-
1
-
-
84875200257
-
Long noncoding RNAs: cellular address codes in development and disease
-
Batista, P.J. et al. (2013) Long noncoding RNAs: cellular address codes in development and disease. Cell, 152, 1298-1307.
-
(2013)
Cell
, vol.152
, pp. 1298-1307
-
-
Batista, P.J.1
-
2
-
-
70349318211
-
The impact of retrotransposons on human genome evolution
-
Cordaux, R. et al. (2009) The impact of retrotransposons on human genome evolution. Nat. Rev. Genet., 10, 691-703.
-
(2009)
Nat. Rev. Genet
, vol.10
, pp. 691-703
-
-
Cordaux, R.1
-
3
-
-
52949095077
-
Retrotransposons revisited: the restraint and rehabilitation of parasites
-
Goodier, J.L. et al. (2008) Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell, 135, 23-35.
-
(2008)
Cell
, vol.135
, pp. 23-35
-
-
Goodier, J.L.1
-
4
-
-
72849106592
-
RNA processing and its regulation: global insights into biological networks
-
Licatalosi, D.D. et al. (2010) RNA processing and its regulation: global insights into biological networks. Nat. Rev. Genet., 11, 75-87.
-
(2010)
Nat. Rev. Genet
, vol.11
, pp. 75-87
-
-
Licatalosi, D.D.1
-
5
-
-
84861904178
-
Genome regulation by long noncoding RNAs
-
Rinn, J.L. et al. (2012) Genome regulation by long noncoding RNAs. Annu. Rev. Biochem., 81, 145-166.
-
(2012)
Annu. Rev. Biochem
, vol.81
, pp. 145-166
-
-
Rinn, J.L.1
-
6
-
-
3042767202
-
MicroRNAs: small RNAs with a big role in gene regulation
-
He, L. et al. (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet., 5, 522-531.
-
(2004)
Nat. Rev. Genet
, vol.5
, pp. 522-531
-
-
He, L.1
-
7
-
-
0141843656
-
The nuclear RNase III Drosha initiates microRNA processing
-
Lee, Y. et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415-419.
-
(2003)
Nature
, vol.425
, pp. 415-419
-
-
Lee, Y.1
-
8
-
-
1842816517
-
Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways
-
Lee, Y.S. et al. (2004) Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell, 117, 69-81.
-
(2004)
Cell
, vol.117
, pp. 69-81
-
-
Lee, Y.S.1
-
9
-
-
0037144546
-
A microRNA in a multiple-turnover RNAi enzyme complex
-
Hutvágner, G. et al. (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science, 297, 2056-2060.
-
(2002)
Science
, vol.297
, pp. 2056-2060
-
-
Hutvágner, G.1
-
10
-
-
58249088751
-
MicroRNAs: target recognition and regulatory functions
-
Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
-
(2009)
Cell
, vol.136
, pp. 215-233
-
-
Bartel, D.P.1
-
11
-
-
0033572660
-
Targeted mRNA degradation by double-stranded RNA in vitro
-
Tuschl, T. et al. (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev., 13, 3191-3197.
-
(1999)
Genes Dev
, vol.13
, pp. 3191-3197
-
-
Tuschl, T.1
-
12
-
-
0034673638
-
An RNA-directed nuclease mediates posttranscriptional gene silencing in Drosophila cells
-
Hammond, S.M. et al. (2000) An RNA-directed nuclease mediates posttranscriptional gene silencing in Drosophila cells. Nature, 404, 293-296.
-
(2000)
Nature
, vol.404
, pp. 293-296
-
-
Hammond, S.M.1
-
13
-
-
24644480213
-
Inhibition of translational initiation by Let-7 MicroRNA in human cells
-
Pillai, R.S. et al. (2005) Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science, 309, 1573-1576.
-
(2005)
Science
, vol.309
, pp. 1573-1576
-
-
Pillai, R.S.1
-
14
-
-
33745168962
-
microRNAs exhibit high frequency genomic alterations in human cancer
-
Zhang, L. et al. (2006) microRNAs exhibit high frequency genomic alterations in human cancer. Proc. Natl Acad. Sci. USA, 103, 9136-9141.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 9136-9141
-
-
Zhang, L.1
-
15
-
-
20444467290
-
A microRNA polycistron as a potential human oncogene
-
He, L. et al. (2005) A microRNA polycistron as a potential human oncogene. Nature, 435, 828-833.
-
(2005)
Nature
, vol.435
, pp. 828-833
-
-
He, L.1
-
16
-
-
78650004201
-
MicroRNA: biogenesis, function and role in cancer
-
Macfarlane, L.-A. et al. (2010) MicroRNA: biogenesis, function and role in cancer. Curr. Genomics, 11, 537-561.
