Casavant, N.C., Funk, F.D., and Hutchison, C.A. III 1987. The L1 family in mice. Prog. Clin. Biol. Res., 251, 104-129.

Edgell MH. 1994. Tracing Transposable elements. Nat. Gen. 7:120-121.

Front section commentary on the paper discovering LRE-2.
It emphasizes the impact of LINE-1 insertional mutagenesi and ectopic exchange on the human mutation rate.

Eickbush, T.H. 1992. Transposing without ends: the non-LTR retrotransposable elements. New Biol. 4:430-440.

Engels WR. 1989. P elements in Drosophila melanogaster. In Mobile DNA (Berg, DE and Howe, MM, eds.) pp. 437-484. ASM, Washington DC.

Engels WR. 1992. The origin of P elements in Drosophila melanogaster. BioEssays 14:681-686.

Feng Q Moran JV Kazzazian HH Jr, Boeke JD. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905-916.

Finnegan DJ. 1989. The I factor and I-R hybrid dysgenesis in Drosophila melanogaster. In Mobile DNA (DH Berg and MM Mowe, eds.) pp.503-517. ASM, Washington DC.

Furano AV. 2000. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Progress in Nucleic Acid Research & Molecular Biology. 64:255-94, 2000.

Furano AV, Hayward BE, Chevret P, Catzeflis F, and Usdin K. 1994. Amplification of the ancient murine Lx family of long interspersed repeated DNA occurred during the murine radiation. J. Mol. Evol. 38:18-27.

Furano AV, and Usdin K. 1995. DNA "Fossils" and Phylogenetic Analysis. J. Biol. Chem. 270: 25301-25304.

Gebhard W, Meitinger T, Hochtl J, and Zachau HG. 1982. A new family of interspersed repetitive DNA sequences in the mouse genome. J. Mol. Biol. 147:453-471.

The source of the original 100,000 LINE-1 copy number estimate for mouse L1.
Since it was done by hybridization, it's really the number of LINE-1s easily detected by hybridization (down to about 80% identity).

Daniel L. Hartl, Andrew G. Clark 1989. Principles of Population Genetics, Sinauer, 1989, Sunderland, Massachusetts.

Hartl DL, Lohe AR, Lozovskaya ER. 1997. Modern thoughts on an ancyent marinere: function, evolution, regulation. Annual Rev. of Genetics 31:337-358.

Reviews relation of mariner to Tc1 family & DDD vs. DDE motifs.
Reviews cut and paste mechanism of insertion.
Reviews species distribution and copy numbers.
Defines subgroups: mauritiana, cecropia, mellifera, irritan, & capitata; more than one lineage can co-exist in a species.
Mentions case of human mariner thought to be hotspot for recombination and initiation of a genetic disorder: see

Kiyosawa and Chance . 1996. Hum. Mol. Genet. 5:745-53.
Reiter et al. 1996. Nat. Genet. 12:288-97.

Describes vertical inactivation and stochastic loss.
Describes regulatory interactions:

Overproduction inhibition
Dominant negative regulation.
A case where mariner is activated during hybrid dysgenesis

Hattori, M., Kuhara, S., Takenaka, O., and Sakaki, Y. 1986. L1 family of repetitive DNA sequences in primates may be derived from a sequence encoding a reverse transcriptase-related protein. Nature 321: 625-628.

Hayward BE, Zavanelli M, and Furano AV. 1997. Recombination creates novel L1 (LINE-1) elements in Rattus norvegicus. Genetics 164:641-654.

Hohjoh H, and MF Singer.1996. Cytoplasmic ribonucleoprotein complexes containing human LINE-1
protein and RNA. EMBO 15: 630-639.

Complexes fall apart with RNAse treatment.
Can crosslink recombinant L1orf1p up to 250 kD.
Says amino terminus important for complex stability (meaning the 1st half of the coiled-coil..
Start calling the coiled-coil domain coiled coil instead of leucine zipper.

