-
1
-
-
0021810791
-
Transcription, processing and nuclear transport of a B1 Alu RNA species complementary to an intron of the murine alpha-fetoprotein gene
-
Adeniyi-Jones, S., and Zasloff, M. (1985) Transcription, processing and nuclear transport of a B1 Alu RNA species complementary to an intron of the murine alpha-fetoprotein gene. Nature 317, 81-84.
-
(1985)
Nature
, vol.317
, pp. 81-84
-
-
Adeniyi-Jones, S.1
Zasloff, M.2
-
2
-
-
4344579113
-
The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock
-
Allen, T. A., Von Kaenel, S., Goodrich, J. A., and Kugel, J. F. (2004) The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat. Struct. Mol. Biol. 11, 816-821.
-
(2004)
Nat. Struct. Mol. Biol
, vol.11
, pp. 816-821
-
-
Allen, T.A.1
von Kaenel, S.2
Goodrich, J.A.3
Kugel, J.F.4
-
3
-
-
17144380460
-
Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm
-
Anzai, T., Osanai, M., Hamada, M., and Fujiwara, H. (2005) Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm. Nucleic Acids Res. 33, 1993-2002.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1993-2002
-
-
Anzai, T.1
Osanai, M.2
Hamada, M.3
Fujiwara, H.4
-
4
-
-
46149115158
-
Virus infection induces NFkappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression
-
Apostolou, E., and Thanos, D. (2008) Virus infection induces NFkappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression. Cell 134, 85-96.
-
(2008)
Cell
, vol.134
, pp. 85-96
-
-
Apostolou, E.1
Thanos, D.2
-
5
-
-
34248160438
-
Developmentally regulated piRNA clusters implicate MILI in transposon control
-
Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K., and Hannon, G. J. (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316, 744-747.
-
(2007)
Science
, vol.316
, pp. 744-747
-
-
Aravin, A.A.1
Sachidanandam, R.2
Girard, A.3
Fejes-Toth, K.4
Hannon, G.J.5
-
6
-
-
12344300804
-
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome
-
Athanasiadis, A., Rich, A., and Maas, S. (2004) Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2, e391.
-
(2004)
PLoS Biol
, vol.2
-
-
Athanasiadis, A.1
Rich, A.2
Maas, S.3
-
7
-
-
0024245366
-
Small B2 RNAs in mouse oocytes, embryos, and somatic tissues
-
Bachvarova, R. (1988) Small B2 RNAs in mouse oocytes, embryos, and somatic tissues. Dev. Biol. 130, 513-523.
-
(1988)
Dev. Biol
, vol.130
, pp. 513-523
-
-
Bachvarova, R.1
-
8
-
-
33646928347
-
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
-
Bejerano, G., Lowe, C. B., Ahituv, N., King, B., Siepel, A., Salama, S. R., Rubin, E. M., Kent, W. J., and Haussler, D. (2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441, 87-90.
-
(2006)
Nature
, vol.441
, pp. 87-90
-
-
Bejerano, G.1
Lowe, C.B.2
Ahituv, N.3
King, B.4
Siepel, A.5
Salama, S.R.6
Rubin, E.M.7
Kent, W.J.8
Haussler, D.9
-
9
-
-
0025063806
-
DNA methylation inhibits transcription by RNA polymerase III of a tRNA gene, but not of a 5S rRNA gene
-
Besser, D., Gotz, F., Schulze-Forster, K., Wagner, H., Kroger, H., and Simon, D. (1990) DNA methylation inhibits transcription by RNA polymerase III of a tRNA gene, but not of a 5S rRNA gene. FEBS Lett. 269, 358-362.
-
(1990)
FEBS Lett
, vol.269
, pp. 358-362
-
-
Besser, D.1
Gotz, F.2
Schulze-Forster, K.3
Wagner, H.4
Kroger, H.5
Simon, D.6
-
10
-
-
79957660882
-
Human nucleosomes: Special role of CG dinucleotides and Alunucleosomes
-
Bettecken, T., Frenkel, Z. M., and Trifonov, E. N. (2011) Human nucleosomes: special role of CG dinucleotides and Alunucleosomes. BMC Genomics 12, 273.
-
(2011)
BMC Genomics
, vol.12
, pp. 273
-
-
Bettecken, T.1
Frenkel, Z.M.2
Trifonov, E.N.3
-
11
-
-
0036144048
-
DNA methylation patterns and epigenetic memory
-
Bird, A. (2002) DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6-21.
-
(2002)
Genes Dev
, vol.16
, pp. 6-21
-
-
Bird, A.1
-
12
-
-
21844444077
-
Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes
-
Bolzer, A., Kreth, G., Solovei, I., Koehler, D., Saracoglu, K., Fauth, C., Muller, S., Eils, R., Cremer, C., Speicher, M. R., et al. (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 3, e157.
-
(2005)
PLoS Biol
, vol.3
-
-
Bolzer, A.1
Kreth, G.2
Solovei, I.3
Koehler, D.4
Saracoglu, K.5
Fauth, C.6
Muller, S.7
Eils, R.8
Cremer, C.9
Speicher, M.R.10
-
13
-
-
4544223707
-
Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L
-
Bourc'his, D., and Bestor, T. H. (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96-99.
-
(2004)
Nature
, vol.431
, pp. 96-99
-
-
Bourc'his, D.1
Bestor, T.H.2
-
14
-
-
0029796901
-
DNA sequence insertion and evolutionary variation in gene regulation
-
Britten, R. J. (1996) DNA sequence insertion and evolutionary variation in gene regulation. Proc. Natl. Acad. Sci. USA 93, 9374-9377.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 9374-9377
-
-
Britten, R.J.1
-
15
-
-
84855288772
-
Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells
-
Carriere, L., Graziani, S., Alibert, O., Ghavi-Helm, Y., Boussouar, F., Humbertclaude, H., Jounier, S., Aude, J. C., Keime, C., Murvai, J., et al. (2012) Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells. Nucleic Acids Res. 40, 270-283.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 270-283
-
-
Carriere, L.1
Graziani, S.2
Alibert, O.3
Ghavi-Helm, Y.4
Boussouar, F.5
Humbertclaude, H.6
Jounier, S.7
Aude, J.C.8
Keime, C.9
Murvai, J.10
-
16
-
-
0031982714
-
Potential Alu function: Regulation of the activity of double-stranded RNA-activated kinase PKR
-
Chu, W. M., Ballard, R., Carpick, B. W., Williams, B. R., and Schmid, C. W. (1998) Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol. Cell. Biol. 18, 58-68.