-
(2010)
Curr. Genomics
, vol.11
, pp. 537-561
-
-
Macfarlane, L.-A.1
-
17
-
-
33645294070
-
Oncomirs-microRNAs with a role in cancer
-
Esquela-Kerscher, A. et al. (2006) Oncomirs-microRNAs with a role in cancer. Nat. Rev. Cancer, 6, 259-269.
-
(2006)
Nat. Rev. Cancer
, vol.6
, pp. 259-269
-
-
Esquela-Kerscher, A.1
-
18
-
-
84858379476
-
MicroRNAs in stress signaling and human disease
-
Mendell, J.T. et al. (2012) MicroRNAs in stress signaling and human disease. Cell, 148, 1172-1187.
-
(2012)
Cell
, vol.148
, pp. 1172-1187
-
-
Mendell, J.T.1
-
19
-
-
84863458292
-
Embryonic stem cell potency fluctuates with endogenous retrovirus activity
-
Macfarlan, T.S. et al. (2012) Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature, 487, 57-63.
-
(2012)
Nature
, vol.487
, pp. 57-63
-
-
Macfarlan, T.S.1
-
20
-
-
84898010302
-
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
-
Lu, X. et al. (2014) The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat. Struct. Mol. Biol., 21, 423-425.
-
(2014)
Nat. Struct. Mol. Biol
, vol.21
, pp. 423-425
-
-
Lu, X.1
-
21
-
-
55549096355
-
Murine endogenous retroviruses
-
Stocking, C. et al. (2008) Murine endogenous retroviruses. Cell. Mol. Life Sci., 65, 3383-3398.
-
(2008)
Cell. Mol. Life Sci
, vol.65
, pp. 3383-3398
-
-
Stocking, C.1
-
22
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander, E.S. 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
-
23
-
-
80052012833
-
LINE-1 elements in structural variation and disease
-
Beck, C.R. et al. (2011) LINE-1 elements in structural variation and disease. Annu. Rev. Genomics Hum. Genet., 12, 187-215.
-
(2011)
Annu. Rev. Genomics Hum. Genet
, vol.12
, pp. 187-215
-
-
Beck, C.R.1
-
24
-
-
77953892366
-
Mobile interspersed repeats are major structural variants in the human genome
-
Huang, C.R. et al. (2010) Mobile interspersed repeats are major structural variants in the human genome. Cell, 141, 1171-1182.
-
(2010)
Cell
, vol.141
, pp. 1171-1182
-
-
Huang, C.R.1
-
25
-
-
28444448708
-
SVA elements: a hominid-specific retroposon family
-
Wang, H. et al. (2005) SVA elements: a hominid-specific retroposon family. J. Mol. Biol., 354, 994-1007.
-
(2005)
J. Mol. Biol
, vol.354
, pp. 994-1007
-
-
Wang, H.1
-
26
-
-
0026503996
-
Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer
-
Miki, Y. et al. (1992) Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res., 52, 643-645.
-
(1992)
Cancer Res
, vol.52
, pp. 643-645
-
-
Miki, Y.1
-
27
-
-
84870482898
-
Extensive somatic L1 retrotransposition in colorectal tumors
-
Solyom, S. et al. (2012) Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res., 22, 2328-2338.
-
(2012)
Genome Res
, vol.22
, pp. 2328-2338
-
-
Solyom, S.1
-
28
-
-
84865285978
-
Landscape of somatic retrotransposition in human cancers
-
Lee, E. et al. (2012) Landscape of somatic retrotransposition in human cancers. Science, 337, 967-971.
-
(2012)
Science
, vol.337
, pp. 967-971
-
-
Lee, E.1
-
29
-
-
33645777446
-
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure
-
Bock, C. et al. (2006) CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet., 2, e26.
-
(2006)
PLoS Genet
, vol.2
-
-
Bock, C.1
-
30
-
-
33746051706
-
Computational prediction of methylation status in human genomic sequences
-
Das, R. et al. (2006) Computational prediction of methylation status in human genomic sequences. Proc. Natl Acad. Sci. USA, 103, 10713-10716.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 10713-10716
-
-
Das, R.1
-
31
-
-
55549102967
-
Keeping active endogenous retroviral-like elements in check: the epigenetic perspective
-
Maksakova, I.A. et al. (2008) Keeping active endogenous retroviral-like elements in check: the epigenetic perspective. Cell. Mol. Life Sci., 65, 3329-3347.
-
(2008)
Cell. Mol. Life Sci
, vol.65
, pp. 3329-3347
-
-
Maksakova, I.A.1
-
32
-
-
34248160438
-
Developmentally regulated piRNA clusters implicate MILI in transposon control
-
Aravin, A.A. et al. (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
-
33
-
-
84888209464
-
RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells
-
Ciaudo, C. et al. (2013) RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet., 9, e1003791.
