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1
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0030479536
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The origin of interspersed repeats in the human genome
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Smit A.F.A. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 6:1996;743-748.
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Curr Opin Genet Dev
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Smit, A.F.A.1
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85031635620
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RepeatMasker server on World Wide Web URL
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RepeatMasker server on World Wide Web URL: http://repeatmasker.genome.washington.edu.
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3
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85031622650
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RepBase Update 1999 on World Wide Web URL Widely used in the genomics world for the elimination of repeats before sequence analysis, this database of reconstructed transposable elements is still underutilized as a source of information for transposon research. Much of the data is not published elsewhere nor available in general databases
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RepBase Update 1999 on World Wide Web URL: http://www.girinst.org/~server/repbase.html . Widely used in the genomics world for the elimination of repeats before sequence analysis, this database of reconstructed transposable elements is still underutilized as a source of information for transposon research. Much of the data is not published elsewhere nor available in general databases.
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4
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85031632711
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Entries in RepBase Update on World Wide Web URL
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Smit, A.F.A.; Jurka, J., Kapitonov, V., Niak, A.: Entries in RepBase Update on World Wide Web URL: http://www.girinst.org/~server/repbase.html.
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Smit, A.F.A.1
Jurka, J.2
Kapitonov, V.3
Niak, A.4
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5
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0029991222
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Tiggers and other DNA transposon fossils in the human genome
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Smit A.F.A., Riggs A.D. Tiggers and other DNA transposon fossils in the human genome. Proc Natl Acad Sci USA. 93:1996;1443-1448.
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Proc Natl Acad Sci USA
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Smit, A.F.A.1
Riggs, A.D.2
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6
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2642698856
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Transposon Tc1 of the nematode Caenorhabditis elegans jumps in human cells
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One of several papers describing the activity of foreign DNA transposons in mammalian cells. Besides being of evolutionary interest, the importance of this work lies in the prospect of using DNA transposons as vehicles in human gene therapy and as tools in mammalian genetics
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Schouten G.J., Van Luenen H.G.A.M., Verra N.C.V., Valerio D., Plasterk R.H.A. Transposon Tc1 of the nematode Caenorhabditis elegans jumps in human cells. Nucleic Acids Res. 26:1998;3013-3017. One of several papers describing the activity of foreign DNA transposons in mammalian cells. Besides being of evolutionary interest, the importance of this work lies in the prospect of using DNA transposons as vehicles in human gene therapy and as tools in mammalian genetics.
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(1998)
Nucleic Acids Res
, vol.26
, pp. 3013-3017
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Schouten, G.J.1
Van Luenen, H.G.A.M.2
Verra, N.C.V.3
Valerio, D.4
Plasterk, R.H.A.5
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8
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0033015742
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ERV-L elements: A family of endogenous retrovirus-like elements active throughout the evolution of mammals
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Benit L., Lallemand J.B., Casella J.F., Philippe H., Heidmann T. ERV-L elements: a family of endogenous retrovirus-like elements active throughout the evolution of mammals. J Virol. 73:1999;3301-3308.
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(1999)
J Virol
, vol.73
, pp. 3301-3308
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Benit, L.1
Lallemand, J.B.2
Casella, J.F.3
Philippe, H.4
Heidmann, T.5
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9
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0032976398
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The age and evolution of non LTR retrotransposable elements
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A phylogenetic study that provides welcome clarity in the relationships of the daunting number of LINE-like elements. Telomerases appear to be descendants of non-LTR retrotransposons, rather than vise versa, when all the currently available information is taken into account
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Malik H.S., Burke W.D., Eickbush T.H. The age and evolution of non LTR retrotransposable elements. Mol Biol Evol. 16:1999;793-805. A phylogenetic study that provides welcome clarity in the relationships of the daunting number of LINE-like elements. Telomerases appear to be descendants of non-LTR retrotransposons, rather than vise versa, when all the currently available information is taken into account.
