-
1
-
-
67349173665
-
The regulated retrotransposon transcriptome of mammalian cells
-
Faulkner GJ, Kimura Y, Daub CO 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
Kimura, Y.2
Daub, C.O.3
-
2
-
-
58149507192
-
Effects of retroviruses on host genome function
-
Jern P, Coffin JM (2008) Effects of retroviruses on host genome function. Annu Rev Genet 42:709–732
-
(2008)
Annu Rev Genet
, vol.42
, pp. 709-732
-
-
Jern, P.1
Coffin, J.M.2
-
3
-
-
84876116910
-
A repetitive elements perspective in polycomb epigenetics
-
Casa V, Gabellini D (2012) A repetitive elements perspective in polycomb epigenetics. Front Genet 3:199
-
(2012)
Front Genet
, vol.3
, pp. 199
-
-
Casa, V.1
Gabellini, D.2
-
4
-
-
49649094943
-
A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements
-
Elisaphenko EA, Kolesnikov NN, Shevchenko AI et al (2008) A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements. PLoS ONE 3:e2521
-
(2008)
PLoS ONE
, vol.3
, pp. e2521
-
-
Elisaphenko, E.A.1
Kolesnikov, N.N.2
Shevchenko, A.I.3
-
5
-
-
70349318211
-
The impact of retrotransposons on human genome evolution
-
Cordaux R, Batzer MA (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
Batzer, M.A.2
-
6
-
-
52949095077
-
Retrotransposons revisited: the restraint and rehabilitation of parasites
-
Goodier JL, Kazazian HH Jr (2008) Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 135:23–35
-
(2008)
Cell
, vol.135
, pp. 23-35
-
-
Goodier, J.L.1
Kazazian, H.H.2
-
7
-
-
84876799419
-
Transposable elements as genetic regulatory substrates in early development
-
Gifford WD, Pfaff SL, Macfarlan TS (2013) Transposable elements as genetic regulatory substrates in early development. Trends Cell Biol 23:218–226
-
(2013)
Trends Cell Biol
, vol.23
, pp. 218-226
-
-
Gifford, W.D.1
Pfaff, S.L.2
Macfarlan, T.S.3
-
8
-
-
0141856317
-
Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins
-
de Parseval N, Lazar V, Casella JF et al (2003) Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. J Virol 77:10414–10422
-
(2003)
J Virol
, vol.77
, pp. 10414-10422
-
-
de Parseval, N.1
Lazar, V.2
Casella, J.F.3
-
9
-
-
18144416982
-
Identification of endogenous retroviral reading frames in the human genome
-
Villesen P, Aagaard L, Wiuf C et al (2004) Identification of endogenous retroviral reading frames in the human genome. Retrovirology 1:32
-
(2004)
Retrovirology
, vol.1
, pp. 32
-
-
Villesen, P.1
Aagaard, L.2
Wiuf, C.3
-
10
-
-
80455158263
-
Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses
-
Subramanian RP, Wildschutte JH, Russo C et al (2011) Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. Retrovirology 8:90
-
(2011)
Retrovirology
, vol.8
, pp. 90
-
-
Subramanian, R.P.1
Wildschutte, J.H.2
Russo, C.3
-
11
-
-
77953880842
-
LINE-1 retrotransposition activity in human genomes
-
Beck CR, Collier P, Macfarlane C et al (2010) LINE-1 retrotransposition activity in human genomes. Cell 141:1159–1170
-
(2010)
Cell
, vol.141
, pp. 1159-1170
-
-
Beck, C.R.1
Collier, P.2
Macfarlane, C.3
-
12
-
-
0042856395
-
Alu: a parasite’s parasite?