Hohjoh H, and Singer MF. 1997. Ribonuclease and High Salt Sensitivity of the Ribonucleoprotein Complex Formed by the Human LINE-1 Retrotransposon . J. Mol. Biol. 271: 7-12.

Says 0.5 M NaCl dissociates in vivo complex, leaving a multimeric L1orf1p not bound to RNA.

Hohjoh H, and Singer MF. 1997. Sequence-specific single-strand RNA binding protein encoded by
the human LINE-1 retrotransposon. EMBO 16: 6034-6043.

Use heterogeneous preparation of human L1orf1p directly isolated from human cells.
Binds in vitro to L1 RNA.
Two specific sites on the two largest T1 fragments.
Binding appears tight and RNA-specific by competition assays.

Holmes, S.E., Singer, M.F., Swergold, G.D. 1992. Studies on p40, the leucine zipper motif-containing protein encoded by the first open reading frame of an active human LINE-1 transposable element. J. Biol. Chem. 267: 19765-19768.

Holmes SE, Dombroski BA, Krebs CM, Boehm CD, and Kazazian HH Jr. 1994. A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion. Nat. Genet. 7: 143-148.

Hutchison III, C.A., S.C. Hardies, D.D. Loeb, W.R. Shehee, & M.H. Edgell. 1989. LINES and related retroposons: Long interspersed repeated sequences in the eukaryotic genome. In Mobile DNA. (Eds. Douglas E. Berg and Martha M. Howe) pp. 593-617, ASM, Washington D.C.

Jakubczak, J.L., Burke, W.D., Eickbush, T.H. 1991. Retrotransposable elements R1 & R2 interrupt the rRNA genes of most insects. Proc. Natl. Acad. Sci. USA 88: 3295-3299.

Jubier-Maurin V, Wincker P, Cuny G, Roizes G. 1987. The relationships between the 5' end repeats and the largest members of the L1 interspersed repeated family in the mouse genome. Nucl. Acids Res. 15:7395-7410.

By hybridization with A and F promoter probes shows both are present in M. cervicolor and M. setulosus Those are at the same depth as M. caroli and M. pahari, respectively.

Kass DH, Peppers JA, Maltbie M, Baker RJ. (1998) Enrichment of a LINE subfamily in a single chromosomal region in Peromyscus. Mamm. Genome 9:488-490.

Shows how you can get a LINE-1 subfamily composed of all old, defective- looking elements by an old LINE-1 getting caught up in a DNA amplification having nothing to do with LINE-1 activity.

Kazazian, H.H., Wong, C., Youssoufian, H., Scott, A.F., Phillips, D.G., Antonarakis, S.E. 1988. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 332: 164-166.

Kazazian HH Jr., Moran JV. 1998. The impact of L1 retrotransposons on the human genome. Nat. Genetics 19: 19-24.

A review.
Points out that 4 of 160 molecularly characterized mouse mutants are L1 insertions:

orleans reeler
spastic
med
beige

Kidwell, M.G. 1993. Voyage of an ancient mariner. Nature 362:202.

Kimmel, B.E., Ole-Moiyoi, O.K., and Young, J.R. 1987. Ingi, a 5.2-kb dispersed sequence element from Trypanosoma brucei that carries half of a smaller mobile element at either end and has homology with mammalian LINEs. Mol. Cell. Biol. 7:1465-1475.

Kingsmore, S. F., Giros, B., Suh, D., Bieniarz, M., Caron, M.G. and Seldin, M.F. 1994. Glycine receptor Beta-subunit gene mutation in the spastic mouse associated with LINE-1 element insertion. Nat. Genet. 7: 136-141.

Kohrman DC, Harris JB, Meisler MH. 1996. Mutation detection in the med and medj alleles of the sodium channel Scn8a. Unusual splicing due to a minor class AT-AC intron. J. Biol. Chem. 271: 17576-17581.

Kolosha, V.O., and Martin, S.L. 1995. Polymorphic sequences encoding the first open reading frame protein from LINE-1 ribonucleoprotein particles. J. Biol. Chem. 270:2868-2873.