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(1999)
Mol Biol Evol
, vol.16
, pp. 793-805
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Malik, H.S.1
Burke, W.D.2
Eickbush, T.H.3
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10
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0030870342
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Sequence-specific single-strand RNA binding protein encoded by the human LINE1-retrotransposon
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Hohjoh H., Singer M.F. Sequence-specific single-strand RNA binding protein encoded by the human LINE1-retrotransposon. EMBO J. 16:1997;l6034-6043.
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(1997)
EMBO J
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Hohjoh, H.1
Singer, M.F.2
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11
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0032559061
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Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure
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Cost G.J., Boeke J.D. Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry. 37:1998;18081-18093.
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(1998)
Biochemistry
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, pp. 18081-18093
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Cost, G.J.1
Boeke, J.D.2
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12
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0032531815
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Does SINE evolution preclude Alu function?
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A scholarly study on whether Alu SINEs have spread as intragenomic parasites or have a more symbiotic relationship with the host. As most aspects of Alu biology and evolution are touched upon, this is the review to read when you're interested in Alus
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Schmid C.W. Does SINE evolution preclude Alu function? Nucleic Acids Res. 26:1998;4541-4550. A scholarly study on whether Alu SINEs have spread as intragenomic parasites or have a more symbiotic relationship with the host. As most aspects of Alu biology and evolution are touched upon, this is the review to read when you're interested in Alus.
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(1998)
Nucleic Acids Res
, vol.26
, pp. 4541-4550
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Schmid, C.W.1
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13
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0031982714
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Potential Alu function: Regulation of the activity of double-stranded RNA-activated kinase PKR
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A set of carefully performed experiments shows that levels of Alu transcripts observed in cells under stress, but not those of related RNA molecules, can antagonize PKR activation and increase translation of a reporter gene
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Chu W.M., Ballard R., Carpick B.W., Williams B.R., Schmid C.W. Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol. 18:1998;58-68. A set of carefully performed experiments shows that levels of Alu transcripts observed in cells under stress, but not those of related RNA molecules, can antagonize PKR activation and increase translation of a reporter gene.
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(1998)
Mol Cell Biol
, vol.18
, pp. 58-68
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Chu, W.M.1
Ballard, R.2
Carpick, B.W.3
Williams, B.R.4
Schmid, C.W.5
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14
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0032515087
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Distribution of the mammalian-wide interspersed repeats (MIRs) in the isochores of the human genome
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Matassi G., Labuda D., Bernardi G. Distribution of the mammalian-wide interspersed repeats (MIRs) in the isochores of the human genome. FEBS Lett. 439:1998;63-65.
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(1998)
FEBS Lett
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, pp. 63-65
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Matassi, G.1
Labuda, D.2
Bernardi, G.3
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15
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0033567043
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Silk worm Bm1 SINE RNA increases following cellular insults
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Kimura R.H., Choudary P.V., Schmid C.W. Silk worm Bm1 SINE RNA increases following cellular insults. Nucleic Acids Res. 27:1999;3380-3387.
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(1999)
Nucleic Acids Res
, vol.27
, pp. 3380-3387
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Kimura, R.H.1
Choudary, P.V.2
Schmid, C.W.3
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16
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0031055331
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Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons
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Jurka J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA. 94:1997;1872-1877.
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(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 1872-1877
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Jurka, J.1
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17
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0032483407
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High-resolution cartography of recently integrated human chromosome 19-specific Alu fossils
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Although reported earlier by the same authors, these larger scale observations that recent distribution patterns of Alu appear random (not targeted to GC-rich DNA) demand consideration in the theory of Alu evolution and possible function
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Arcot S.S., Adamson A.W., Risch G.W., LaFleur J., Robichaux M.B., Lamerdin J.E., Carrano A.V., Batzer M.A. High-resolution cartography of recently integrated human chromosome 19-specific Alu fossils. J Mol Biol. 281:1998;843-856. Although reported earlier by the same authors, these larger scale observations that recent distribution patterns of Alu appear random (not targeted to GC-rich DNA) demand consideration in the theory of Alu evolution and possible function.