-
(1998)
Mol. Cell. Biol
, vol.18
, pp. 58-68
-
-
Chu, W.M.1
Ballard, R.2
Carpick, B.W.3
Williams, B.R.4
Schmid, C.W.5
-
18
-
-
0032559061
-
Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure
-
Cost, G. J., and Boeke, J. D. (1998) Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry 37, 18081-18093.
-
(1998)
Biochemistry
, vol.37
, pp. 18081-18093
-
-
Cost, G.J.1
Boeke, J.D.2
-
19
-
-
0022388991
-
Repeat sequence families derived from mammalian tRNA genes
-
Daniels, G. R., and Deininger, P. L. (1985) Repeat sequence families derived from mammalian tRNA genes. Nature 317, 819-822.
-
(1985)
Nature
, vol.317
, pp. 819-822
-
-
Daniels, G.R.1
Deininger, P.L.2
-
20
-
-
0036796354
-
Mammalian retroelements
-
Deininger, P. L., and Batzer, M. A. (2002) Mammalian retroelements. Genome Res. 12, 1455-1465.
-
(2002)
Genome Res
, vol.12
, pp. 1455-1465
-
-
Deininger, P.L.1
Batzer, M.A.2
-
21
-
-
0019868389
-
Base sequence studies of 300 nucleotide renatured repeated human DNA clones
-
Deininger, P. L., Jolly, D. J., Rubin, C. M., Friedmann, T., and Schmid, C. W. (1981) Base sequence studies of 300 nucleotide renatured repeated human DNA clones. J. Mol. Biol. 151, 17-33.
-
(1981)
J. Mol. Biol
, vol.151
, pp. 17-33
-
-
Deininger, P.L.1
Jolly, D.J.2
Rubin, C.M.3
Friedmann, T.4
Schmid, C.W.5
-
22
-
-
0026757177
-
Master genes in mammalian repetitive DNA amplification
-
Deininger, P. L., Batzer, M. A., Hutchison, C. A., 3rd, and Edgell, M. H. (1992) Master genes in mammalian repetitive DNA amplification. Trends Genet. 8, 307-311.
-
(1992)
Trends Genet
, vol.8
, pp. 307-311
-
-
Deininger, P.L.1
Batzer, M.A.2
Hutchison III., C.A.3
Edgell, M.H.4
-
23
-
-
0344585056
-
Mobile elements and mammalian genome evolution
-
Deininger, P. L., Moran, J. V., Batzer, M. A., and Kazazian, H. H. Jr. (2003) Mobile elements and mammalian genome evolution. Curr. Opin. Genet. Dev. 13, 651-658.
-
(2003)
Curr. Opin. Genet. Dev
, vol.13
, pp. 651-658
-
-
Deininger, P.L.1
Moran, J.V.2
Batzer, M.A.3
Kazazian Jr., H.H.4
-
24
-
-
18844365062
-
L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells
-
Dewannieux, M., and Heidmann, T. (2005) L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells. J. Mol. Biol. 349, 241-247.
-
(2005)
J. Mol. Biol
, vol.349
, pp. 241-247
-
-
Dewannieux, M.1
Heidmann, T.2
-
25
-
-
0041353551
-
LINEmediated retrotransposition of marked Alu sequences
-
Dewannieux, M., Esnault, C., and Heidmann, T. (2003) LINEmediated retrotransposition of marked Alu sequences. Nat. Genet. 35, 41-48.
-
(2003)
Nat. Genet
, vol.35
, pp. 41-48
-
-
Dewannieux, M.1
Esnault, C.2
Heidmann, T.3
-
26
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., and Ren, B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376-380.
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
Selvaraj, S.2
Yue, F.3
Kim, A.4
Li, Y.5
Shen, Y.6
Hu, M.7
Liu, J.S.8
Ren, B.9
-
27
-
-
0018894384
-
Selfish genes, the phenotype paradigm and genome evolution
-
Doolittle, W. F., and Sapienza, C. (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284, 601-603.
-
(1980)
Nature
, vol.284
, pp. 601-603
-
-
Doolittle, W.F.1
Sapienza, C.2
-
28
-
-
77951621301
-
The genome sequence of taurine cattle: A window to ruminant biology and evolution
-
Elsik, C. G., Tellam, R. L., Worley, K. C., Gibbs, R. A., Muzny, D. M., Weinstock, G. M., Adelson, D. L., Eichler, E. E., Elnitski, L., Guigo, R., et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522-528.
-
(2009)
Science
, vol.324
, pp. 522-528
-
-
Elsik, C.G.1
Tellam, R.L.2
Worley, K.C.3
Gibbs, R.A.4
Muzny, D.M.5
Weinstock, G.M.6
Adelson, D.L.7
Eichler, E.E.8
Elnitski, L.9
Guigo, R.10
-
29
-
-
0028951144
-
Nucleosome positioning by human Alu elements in chromatin
-
Englander, E. W., and Howard, B. H. (1995) Nucleosome positioning by human Alu elements in chromatin. J. Biol. Chem. 270, 10091-10096.
-
(1995)
J. Biol. Chem
, vol.270
, pp. 10091-10096
-
-
Englander, E.W.1
Howard, B.H.2
-
30
-
-
0027304429
-
Nucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation
-
Englander, E. W., Wolffe, A. P., and Howard, B. H. (1993) Nucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation. J. Biol. Chem. 268, 19565-19573.
-
(1993)
J. Biol. Chem
, vol.268
, pp. 19565-19573
-
-
Englander, E.W.1
Wolffe, A.P.2
Howard, B.H.3
-
31
-
-
4344583992
-
B2 RNA binds directly to RNA polymerase II to repress transcript synthesis
-
Espinoza, C. A., Allen, T. A., Hieb, A. R., Kugel, J. F., and Goodrich, J. A. (2004) B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat. Struct. Mol. Biol. 11, 822-829.
-
(2004)
Nat. Struct. Mol. Biol
, vol.11
, pp. 822-829
-
-
Espinoza, C.A.1
Allen, T.A.2
Hieb, A.R.3
Kugel, J.F.4
Goodrich, J.A.5
-
32
-
-
0035042431
-
Transposable B2 SINE elements can provide mobile RNA polymerase II promoters
-
Ferrigno, O., Virolle, T., Djabari, Z., Ortonne, J. P., White, R. J., and Aberdam, D. (2001) Transposable B2 SINE elements can provide mobile RNA polymerase II promoters. Nat. Genet. 28, 77-81.