Vladimir O. Kolosha, V.O. and Sandra L. Martin, S.L. 2003. High-affinity, Non-sequence-specific RNA Binding by the Open Reading Frame 1 (ORF1) Protein from Long Interspersed Nuclear Element 1 (LINE-1) J. Biol. Chem. 2003 278: 8112-8117.

Kraft,R., Kadyk,L. and Leinwand,L.A. Sequence organization of variant mouse 4.5 S RNA genes and pseudogenes Genomics 12 (3), 555-566 (1992)

GenBank MDD645GE, X60028
Contained 3 truncated LINE-1s, which they named L1MdX, L1MdY, and L1MdZ.
Since these three fall in 3 previously unnamed large families, we are using them as namesakes for those families.
The L1MdX family is also called the L2 or L1Md2 family and may be the same as the A/F composite family.

Langley, C.H, Montgomery, E., Hudson, R., Kaplan, N. and Charlesworth, B. 1988. On the role of unequal exchange in the containment of transposable element copy number. Genet. Res. Camb. 52: 223-235.

Leibold DM. Swergold GD. Singer MF. Thayer RE. Dombroski BA. Fanning TG. 1990. Translation of LINE-1 DNA elements in vitro
and in human cells. Proceedings of the National Academy of Sciences of the United States of America. 87(18):6990-4.

Loeb, D.D., Padgett, R.W., Hardies, S.C., Shehee, W.R., Comer, M.B., Edgell, M.H., and Hutchison, C.A. III. 1986. The sequence of a large L1Md element reveals a tandemly repeated 5' end and several features found in retrotransposons. Mol. Cell. Biol. 6, 168-182.

Prototypical mouse A-type full length LINE-1
Source of standard coordinate system
GenBank M13002

Luan, D.D., Korman, M.H., Jakubczak, J.L., and Eickbush, T.H. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LT retrotransposition. Cell 72: 595-605.

Luan, D.D. and Eickbush, T.H. 1995. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol. Cell. Biol. 15: 3882-3891.

Martin SL. Bushman FD. 2001. Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Molecular & Cellular Biology. 21(2):467-75.

Martin SL. Li J. Weisz JA. 2000. Deletion analysis defines distinct functional domains for protein-protein and nucleic acid interactions in the
ORF1 protein of mouse LINE-1.Journal of Molecular Biology. 304(1):11-20, 2000.

Martin SL. Li J. Epperson LE. Lieberman B. 1998. Functional reverse transcriptases encoded by A-type mouse LINE-1: defining the minimal
domain by deletion analysis. Gene. 215(1):69-75.

Martin, SL. 1991. Ribonucleoprotien particles with LINE-1 RNA in mouse embryonal carcinoma cells. Mol. Cell. Biol. 11:4804-4807.

Martin, S. 1991. LINEs. Curr. Opin. Genet. Dev. 1: 505- 508.

Mathias, S.L., Scott, A.F., Kazazian, H.H., Jr., Boike, J.D., and Gabriel, A. 1991. Reverse transcriptase encoded by a human transposable element. Science 245: 1808-1810.

McMillan, J.P., and Singer, M.F. 1993. Translation of the human LINE-1 element, L1Hs. Proc. Natl. Acad. Sci. USA 90:11533-11537.

Miki, Y., Nishisho, I., Horii, A., Miyoshi, Y., and Utsumnomiya, J. 1992. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 52: 643-645.

Misra S, and Rio DC 1990. Cytotype control of Drosophila P element transposition: the 66 kd protein is a repressor of transposase activity. Cell 62: 269-284.

Misra S, Buratowski RM, Ohkawa T, and Rio DC. 1993. Cytotype control of Drosophila melanogaster P element transposition: genomic position determines maternal repression. Genetics 135:785-800.

Mizrokhi, L.J., and Mazo, A.M. 1990. Evidence for horizontal transmission of the mobile element jockey between distant Drosophila species. Proc. Natl. Acad. Sci. USA 87: 9216-9220.

Modi WS. 1996. Phylogenetic history of LINE-1 among arvicolid rodents. Mol. Biol. Evol. 13:633-641.