-
Schmid CW (2003) Alu: a parasite’s parasite? Nat Genet 35:15–16
-
(2003)
Nat Genet
, vol.35
, pp. 15-16
-
-
Schmid, C.W.1
-
13
-
-
22744445703
-
RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons
-
Kapitonov VV, Jurka J (2005) RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3:e181
-
(2005)
PLoS Biol
, vol.3
, pp. e181
-
-
Kapitonov, V.V.1
Jurka, J.2
-
14
-
-
84961287889
-
Retroviral transcriptional regulation and embryonic stem cells: war and peace
-
Schlesinger S, Goff SP (2015) Retroviral transcriptional regulation and embryonic stem cells: war and peace. Mol Cell Biol 35:770–777
-
(2015)
Mol Cell Biol
, vol.35
, pp. 770-777
-
-
Schlesinger, S.1
Goff, S.P.2
-
15
-
-
84930205085
-
Retrotransposons shape species-specific embryonic stem cell gene expression
-
Robbez-Masson L, Rowe HM (2015) Retrotransposons shape species-specific embryonic stem cell gene expression. Retrovirology 12:45
-
(2015)
Retrovirology
, vol.12
, pp. 45
-
-
Robbez-Masson, L.1
Rowe, H.M.2
-
16
-
-
33748526495
-
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication
-
Johnson R, Gamblin RJ, Ooi L et al (2006) Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res 34:3862–3877
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3862-3877
-
-
Johnson, R.1
Gamblin, R.J.2
Ooi, L.3
-
17
-
-
77954100084
-
Transposable elements have rewired the core regulatory network of human embryonic stem cells
-
Kunarso G, Chia NY, Jeyakani J et al (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42:631–634
-
(2010)
Nat Genet
, vol.42
, pp. 631-634
-
-
Kunarso, G.1
Chia, N.Y.2
Jeyakani, J.3
-
18
-
-
23844534414
-
Impact of transposable elements on the evolution of mammalian gene regulation
-
Medstrand P, van de Lagemaat LN, Dunn CA et al (2005) Impact of transposable elements on the evolution of mammalian gene regulation. Cytogenet Genome Res 110:342–352
-
(2005)
Cytogenet Genome Res
, vol.110
, pp. 342-352
-
-
Medstrand, P.1
van de Lagemaat, L.N.2
Dunn, C.A.3
-
19
-
-
84902682913
-
The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs
-
Johnson R, Guigo R (2014) The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA 20:959–976
-
(2014)
RNA
, vol.20
, pp. 959-976
-
-
Johnson, R.1
Guigo, R.2
-
20
-
-
0021798378
-
Spatial distribution of transcripts of the long repeated ETn sequence during early mouse embryogenesis
-
Brulet P, Condamine H, Jacob F (1985) Spatial distribution of transcripts of the long repeated ETn sequence during early mouse embryogenesis. Proc Natl Acad Sci USA 82:2054–2058
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, pp. 2054-2058
-
-
Brulet, P.1
Condamine, H.2
Jacob, F.3
-
21
-
-
0021348844
-
Amounts, synthesis, and some properties of intracisternal a particle-related RNA in early mouse embryos
-
Piko L, Hammons MD, Taylor KD (1984) Amounts, synthesis, and some properties of intracisternal a particle-related RNA in early mouse embryos. Proc Natl Acad Sci USA 81:488–492
-
(1984)
Proc Natl Acad Sci USA
, vol.81
, pp. 488-492
-
-
Piko, L.1
Hammons, M.D.2
Taylor, K.D.3
-
22
-
-
5044251591
-
Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos
-
Peaston AE, Evsikov AV, Graber JH et al (2004) Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell 7:597–606
-
(2004)
Dev Cell
, vol.7
, pp. 597-606
-
-
Peaston, A.E.1
Evsikov, A.V.2
Graber, J.H.3
-
23
-
-
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
-
25
-
-
84930227422
-
Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
-
Grow EJ, Flynn RA, Chavez SL et al (2015) Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature 522:221–225
-
(2015)
Nature
, vol.522
, pp. 221-225
-
-
Grow, E.J.1
Flynn, R.A.2
Chavez, S.L.3
-
26
-
-
39549099581
-
Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles
-
Boller K, Schonfeld K, Lischer S et al (2008) Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles. J Gen Virol 89:567–572
-
(2008)
J Gen Virol
, vol.89
, pp. 567-572
-
-
Boller, K.1
Schonfeld, K.2
Lischer, S.3
-
28
-
-
84924907701
-
Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells
-
Goke J, Lu X, Chan YS et al (2015) Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. Cell Stem Cell 16:135–141
-
(2015)
Cell Stem Cell
, vol.16
, pp. 135-141
-
-
Goke, J.1
Lu, X.2
Chan, Y.S.3
-
29
-
-
84901651635
-
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
-
Fort A, Hashimoto K, Yamada D et al (2014) Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat Genet 46:558–566
-
(2014)
Nat Genet
, vol.46
, pp. 558-566
-
-
Fort, A.1
Hashimoto, K.2
Yamada, D.3
-
30
-
-
0037307630
-
MuERV-L is one of the earliest transcribed genes in mouse one-cell embryos
-
Kigami D, Minami N, Takayama H et al (2003) MuERV-L is one of the earliest transcribed genes in mouse one-cell embryos. Biol Reprod 68:651–654
-
(2003)
Biol Reprod
, vol.68
, pp. 651-654
-
-
Kigami, D.1
Minami, N.2
Takayama, H.3
-
31
-
-
34249279527
-
Stability and flexibility of epigenetic gene regulation in mammalian development
-
Reik W (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447:425–432
-
(2007)
Nature
, vol.447
, pp. 425-432
-
-
Reik, W.1
-
32
-
-
84871927765
-
Silencing of proviruses in embryonic cells: efficiency, stability and chromatin modifications
-
Schlesinger S, Goff SP (2013) Silencing of proviruses in embryonic cells: efficiency, stability and chromatin modifications. EMBO Rep 14:73–79
-
(2013)
EMBO Rep
, vol.14
, pp. 73-79
-
-
Schlesinger, S.1
Goff, S.P.2
-
33
-
-
0033915781
-
Mice lacking the transcriptional corepressor TIF1beta are defective in early postimplantation development
-
Cammas F, Mark M, Dolle P et al (2000) Mice lacking the transcriptional corepressor TIF1beta are defective in early postimplantation development. Development 127:2955–2963
-
(2000)
Development
, vol.127
, pp. 2955-2963
-
-
Cammas, F.1
Mark, M.2
Dolle, P.3
-
34
-
-
84858770341
-
Trim28 is required for epigenetic stability during mouse oocyte to embryo transition
-
Messerschmidt DM, de Vries W, Ito M et al (2012) Trim28 is required for epigenetic stability during mouse oocyte to embryo transition. Science 335:1499–1502
-
(2012)
Science
, vol.335
, pp. 1499-1502
-
-
Messerschmidt, D.M.1
de Vries, W.2
Ito, M.3
-
35
-
-
84874626481
-
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells
-
Rowe HM, Kapopoulou A, Corsinotti A et al (2013) TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res 23:452–461
-
(2013)
Genome Res
, vol.23
, pp. 452-461
-
-
Rowe, H.M.1
Kapopoulou, A.2
Corsinotti, A.3
-
36
-
-
74549116659
-
KAP1 controls endogenous retroviruses in embryonic stem cells
-
Rowe HM, Jakobsson J, Mesnard D et al (2010) KAP1 controls endogenous retroviruses in embryonic stem cells. Nature 463:237–240
-
(2010)
Nature
, vol.463
, pp. 237-240
-
-
Rowe, H.M.1
Jakobsson, J.2
Mesnard, D.3
-
37
-
-
33751007001
-
The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression
-
Sripathy SP, Stevens J, Schultz DC (2006) The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression. Mol Cell Biol 26:8623–8638
-
(2006)
Mol Cell Biol
, vol.26
, pp. 8623-8638
-
-
Sripathy, S.P.1
Stevens, J.2
Schultz, D.C.3
-
38
-
-
77950862656
-
Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
-
Matsui T, Leung D, Miyashita H et al (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
-
39
-
-
67349170854
-
Embryonic stem cells use ZFP809 to silence retroviral DNAs
-
Wolf D, Goff SP (2009) Embryonic stem cells use ZFP809 to silence retroviral DNAs. Nature 458:1201–1204
-
(2009)
Nature
, vol.458
, pp. 1201-1204
-
-
Wolf, D.1
Goff, S.P.2
-
40
-
-
84924666261
-
The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses
-
Wolf G, Yang P, Fuchtbauer AC et al (2015) The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses. Genes Dev 29:538–554
-
(2015)
Genes Dev
, vol.29
, pp. 538-554
-
-
Wolf, G.1
Yang, P.2
Fuchtbauer, A.C.3
-
41
-
-
84892437617
-
Proviral silencing in embryonic cells is regulated by Yin Yang 1
-
Schlesinger S, Lee AH, Wang GZ et al (2013) Proviral silencing in embryonic cells is regulated by Yin Yang 1. Cell Rep 4:50–58
-
(2013)
Cell Rep
, vol.4
, pp. 50-58
-
-
