-
1
-
-
0034652141
-
Positive and negative regulation of endogenous genes by designed transcription factors
-
Beerli, R.R., Dreier, B., & Barbas, C.F. III Positive and negative regulation of endogenous genes by designed transcription factors. Proc. Natl. Acad. Sci. USA 97, 1495-1500 (2000
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 1495-1500
-
-
Beerli, R.R.1
Dreier, B.2
Barbas, C.F.3
-
2
-
-
0037164741
-
Gene-specific targeting of H3K9 methylation is sufficient for initiating repression in vivo
-
Snowden, A.W., Gregory, P.D., Case, C.C., & Pabo, C.O. Gene-specific targeting of H3K9 methylation is sufficient for initiating repression in vivo. Curr. Biol. 12, 2159-2166 (2002
-
(2002)
Curr. Biol
, vol.12
, pp. 2159-2166
-
-
Snowden, A.W.1
Gregory, P.D.2
Case, C.C.3
Pabo, C.O.4
-
3
-
-
84864856835
-
Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains
-
Cong, L., Zhou, R., Kuo, Y.C., Cunniff, M., & Zhang, F. Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat. Commun. 3, 968 (2012
-
(2012)
Nat. Commun
, vol.3
, pp. 968
-
-
Cong, L.1
Zhou, R.2
Kuo, Y.C.3
Cunniff, M.4
Zhang, F.5
-
4
-
-
84882976110
-
Optical control of mammalian endogenous transcription and epigenetic states
-
Konermann, S., et al. Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472-476 (2013
-
(2013)
Nature
, vol.500
, pp. 472-476
-
-
Konermann, S.1
-
5
-
-
84886084801
-
Locus-specific editing of histone modifications at endogenous enhancers
-
Mendenhall, E.M., et al. Locus-specific editing of histone modifications at endogenous enhancers. Nat. Biotechnol. 31, 1133-1136 (2013
-
(2013)
Nat. Biotechnol
, vol.31
, pp. 1133-1136
-
-
Mendenhall, E.M.1
-
6
-
-
84880571335
-
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes
-
Gilbert, L.A., et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442-451 (2013
-
(2013)
Cell
, vol.154
, pp. 442-451
-
-
Gilbert, L.A.1
-
7
-
-
84884906690
-
RNA-guided gene activation by CRISPR-Cas9-based transcription factors
-
Perez-Pinera, P., et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat. Methods 10, 973-976 (2013
-
(2013)
Nat. Methods
, vol.10
, pp. 973-976
-
-
Perez-Pinera, P.1
-
8
-
-
84884907424
-
CRISPR RNA-guided activation of endogenous human genes
-
Maeder, M.L., et al. CRISPR RNA-guided activation of endogenous human genes. Nat. Methods 10, 977-979 (2013
-
(2013)
Nat. Methods
, vol.10
, pp. 977-979
-
-
Maeder, M.L.1
-
9
-
-
84928924333
-
Functional annotation of native enhancers with a Cas9-histone demethylase fusion
-
Kearns, N.A., et al. Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat. Methods 12, 401-403 (2015
-
(2015)
Nat. Methods
, vol.12
, pp. 401-403
-
-
Kearns, N.A.1
-
10
-
-
84929135130
-
Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers
-
Hilton, I.B., et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33, 510-517 (2015
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 510-517
-
-
Hilton, I.B.1
-
11
-
-
84890048526
-
Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins
-
Maeder, M.L., et al. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat. Biotechnol. 31, 1137-1142 (2013
-
(2013)
Nat. Biotechnol
, vol.31
, pp. 1137-1142
-
-
Maeder, M.L.1
-
12
-
-
84860561774
-
Epigenetic reprogramming of cancer cells via targeted DNA methylation
-
Rivenbark, A.G., et al. Epigenetic reprogramming of cancer cells via targeted DNA methylation. Epigenetics 7, 350-360 (2012
-
(2012)
Epigenetics
, vol.7
, pp. 350-360
-
-
Rivenbark, A.G.1
-
13
-
-
84865070369
-
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
-
Jinek, M., et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012
-
(2012)
Science
, vol.337
, pp. 816-821
-
-
Jinek, M.1
-
14
-
-
84873729095
-
Multiplex genome engineering using CRISPR/Cas systems
-
Cong, L., et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013
-
(2013)
Science
, vol.339
, pp. 819-823
-
-
Cong, L.1
-
15
-
-
84873734105
-
RNA-guided human genome engineering via Cas9
-
Mali, P., et al RNA-guided Human Genome Engineering Via Cas9. Science 339, 823-826 (2013
-
(2013)
Science
, vol.339
, pp. 823-826
-
-
Mali, P.1
-
16
-
-
84908352138
-
Genome-Scale CRISPR-mediated control of gene repression and activation
-
Gilbert, L.A., et al. Genome-Scale CRISPR-mediated control of gene repression and activation. Cell 159, 647-661 (2014
-
(2014)
Cell
, vol.159
, pp. 647-661
-
-
Gilbert, L.A.1
-
17
-
-
84923096541
-
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
-
Konermann, S., et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583-588 (2015
-
(2015)
Nature
, vol.517
, pp. 583-588
-
-
Konermann, S.1
-
18
-
-
84964313405
-
Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers
-
Gao, X., et al. Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers. Nucleic Acids Res. 42, e155 (2014