-
(2013)
PLoS Genet
, vol.9
-
-
Ciaudo, C.1
-
34
-
-
77952411179
-
Epigenetic regulation of a murine retrotransposon by a dual histone modification mark
-
Brunmeir, R. et al. (2010) Epigenetic regulation of a murine retrotransposon by a dual histone modification mark. PLoS Genet., 6, e1000927.
-
(2010)
PLoS Genet
, vol.6
-
-
Brunmeir, R.1
-
35
-
-
84890815968
-
Lsh regulates LTR retrotransposon repression independently of Dnmt3b function
-
Dunican, D.S. et al. (2013) Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. Genome Biol., 14, R146.
-
(2013)
Genome Biol
, vol.14
, pp. R146
-
-
Dunican, D.S.1
-
36
-
-
84875226981
-
Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA
-
Fadloun, A. et al. (2013) Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA. Nat. Struct. Mol. Biol., 20, 332-338.
-
(2013)
Nat. Struct. Mol. Biol
, vol.20
, pp. 332-338
-
-
Fadloun, A.1
-
37
-
-
41649116098
-
DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes
-
Kuramochi-Miyagawa, S. 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
-
38
-
-
84861142040
-
Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells
-
Reichmann, J. et al. (2012) Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells. PLoS Comput. Biol., 8, e1002486.
-
(2012)
PLoS Comput. Biol
, vol.8
-
-
Reichmann, J.1
-
39
-
-
78649274945
-
Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer
-
Estécio, M.R. et al. (2010) Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res., 20, 1369-1382.
-
(2010)
Genome Res
, vol.20
, pp. 1369-1382
-
-
Estécio, M.R.1
-
40
-
-
22844457491
-
DNA methylation and human disease
-
Robertson, K.D. (2005) DNA methylation and human disease. Nat. Rev. Genet., 6, 597-610.
-
(2005)
Nat. Rev. Genet
, vol.6
, pp. 597-610
-
-
Robertson, K.D.1
-
41
-
-
0029030242
-
Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts
-
Liu, W.M. et al. (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
-
42
-
-
33645079143
-
Activation of human long interspersed nuclear element 1 retrotransposition by benzo(a)pyrene, an ubiquitous environmental carcinogen
-
Stribinskis, V. et al. (2006) Activation of human long interspersed nuclear element 1 retrotransposition by benzo(a)pyrene, an ubiquitous environmental carcinogen. Cancer Res., 66, 2616-2620.
-
(2006)
Cancer Res
, vol.66
, pp. 2616-2620
-
-
Stribinskis, V.1
-
43
-
-
79952402071
-
Reactivation of L1 retrotransposon by benzo(a)pyrene involves complex genetic and epigenetic regulation
-
Teneng, I. et al. (2011) Reactivation of L1 retrotransposon by benzo(a)pyrene involves complex genetic and epigenetic regulation. Epigenetics, 6, 355-367.
-
(2011)
Epigenetics
, vol.6
, pp. 355-367
-
-
Teneng, I.1
-
44
-
-
0009969062
-
Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition
-
Feng, Q. et al. (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell, 87, 905-916.
-
(1996)
Cell
, vol.87
, pp. 905-916
-
-
Feng, Q.1
-
45
-
-
0026428975
-
Reverse transcriptase encoded by a human transposable element
-
Mathias, S.L. et al. (1991) Reverse transcriptase encoded by a human transposable element. Science, 254, 1808-1810.
-
(1991)
Science
, vol.254
, pp. 1808-1810
-
-
Mathias, S.L.1
-
46
-
-
80052449321
-
Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition
-
Khazina, E. et al. (2011) Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition. Nat. Struct. Mol. Biol., 18, 1006-1014.
-
(2011)
Nat. Struct. Mol. Biol
, vol.18
, pp. 1006-1014
-
-
Khazina, E.1
-
47
-
-
0030961149
-
In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition
-
Kolosha, V.O. et al. (1997) In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition. Proc. Natl Acad. Sci. USA. 94, 10155-10160.
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 10155-10160
-
-
Kolosha, V.O.1
-
48
-
-
0003308786
-
Molecular archeology of L1 insertions in the human genome
-
research0052.1-research0052.18
-
Szak, S. et al. (2002) Molecular archeology of L1 insertions in the human genome. Genome Biol., 3, research0052.1-research0052.18.
-
(2002)
Genome Biol
, vol.3
-
-
Szak, S.1
-
49
-
-
0033525586
-
Exon shuffling by L1 retrotransposition
-
Moran, J.V. et al. (1999) Exon shuffling by L1 retrotransposition. Science, 283, 1530-1534.