Schlesinger, S.1
Lee, A.H.2
Wang, G.Z.3
-
42
-
-
84882800012
-
Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells
-
Tan X, Xu X, Elkenani M et al (2013) Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells. Stem Cell Res 11:1045–1059
-
(2013)
Stem Cell Res
, vol.11
, pp. 1045-1059
-
-
Tan, X.1
Xu, X.2
Elkenani, M.3
-
43
-
-
84867553284
-
Expression of endogenous retroviruses is negatively regulated by the pluripotency marker Rex1/Zfp42
-
Guallar D, Perez-Palacios R, Climent M et al (2012) Expression of endogenous retroviruses is negatively regulated by the pluripotency marker Rex1/Zfp42. Nucleic Acids Res 40:8993–9007
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 8993-9007
-
-
Guallar, D.1
Perez-Palacios, R.2
Climent, M.3
-
44
-
-
84929152789
-
C2H2 zinc finger proteins greatly expand the human regulatory lexicon
-
Najafabadi HS, Mnaimneh S, Schmitges FW et al (2015) C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol 33:555–562
-
(2015)
Nat Biotechnol
, vol.33
, pp. 555-562
-
-
Najafabadi, H.S.1
Mnaimneh, S.2
Schmitges, F.W.3
-
45
-
-
80555142988
-
Coevolution of retroelements and tandem zinc finger genes
-
Thomas JH, Schneider S (2011) Coevolution of retroelements and tandem zinc finger genes. Genome Res 21:1800–1812
-
(2011)
Genome Res
, vol.21
, pp. 1800-1812
-
-
Thomas, J.H.1
Schneider, S.2
-
46
-
-
84922971647
-
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
-
Jacobs FM, Greenberg D, Nguyen N et al (2014) An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature 516:242–245
-
(2014)
Nature
, vol.516
, pp. 242-245
-
-
Jacobs, F.M.1
Greenberg, D.2
Nguyen, N.3
-
47
-
-
84906342313
-
Ectopic DNMT3L triggers assembly of a repressive complex for retroviral silencing in somatic cells
-
Kao TH, Liao HF, Wolf D et al (2014) Ectopic DNMT3L triggers assembly of a repressive complex for retroviral silencing in somatic cells. J Virol 88:10680–10695
-
(2014)
J Virol
, vol.88
, pp. 10680-10695
-
-
Kao, T.H.1
Liao, H.F.2
Wolf, D.3
-
48
-
-
33644873184
-
BioGRID: a general repository for interaction datasets
-
Stark C, Breitkreutz BJ, Reguly T et al (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34:D535–D539
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D535-D539
-
-
Stark, C.1
Breitkreutz, B.J.2
Reguly, T.3
-
49
-
-
79952614013
-
Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A
-
Macfarlan TS, Gifford WD, Agarwal S et al (2011) Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev 25:594–607
-
(2011)
Genes Dev
, vol.25
, pp. 594-607
-
-
Macfarlan, T.S.1
Gifford, W.D.2
Agarwal, S.3
-
50
-
-
78049357469
-
Lysine-specific demethylase 1 regulates the embryonic transcriptome and CoREST stability
-
Foster CT, Dovey OM, Lezina L et al (2010) Lysine-specific demethylase 1 regulates the embryonic transcriptome and CoREST stability. Mol Cell Biol 30:4851–4863
-
(2010)
Mol Cell Biol
, vol.30
, pp. 4851-4863
-
-
Foster, C.T.1
Dovey, O.M.2
Lezina, L.3
-
51
-
-
77954652028
-
TIF1beta regulates the pluripotency of embryonic stem cells in a phosphorylation-dependent manner
-
Seki Y, Kurisaki A, Watanabe-Susaki K et al (2010) TIF1beta regulates the pluripotency of embryonic stem cells in a phosphorylation-dependent manner. Proc Natl Acad Sci USA 107:10926–10931
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 10926-10931
-
-
Seki, Y.1
Kurisaki, A.2
Watanabe-Susaki, K.3
-
52
-
-
84988299282
-
Role of Oct4 in the early embryo development
-
Wu G, Scholer HR (2014) Role of Oct4 in the early embryo development. Cell Regen (Lond) 3:7
-
(2014)
Cell Regen (Lond)
, vol.3
, pp. 7
-
-
Wu, G.1
Scholer, H.R.2
-
53
-
-
84904537943
-
Suv39 h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells
-
Bulut-Karslioglu A, De La Rosa-Velazquez IA, Ramirez F et al (2014) Suv39 h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells. Mol Cell 55:277–290
-
(2014)
Mol Cell
, vol.55
, pp. 277-290
-
-
Bulut-Karslioglu, A.1
De La Rosa-Velazquez, I.A.2
Ramirez, F.3
-
54
-
-
84878422484
-
Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells
-
Maksakova IA, Thompson PJ, Goyal P et al (2013) Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. Epigenetics Chromatin 6:15
-
(2013)
Epigenetics Chromatin
, vol.6
, pp. 15
-
-
Maksakova, I.A.1
Thompson, P.J.2
Goyal, P.3
-
55
-
-
84924359019
-
hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells
-
Thompson PJ, Dulberg V, Moon KM et al (2015) hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells. PLoS Genet 11:e1004933
-
(2015)
PLoS Genet
, vol.11
, pp. e1004933
-
-
Thompson, P.J.1
Dulberg, V.2
Moon, K.M.3
-
56
-
-
80051571400
-
Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells
-
Yu HB, Johnson R, Kunarso G et al (2011) Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells. Genome Res 21:1284–1293
-
(2011)
Genome Res
, vol.21
, pp. 1284-1293
-
-
Yu, H.B.1
Johnson, R.2
Kunarso, G.3
-
57
-
-
80054684150
-
Endogenous APOBEC3B restricts LINE-1 retrotransposition in transformed cells and human embryonic stem cells
-
Wissing S, Montano M, Garcia-Perez JL et al (2011) Endogenous APOBEC3B restricts LINE-1 retrotransposition in transformed cells and human embryonic stem cells. J Biol Chem 286:36427–36437
-
(2011)
J Biol Chem
, vol.286
, pp. 36427-36437
-
-
Wissing, S.1
Montano, M.2
Garcia-Perez, J.L.3
-
58
-
-
66149168927
-
L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism
-
Kano H, Godoy I, Courtney C et al (2009) L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev 23:1303–1312
-
(2009)
Genes Dev
, vol.23
, pp. 1303-1312
-
-
Kano, H.1
Godoy, I.2
Courtney, C.3
-
59
-
-
84857845592
-
RYBP represses endogenous retroviruses and preimplantation- and germ line-specific genes in mouse embryonic stem cells
-
Hisada K, Sanchez C, Endo TA et al (2012) RYBP represses endogenous retroviruses and preimplantation- and germ line-specific genes in mouse embryonic stem cells. Mol Cell Biol 32:1139–1149
-
(2012)
Mol Cell Biol
, vol.32
, pp. 1139-1149
-
-
Hisada, K.1
Sanchez, C.2
Endo, T.A.3
-
60
-
-
0344223442
-
RYBP, a new repressor protein that interacts with components of the mammalian polycomb complex, and with the transcription factor YY1
-
Garcia E, Marcos-Gutierrez C, del Mar Lorente M et al (1999) RYBP, a new repressor protein that interacts with components of the mammalian polycomb complex, and with the transcription factor YY1. EMBO J 18:3404–3418
-
(1999)
EMBO J
, vol.18
, pp. 3404-3418
-
-
Garcia, E.1
Marcos-Gutierrez, C.2
del Mar, L.M.3
-
61
-
-
76149142791
-
Polycomb complexes act redundantly to repress genomic repeats and genes
-
Leeb M, Pasini D, Novatchkova M et al (2010) Polycomb complexes act redundantly to repress genomic repeats and genes. Genes Dev 24:265–276
-
(2010)
Genes Dev
, vol.24
, pp. 265-276
-
-
Leeb, M.1
Pasini, D.2
Novatchkova, M.3
-
62
-
-
84930939091
-
Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells
-
Elsasser SJ, Noh KM, Diaz N et al (2015) Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature 522:240–244
-
(2015)
Nature
, vol.522
, pp. 240-244
-
-
Elsasser, S.J.1
Noh, K.M.2
Diaz, N.3
-
63
-
-
0035890090
-
Lsh, a member of the SNF2 family, is required for genome-wide methylation
-
Dennis K, Fan T, Geiman T et al (2001) Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev 15:2940–2944
-
(2001)
Genes Dev
, vol.15
, pp. 2940-2944
-
-
Dennis, K.1
Fan, T.2
Geiman, T.3
-
64
-
-
1842665566
-
RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos
-
Svoboda P, Stein P, Anger M et al (2004) RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos. Dev Biol 269:276–285
-
(2004)
Dev Biol
, vol.269
, pp. 276-285
-
-
Svoboda, P.1
Stein, P.2
Anger, M.3
-
65
-
-
13844294261
-
Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing
-
Kanellopoulou C, Muljo SA, Kung AL et al (2005) Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19:489–501
-
(2005)
Genes Dev
, vol.19
, pp. 489-501
-
-
Kanellopoulou, C.1
Muljo, S.A.2
Kung, A.L.3
-
66
-
-
60149098474
-
Small RNAs as guardians of the genome
-
Malone CD, Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 136:656–668
-
(2009)
Cell
, vol.136