-
(2001)
Nat. Genet
, vol.28
, pp. 77-81
-
-
Ferrigno, O.1
Virolle, T.2
Djabari, Z.3
Ortonne, J.P.4
White, R.J.5
Aberdam, D.6
-
33
-
-
42349096534
-
Transposable elements and the evolution of regulatory networks
-
Feschotte, C. (2008) Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 9, 397-405.
-
(2008)
Nat. Rev. Genet
, vol.9
, pp. 397-405
-
-
Feschotte, C.1
-
34
-
-
0023056872
-
Induction of B2 RNA polymerase III transcription by heat shock: Enrichment for heat shock induced sequences in rodent cells by hybridization subtraction
-
Fornace, A. J. Jr., and Mitchell, J. B. (1986) Induction of B2 RNA polymerase III transcription by heat shock: enrichment for heat shock induced sequences in rodent cells by hybridization subtraction. Nucleic Acids Res. 14, 5793-5811.
-
(1986)
Nucleic Acids Res
, vol.14
, pp. 5793-5811
-
-
Fornace Jr., A.J.1
Mitchell, J.B.2
-
35
-
-
0035967858
-
The RNA polymerase III transcription apparatus
-
Geiduschek, E. P., and Kassavetis, G. A. (2001) The RNA polymerase III transcription apparatus. J. Mol. Biol. 310, 1-26.
-
(2001)
J. Mol. Biol
, vol.310
, pp. 1-26
-
-
Geiduschek, E.P.1
Kassavetis, G.A.2
-
36
-
-
33646145936
-
Do transposable elements really contribute to proteomes?
-
Gotea, V., and Makalowski, W. (2006) Do transposable elements really contribute to proteomes? Trends Genet. 22, 260-267.
-
(2006)
Trends Genet
, vol.22
, pp. 260-267
-
-
Gotea, V.1
Makalowski, W.2
-
37
-
-
45149084413
-
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
-
Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M. B., Talhout, W., Eussen, B. H,., de Klein, A., Wessels, L., de Laat, W. et al. (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948-951.
-
(2008)
Nature
, vol.453
, pp. 948-951
-
-
Guelen, L.1
Pagie, L.2
Brasset, E.3
Meuleman, W.4
Faza, M.B.5
Talhout, W.6
Eussen, B.H.7
de Klein, A.8
Wessels, L.9
de Laat, W.10
-
38
-
-
0027296641
-
Developmental differences in methylation of human Alu repeats
-
Hellmann-Blumberg, U., Hintz, M. F., Gatewood, J. M., and Schmid, C. W. (1993) Developmental differences in methylation of human Alu repeats. Mol. Cell. Biol. 13, 4523-4530.
-
(1993)
Mol. Cell. Biol
, vol.13
, pp. 4523-4530
-
-
Hellmann-Blumberg, U.1
Hintz, M.F.2
Gatewood, J.M.3
Schmid, C.W.4
-
39
-
-
33846021959
-
Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts
-
Ichiyanagi, K., Nakajima, R., Kajikawa, M., and Okada, N. (2007) Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts. Genome Res. 17, 33-41.
-
(2007)
Genome Res
, vol.17
, pp. 33-41
-
-
Ichiyanagi, K.1
Nakajima, R.2
Kajikawa, M.3
Okada, N.4
-
40
-
-
83055163677
-
Locus-and domaindependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development
-
Ichiyanagi, K., Li, Y., Watanabe, T., Ichiyanagi, T., Fukuda, K., Kitayama, J., Yamamoto, Y., Kuramochi-Miyagawa, S., Nakano, T., Yabuta, Y., et al. (2011) Locus-and domaindependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development. Genome Res. 21, 2058-2066.
-
(2011)
Genome Res
, vol.21
, pp. 2058-2066
-
-
Ichiyanagi, K.1
Li, Y.2
Watanabe, T.3
Ichiyanagi, T.4
Fukuda, K.5
Kitayama, J.6
Yamamoto, Y.7
Kuramochi-Miyagawa, S.8
Nakano, T.9
Yabuta, Y.10
-
41
-
-
84877892296
-
Small RNAs and regulation of transposons in plants
-
Ito, H. (2013) Small RNAs and regulation of transposons in plants. Genes Genet. Syst. 88, 3-7.
-
(2013)
Genes Genet. Syst
, vol.88
, pp. 3-7
-
-
Ito, H.1
-
42
-
-
0019869111
-
Short interspersed repetitive DNA elements in eucaryotes: Transposable DNA elements generated by reverse transcription of RNA pol III transcripts?
-
Jagadeeswaran, P., Forget, B. G., and Weissman, S. M. (1981) Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell 26, 141-142.
-
(1981)
Cell
, vol.26
, pp. 141-142
-
-
Jagadeeswaran, P.1
Forget, B.G.2
Weissman, S.M.3
-
43
-
-
0031055331
-
Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons
-
Jurka, J. (1997) Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94, 1872-1877.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 1872-1877
-
-
Jurka, J.1
-
44
-
-
0842277811
-
Duplication, coclustering, and selection of human Alu retrotransposons
-
Jurka, J., Kohany, O., Pavlicek, A., Kapitonov, V. V., and Jurka, M. V. (2004) Duplication, coclustering, and selection of human Alu retrotransposons. Proc. Natl. Acad. Sci. USA 101, 1268-1272.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 1268-1272
-
-
Jurka, J.1
Kohany, O.2
Pavlicek, A.3
Kapitonov, V.V.4
Jurka, M.V.5
-
45
-
-
0036849412
-
LINEs mobilize SINEs in the eel through a shared 3' sequence
-
Kajikawa, M., and Okada, N. (2002) LINEs mobilize SINEs in the eel through a shared 3' sequence. Cell 111, 433-444.
-
(2002)
Cell
, vol.111
, pp. 433-444
-
-
Kajikawa, M.1
Okada, N.2
-
46
-
-
0038709269
-
A novel class of SINE elements derived from 5S rRNA
-
Kapitonov, V. V., and Jurka, J. (2003) A novel class of SINE elements derived from 5S rRNA. Mol. Biol. Evol. 20, 694-702.
-
(2003)
Mol. Biol. Evol
, vol.20
, pp. 694-702
-
-
Kapitonov, V.V.1
Jurka, J.2
-
47
-
-
0021882531
-
Repetitive sequence transcripts and U1 RNA in mouse oocytes and eggs
-
Kaplan, G., Jelinek, W. R., and Bachvarova, R. (1985) Repetitive sequence transcripts and U1 RNA in mouse oocytes and eggs. Dev. Biol. 109, 15-24.