Montgomery, E.A., Langley, C.H. 1983. Transposable elements in Medeelian populations. II. Distribution of three copia-like elements in a natural population. Genetics 104:473-83.

Moran JV. 1999. Human L1 retrotransposition: insights and peculiarities learned from a cultured cell retrotransposition assay. Genetica. 107(1-3):39-51.

Moran, J.V., Holmes, S.E., Naas, T.P., DeBerardinis, R.J., Boeke, J.D., and Kazazian, H.H. Jr. 1996. High Frequency Retrotransposition in cultured mammalian cells. Cell 87: 917-927.

Assayed insertion rates for neo marked L1.2 or LRE2 expressed off a moderate copy number episome in HeLa cells.
Was expressed off of either the CMV promoter or the L1 promoter.
Got frequency of 0.5 x 10^-3.
Insertion required ORF1.
Trans-mobilization (ORF2^-) was 10^-6. Ie. Trans-mobilization was 10^-3 of cis-mobilization, although the experiments weren't done in a strictly comparable way.
Got some very long target site duplications and some deletions of target site sequence, instead of the normal L1 TSD pattern.
The 3' UTR Purine tract was not required.

Moran JV. DeBerardinis RJ. Kazazian HH Jr. 1999. Exon shuffling by L1 retrotransposition. Science.
283(5407):1530-4, 1999

Naas TP, DeBerardinis RJ, Moran JV, Ostertag EM, Kingsmore SF, Seldin MF, Hayashizaki Y, Martin SL, and Kazazian HH Jr. 1998. An actively retrotransposing novel subfamily of mouse L1 elements. EMBO J. 17:590-597.

Two full length spontaneous mouse L1 inserts have nearly identical seq. (99.4%).

L1_Orl, aka L1 insert in Orleans reeler, aka L1reeler, aka D84391.
L1_spa, aka L1 in spastic, aka AF016099

The both have F-type promoters; 5 2/3, and 7 1/2 promoter repeats, respectively.
They form a family separate from the A family (actually from the A2 family) which the authors name T_F. [Note: T_F is the same as our previous L1Md4 family, and is the same family as the spretus oMS475 and oMs7024 families.]
The new F-type promoter is 73% identical to the "old" F-type promoter consensus.
They determine 2000-3000 copies of this 5' UTR in the mouse. Notes by contrast that there are only about 160 full length members of human Ta subfamily.
They were active by promoter assay, and RT assay; in the latter, they were comparable to human L1.2.
By in culture transposition assay, they were 25% and 4% as active as L1.2, respectively.
See also DeBerardinis et al., 1998.

Narita, N., Nishio, H., Kitoh, Y., Ishikawa, Y., Ishikawa, Y., Minami, R., Nakamura, H., and Matsuo, M. 1992. Insertion of a 5' truncated L1 element into the 3' end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystropy. J. Clin. Invest 91: 1862-1876.

Nevers P, Saedler H. 1977. Transposable genetic elements as agents of instability and chromosomal rearrangements. Nature 268:109-115.

Orgel LE, Crick FH (1980) Selfish DNA: the ultimate parasite. Nature 284:604.

Ostertag EM. Prak ET. DeBerardinis RJ. Moran JV. Kazazian HH Jr. 2000. Determination of L1 retrotransposition kinetics in cultured cells.
Nucleic Acids Research. 28(6):1418-23.

Padgett RW, Hutchison CA III, Edgell MH. 1988. 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. Nucl. Acids Res. 16:739-749.

Pardue ML, Danilevskaya ON, Lowenhaupt K, Slot F, Traverse KL. 1996. Drosophila telomeres: new views on chromosome evolution. Trends in Genetics 12(2):48-52.

Perou CM, Pryor RJ, Naas TP, Kaplan J. 1997. The bg allele mutation is due to a LINE-1 element retrotransposition. Genomics 42: 366-368.

Plasterk RHA, Izsvak Z, Ivics Z. 1999. Residents aliens. Trends in Genetics 15:326-332.

About mariner elements.