, pp. 656-668
-
-
Malone, C.D.1
Hannon, G.J.2
-
67
-
-
77953935308
-
Estimating enrichment of repetitive elements from high-throughput sequence data
-
Day DS, Luquette LJ, Park PJ et al (2010) Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol 11:R69
-
(2010)
Genome Biol
, vol.11
, pp. R69
-
-
Day, D.S.1
Luquette, L.J.2
Park, P.J.3
-
68
-
-
0031662164
-
Transcription of IAP endogenous retroviruses is constrained by cytosine methylation
-
Walsh CP, Chaillet JR, Bestor TH (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
-
69
-
-
84872088060
-
De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET
-
Rowe HM, Friedli M, Offner S et al (2013) De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development 140:519–529
-
(2013)
Development
, vol.140
, pp. 519-529
-
-
Rowe, H.M.1
Friedli, M.2
Offner, S.3
-
70
-
-
79251558860
-
Chromatin plasticity in pluripotent cells
-
Melcer S, Meshorer E (2010) Chromatin plasticity in pluripotent cells. Essays Biochem 48:245–262
-
(2010)
Essays Biochem
, vol.48
, pp. 245-262
-
-
Melcer, S.1
Meshorer, E.2
-
71
-
-
83455169070
-
Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility
-
Wissing S, Munoz-Lopez M, Macia A et al (2012) Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility. Hum Mol Genet 21:208–218
-
(2012)
Hum Mol Genet
, vol.21
, pp. 208-218
-
-
Wissing, S.1
Munoz-Lopez, M.2
Macia, A.3
-
72
-
-
84902673290
-
Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency
-
Friedli M, Turelli P, Kapopoulou A et al (2014) Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency. Genome Res 24:1251–1259
-
(2014)
Genome Res
, vol.24
, pp. 1251-1259
-
-
Friedli, M.1
Turelli, P.2
Kapopoulou, A.3
-
73
-
-
84937203002
-
Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
-
Cacchiarelli D, Trapnell C, Ziller MJ et al (2015) Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency. Cell 162:412–424
-
(2015)
Cell
, vol.162
, pp. 412-424
-
-
Cacchiarelli, D.1
Trapnell, C.2
Ziller, M.J.3
-
74
-
-
79957884078
-
LSD1 regulates the balance between self-renewal and differentiation in human embryonic stem cells
-
Adamo A, Sese B, Boue S et al (2011) LSD1 regulates the balance between self-renewal and differentiation in human embryonic stem cells. Nat Cell Biol 13:652–659
-
(2011)
Nat Cell Biol
, vol.13
, pp. 652-659
-
-
Adamo, A.1
Sese, B.2
Boue, S.3
-
75
-
-
46949085597
-
Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds
-
Huangfu D, Maehr R, Guo W et al (2008) Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat Biotechnol 26:795–797
-
(2008)
Nat Biotechnol
, vol.26
, pp. 795-797
-
-
Huangfu, D.1
Maehr, R.2
Guo, W.3
-
76
-
-
47149108349
-
Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis
-
Karantzali E, Schulz H, Hummel O et al (2008) Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis. Genome Biol 9:R65
-
(2008)
Genome Biol
, vol.9
, pp. R65
-
-
Karantzali, E.1
Schulz, H.2
Hummel, O.3
-
77
-
-
73049112178
-
Vitamin C enhances the generation of mouse and human induced pluripotent stem cells
-
Esteban MA, Wang T, Qin B et al (2010) Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell 6:71–79
-
(2010)
Cell Stem Cell
, vol.6
, pp. 71-79
-
-
Esteban, M.A.1
Wang, T.2
Qin, B.3
-
78
-
-
84871990064
-
H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs
-
Chen J, Liu H, Liu J et al (2013) H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat Genet 45:34–42
-
(2013)
Nat Genet
, vol.45
, pp. 34-42
-
-
Chen, J.1
Liu, H.2
Liu, J.3
-
79
-
-
84863458292
-
Embryonic stem cell potency fluctuates with endogenous retrovirus activity
-
Macfarlan TS, Gifford WD, Driscoll 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
Gifford, W.D.2
Driscoll, S.3
-
81
-
-
33751357219
-
CAF-1 is essential for heterochromatin organization in pluripotent embryonic cells
-
Houlard M, Berlivet S, Probst AV et al (2006) CAF-1 is essential for heterochromatin organization in pluripotent embryonic cells. PLoS Genet 2:e181
-
(2006)
PLoS Genet
, vol.2
, pp. e181
-
-
Houlard, M.1
Berlivet, S.2
Probst, A.V.3
-
82
-
-