-
(1985)
Dev. Biol
, vol.109
, pp. 15-24
-
-
Kaplan, G.1
Jelinek, W.R.2
Bachvarova, R.3
-
48
-
-
79957844585
-
DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs
-
Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M., et al. (2011) DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell 8, 676-687.
-
(2011)
Cell Stem Cell
, vol.8
, pp. 676-687
-
-
Karimi, M.M.1
Goyal, P.2
Maksakova, I.A.3
Bilenky, M.4
Leung, D.5
Tang, J.X.6
Shinkai, Y.7
Mager, D.L.8
Jones, S.9
Hirst, M.10
-
49
-
-
4644324088
-
Widespread RNA editing of embedded Alu elements in the human transcriptome
-
Kim, D. D., Kim, T. T., Walsh, T., Kobayashi, Y., Matise, T. C., Buyske, S., and Gabriel, A. (2004) Widespread RNA editing of embedded Alu elements in the human transcriptome. Genome Res. 14, 1719-1725.
-
(2004)
Genome Res
, vol.14
, pp. 1719-1725
-
-
Kim, D.D.1
Kim, T.T.2
Walsh, T.3
Kobayashi, Y.4
Matise, T.C.5
Buyske, S.6
Gabriel, A.7
-
50
-
-
0027474543
-
DNA methylation in the Alu sequences of diploid and haploid primary human cells
-
Kochanek, S., Renz, D., and Doerfler, W. (1993) DNA methylation in the Alu sequences of diploid and haploid primary human cells. EMBO J. 12, 1141-1151.
-
(1993)
EMBO J
, vol.12
, pp. 1141-1151
-
-
Kochanek, S.1
Renz, D.2
Doerfler, W.3
-
51
-
-
0042346386
-
Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells
-
Kondo, Y., and Issa, J. P. (2003) Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J. Biol. Chem. 278, 27658-27662.
-
(2003)
J. Biol. Chem
, vol.278
, pp. 27658-27662
-
-
Kondo, Y.1
Issa, J.P.2
-
52
-
-
0023946286
-
Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands
-
Korenberg, J. R., and Rykowski, M. C. (1988) Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands. Cell 53, 391-400.
-
(1988)
Cell
, vol.53
, pp. 391-400
-
-
Korenberg, J.R.1
Rykowski, M.C.2
-
53
-
-
0018432209
-
Long double-stranded sequences (dsRNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: Evidence from DNA cloning experiments
-
Kramerov, D. A., Grigoryan, A. A., Ryskov, A. P., and Georgiev, G. P. (1979) Long double-stranded sequences (dsRNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments. Nucleic Acids Res. 6, 697-713.
-
(1979)
Nucleic Acids Res
, vol.6
, pp. 697-713
-
-
Kramerov, D.A.1
Grigoryan, A.A.2
Ryskov, A.P.3
Georgiev, G.P.4
-
54
-
-
41649116098
-
DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes
-
Kuramochi-Miyagawa, S., Watanabe, T., Gotoh, K., Totoki, Y., Toyoda, A., Ikawa, M., Asada, N., Kojima, K., Yamaguchi, Y., Ijiri, T. W., et al. (2008) DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 22, 908-917.
-
(2008)
Genes Dev
, vol.22
, pp. 908-917
-
-
Kuramochi-Miyagawa, S.1
Watanabe, T.2
Gotoh, K.3
Totoki, Y.4
Toyoda, A.5
Ikawa, M.6
Asada, N.7
Kojima, K.8
Yamaguchi, Y.9
Ijiri, T.W.10
-
55
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
Fitzhugh, W.10
-
56
-
-
0038701605
-
The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons
-
Lev-Maor, G., Sorek, R., Shomron, N., and Ast, G. (2003) The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science 300, 1288-1291.
-
(2003)
Science
, vol.300
, pp. 1288-1291
-
-
Lev-Maor, G.1
Sorek, R.2
Shomron, N.3
Ast, G.4
-
57
-
-
3543004084
-
Systematic identification of abundant A-to-I editing sites in the human transcriptome
-
Levanon, E. Y., Eisenberg, E., Yelin, R., Nemzer, S., Hallegger, M., Shemesh, R., Fligelman, Z. Y., Shoshan, A., Pollock, S. R., Sztybel, D., et al. (2004) Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 22, 1001-1005.
-
(2004)
Nat. Biotechnol
, vol.22
, pp. 1001-1005
-
-
Levanon, E.Y.1
Eisenberg, E.2
Yelin, R.3
Nemzer, S.4
Hallegger, M.5
Shemesh, R.6
Fligelman, Z.Y.7
Shoshan, A.8
Pollock, S.R.9
Sztybel, D.10
-
58
-
-
0032735573
-
Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo
-
Li, T., Spearow, J., Rubin, C. M., and Schmid, C. W. (1999) Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 239, 367-372.
-
(1999)
Gene
, vol.239
, pp. 367-372
-
-
Li, T.1
Spearow, J.2
Rubin, C.M.3
Schmid, C.W.4
-
59
-
-
28644447707
-
Genome sequence, comparative analysis and haplotype structure of the domestic dog
-
Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., 3rd, Zody, M. C., et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803-819.
-
(2005)
Nature
, vol.438
, pp. 803-819
-
-
Lindblad-Toh, K.1
Wade, C.M.2
Mikkelsen, T.S.3
Karlsson, E.K.4
Jaffe, D.B.5
Kamal, M.6
Clamp, M.7
Chang, J.L.8
Kulbokas III., E.J.9
Zody, M.C.10
-
60
-
-
0027251502
-
Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation
-
Liu, W. M., and Schmid, C. W. (1993) Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation. Nucleic Acids Res. 21, 1351-1359.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 1351-1359
-
-
Liu, W.M.1
Schmid, C.W.2
-
61
-
-
0029030242
-
Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts
-
Liu, W. M., Chu, W. M., Choudary, P. V., and Schmid, C. W. (1995) Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res. 23, 1758-1765.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 1758-1765
-
-
Liu, W.M.1
Chu, W.M.2
Choudary, P.V.3
Schmid, C.W.4
-
62
-
-
0027450385
-
Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition
-
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-LTR retrotransposition. Cell 72, 595-605.