-
(1999)
Science
, vol.283
, pp. 1530-1534
-
-
Moran, J.V.1
-
50
-
-
76249132036
-
Many LINE1 elements contribute to the transcriptome of human somatic cells
-
Rangwala, S.H. et al. (2009) Many LINE1 elements contribute to the transcriptome of human somatic cells. Genome Biol., 10, R100.
-
(2009)
Genome Biol
, vol.10
, pp. R100
-
-
Rangwala, S.H.1
-
51
-
-
0034999474
-
Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes
-
Speek, M. (2001) Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol. Cell. Biol., 21, 1973-1985.
-
(2001)
Mol. Cell. Biol
, vol.21
, pp. 1973-1985
-
-
Speek, M.1
-
52
-
-
0037965788
-
Hot L1s account for the bulk of retrotransposition in the human population
-
Brouha, B. et al. (2003) Hot L1s account for the bulk of retrotransposition in the human population. Proc. Natl Acad. Sci. USA, 100, 5280-5285.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 5280-5285
-
-
Brouha, B.1
-
53
-
-
0030903621
-
Many human L1 elements are capable of retrotransposition
-
Sassaman, D.M. et al. (1997) Many human L1 elements are capable of retrotransposition. Nat. Genet., 16, 37-43.
-
(1997)
Nat. Genet
, vol.16
, pp. 37-43
-
-
Sassaman, D.M.1
-
54
-
-
0025913154
-
Identity of rearranged LINE/c-MYC junction sequences specific for the canine transmissible venereal tumor
-
Amariglio, E.N. et al. (1991) Identity of rearranged LINE/c-MYC junction sequences specific for the canine transmissible venereal tumor. Proc. Natl Acad. Sci. USA, 88, 8136-8139.
-
(1991)
Proc. Natl Acad. Sci. USA
, vol.88
, pp. 8136-8139
-
-
Amariglio, E.N.1
-
55
-
-
0343534267
-
"Retroposon" insertion into the cellular oncogene c-myc in canine transmissible venereal tumor
-
Katzir, N. et al. (1985) "Retroposon" insertion into the cellular oncogene c-myc in canine transmissible venereal tumor. Proc. Natl Acad. Sci. USA, 82, 1054-1058.
-
(1985)
Proc. Natl Acad. Sci. USA
, vol.82
, pp. 1054-1058
-
-
Katzir, N.1
-
56
-
-
33746668116
-
Clonal origin and evolution of a transmissible cancer
-
Murgia, C. et al. (2006) Clonal origin and evolution of a transmissible cancer. Cell, 126, 477-487.
-
(2006)
Cell
, vol.126
, pp. 477-487
-
-
Murgia, C.1
-
57
-
-
77955160719
-
High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
-
Ewing, A.D. et al. (2010) High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res. 20, 1262-1270.
-
(2010)
Genome Res
, vol.20
, pp. 1262-1270
-
-
Ewing, A.D.1
-
58
-
-
77953889472
-
Natural mutagenesis of human genomes by endogenous retrotransposons
-
Iskow, R.C. et al. (2010) Natural mutagenesis of human genomes by endogenous retrotransposons. Cell, 141, 1253-1261.
-
(2010)
Cell
, vol.141
, pp. 1253-1261
-
-
Iskow, R.C.1
-
59
-
-
84875698271
-
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma
-
Shukla, R. et al. (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell, 153, 101-111.
-
(2013)
Cell
, vol.153
, pp. 101-111
-
-
Shukla, R.1
-
60
-
-
84870224456
-
LINE-1 retrotransposition in the nervous system
-
Thomas, C.A. et al. (2012) LINE-1 retrotransposition in the nervous system. Annu. Rev. Cell Dev. Biol., 28, 555-573.
-
(2012)
Annu. Rev. Cell Dev. Biol
, vol.28
, pp. 555-573
-
-
Thomas, C.A.1
-
61
-
-
0032796376
-
Alu repeats and human disease
-
Deininger, P.L. et al. (1999) Alu repeats and human disease. Mol. Genet. Metab., 67, 183-193.
-
(1999)
Mol. Genet. Metab
, vol.67
, pp. 183-193
-
-
Deininger, P.L.1
-
62
-
-
0036250811
-
Alu repeats and human genomic diversity
-
Batzer, M.A. et al. (2002) Alu repeats and human genomic diversity. Nat. Rev. Genet., 3, 370-379.
-
(2002)
Nat. Rev. Genet
, vol.3
, pp. 370-379
-
-
Batzer, M.A.1
-
63
-
-
0036796354
-
Mammalian retroelements
-
Deininger, P.L. et al. (2002) Mammalian retroelements. Genome Res., 12, 1455-1465.
-
(2002)
Genome Res
, vol.12
, pp. 1455-1465
-
-
Deininger, P.L.1
-
64
-
-
57149120574
-
Active Alu retrotransposons in the human genome
-
Bennett, E.A. et al. (2008) Active Alu retrotransposons in the human genome. Genome Res., 18, 1875-1883.