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(1998)
J Mol Biol
, vol.281
, pp. 843-856
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Arcot, S.S.1
Adamson, A.W.2
Risch, G.W.3
Lafleur, J.4
Robichaux, M.B.5
Lamerdin, J.E.6
Carrano, A.V.7
Batzer, M.A.8
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18
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0032054301
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Placental endogenous retrovirus (ERV): Structural, functional, and evolutionary significance
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This paper summarizes the evidence for a correlation between ERVs and placental function and evolution. An intriguing subject which is worth a look for outsiders
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Harris J.R. Placental endogenous retrovirus (ERV): structural, functional, and evolutionary significance. BioEssays. 20:1998;307-316. This paper summarizes the evidence for a correlation between ERVs and placental function and evolution. An intriguing subject which is worth a look for outsiders.
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(1998)
BioEssays
, vol.20
, pp. 307-316
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Harris, J.R.1
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19
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0027363236
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The human endogenous retrovirus ERV-3 is upregulated in differentiating placental trophoblast cells
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Boyd M.T., Bax C.M.R., Bax B.E., Bloxam D.L., Weiss R.A. The human endogenous retrovirus ERV-3 is upregulated in differentiating placental trophoblast cells. Virology. 196:1993;349-353.
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(1993)
Virology
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, pp. 349-353
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Boyd, M.T.1
Bax, C.M.R.2
Bax, B.E.3
Bloxam, D.L.4
Weiss, R.A.5
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20
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0032952553
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Expression of endogenous retrovirus ERV-3 induces differentiation in BeWo, a choriocarcinoma model of human placental trophoblast
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Evidence that ERV-3, once an HERV-R envelope gene, is now directly involved in the development of the placenta, specifically in cell fusions to form the syncytiotrophoblasts
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Lin L., Xu B., Rote N.S. Expression of endogenous retrovirus ERV-3 induces differentiation in BeWo, a choriocarcinoma model of human placental trophoblast. Placenta. 20:1999;109-118. Evidence that ERV-3, once an HERV-R envelope gene, is now directly involved in the development of the placenta, specifically in cell fusions to form the syncytiotrophoblasts.
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(1999)
Placenta
, vol.20
, pp. 109-118
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Lin, L.1
Xu, B.2
Rote, N.S.3
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21
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0344931799
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Endogenous retroviruses and multiple sclerosis. II. HERV-7q
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Alliel P.M., Perin J.P., Pierig R., Nussbaum J.L., Menard A., Rieger F. Endogenous retroviruses and multiple sclerosis. II. HERV-7q. C R Acad Sci III. 321:1998;857-863.
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(1998)
C R Acad Sci III
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, pp. 857-863
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Alliel, P.M.1
Perin, J.P.2
Pierig, R.3
Nussbaum, J.L.4
Menard, A.5
Rieger, F.6
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22
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0344450781
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Molecular characterization and placental expression of HERV-W, a new human endogenous retrovirus family
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•]
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•].
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(1999)
J Virol
, vol.73
, pp. 1175-1185
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Blond, J.L.1
Beseme, F.2
Duret, L.3
Bouton, O.4
Bedin, F.5
Perron, H.6
Mandrand, B.7
Mallet, F.8
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23
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0032036690
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Fv1, the mouse retrovirus resistance gene
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Stoye J.P. Fv1, the mouse retrovirus resistance gene. Rev Sci Tech. 17:1998;269-277.