-
(1993)
Cell
, vol.72
, pp. 595-605
-
-
Luan, D.D.1
Korman, M.H.2
Jakubczak, J.L.3
Eickbush, T.H.4
-
63
-
-
80053990356
-
Genomic relationship between SINE retrotransposons, Pol III-Pol II transcription, and chromatin organization: The journey from junk to jewel
-
Lunyak, V. V., and Atallah, M. (2011) Genomic relationship between SINE retrotransposons, Pol III-Pol II transcription, and chromatin organization: the journey from junk to jewel. Biochem. Cell Biol. 89, 495-504.
-
(2011)
Biochem. Cell Biol
, vol.89
, pp. 495-504
-
-
Lunyak, V.V.1
Atallah, M.2
-
64
-
-
34447515727
-
Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis
-
Lunyak, V. V., Prefontaine, G. G., Nunez, E., Cramer, T., Ju, B. G., Ohgi, K. A., Hutt, K., Roy, R., Garcia-Diaz, A., Zhu, X., et al. (2007) Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science 317, 248-251.
-
(2007)
Science
, vol.317
, pp. 248-251
-
-
Lunyak, V.V.1
Prefontaine, G.G.2
Nunez, E.3
Cramer, T.4
Ju, B.G.5
Ohgi, K.A.6
Hutt, K.7
Roy, R.8
Garcia-Diaz, A.9
Zhu, X.10
-
65
-
-
39549103642
-
Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock
-
Mariner, P. D., Walters, R. D., Espinoza, C. A., Drullinger, L. F., Wagner, S. D., Kugel, J. F., and Goodrich, J. A. (2008) Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol. Cell 29, 499-509.
-
(2008)
Mol. Cell
, vol.29
, pp. 499-509
-
-
Mariner, P.D.1
Walters, R.D.2
Espinoza, C.A.3
Drullinger, L.F.4
Wagner, S.D.5
Kugel, J.F.6
Goodrich, J.A.7
-
66
-
-
77950862656
-
Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
-
Matsui, T., Leung, D., Miyashita, H., Maksakova, I. A., Miyachi, H., Kimura, H., Tachibana, M., Lorincz, M. C., and Shinkai, Y. (2010) Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 464, 927-931.
-
(2010)
Nature
, vol.464
, pp. 927-931
-
-
Matsui, T.1
Leung, D.2
Miyashita, H.3
Maksakova, I.A.4
Miyachi, H.5
Kimura, H.6
Tachibana, M.7
Lorincz, M.C.8
Shinkai, Y.9
-
67
-
-
0036798062
-
Retroelement Distributions In the Human Genome: Variations Associated With Age and Proximity to Genes
-
Medstrand, P., van de Lagemaat, L. N., and Mager, D. L. (2002) Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res. 12, 1483-1495.
-
(2002)
Genome Res
, vol.12
, pp. 1483-1495
-
-
Medstrand, P.1
van de Lagemaat, L.N.2
Mager, D.L.3
-
68
-
-
24344500211
-
Initial sequence of the chimpanzee genome and comparison with the human genome
-
Mikkelsen, T. S., Hillier, L. W., Eichler, E. E., Zody, M. C., Jaffe, D. B., Yang, S., Enard, W., Hellmann, I., Lindblad-Toh, K., Altheide, T. K., et al. (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87.
-
(2005)
Nature
, vol.437
, pp. 69-87
-
-
Mikkelsen, T.S.1
Hillier, L.W.2
Eichler, E.E.3
Zody, M.C.4
Jaffe, D.B.5
Yang, S.6
Enard, W.7
Hellmann, I.8
Lindblad-Toh, K.9
Altheide, T.K.10
-
69
-
-
34248576291
-
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
-
Mikkelsen, T. S., Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., Garber, M., Gentles, A. J., Goodstadt, L., Heger, A., et al. (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447, 167-177.
-
(2007)
Nature
, vol.447
, pp. 167-177
-
-
Mikkelsen, T.S.1
Wakefield, M.J.2
Aken, B.3
Amemiya, C.T.4
Chang, J.L.5
Duke, S.6
Garber, M.7
Gentles, A.J.8
Goodstadt, L.9
Heger, A.10
-
70
-
-
77951962545
-
Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells
-
Moqtaderi, Z., Wang, J., Raha, D., White, R. J., Snyder, M., Weng, Z., and Struhl, K. (2010) Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat. Struct. Mol. Biol. 17, 635-640.
-
(2010)
Nat. Struct. Mol. Biol
, vol.17
, pp. 635-640
-
-
Moqtaderi, Z.1
Wang, J.2
Raha, D.3
White, R.J.4
Snyder, M.5
Weng, Z.6
Struhl, K.7
-
71
-
-
0030606320
-
High frequency retrotransposition in cultured mammalian cells
-
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.
-
(1996)
Cell
, vol.87
, pp. 917-927
-
-
Moran, J.V.1
Holmes, S.E.2
Naas, T.P.3
Deberardinis, R.J.4
Boeke, J.D.5
Kazazian Jr., H.H.6
-
72
-
-
84865286053
-
A SINE-derived element constitutes a unique modular enhancer for mammalian diencephalic Fgf8
-
Nakanishi, A., Kobayashi, N., Suzuki-Hirano, A., Nishihara, H., Sasaki, T., Hirakawa, M., Sumiyama, K., Shimogori, T., and Okada, N. (2012) A SINE-derived element constitutes a unique modular enhancer for mammalian diencephalic Fgf8. PLoS ONE 7, e43785.
-
(2012)
PLoS ONE
, vol.7
-
-
Nakanishi, A.1
Kobayashi, N.2
Suzuki-Hirano, A.3
Nishihara, H.4
Sasaki, T.5
Hirakawa, M.6
Sumiyama, K.7
Shimogori, T.8
Okada, N.9
-
73
-
-
33745620751
-
Functional noncoding sequences derived from SINEs in the mammalian genome
-
Nishihara, H., Smit, A. F., and Okada, N. (2006) Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 16, 864-874.
-
(2006)
Genome Res
, vol.16
, pp. 864-874
-
-
Nishihara, H.1
Smit, A.F.2
Okada, N.3
-
74
-
-
33646912186
-
A role for TFIIIC transcription factor complex in genome organization
-
Noma, K., Cam, H. P., Maraia, R. J., and Grewal, S. I. (2006) A role for TFIIIC transcription factor complex in genome organization. Cell 125, 859-872.
-
(2006)
Cell
, vol.125
, pp. 859-872
-
-
Noma, K.1
Cam, H.P.2
Maraia, R.J.3
Grewal, S.I.4
-
75
-
-
1842665155
-
Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters
-
Oei, S. L., Babich, V. S., Kazakov, V. I., Usmanova, N. M., Kropotov, A. V., and Tomilin, N. V. (2004) Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters. Genomics 83, 873-882.