-
(2014)
Nucleic Acids Res
, vol.42
, pp. e155
-
-
Gao, X.1
-
19
-
-
84923798099
-
A CRISPR/Cas9-based system for reprogramming cell lineage specification
-
Chakraborty, S., et al. A CRISPR/Cas9-based system for reprogramming cell lineage specification. Stem Cell Reports 3, 940-947 (2014
-
(2014)
Stem Cell Reports
, vol.3
, pp. 940-947
-
-
Chakraborty, S.1
-
20
-
-
84926521955
-
Highly efficient Cas9-mediated transcriptional programming
-
Chavez, A., et al. Highly efficient Cas9-mediated transcriptional programming. Nat. Methods 12, 326-328 (2015
-
(2015)
Nat. Methods
, vol.12
, pp. 326-328
-
-
Chavez, A.1
-
21
-
-
84901195977
-
Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells
-
Nissim, L., Perli, S.D., Fridkin, A., Perez-Pinera, P., & Lu, T.K. Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol. Cell 54, 698-710 (2014
-
(2014)
Mol. Cell
, vol.54
, pp. 698-710
-
-
Nissim, L.1
Perli, S.D.2
Fridkin, A.3
Perez-Pinera, P.4
Lu, T.K.5
-
22
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman, R.E., et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
-
23
-
-
38649099445
-
High-resolution mapping and characterization of open chromatin across the genome
-
Boyle, A.P., et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311-322 (2008
-
(2008)
Cell
, vol.132
, pp. 311-322
-
-
Boyle, A.P.1
-
24
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Encode Project Consortium., et al.
-
ENCODE Project Consortium., et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
25
-
-
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, S.P., Stevens, J., & Schultz, D.C. 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
-
(2006)
Mol. Cell. Biol
, vol.26
, pp. 8623-8638
-
-
Sripathy, S.P.1
Stevens, J.2
Schultz, D.C.3
-
26
-
-
77950421703
-
KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading
-
Groner, A.C., et al. KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet. 6, e1000869 (2010
-
(2010)
PLoS Genet
, vol.6
, pp. e1000869
-
-
Groner, A.C.1
-
27
-
-
0037089626
-
3rd SETDB1: A novel KAP-1-Associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins
-
Schultz, D.C., Ayyanathan, K., Negorev, D., Maul, G.G., & Rauscher, F.J. 3rd SETDB1: a novel KAP-1-Associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 16, 919-932 (2002
-
(2002)
Genes Dev
, vol.16
, pp. 919-932
-
-
Schultz, D.C.1
Ayyanathan, K.2
Negorev, D.3
Maul, G.G.4
Rauscher, F.J.5
-
28
-
-
84856431427
-
NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression
-
Reynolds, N., et al. NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression. EMBO J. 31, 593-605 (2012
-
(2012)
EMBO J.
, vol.31
, pp. 593-605
-
-
Reynolds, N.1
-
29
-
-
84902095352
-
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
-
Wu, X., et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. 32, 670-676 (2014
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 670-676
-
-
Wu, X.1
-
30
-
-
84903545084
-
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
-
Kuscu, C., Arslan, S., Singh, R., Thorpe, J., & Adli, M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol. 32, 677-683 (2014
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 677-683
-
-
Kuscu, C.1
Arslan, S.2
Singh, R.3
Thorpe, J.4
Adli, M.5
-
31
-
-
84913620157
-
Analysis of an artificial zinc finger epigenetic modulator: Widespread binding but limited regulation
-
Grimmer, M.R., et al. Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Res. 42, 10856-10868 (2014
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 10856-10868
-
-
Grimmer, M.R.1
-
32
-
-
0041624239
-
Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: A mammalian cell culture model of gene variegation
-
Ayyanathan, K., et al. Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. Genes Dev. 17, 1855-1869 (2003
-
(2003)
Genes Dev
, vol.17
, pp. 1855-1869
-
-
Ayyanathan, K.1
-
33
-
-
84862662420
-
Dynamics and memory of heterochromatin in living cells
-
Hathaway, N.A., et al. Dynamics and memory of heterochromatin in living cells. Cell 149, 1447-1460 (2012
-
(2012)
Cell
, vol.149
, pp. 1447-1460
-
-
Hathaway, N.A.1
-
34
-
-
0031593199
-
Locus control regions of mammalian beta-globin gene clusters: Combining phylogenetic analyses and experimental results to gain functional insights
-
Hardison, R., et al. Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene 205, 73-94 (1997
-
(1997)
Gene
, vol.205
, pp. 73-94
-
-
Hardison, R.1
-
35
-
-
0026482145
-
Transcription of the hypersensitive site HS2 enhancer in erythroid cells
-
Tuan, D., Kong, S., & Hu, K. Transcription of the hypersensitive site HS2 enhancer in erythroid cells. Proc. Natl. Acad. Sci. USA 89, 11219-11223 (1992
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 11219-11223