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(1998)
Rev Sci Tech
, vol.17
, pp. 269-277
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Stoye, J.P.1
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24
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0031820331
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X-chromosome inactivation: A repeat hypothesis
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The apparent necessity for an X-chromosome-specific factor to bind Xist RNA and observations of repeat-induced gene silencing in other species are elegantly combined to suggest that contact of an interspersed repeat with Xist RNA may lead to the silencing of these elements and the intervening unique sequences by their conversion to heterochromatin
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Lyon M.F. X-chromosome inactivation: a repeat hypothesis. Cytogenet Cell Genet. 80:1998;133-137. The apparent necessity for an X-chromosome-specific factor to bind Xist RNA and observations of repeat-induced gene silencing in other species are elegantly combined to suggest that contact of an interspersed repeat with Xist RNA may lead to the silencing of these elements and the intervening unique sequences by their conversion to heterochromatin.
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(1998)
Cytogenet Cell Genet
, vol.80
, pp. 133-137
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Lyon, M.F.1
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25
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0032898752
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Xist RNA exhibits a banded localization on the inactive X chromosome and is excluded from autosomal material in cis
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Duthie S.M., Nesterova T.B., Formstone E.J., Keohane A.M., Turner B.M., Zakian S.M., Brockdorff N. Xist RNA exhibits a banded localization on the inactive X chromosome and is excluded from autosomal material in cis. Hum Mol net. 8:1999;195-204.
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(1999)
Hum Mol Net
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, pp. 195-204
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Duthie, S.M.1
Nesterova, T.B.2
Formstone, E.J.3
Keohane, A.M.4
Turner, B.M.5
Zakian, S.M.6
Brockdorff, N.7
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27
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0032102720
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Mobile elements and disease
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A good introduction to the (limited) contribution of transposable elements to human diseases
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Kazazian H.H. Jr. Mobile elements and disease. Curr Opin Genet Dev. 8:1998;343-350. A good introduction to the (limited) contribution of transposable elements to human diseases.
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(1998)
Curr Opin Genet Dev
, vol.8
, pp. 343-350
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Kazazian H.H., Jr.1
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28
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0032560851
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An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy
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Kobayashi K., Nakahori Y., Miyake M., Matsumura K., Kondo-Iida E., Nomura Y., Segawa M., Yoshioka M., Saito K., Osawa M.et al. An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy. Nature. 394:1998;388-392.
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(1998)
Nature
, vol.394
, pp. 388-392
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Kobayashi, K.1
Nakahori, Y.2
Miyake, M.3
Matsumura, K.4
Kondo-Iida, E.5
Nomura, Y.6
Segawa, M.7
Yoshioka, M.8
Saito, K.9
Osawa, M.10
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29
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0032911903
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Unusual mutations in Btk: An insertion, a duplication, an inversion, and four large deletions
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These two papers report the first non-Alu/L1 insertional mutations by a transposable element in human. The inserted SVA or SINE-R is a composite element containing several degraded copies of Alu, a GC-rich, 49-bp unit tandem repeat region, and a fragment of the HERV-K LTR. Although it is entirely unclear how this element 'gets around', the variable length target site and poly(A) tail seem to implicate the L1 machinery again
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Rohrer J., Minegishi Y., Richter D., Eguiguren J., Conley M.E. Unusual mutations in Btk: an insertion, a duplication, an inversion, and four large deletions. Clin Immunol. 90:1999;28-37. These two papers report the first non-Alu/L1 insertional mutations by a transposable element in human. The inserted SVA or SINE-R is a composite element containing several degraded copies of Alu, a GC-rich, 49-bp unit tandem repeat region, and a fragment of the HERV-K LTR. Although it is entirely unclear how this element 'gets around', the variable length target site and poly(A) tail seem to implicate the L1 machinery again.