-
(2004)
Genomics
, vol.83
, pp. 873-882
-
-
Oei, S.L.1
Babich, V.S.2
Kazakov, V.I.3
Usmanova, N.M.4
Kropotov, A.V.5
Tomilin, N.V.6
-
76
-
-
84860327228
-
Active role of small non-coding RNAs derived from SINE/B1 retrotransposon during early mouse development
-
Ohnishi, Y., Totoki, Y., Toyoda, A., Watanabe, T., Yamamoto, Y., Tokunaga, K., Sakaki, Y., Sasaki, H., and Hohjoh, H. (2012) Active role of small non-coding RNAs derived from SINE/B1 retrotransposon during early mouse development. Mol. Biol. Rep. 39, 903-909.
-
(2012)
Mol. Biol. Rep
, vol.39
, pp. 903-909
-
-
Ohnishi, Y.1
Totoki, Y.2
Toyoda, A.3
Watanabe, T.4
Yamamoto, Y.5
Tokunaga, K.6
Sakaki, Y.7
Sasaki, H.8
Hohjoh, H.9
-
77
-
-
0015271630
-
So much "junk" DNA in our genome
-
Ohno, S. (1972) So much "junk" DNA in our genome. Brookhaven Symp. Biol. 23, 366-370.
-
(1972)
Brookhaven Symp. Biol
, vol.23
, pp. 366-370
-
-
Ohno, S.1
-
78
-
-
23844437243
-
SINEs and LINEs: Symbionts of eukaryotic genomes with a common tail
-
Ohshima, K., and Okada, N. (2005) SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet. Genome Res. 110, 475-490.
-
(2005)
Cytogenet. Genome Res
, vol.110
, pp. 475-490
-
-
Ohshima, K.1
Okada, N.2
-
79
-
-
0029927086
-
The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements
-
Ohshima, K., Hamada, M., Terai, Y., and Okada, N. (1996) The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements. Mol. Cell. Biol. 16, 3756-3764.
-
(1996)
Mol. Cell. Biol
, vol.16
, pp. 3756-3764
-
-
Ohshima, K.1
Hamada, M.2
Terai, Y.3
Okada, N.4
-
80
-
-
1542682570
-
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
-
Ohshima, K., Hattori, M., Yada, T., Gojobori, T., Sakaki, Y., and Okada, N. (2003) Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol. 4, R74.
-
(2003)
Genome Biol
, vol.4
-
-
Ohshima, K.1
Hattori, M.2
Yada, T.3
Gojobori, T.4
Sakaki, Y.5
Okada, N.6
-
82
-
-
77954693443
-
Emergence of mammals by emergency: Exaptation
-
Okada, N., Sasaki, T., Shimogori, T., and Nishihara, H. (2010) Emergence of mammals by emergency: exaptation. Genes Cells 15, 801-812.
-
(2010)
Genes Cells
, vol.15
, pp. 801-812
-
-
Okada, N.1
Sasaki, T.2
Shimogori, T.3
Nishihara, H.4
-
83
-
-
77951943463
-
Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors
-
Oler, A. J., Alla, R. K., Roberts, D. N., Wong, A., Hollenhorst, P. C., Chandler, K. J., Cassiday, P. A., Nelson, C. A., Hagedorn, C. H., Graves, B. J., et al. (2010) Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat. Struct. Mol. Biol. 17, 620-628.
-
(2010)
Nat. Struct. Mol. Biol
, vol.17
, pp. 620-628
-
-
Oler, A.J.1
Alla, R.K.2
Roberts, D.N.3
Wong, A.4
Hollenhorst, P.C.5
Chandler, K.J.6
Cassiday, P.A.7
Nelson, C.A.8
Hagedorn, C.H.9
Graves, B.J.10
-
84
-
-
0018857680
-
Selfish DNA: The ultimate parasite
-
Orgel, L. E., and Crick, F. H. (1980) Selfish DNA: the ultimate parasite. Nature 284, 604-607.
-
(1980)
Nature
, vol.284
, pp. 604-607
-
-
Orgel, L.E.1
Crick, F.H.2
-
85
-
-
0023046916
-
Transcriptional inactivity of Alu repeats in HeLa cells
-
Paulson, K. E., and Schmid, C. W. (1986) Transcriptional inactivity of Alu repeats in HeLa cells. Nucleic Acids Res. 14, 6145-6158.
-
(1986)
Nucleic Acids Res
, vol.14
, pp. 6145-6158
-
-
Paulson, K.E.1
Schmid, C.W.2
-
86
-
-
67549119096
-
CTCF: Master weaver of the genome
-
Phillips, J. E., and Corces, V. G. (2009) CTCF: master weaver of the genome. Cell 137, 1194-1211.
-
(2009)
Cell
, vol.137
, pp. 1194-1211
-
-
Phillips, J.E.1
Corces, V.G.2
-
87
-
-
0029999154
-
An Alu element in the myeloperoxidase promoter contains a composite SP1-thyroid hormone-retinoic acid response element
-
Piedrafita, F. J., Molander, R. B., Vansant, G., Orlova, E. A., Pfahl, M., and Reynolds, W. F. (1996) An Alu element in the myeloperoxidase promoter contains a composite SP1-thyroid hormone-retinoic acid response element. J. Biol. Chem. 271, 14412-14420.
-
(1996)
J. Biol. Chem
, vol.271
, pp. 14412-14420
-
-
Piedrafita, F.J.1
Molander, R.B.2
Vansant, G.3
Orlova, E.A.4
Pfahl, M.5
Reynolds, W.F.6
-
88
-
-
33746377600
-
Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes
-
Polak, P., and Domany, E. (2006) Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics 7, 133.
-
(2006)
BMC Genomics
, vol.7
, pp. 133
-
-
Polak, P.1
Domany, E.2
-
89
-
-
0035839126
-
Epigenetic reprogramming in mammalian development
-
Reik, W., Dean, W., and Walter, J. (2001) Epigenetic reprogramming in mammalian development. Science 293, 1089-1093.