-
-
Tuan, D.1
Kong, S.2
Hu, K.3
-
36
-
-
0032747826
-
Structural and functional cross-talk between a distant enhancer and the epsilon-globin gene promoter shows interdependence of the two elements in chromatin
-
McDowell, J.C., & Dean, A. Structural and functional cross-talk between a distant enhancer and the epsilon-globin gene promoter shows interdependence of the two elements in chromatin. Mol. Cell. Biol. 19, 7600-7609 (1999
-
(1999)
Mol. Cell. Biol
, vol.19
, pp. 7600-7609
-
-
McDowell, J.C.1
Dean, A.2
-
37
-
-
13244272059
-
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1
-
Vakoc, C.R., et al. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol. Cell 17, 453-462 (2005
-
(2005)
Mol Cell
, vol.17
, pp. 453-462
-
-
Vakoc, C.R.1
-
38
-
-
33749400168
-
Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
-
Dostie, J., et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299-1309 (2006
-
(2006)
Genome Res
, vol.16
, pp. 1299-1309
-
-
Dostie, J.1
-
39
-
-
0021057680
-
Inducible transcription of five globin genes in K562 human leukemia cells
-
Dean, A., Ley, T.J., Humphries, R.K., Fordis, M., & Schechter, A.N. Inducible transcription of five globin genes in K562 human leukemia cells. Proc. Natl. Acad. Sci. USA 80, 5515-5519 (1983
-
(1983)
Proc. Natl. Acad. Sci. USA
, vol.80
, pp. 5515-5519
-
-
Dean, A.1
Ley, T.J.2
Humphries, R.K.3
Fordis, M.4
Schechter, A.N.5
-
40
-
-
84938857368
-
Genome-wide specificity of DNA-binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
-
Polstein, L.R., et al. Genome-wide specificity of DNA-binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Res. 25, 1158-1169 (2015
-
(2015)
Genome Res
, vol.25
, pp. 1158-1169
-
-
Polstein, L.R.1
-
41
-
-
84938836171
-
A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
-
O'Geen, H., Henry, I.M., Bhakta, M.S., Meckler, J.F., & Segal, D.J. A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. Nucleic Acids Res. 43, 3389-3404 (2015
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 3389-3404
-
-
O'Geen, H.1
Henry, I.M.2
Bhakta, M.S.3
Meckler, J.F.4
Segal, D.J.5
-
42
-
-
0034739815
-
Levels of GATA-1/GATA-2 transcription factors modulate expression of embryonic and fetal hemoglobins
-
Ikonomi, P., et al. Levels of GATA-1/GATA-2 transcription factors modulate expression of embryonic and fetal hemoglobins. Gene 261, 277-287 (2000
-
(2000)
Gene
, vol.261
, pp. 277-287
-
-
Ikonomi, P.1
-
43
-
-
84908439526
-
Reactivation of developmentally silenced globin genes by forced chromatin looping
-
Deng, W., et al. Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell 158, 849-860 (2014
-
(2014)
Cell
, vol.158
, pp. 849-860
-
-
Deng, W.1
-
44
-
-
84922535144
-
Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector
-
Kabadi, A.M., Ousterout, D.G., Hilton, I.B., & Gersbach, C.A. Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector. Nucleic Acids Res. 42, e147 (2014
-
(2014)
Nucleic Acids Res
, vol.42
, pp. e147
-
-
Kabadi, A.M.1
Ousterout, D.G.2
Hilton, I.B.3
Gersbach, C.A.4
-
45
-
-
44449120988
-
Production and titration of lentiviral vectors
-
Chapter 4 Unit 4.21
-
Salmon, P., & Trono, D. Production and titration of lentiviral vectors. Curr. Protoc. Neurosci. Chapter 4, Unit 4.21 (2006
-
(2006)
Curr. Protoc. Neurosci
-
-
Salmon, P.1
Trono, D.2
-
46
-
-
84855331824
-
Transposase mediated construction of RNA-seq libraries
-
Gertz, J., et al. Transposase mediated construction of RNA-seq libraries. Genome Res. 22, 134-141 (2012
-
(2012)
Genome Res
, vol.22
, pp. 134-141
-
-
Gertz, J.1
-
47
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
48
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S., & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010
-
(2010)
Genome Biol
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
49
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
50
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS
-
Zhang, Y., et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008
-
(2008)
Genome Biol
, vol.9
, pp. R137
-
-
Zhang, Y.1
-
51
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A.R., & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
52
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M.I., Huber, W., & Anders, S Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014
-
(2014)
Genome Biol
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
53
-
-
77956276383
-
DNase-seq: A high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
-
February
-
Song, L., & Crawford, G.E. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb. Protoc. 2010 doi:10.1101/pdb.prot5384 (February 2010
-
(2010)
Cold Spring Harb. Protoc
, vol.2010
-
-
Song, L.1
Crawford, G.E.2
-
54
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
|