-
(2008)
Genome Res
, vol.18
, pp. 1875-1883
-
-
Bennett, E.A.1
-
65
-
-
79953108463
-
Alu distribution and mutation types of cancer genes
-
Zhang, W. et al. (2011) Alu distribution and mutation types of cancer genes. BMC Genomics, 12, 157.
-
(2011)
BMC Genomics
, vol.12
, pp. 157
-
-
Zhang, W.1
-
66
-
-
27444436452
-
Founder SVA retrotransposal insertion in Fukuyama-type congenital muscular dystrophy and its origin in Japanese and Northeast Asian populations
-
Watanabe, M. et al. (2005) Founder SVA retrotransposal insertion in Fukuyama-type congenital muscular dystrophy and its origin in Japanese and Northeast Asian populations. Am. J. Med. Genet. A, 138, 344-348.
-
(2005)
Am. J. Med. Genet. A
, vol.138
, pp. 344-348
-
-
Watanabe, M.1
-
67
-
-
24144489347
-
Two independent retrotransposon insertions at the same site within the coding region of BTK
-
Conley, M.E. et al. (2005) Two independent retrotransposon insertions at the same site within the coding region of BTK. Hum. Mutat., 25, 324-325.
-
(2005)
Hum. Mutat
, vol.25
, pp. 324-325
-
-
Conley, M.E.1
-
68
-
-
77956849313
-
Genomic rearrangements in inherited disease and cancer
-
Chen, J.M. et al. (2010) Genomic rearrangements in inherited disease and cancer. Semin. Cancer Biol., 20, 222-233.
-
(2010)
Semin. Cancer Biol
, vol.20
, pp. 222-233
-
-
Chen, J.M.1
-
69
-
-
67651098662
-
Mechanisms of change in gene copy number
-
Hastings, P.J. et al. (2009) Mechanisms of change in gene copy number. Nat. Rev. Genet., 10, 551-564.
-
(2009)
Nat. Rev. Genet
, vol.10
, pp. 551-564
-
-
Hastings, P.J.1
-
70
-
-
77951810932
-
The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important
-
Kvikstad, E.M. et al. (2010) The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res., 20, 600-613.
-
(2010)
Genome Res
, vol.20
, pp. 600-613
-
-
Kvikstad, E.M.1
-
71
-
-
33750279751
-
The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model
-
Abrusán, G. et al. (2006) The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model. J. Mol. Evol., 63, 484-492.
-
(2006)
J. Mol. Evol
, vol.63
, pp. 484-492
-
-
Abrusán, G.1
-
72
-
-
0029804093
-
Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1
-
Smith, T.M. et al. (1996) Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1. Genome Res., 6, 1029-1049.
-
(1996)
Genome Res
, vol.6
, pp. 1029-1049
-
-
Smith, T.M.1
-
73
-
-
0036206745
-
Distinct BRCA1 rearrangements involving the BRCA1 pseudogene suggest the existence of a recombination hot spot
-
Puget, N. et al. (2002) Distinct BRCA1 rearrangements involving the BRCA1 pseudogene suggest the existence of a recombination hot spot. Am. J. Hum. Genet., 70, 858-865.
-
(2002)
Am. J. Hum. Genet
, vol.70
, pp. 858-865
-
-
Puget, N.1
-
74
-
-
0031035045
-
A 1-kb Alu-mediated germ-line deletion removing BRCA1 exon 17
-
Puget, N. et al. (1997) A 1-kb Alu-mediated germ-line deletion removing BRCA1 exon 17. Cancer Res., 57, 828-831.
-
(1997)
Cancer Res
, vol.57
, pp. 828-831
-
-
Puget, N.1
-
75
-
-
84875464936
-
Genomic characterization of two large Alumediated rearrangements of the BRCA1 gene
-
Peixoto, A. et al. (2013) Genomic characterization of two large Alumediated rearrangements of the BRCA1 gene. J. Hum. Genet., 58, 78-83.
-
(2013)
J. Hum. Genet
, vol.58
, pp. 78-83
-
-
Peixoto, A.1
-
76
-
-
5144227841
-
Retroelements and the human genome: new perspectives on an old relation
-
Bannert, N. et al. (2004) Retroelements and the human genome: new perspectives on an old relation. Proc. Natl Acad. Sci. USA, 101, 14572-14579.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 14572-14579
-
-
Bannert, N.1
-
77
-
-
84876095725
-
Human-specific HERV-K insertion causes genomic variations in the human genome
-
Shin, W. et al. (2013) Human-specific HERV-K insertion causes genomic variations in the human genome. PLoS One, 8, e60605.