-
(2001)
Science
, vol.293
, pp. 1089-1093
-
-
Reik, W.1
Dean, W.2
Walter, J.3
-
90
-
-
40349112875
-
Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo
-
Roman, A. C., Benitez, D. A., Carvajal-Gonzalez, J. M., and Fernandez-Salguero, P. M. (2008) Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo. Proc. Natl. Acad. Sci. USA 105, 1632-1637.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 1632-1637
-
-
Roman, A.C.1
Benitez, D.A.2
Carvajal-Gonzalez, J.M.3
Fernandez-Salguero, P.M.4
-
91
-
-
79952261267
-
Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch
-
Roman, A. C., Gonzalez-Rico, F. J., Molto, E., Hernando, H., Neto, A., Vicente-Garcia, C., Ballestar, E., Gomez--Skarmeta, J. L., Vavrova-Anderson, J., White, R. J., et al. (2011) Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch. Genome Res. 21, 422-432.
-
(2011)
Genome Res
, vol.21
, pp. 422-432
-
-
Roman, A.C.1
Gonzalez-Rico, F.J.2
Molto, E.3
Hernando, H.4
Neto, A.5
Vicente-Garcia, C.6
Ballestar, E.7
Gomez--skarmeta, J.L.8
Vavrova-Anderson, J.9
White, R.J.10
-
92
-
-
0018896269
-
Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences
-
Rubin, C. M., Houck, C. M., Deininger, P. L., Friedmann, T., and Schmid, C. W. (1980) Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences. Nature 284, 372-374.
-
(1980)
Nature
, vol.284
, pp. 372-374
-
-
Rubin, C.M.1
Houck, C.M.2
Deininger, P.L.3
Friedmann, T.4
Schmid, C.W.5
-
93
-
-
84877898486
-
The epigenetic regulation of transposable elements by PIWI-interacting RNAs in Drosophila
-
Saito, K. (2013) The epigenetic regulation of transposable elements by PIWI-interacting RNAs in Drosophila. Genes Genet. Syst. 88, 9-17.
-
(2013)
Genes Genet. Syst
, vol.88
, pp. 9-17
-
-
Saito, K.1
-
94
-
-
0022315823
-
Rodent type 2 Alu family, rat identifier sequence, rabbit C family, and bovine or goat 73-bp repeat may have evolved from tRNA genes
-
Sakamoto, K., and Okada, N. (1985) Rodent type 2 Alu family, rat identifier sequence, rabbit C family, and bovine or goat 73-bp repeat may have evolved from tRNA genes. J. Mol. Evol. 22, 134-140.
-
(1985)
J. Mol. Evol
, vol.22
, pp. 134-140
-
-
Sakamoto, K.1
Okada, N.2
-
95
-
-
35948981635
-
Ancient Exaptation of a CORE-SINE Retroposon Into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene
-
Santangelo, A. M., de Souza, F. S., Franchini, L. F., Bumaschny, V. F., Low, M. J., and Rubinstein, M. (2007) Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene. PLoS Genet. 3, 1813-1826.
-
(2007)
PLoS Genet
, vol.3
, pp. 1813-1826
-
-
Santangelo, A.M.1
de Souza, F.S.2
Franchini, L.F.3
Bumaschny, V.F.4
Low, M.J.5
Rubinstein, M.6
-
96
-
-
38349100549
-
Epigenetic events in mammalian germ-cell development: Reprogramming and beyond
-
Sasaki, H., and Matsui, Y. (2008) Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat. Rev. Genet. 9, 129-140.
-
(2008)
Nat. Rev. Genet
, vol.9
, pp. 129-140
-
-
Sasaki, H.1
Matsui, Y.2
-
97
-
-
41949093041
-
Possible involvement of SINEs in mammalian-specific brain formation
-
Sasaki, T., Nishihara, H., Hirakawa, M., Fujimura, K., Tanaka, M., Kokubo, N., Kimura-Yoshida, C., Matsuo, I., Sumiyama, K., Saitou, N., et al. (2008) Possible involvement of SINEs in mammalian-specific brain formation. Proc. Natl. Acad. Sci. USA 105, 4220-4225.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 4220-4225
-
-
Sasaki, T.1
Nishihara, H.2
Hirakawa, M.3
Fujimura, K.4
Tanaka, M.5
Kokubo, N.6
Kimura-Yoshida, C.7
Matsuo, I.8
Sumiyama, K.9
Saitou, N.10
-
98
-
-
0032531815
-
Does SINE evolution preclude Alu function?
-
Schmid, C. W. (1998) Does SINE evolution preclude Alu function? Nucleic Acids Res. 26, 4541-4550.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 4541-4550
-
-
Schmid, C.W.1
-
99
-
-
84863393570
-
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages
-
Schmidt, D., Schwalie, P. C., Wilson, M. D., Ballester, B., Goncalves, A., Kutter, C., Brown, G. D., Marshall, A., Flicek, P., and Odom, D. T. (2012) Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148, 335-348.
-
(2012)
Cell
, vol.148
, pp. 335-348
-
-
Schmidt, D.1
Schwalie, P.C.2
Wilson, M.D.3
Ballester, B.4
Goncalves, A.5
Kutter, C.6
Brown, G.D.7
Marshall, A.8
Flicek, P.9
Odom, D.T.10
-
100
-
-
0037108150
-
Recruitment of RNA polymerase III to its target promoters
-
Schramm, L., and Hernandez, N. (2002) Recruitment of RNA polymerase III to its target promoters. Genes Dev. 16, 2593-2620.
-
(2002)
Genes Dev
, vol.16
, pp. 2593-2620
-
-
Schramm, L.1
Hernandez, N.2
-
101
-
-
0020332775
-
Highly repeated sequences in mammalian genomes
-
Singer, M. F. (1982) Highly repeated sequences in mammalian genomes. Int. Rev. Cytol. 76, 67-112.
-
(1982)
Int. Rev. Cytol
, vol.76
, pp. 67-112
-
-
Singer, M.F.1
-
102
-
-
79953089167
-
PIWIinteracting small RNAs: The vanguard of genome defence
-
Siomi, M. C., Sato, K., Pezic, D., and Aravin, A. A. (2011) PIWIinteracting small RNAs: the vanguard of genome defence. Nat. Rev. Mol. Cell Biol. 12, 246-258.
-
(2011)
Nat. Rev. Mol. Cell Biol
, vol.12
, pp. 246-258
-
-
Siomi, M.C.1
Sato, K.2
Pezic, D.3
Aravin, A.A.4
-
103
-
-
64249139170
-
Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution
-
Solovei, I., Kreysing, M., Lanctot, C., Kosem, S., Peichl, L., Cremer, T., Guck, J., and Joffe, B. (2009) Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell 137, 356-368.