33751189184
-
Transcriptional and post-transcriptional regulation of retrotransposons IAP and MuERV-L affect pluripotency of mice ES cells
-
Ramirez MA, Pericuesta E, Fernandez-Gonzalez R et al (2006) Transcriptional and post-transcriptional regulation of retrotransposons IAP and MuERV-L affect pluripotency of mice ES cells. Reprod Biol Endocrinol 4:55
-
(2006)
Reprod Biol Endocrinol
, vol.4
, pp. 55
-
-
Ramirez, M.A.1
Pericuesta, E.2
Fernandez-Gonzalez, R.3
-
83
-
-
84897989106
-
Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming
-
Hu X, Zhang L, Mao SQ et al (2014) Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell 14:512–522
-
(2014)
Cell Stem Cell
, vol.14
, pp. 512-522
-
-
Hu, X.1
Zhang, L.2
Mao, S.Q.3
-
84
-
-
77957551870
-
A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts
-
Li R, Liang J, Ni S et al (2010) A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell 7:51–63
-
(2010)
Cell Stem Cell
, vol.7
, pp. 51-63
-
-
Li, R.1
Liang, J.2
Ni, S.3
-
85
-
-
79960046168
-
Rational optimization of reprogramming culture conditions for the generation of induced pluripotent stem cells with ultra-high efficiency and fast kinetics
-
Chen J, Liu J, Chen Y et al (2011) Rational optimization of reprogramming culture conditions for the generation of induced pluripotent stem cells with ultra-high efficiency and fast kinetics. Cell Res 21:884–894
-
(2011)
Cell Res
, vol.21
, pp. 884-894
-
-
Chen, J.1
Liu, J.2
Chen, Y.3
-
86
-
-
84865727393
-
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
-
Derrien T, Johnson R, Bussotti G et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789
-
(2012)
Genome Res
, vol.22
, pp. 1775-1789
-
-
Derrien, T.1
Johnson, R.2
Bussotti, G.3
-
87
-
-
84869881863
-
Transposable elements reveal a stem cell-specific class of long noncoding RNAs
-
Kelley D, Rinn J (2012) Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol 13:R107
-
(2012)
Genome Biol
, vol.13
, pp. R107
-
-
Kelley, D.1
Rinn, J.2
-
88
-
-
84876864345
-
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs
-
Kapusta A, Kronenberg Z, Lynch VJ et al (2013) Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet 9:e1003470
-
(2013)
PLoS Genet
, vol.9
, pp. e1003470
-
-
Kapusta, A.1
Kronenberg, Z.2
Lynch, V.J.3
-
89
-
-
78649467088
-
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells
-
Loewer S, Cabili MN, Guttman M et al (2010) Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet 42:1113–1117
-
(2010)
Nat Genet
, vol.42
, pp. 1113-1117
-
-
Loewer, S.1
Cabili, M.N.2
Guttman, M.3
-
90
-
-
84876367541
-
Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal
-
Wang Y, Xu Z, Jiang J et al (2013) Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell 25:69–80
-
(2013)
Dev Cell
, vol.25
, pp. 69-80
-
-
Wang, Y.1
Xu, Z.2
Jiang, J.3
-
91
-
-
84856492490
-
Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors
-
Ng SY, Johnson R, Stanton LW (2012) Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J 31:522–533
-
(2012)
EMBO J
, vol.31
, pp. 522-533
-
-
Ng, S.Y.1
Johnson, R.2
Stanton, L.W.3
-
92
-
-
84920267059
-
The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters
-
Bao X, Wu H, Zhu X et al (2015) The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Res 25:80–92
-
(2015)
Cell Res
, vol.25
, pp. 80-92
-
-
Bao, X.1
Wu, H.2
Zhu, X.3
-
93
-
-
84857498937
-
RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation
-
Narva E, Rahkonen N, Emani MR et al (2012) RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells 30:452–460
-
(2012)
Stem Cells
, vol.30
, pp. 452-460
-
-
Narva, E.1
Rahkonen, N.2
Emani, M.R.3
-
94
-
-
79957573197
-
ECAT11/L1td1 is enriched in ESCs and rapidly activated during iPSC generation, but it is dispensable for the maintenance and induction of pluripotency
-
Iwabuchi KA, Yamakawa T, Sato Y et al (2011) ECAT11/L1td1 is enriched in ESCs and rapidly activated during iPSC generation, but it is dispensable for the maintenance and induction of pluripotency. PLoS ONE 6:e20461
-
(2011)
PLoS ONE
, vol.6
, pp. e20461