Sassaman, D. M., Dombroski, B. A., Moran, J. V., Kimberland, M. L., Naas, T. P., DeBerardinis, R. J., Gabriel, A., Swergold, G. D. & Kazazian, H. H., Jr. (1997). Many human L1 elements are capable of ret- rotransposition. Nature Genet. 16, 37-43.

Saxton JA and Martin SL. 1998. Recombination between subtypes creates a mosaic lineage of LINE-1 that is expressed and actively retrotransposing in the mouse genome. J. Mol. Biol. 280:611-622.

Schichman, S.A., Adey, N.B., Edgell, M.H., Hutchison, C.A. III. 1993. L1 A-monomer tandem arrays have expanded during the course of mouse L1 evolution. Mol. Biol. Evol. 10:552-570.

Schichman SA, Severynse DM, Edgell MH, Hutchison CA III. 1992. Strand-specific LINE-1 transcription in mouse F9 cells originates from the youngest phylogenetic subgroup of LINE-1 elements. J. Mol. Biol. 224:559-574.

Schwarz-Summer, Z., Leclercq, L., Gobel, E., and Saedler, H. 1987. Cin4, an insert altering the structure of the A1 gene in Zea mays, exhibits properties of nonviral retrotransposons. EMBO J. 6:3873-3880.

Scott, A.F., Schmeckpeper, B.J., Abdelrazik, M., Comey, C.T., O'Hara,B., Rossiter, J.P., Cooley, T., Heath, P., Smith, K.D., and Margolet, L. 1987. Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence. Genomics 1: 113-125

Severynse, D.M., Hutchison, C.A. III, and Edgell, M.H. 1992. Identification of transcriptional regulatory activity within the 5' A- type monomer sequence of the mouse LINE-1 retroposon. Mammalian Genome 2: 41-50.

She JX, Bonhomme F, Boursot P, Thaler L, and Catzeflis F. (1990) Molecular phylogenies in the genus Mus: Comparative analysis of electrophoretic, scnDNA hybridization, and mt DNA RFLP data. Biol. J. Linnean Soc. 41:83-103.

Summarizes data that spretus, spicilegus, and the musculus ancestral species split 1.1 Mya.
Based on 10 Mya rat/mouse split.

Shehee, W.R., Chao, S.-F., Loeb, D.D., Comer, M.B., Hutchison, C.A. III, and Edgell, M.H. 1987. Determination of a functional ancestral sequence and definition of the 5' end of A-type mouse L1 elements. J. Mol. Biol. 196: 757-767.

Reports L1MdA13 and L1Md9 sequences
Reconstructs ancestral sequence for A2 & A13, which would be the sequence responsible for the terminal transposition burst of the domesticus A2 lineage.

Shehee WR, Loeb DD, Adey NB, Burton FH, Casavant NC, Cole P, Davies CJ, McGraw RA, Schichman SA, Severynse DM, Voliva CF, Weyter FW, Wisely GB, Edgell MH, and Hutchison CA III. 1989. Nucleotide sequence of the BALB/c mouse beta-globin complex. J Mol Biol 205:41-62.

Singer, M.F., Krek, V., McMillan, J.P., Swergold, G.D., and Thayer, R.E. 1993. LINE-1: a human transposable element. Gene 135:183-188.

Skowronski, J., and Singer, M.F. 1986. The abundant LINE-1 family of repeated sequences in mammals, genes and pseudogenes. Cold Spring Harbor Symp. Quant. Biol. 51: 457-464.

Skowronski, J., Fanning, T.G., and Singer, M.F. 1988. Unit- length LINE- 1 transcripts in human teratocarcinoma cells. Mol. Cell Biol. 8: 1385- 1397.

Smit, A.F.A, Toth, G., Riggs, A.D., Jurka, J. 1995. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 246: 401-417.

They made a mammoth compilation of mammalian LINE-1 sequences, and defined subfamilies (age cohorts). With this approach, they showed that they could track remnants of LINE-1 evolution back to the mammalian radiation.

Syvanen M. 1984. The evolutionary implication of mobile genetic elements. Annual Rev. Genetics 18:271-293.