-
(2013)
PLoS One
, vol.8
-
-
Shin, W.1
-
78
-
-
0035734951
-
Evidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution
-
Hughes, J.F. et al. (2001) Evidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution. Nat. Genet., 29, 487-489.
-
(2001)
Nat. Genet
, vol.29
, pp. 487-489
-
-
Hughes, J.F.1
-
79
-
-
0031453779
-
Barbara McClintock and the transposition concept
-
Barahona, A. (1997) Barbara McClintock and the transposition concept. Arch. Int. Hist. Sci. (Paris)., 46, 309-329.
-
(1997)
Arch. Int. Hist. Sci. (Paris)
, vol.46
, pp. 309-329
-
-
Barahona, A.1
-
80
-
-
36749061982
-
Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53
-
Wang, T. et al. (2007) Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc. Natl Acad. Sci. USA, 104, 18613-18618.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 18613-18618
-
-
Wang, T.1
-
81
-
-
55549117831
-
Evolution of the mammalian transcription factor binding repertoire via transposable elements
-
Bourque, G. et al. (2008) Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res., 18, 1752-1762.
-
(2008)
Genome Res
, vol.18
, pp. 1752-1762
-
-
Bourque, G.1
-
82
-
-
77952238354
-
Genomic gems: SINE RNAs regulate mRNA production
-
Ponicsan, S.L. et al. (2010) Genomic gems: SINE RNAs regulate mRNA production. Curr. Opin. Genet. Dev., 20, 149-155.
-
(2010)
Curr. Opin. Genet. Dev
, vol.20
, pp. 149-155
-
-
Ponicsan, S.L.1
-
83
-
-
2442667886
-
Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes
-
Han, J.S. et al. (2004) Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature, 429, 268-274.
-
(2004)
Nature
, vol.429
, pp. 268-274
-
-
Han, J.S.1
-
84
-
-
12244275645
-
Widespread occurrence of antisense transcription in the human genome
-
Yelin, R. et al. (2003) Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol., 21, 379-386.
-
(2003)
Nat. Biotechnol
, vol.21
, pp. 379-386
-
-
Yelin, R.1
-
85
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
-
86
-
-
67349173665
-
The regulated retrotransposon transcriptome of mammalian cells
-
Faulkner, G.J. et al. (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet., 41, 563-571.
-
(2009)
Nat. Genet
, vol.41
, pp. 563-571
-
-
Faulkner, G.J.1
-
87
-
-
33644801773
-
Alternative initiation and splicing in dicer gene expression in human breast cells
-
Irvin-Wilson, C.V. et al. (2005) Alternative initiation and splicing in dicer gene expression in human breast cells. Breast Cancer Res., 7, R563-R569.
-
(2005)
Breast Cancer Res
, vol.7
, pp. R563-R569
-
-
Irvin-Wilson, C.V.1
-
88
-
-
50849114182
-
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
-
Singer, G.A. et al. (2008) Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array. BMC Genomics, 9, 349.
-
(2008)
BMC Genomics
, vol.9
, pp. 349
-
-
Singer, G.A.1
-
89
-
-
80053970951
-
Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis
-
Thorsen, K. et al. (2011) Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis. BMC Genomics, 12, 505.
-
(2011)
BMC Genomics
, vol.12
, pp. 505
-
-
Thorsen, K.1
-
90
-
-
77952414230
-
Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer
-
Wolff, E.M. et al. (2010) Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet., 6, e1000917.
-
(2010)
PLoS Genet
, vol.6
-
-
Wolff, E.M.1
-
91
-
-
1942467065
-
Genomic variants in exons and introns: identifying the splicing spoilers
-
Pagani, F. et al. (2004) Genomic variants in exons and introns: identifying the splicing spoilers. Nat. Rev. Genet., 5, 389-396.
-
(2004)
Nat. Rev. Genet
, vol.5
, pp. 389-396
-
-
Pagani, F.1
-
92
-
-
56749164864
-
Expression of 24, 426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines
-
Castle, J.C. et al. (2008) Expression of 24, 426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat. Genet., 40, 1416-1425.
-
(2008)
Nat. Genet
, vol.40
, pp. 1416-1425
-
-
Castle, J.C.1
-
93
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang, E.T. et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
-
94
-
-
79952615527
-
Widespread establishment and regulatory impact of Alu exons in human genes
-
Shen, S. et al. (2011) Widespread establishment and regulatory impact of Alu exons in human genes. Proc. Natl Acad. Sci. USA, 108, 2837-2842.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 2837-2842
-
-
Shen, S.1
-
95
-
-
12344300804
-
Widespread A-to-I RNA editing of Alucontaining mRNAs in the human transcriptome
-
Athanasiadis, A. et al. (2004) Widespread A-to-I RNA editing of Alucontaining mRNAs in the human transcriptome. PLoS Biol., 2, e391.