-
(2009)
Cell
, vol.137
, pp. 356-368
-
-
Solovei, I.1
Kreysing, M.2
Lanctot, C.3
Kosem, S.4
Peichl, L.5
Cremer, T.6
Guck, J.7
Joffe, B.8
-
104
-
-
0036064148
-
Alu-containing exons are alternatively spliced
-
Sorek, R., Ast, G., and Graur, D. (2002) Alu-containing exons are alternatively spliced. Genome Res. 12, 1060-1067.
-
(2002)
Genome Res
, vol.12
, pp. 1060-1067
-
-
Sorek, R.1
Ast, G.2
Graur, D.3
-
105
-
-
77952121837
-
Effects of Alu elements on global nucleosome positioning in the human genome
-
Tanaka, Y., Yamashita, R., Suzuki, Y., and Nakai, K. (2010) Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics 11, 309.
-
(2010)
BMC Genomics
, vol.11
, pp. 309
-
-
Tanaka, Y.1
Yamashita, R.2
Suzuki, Y.3
Nakai, K.4
-
106
-
-
82955188747
-
A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons
-
Tashiro, K., Teissier, A., Kobayashi, N., Nakanishi, A., Sasaki, T., Yan, K., Tarabykin, V., Vigier, L., Sumiyama, K., Hirakawa, M., et al. (2011) A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons. PLoS One 6, e28497.
-
(2011)
PLoS One
, vol.6
-
-
Tashiro, K.1
Teissier, A.2
Kobayashi, N.3
Nakanishi, A.4
Sasaki, T.5
Yan, K.6
Tarabykin, V.7
Vigier, L.8
Sumiyama, K.9
Hirakawa, M.10
-
107
-
-
74549153240
-
Alu and B1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes
-
Tsirigos, A., and Rigoutsos, I. (2009) Alu and B1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput. Biol. 5, e1000610.
-
(2009)
PLoS Comput. Biol
, vol.5
-
-
Tsirigos, A.1
Rigoutsos, I.2
-
108
-
-
33745270104
-
Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b
-
Tsumura, A., Hayakawa, T., Kumaki, Y., Takebayashi, S., Sakaue, M., Matsuoka, C., Shimotohno, K., Ishikawa, F., Li, E., Ueda, H. R., et al. (2006) Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11, 805-814.
-
(2006)
Genes Cells
, vol.11
, pp. 805-814
-
-
Tsumura, A.1
Hayakawa, T.2
Kumaki, Y.3
Takebayashi, S.4
Sakaue, M.5
Matsuoka, C.6
Shimotohno, K.7
Ishikawa, F.8
Li, E.9
Ueda, H.R.10
-
109
-
-
0021127698
-
Alu sequences are processed 7SL RNA genes
-
Ullu, E., and Tschudi, C. (1984) Alu sequences are processed 7SL RNA genes. Nature 312, 171-172.
-
(1984)
Nature
, vol.312
, pp. 171-172
-
-
Ullu, E.1
Tschudi, C.2
-
110
-
-
0029153564
-
The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element
-
Vansant, G., and Reynolds, W. F. (1995) The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element. Proc. Natl. Acad. Sci. USA 92, 8229-8233.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 8229-8233
-
-
Vansant, G.1
Reynolds, W.F.2
-
111
-
-
84876581626
-
SINEBase: A database and tool for SINE analysis
-
Vassetzky, N. S., and Kramerov, D. A. (2013) SINEBase: a database and tool for SINE analysis. Nucleic Acids Res. 41, D83-D89.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Vassetzky, N.S.1
Kramerov, D.A.2
-
112
-
-
0031662164
-
Transcription of IAP endogenous retroviruses is constrained by cytosine methylation
-
Walsh, C. P., Chaillet, J. R., and Bestor, T. H. (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20, 116-117.
-
(1998)
Nat. Genet
, vol.20
, pp. 116-117
-
-
Walsh, C.P.1
Chaillet, J.R.2
Bestor, T.H.3
-
113
-
-
79952525007
-
MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline
-
Watanabe, T., Chuma, S., Yamamoto, Y., Kuramochi-Miyagawa, S., Totoki, Y., Toyoda, A., Hoki, Y., Fujiyama, A., Shibata, T., Sado, T., et al. (2011) MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline. Dev. Cell 20, 364-375.
-
(2011)
Dev. Cell
, vol.20
, pp. 364-375
-
-
Watanabe, T.1
Chuma, S.2
Yamamoto, Y.3
Kuramochi-Miyagawa, S.4
Totoki, Y.5
Toyoda, A.6
Hoki, Y.7
Fujiyama, A.8
Shibata, T.9
Sado, T.10
-
114
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
Agarwal, P.6
Agarwala, R.7
Ainscough, R.8
Alexandersson, M.9
An, P.10
-
115
-
-
0035144498
-
Human L1 retrotransposition: Cis preference versus trans complementation
-
Wei, W., Gilbert, N., Ooi, S. L., Lawler, J. F., Ostertag, E. M., Kazazian, H. H., Boeke, J. D., and Moran, J. V. (2001) Human L1 retrotransposition: cis preference versus trans complementation. Mol. Cell. Biol. 21, 1429-1439.
-
(2001)
Mol. Cell. Biol
, vol.21
, pp. 1429-1439
-
-
Wei, W.1
Gilbert, N.2
Ooi, S.L.3
Lawler, J.F.4
Ostertag, E.M.5
Kazazian, H.H.6
Boeke, J.D.7
Moran, J.V.8
-
116
-
-
0019186902
-
An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome
-
Weiner, A. M. (1980) An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 22, 209-218.
-
(1980)
Cell
, vol.22
, pp. 209-218
-
-
Weiner, A.M.1
-
117
-
-
67949092871
-
Highthroughput Sequence-based Epigenomic Analysis of Alu Repeats In Human Cerebellum
-
Xie, H., Wang, M., Bonaldo, Mde, F., Smith, C., Rajaram, V., Goldman, S., Tomita, T., and Soares, M. B. (2009) Highthroughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res. 37, 4331-4340.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 4331-4340
-
-
Xie, H.1
Wang, M.2
Bonaldo, M.F.3
Smith, C.4
Rajaram, V.5
Goldman, S.6
Tomita, T.7
Soares, M.B.8
-
118
-
-
59349083791
-
Methylation and deamination of CpGs generate p53-binding sites on a genomic scale
-
Zemojtel, T., Kielbasa, S. M., Arndt, P. F., Chung, H. R., and Vingron, M. (2009) Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet. 25, 63-66.
-
(2009)
Trends Genet
, vol.25
, pp. 63-66
-
-
Zemojtel, T.1
Kielbasa, S.M.2
Arndt, P.F.3
Chung, H.R.4
Vingron, M.5
|