Takahara T, Ohsumi T, Kuromitsu J, Shibata K, Sasaki N, Okazaki Y, Shibata H, Sato S, Yoshiki A, Kusakabe M, Muramatsu M, Ueki M, Okuda K, and Hayashizaki Y. 1996. Dysfunction of the Orleans reeler gene arising from exon skipping due to transposition of a full-length copy of an active L1 sequene into the skipped exon. Hum. Mol. Genet. 5: 989-993.

See also Naas et al.

Thayer RE. Singer MF. Fanning TG. 1993. Undermethylation of specific LINE-1 sequences in human cells producing a
LINE-1-encoded protein. Gene. 133(2):273-7.

Trelogan, S.A., and Martin, S.L. 1995. Tightly regulated, developmentally specific expression of the first open reading frame from LINE-1 during mouse embryogenesis. Proc. Natl. Acad. Sci. USA 92: 1520-1524.

Usdin K, and Furano AV. 1988. Rat L1 (Long interspersed repeated DNA) elements contain guanine-rich homopurine sequences that induce unpairing of contiguous duplex DNA. Proc. Natl. Acad. Sci. USA: 85:4416-4420.

Usdin K, and Furano AV. 1989. The structure of the guanine-rich polymurine:polypyrimidine sequence at the right end of the rat L1 (LINE-1) element. J. Biol. Chem. 264: 15681-15687.

Usdin K, Chevret P, Catzefils FM, Verona R, and Furano AV. 1995. L1 (LINE-1) retrotransposable elements provide a fossil record of the phylogenetic history of murin rodents. Mol. Biol. Evol 12:73-82.

Vanlerberghe F, Bonhomme F, Hutchison CA III, and Edgell MH. 1993. A major difference between the divergence patterns within the LINE-1 families in mice and voles. Mol. Biol. Evol. 10: 719-731.

Verneau, O., Catzeflis, F., and Furano, A.V. 1997. Determination of the Evolutionary Relationships in Rattus sensu lato (Rodentia:Muridae) using L1 (LINE-1) Amplification Events. J. Mol. Evol. 45:424-436.

They organize the rat LINE-1 sequences into subfamilies (age cohorts), make oligos, and use the presence or absence of a high copy number signal with each oligo as a phylogenetic character to sort out the phylogenetics of the rat.

Verneau O, Catzeflis F, and Furano AV. 1998. Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons. Proc. Natl. Acad. Sci. USA: 95:11284-11280.

Wade MJ, Beeman RW. 1994. The population dynamics of maternal-effect selfish genes. Genetics 138:1309-1314.

Wei W. Gilbert N. Ooi SL. Lawler JF. Ostertag EM. Kazazian HH. Boeke JD. Moran JV. 2001. Human L1 retrotransposition: cis preference
versus trans complementation. Molecular & Cellular Biology. 21(4):1429-39.

Wei W. Morrish TA. Alisch RS. Moran JV. 2000. A transient assay reveals that cultured human cells can accommodate multiple LINE-1
retrotransposition events. Analytical Biochemistry. 284(2):435-8.

Wincker P, Jubier-Maurin, V., and Roizes G. 1987. Unrelated sequences at the 5' end of mouse LINE-1 repeated elements define two distinct subfamilies. Nucl. Acids. Res. 15:8593-8606.

Xiong, Y. and Eickbush, T.H. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353-3362.

Yoder JA, Walsh CP, Bestor TH. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends in Genetics 13:335-340.

Argues in favor of genomic methylation as a defense against transposons.

Zaiss DM, Kloetzel P-M. 1999. A second gene encoding the mouse proteasome activator PA28 beta subunit is part of a LINE1 element and is driven by a LINE1 promoter. J. Mol. Biol. 287:829-835.

Zechner U, Reule M, Orth A, Bonhomme F, Strack B, Guenet J-L, Hameister H, Fundele R 1996 An X-chromosome linked locus contributes to abnormal placental development inmouse interspecific hybrids. Nat Genet 12: 398-403.