-
-
Iwabuchi, K.A.1
Yamakawa, T.2
Sato, Y.3
-
95
-
-
84920730997
-
Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming
-
Kim DH, Marinov GK, Pepke S et al (2015) Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. Cell Stem Cell 16:88–101
-
(2015)
Cell Stem Cell
, vol.16
, pp. 88-101
-
-
Kim, D.H.1
Marinov, G.K.2
Pepke, S.3
-
96
-
-
80052869283
-
lincRNAs act in the circuitry controlling pluripotency and differentiation
-
Guttman M, Donaghey J, Carey BW et al (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477:295–300
-
(2011)
Nature
, vol.477
, pp. 295-300
-
-
Guttman, M.1
Donaghey, J.2
Carey, B.W.3
-
97
-
-
84871215627
-
HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency
-
Santoni FA, Guerra J, Luban J (2012) HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Retrovirology 9:111
-
(2012)
Retrovirology
, vol.9
, pp. 111
-
-
Santoni, F.A.1
Guerra, J.2
Luban, J.3
-
98
-
-
84898010302
-
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
-
Lu X, Sachs F, Ramsay L 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
Sachs, F.2
Ramsay, L.3
-
99
-
-
84922115236
-
Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
-
Wang J, Xie G, Singh M et al (2014) Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature 516:405–409
-
(2014)
Nature
, vol.516
, pp. 405-409
-
-
Wang, J.1
Xie, G.2
Singh, M.3
-
100
-
-
84867908194
-
Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells
-
Hutchins AP, Poulain S, Fujii H et al (2012) Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells. Genomics 100:303–313
-
(2012)
Genomics
, vol.100
, pp. 303-313
-
-
Hutchins, A.P.1
Poulain, S.2
Fujii, H.3
-
101
-
-
34250729138
-
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
-
Rinn JL, Kertesz M, Wang JK et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323
-
(2007)
Cell
, vol.129
, pp. 1311-1323
-
-
Rinn, J.L.1
Kertesz, M.2
Wang, J.K.3
-
102
-
-
84881256653
-
Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds
-
Hou P, Li Y, Zhang X et al (2013) Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science 341:651–654
-
(2013)
Science
, vol.341
, pp. 651-654
-
-
Hou, P.1
Li, Y.2
Zhang, X.3
-
103
-
-
79951495822
-
lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements
-
Gong C, Maquat LE (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470:284–288
-
(2011)
Nature
, vol.470
, pp. 284-288
-
-
Gong, C.1
Maquat, L.E.2
-
104
-
-
84899693328
-
A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins
-
Negishi M, Wongpalee SP, Sarkar S et al (2014) A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins. PLoS ONE 9:e95216
-
(2014)
PLoS ONE
, vol.9
, pp. e95216
-
-
Negishi, M.1
Wongpalee, S.P.2
Sarkar, S.3
-
105
-
-
84869088820
-
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat
-
Carrieri C, Cimatti L, Biagioli M et al (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491:454–457
-
(2012)
Nature
, vol.491
, pp. 454-457
-
-
Carrieri, C.1
Cimatti, L.2
Biagioli, M.3
-
106
-
-
84990931802
-
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions
-
Kelley DR, Hendrickson DG, Tenen D et al (2014) Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. Genome Biol 15:537
-
(2014)
Genome Biol
, vol.15
, pp. 537
-
-
Kelley, D.R.1
Hendrickson, D.G.2
Tenen, D.3
-
107
-
-
84886024597
-
Human endogenous retrovirus K (HML-2) RNA and protein expression is a marker for human embryonic and induced pluripotent stem cells
-
Fuchs NV, Loewer S, Daley GQ et al (2013) Human endogenous retrovirus K (HML-2) RNA and protein expression is a marker for human embryonic and induced pluripotent stem cells. Retrovirology 10:115
-
(2013)
Retrovirology
, vol.10
, pp. 115
-
-
Fuchs, N.V.1
Loewer, S.2
Daley, G.Q.3
-
108
-
-
84945472619
-
Systematic identification of factors for provirus silencing in embryonic stem cells
-
Yang BX, EL Farran CA, Guo HC et al (2015) Systematic identification of factors for provirus silencing in embryonic stem cells. Cell 163:230–245
-
(2015)
Cell
, vol.163
, pp. 230-245
-
-
Yang, B.X.1
EL Farran, C.A.2
Guo, H.C.3
|