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(1999)
Clin Immunol
, vol.90
, pp. 28-37
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Rohrer, J.1
Minegishi, Y.2
Richter, D.3
Eguiguren, J.4
Conley, M.E.5
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30
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0031797726
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Human specific integrations of the HERV-K endogenous retrovirus family
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The authors build a phylogenetic tree of HERV-K elements in our genome and come to the conclusion that probably several hundred copies are specific to humans. Out of eight copies, one showed an ancestral (empty) state in some alleles; however, this copy resides in the HLA locus and the alleles are an estimated 30-million-years old
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Medstrand P., Mager D.L. Human specific integrations of the HERV-K endogenous retrovirus family. J Virol. 72:1998;9782-9787. The authors build a phylogenetic tree of HERV-K elements in our genome and come to the conclusion that probably several hundred copies are specific to humans. Out of eight copies, one showed an ancestral (empty) state in some alleles; however, this copy resides in the HLA locus and the alleles are an estimated 30-million-years old.
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(1998)
J Virol
, vol.72
, pp. 9782-9787
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Medstrand, P.1
Mager, D.L.2
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31
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0033049548
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Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV-K retrovirus
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Berkhout B., Jebbink M., Zsiros J. Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV-K retrovirus. J Virol. 73:1999;2365-2375.
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(1999)
J Virol
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, pp. 2365-2375
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Berkhout, B.1
Jebbink, M.2
Zsiros, J.3
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33
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0031707062
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The paleontology of intergene retrotransposons of maize
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The influence of transposable elements on plant genomes always seems to humble observations in mammals. The authors estimate the age of the LTR retrotransposons in a locus from the divergence of 5′ and 3′ LTRs and come to the conclusion that the maize genome may have doubled in size in the last 3 million years because of retrotransposon insertions
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SanMiguel P., Gaut B.S., Tikhonov A., Nakajima Y., Bennetzen J.L. The paleontology of intergene retrotransposons of maize. Nat Genet. 20:1998;43-45. The influence of transposable elements on plant genomes always seems to humble observations in mammals. The authors estimate the age of the LTR retrotransposons in a locus from the divergence of 5′ and 3′ LTRs and come to the conclusion that the maize genome may have doubled in size in the last 3 million years because of retrotransposon insertions.
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(1998)
Nat Genet
, vol.20
, pp. 43-45
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Sanmiguel, P.1
Gaut, B.S.2
Tikhonov, A.3
Nakajima, Y.4
Bennetzen, J.L.5
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34
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0032954098
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Taming of transposable elements by homology-dependent gene silencing
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Jensen S., Gassama M.P., Heidmann T. Taming of transposable elements by homology-dependent gene silencing. Nat Genet. 21:1999;209-212.
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(1999)
Nat Genet
, vol.21
, pp. 209-212
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Jensen, S.1
Gassama, M.P.2
Heidmann, T.3
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35
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0030840954
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Cytosine methylation and the ecology of intragenomic parasites
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Yoder J.A., Walsh C.P., Bestor T.H. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13:1997;335-340.
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(1997)
Trends Genet
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, pp. 335-340
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Yoder, J.A.1
Walsh, C.P.2
Bestor, T.H.3
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36
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0031877999
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The role of DNA methylation in invertebrates: Developmental regulation or genome defense?
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A learned review combined with a survey of methylation patterns in invertebrate genomes that seems to disfavor the idea that the primary and least dispensable function of DNA methylation lies in defense against intragenomic parasites. The authors observe a correlation of the occurrence of DNA methylation with the number of somatic cell divisions, but not with genome size or abundance of transposable elements
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Regev A., Lamb M.J., Jablonka E. The role of DNA methylation in invertebrates: developmental regulation or genome defense? Mol Biol Evol. 15:1998;880-891. A learned review combined with a survey of methylation patterns in invertebrate genomes that seems to disfavor the idea that the primary and least dispensable function of DNA methylation lies in defense against intragenomic parasites. The authors observe a correlation of the occurrence of DNA methylation with the number of somatic cell divisions, but not with genome size or abundance of transposable elements.