-
(2004)
PLoS Biol
, vol.2
-
-
Athanasiadis, A.1
-
96
-
-
33750460928
-
Multiple effects govern endogenous retrovirus survival patterns in human gene introns
-
Van de Lagemaat, L.N. et al. (2006) Multiple effects govern endogenous retrovirus survival patterns in human gene introns. Genome Biol. 7, R86.
-
(2006)
Genome Biol
, vol.7
, pp. R86
-
-
Van de Lagemaat, L.N.1
-
97
-
-
84877768911
-
RNA sequencing of cancer reveals novel splicing alterations
-
Eswaran, J. et al. (2013) RNA sequencing of cancer reveals novel splicing alterations. Sci. Rep., 3, 1689.
-
(2013)
Sci. Rep
, vol.3
, pp. 1689
-
-
Eswaran, J.1
-
98
-
-
84887460995
-
Misregulation of pre-mRNA alternative splicing in cancer
-
Zhang, J. et al. (2013) Misregulation of pre-mRNA alternative splicing in cancer. Cancer Discov., 3, 1228-1237.
-
(2013)
Cancer Discov
, vol.3
, pp. 1228-1237
-
-
Zhang, J.1
-
99
-
-
84884419292
-
Emerging patterns of somatic mutations in cancer
-
Watson, I.R. et al. (2013) Emerging patterns of somatic mutations in cancer. Nat. Rev. Genet., 14, 703-718.
-
(2013)
Nat. Rev. Genet
, vol.14
, pp. 703-718
-
-
Watson, I.R.1
-
100
-
-
78049416081
-
Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged
-
David, C.J. et al. (2010) Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev. 24, 2343-2364.
-
(2010)
Genes Dev
, vol.24
, pp. 2343-2364
-
-
David, C.J.1
-
101
-
-
84896706322
-
Linear decay of retrotransposon antisense bias across genes is contingent upon tissue specificity
-
Linker, S. et al. (2013) Linear decay of retrotransposon antisense bias across genes is contingent upon tissue specificity. PLoS One, 8, e79402.
-
(2013)
PLoS One
, vol.8
-
-
Linker, S.1
-
102
-
-
0036170433
-
The solitary long terminal repeats of ERV-9 endogenous retrovirus are conserved during primate evolution and possess enhancer activities in embryonic and hematopoietic cells
-
Ling, J. et al. (2002) The solitary long terminal repeats of ERV-9 endogenous retrovirus are conserved during primate evolution and possess enhancer activities in embryonic and hematopoietic cells. J. Virol., 76, 2410-2423.
-
(2002)
J. Virol
, vol.76
, pp. 2410-2423
-
-
Ling, J.1
-
103
-
-
77955627648
-
Long-range function of an intergenic retrotransposon
-
Pi, W. et al. (2010) Long-range function of an intergenic retrotransposon. Proc. Natl Acad. Sci. USA, 107, 12992-12997.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 12992-12997
-
-
Pi, W.1
-
104
-
-
84881484687
-
Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer
-
Cruickshanks, H.A. et al. (2013) Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer. Nucleic Acids Res., 41, 6857-6869.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 6857-6869
-
-
Cruickshanks, H.A.1
-
105
-
-
19444367079
-
Mammalian microRNAs derived from genomic repeats
-
Smalheiser, N.R. et al. (2005) Mammalian microRNAs derived from genomic repeats. Trends Genet., 21, 322-326.
-
(2005)
Trends Genet
, vol.21
, pp. 322-326
-
-
Smalheiser, N.R.1
-
106
-
-
66149157654
-
Human-specific modulation of transcriptional activity provided by endogenous retroviral insertions
-
Gogvadze, E. et al. (2009) Human-specific modulation of transcriptional activity provided by endogenous retroviral insertions. J. Virol., 83, 6098-6105.
-
(2009)
J. Virol
, vol.83
, pp. 6098-6105
-
-
Gogvadze, E.1
-
107
-
-
84856013431
-
Clonal evolution in cancer
-
Greaves, M. et al. (2012) Clonal evolution in cancer, Nature, 481, 306-313.
-
(2012)
Nature
, vol.481
, pp. 306-313
-
-
Greaves, M.1
-
108
-
-
84878988418
-
Visiting "noncodarnia"
-
Perkel, J.M. (2013) Visiting "noncodarnia". Biotechniques, 54, 301, 303-304.
-
(2013)
Biotechniques
, vol.54
-
-
Perkel, J.M.1
-
109
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
-
110
-
-
80053045739
-
Molecular mechanisms of long noncoding RNAs
-
Wang, K.C. et al. (2011) Molecular mechanisms of long noncoding RNAs. Mol. Cell, 43, 904-914.
-
(2011)
Mol. Cell
, vol.43
, pp. 904-914
-
-
Wang, K.C.1
-
111
-
-
0344429906
-
MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer
-
Ji, P. et al. (2003) MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene, 22, 8031-8041.
-
(2003)
Oncogene
, vol.22
, pp. 8031-8041
-
-
Ji, P.1
-
112
-
-
79953888460
-
The functional role of long non-coding RNA in human carcinomas
-
Gibb, E.A. et al. (2011) The functional role of long non-coding RNA in human carcinomas. Mol. Cancer, 10, 38.
-
(2011)
Mol. Cancer
, vol.10
, pp. 38
-
-
Gibb, E.A.1
-
113
-
-
77955323879
-
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response
-
Huarte, M. et al. (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell, 142, 409-419.
-
(2010)
Cell
, vol.142
, pp. 409-419
-
-
Huarte, M.1
-
114
-
-
84874053510
-
Xist RNA is a potent suppressor of hematologic cancer in mice
-
Yildirim, E. et al. (2013) Xist RNA is a potent suppressor of hematologic cancer in mice. Cell, 152, 727-742.
-
(2013)
Cell
, vol.152
, pp. 727-742
-
-
Yildirim, E.1
-
115
-
-
18744372123
-
BRCA1 supports XIST RNA concentration on the inactive X chromosome
-
Ganesan, S. et al. (2002) BRCA1 supports XIST RNA concentration on the inactive X chromosome. Cell, 111, 393-405.
-
(2002)
Cell
, vol.111
, pp. 393-405
-
-
Ganesan, S.1
-
116
-
-
38049155825
-
Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA
-
Yu, W. et al. (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature, 451, 202-206.
-
(2008)
Nature
, vol.451
, pp. 202-206
-
-
Yu, W.1
-
117
-
-
0033955368
-
Vertebrate pseudogenes
-
Mighell, A.J. et al. (2000) Vertebrate pseudogenes. FEBS Lett., 468, 109-114.
-
(2000)
FEBS Lett
, vol.468
, pp. 109-114
-
-
Mighell, A.J.1
-
118
-
-
0346155809
-
Pseudogenes: are they "junk" or functional DNA?
-
Balakirev, E.S. et al. (2003) Pseudogenes: are they "junk" or functional DNA? Annu. Rev. Genet., 37, 123-151.
-
(2003)
Annu. Rev. Genet
, vol.37
, pp. 123-151
-
-
Balakirev, E.S.1
-
119
-
-
84860119507
-
Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer
-
Nie, L. et al. (2012) Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer. Am. J. Transl. Res., 4, 127-150.
-
(2012)
Am. J. Transl. Res
, vol.4
, pp. 127-150
-
-
Nie, L.1
-
120
-
-
84865726286
-
The GENCODE pseudogene resource
-
Pei, B. et al. (2012) The GENCODE pseudogene resource. Genome Biol., 13, R51.
-
(2012)
Genome Biol
, vol.13
, pp. R51
-
-
Pei, B.1
-
121
-
-
84893093139
-
Inhibition of LINE-1 retrotransposonencoded reverse transcriptase modulates the expression of cell differentiation genes in breast cancer cells
-
Patnala, R. et al. (2014) Inhibition of LINE-1 retrotransposonencoded reverse transcriptase modulates the expression of cell differentiation genes in breast cancer cells. Breast Cancer Res. Treat., 143, 239-253.
-
(2014)
Breast Cancer Res. Treat
, vol.143
, pp. 239-253
-
-
Patnala, R.1
-
122
-
-
79961170994
-
A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?
-
Salmena, L. et al. (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell, 146, 353-358.
-
(2011)
Cell
, vol.146
, pp. 353-358
-
-
Salmena, L.1
-
123
-
-
80054689794
-
An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma
-
Sumazin, P. et al. (2011) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell, 147, 370-381.
-
(2011)
Cell
, vol.147
, pp. 370-381
-
-
Sumazin, P.1
-
124
-
-
77953957633
-
A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
-
Poliseno, L. et al. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465, 1033-1038.
-
(2010)
Nature
, vol.465
, pp. 1033-1038
-
-
Poliseno, L.1
-
125
-
-
79952255050
-
Transcriptional regulation of Oct4 by a long noncoding RNA antisense to Oct4-pseudogene 5
-
Hawkins, P.G. et al. (2010) Transcriptional regulation of Oct4 by a long noncoding RNA antisense to Oct4-pseudogene 5. Transcription, 1, 165-175.
-
(2010)
Transcription
, vol.1
, pp. 165-175
-
-
Hawkins, P.G.1
-
126
-
-
33745125901
-
The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene
-
Duret, L. et al. (2006) The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science, 312, 1653-1655.
-
(2006)
Science
, vol.312
, pp. 1653-1655
-
-
Duret, L.1
|