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(1998)
Mol Biol Evol
, vol.15
, pp. 880-891
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Regev, A.1
Lamb, M.J.2
Jablonka, E.3
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37
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0033582623
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Nonmethylated transposable elements and methylated genes in a chordate genome
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This observation of an 'opposite' methylation pattern in a urochordate clearly does not fit in with a host defense function of methylation in this organism
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Simmen M.W., Leitgeb S., Charlton J., Jones S.J., Harris B.R., Clark V.H., Bird A. Nonmethylated transposable elements and methylated genes in a chordate genome. Science. 283:1999;1164-1167. This observation of an 'opposite' methylation pattern in a urochordate clearly does not fit in with a host defense function of methylation in this organism.
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(1999)
Science
, vol.283
, pp. 1164-1167
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Simmen, M.W.1
Leitgeb, S.2
Charlton, J.3
Jones, S.J.4
Harris, B.R.5
Clark, V.H.6
Bird, A.7
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38
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0031662164
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Transcription of IAP endogenous retroviruses is constrained by cytosine methylation
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The authors observe a marked increase of IAP endogenous virus activity in mice in which the DNA methyltransferase gene dmt1 has been knocked out, consistent with a role for methylation in host defense mechanisms
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Walsh C.P., Chaillet J.R., Bestor T.H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet. 20:1998;116-117. The authors observe a marked increase of IAP endogenous virus activity in mice in which the DNA methyltransferase gene dmt1 has been knocked out, consistent with a role for methylation in host defense mechanisms.
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(1998)
Nat Genet
, vol.20
, pp. 116-117
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Walsh, C.P.1
Chaillet, J.R.2
Bestor, T.H.3
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39
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0031984304
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Repeat induced gene silencing in mammals
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The authors show that suppression of transgene expression involves methylation and is correlated with the number of concatemeric repetition of the transgene, hinting at the possible existence of a transcriptional host defense mechanism as has been uncovered in plants and fungi
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Garrick D., Fiering S., Martin D.I.K., Whitelaw E. Repeat induced gene silencing in mammals. Nat Genet. 18:1998;56-59. The authors show that suppression of transgene expression involves methylation and is correlated with the number of concatemeric repetition of the transgene, hinting at the possible existence of a transcriptional host defense mechanism as has been uncovered in plants and fungi.
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(1998)
Nat Genet
, vol.18
, pp. 56-59
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Garrick, D.1
Fiering, S.2
Martin, D.I.K.3
Whitelaw, E.4
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40
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0032126345
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Cytosine methylation of repeated sequences in eukaryotes: The role of DNA pairing
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Bender J. Cytosine methylation of repeated sequences in eukaryotes: the role of DNA pairing. Trends Biochem Sci. 23:1998;252-256.
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(1998)
Trends Biochem Sci
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, pp. 252-256
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Bender, J.1
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0032480226
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DNA hypomethylation leads to elevated mutation rates
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Chen R.Z., Petterson U., Beard C., Jackson-Grusby L., Jaenisch R. DNA hypomethylation leads to elevated mutation rates. Nature. 395:1998;89-93.
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(1998)
Nature
, vol.395
, pp. 89-93
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Chen, R.Z.1
Petterson, U.2
Beard, C.3
Jackson-Grusby, L.4
Jaenisch, R.5
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42
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0009673698
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Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid
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A hybrid of different wallaby species shows extensive chromosomal rearrangements and expansion of centromeres. The hybrid has an extensively undermethylated genome, including undermethylated ERVs which appear to have transposed to and expanded in some centromeres. The latter expansion may be due to concatemerization rather than transposition
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O'Neill R.J.W., O'Neil M.J., Graves J.A.M. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature. 393:1998;68-72. A hybrid of different wallaby species shows extensive chromosomal rearrangements and expansion of centromeres. The hybrid has an extensively undermethylated genome, including undermethylated ERVs which appear to have transposed to and expanded in some centromeres. The latter expansion may be due to concatemerization rather than transposition.
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(1998)
Nature
, vol.393
, pp. 68-72
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O'Neill, R.J.W.1
O'Neil, M.J.2
Graves, J.A.M.3
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43
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0033525586
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