-
1
-
-
0034507632
-
Transcription of eukaryotic protein-coding genes
-
A detailed review of transcriptional regulation, general factors and accessory proteins that control transcription initation and elongation
-
Lee, T. I. & Young, R. A. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34, 77-137 (2000). A detailed review of transcriptional regulation, general factors and accessory proteins that control transcription initation and elongation.
-
(2000)
Annu. Rev. Genet
, vol.34
, pp. 77-137
-
-
Lee, T.I.1
Young, R.A.2
-
2
-
-
34249098071
-
Mammalian RNA polymerase II core promoters: Insights from genome-wide studies
-
Sandelin, A. et al. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nature Rev. Genet. 8, 424-436 (2007).
-
(2007)
Nature Rev. Genet
, vol.8
, pp. 424-436
-
-
Sandelin, A.1
-
3
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
This paper demonstrates how genome-wide studies of transcription factor binding, chromatin structure, DNA replication and sequence conservation can synergize. ENCODE Project Consortium
-
ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007). This paper demonstrates how genome-wide studies of transcription factor binding, chromatin structure, DNA replication and sequence conservation can synergize.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
-
4
-
-
30044451918
-
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome
-
Cooper, S. J., Trinklein, N. D., Anton, E. D., Nguyen, L. & Myers, R. M. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res. 16, 1-10 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 1-10
-
-
Cooper, S.J.1
Trinklein, N.D.2
Anton, E.D.3
Nguyen, L.4
Myers, R.M.5
-
5
-
-
30044442791
-
Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
-
Kimura, K. et al. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res. 16, 55-65 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 55-65
-
-
Kimura, K.1
-
6
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
-
7
-
-
62549128139
-
A census of human transcription factors: Function, expression and evolution
-
A summary of the expression, conservation and activity of the set of human sequence-specific transcription factors
-
Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A. & Luscombe, N. M. A census of human transcription factors: function, expression and evolution. Nature Rev. Genet. 10, 252-263 (2009). A summary of the expression, conservation and activity of the set of human sequence-specific transcription factors.
-
(2009)
Nature Rev. Genet
, vol.10
, pp. 252-263
-
-
Vaquerizas, J.M.1
Kummerfeld, S.K.2
Teichmann, S.A.3
Luscombe, N.M.4
-
8
-
-
0035895505
-
The sequence of the human genome
-
Venter, J. C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
-
(2001)
Science
, vol.291
, pp. 1304-1351
-
-
Venter, J.C.1
-
9
-
-
0035865078
-
Human disease genes
-
Jimenez-Sanchez, G., Childs, B. & Valle, D. Human disease genes. Nature 409, 853-855 (2001).
-
(2001)
Nature
, vol.409
, pp. 853-855
-
-
Jimenez-Sanchez, G.1
Childs, B.2
Valle, D.3
-
10
-
-
49249110970
-
Global analysis of in vivo Foxa2-binding sites in mouse liver using massively parallel sequencing
-
Wederell, E. D. et al. Global analysis of in vivo Foxa2-binding sites in mouse liver using massively parallel sequencing. Nucleic Acids Res. 36, 4549-4564 (2008).
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 4549-4564
-
-
Wederell, E.D.1
-
11
-
-
48249123867
-
-
Reed, B. D., Charos, A. E., Szekely, A. M., Weissman, S. M. & Snyder, M. Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLOS Genet. 4, e1000133 (2008).
-
Reed, B. D., Charos, A. E., Szekely, A. M., Weissman, S. M. & Snyder, M. Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLOS Genet. 4, e1000133 (2008).
-
-
-
-
12
-
-
33646474127
-
Genome-wide analysis of menin binding provides insights to MEN1 tumorigenesis
-
Scacheri, P. C. et al. Genome-wide analysis of menin binding provides insights to MEN1 tumorigenesis. PLoS Genet. 2, e51 (2006).
-
(2006)
PLoS Genet
, vol.2
-
-
Scacheri, P.C.1
-
13
-
-
42149183576
-
Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells
-
Hatzis, P. et al. Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells. Mol. Cell. Biol. 28, 2732-2744 (2008).
-
(2008)
Mol. Cell. Biol
, vol.28
, pp. 2732-2744
-
-
Hatzis, P.1
-
14
-
-
34347353316
-
Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs
-
O'Geen, H. et al. Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet. 3, e89 (2007).
-
(2007)
PLoS Genet
, vol.3
-
-
O'Geen, H.1
-
15
-
-
35949000033
-
A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals iterchangeable roles of E2F family members
-
Xu, X. et al. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals iterchangeable roles of E2F family members. Genome Res. 17, 1550-1561 (2007).
-
(2007)
Genome Res
, vol.17
, pp. 1550-1561
-
-
Xu, X.1
-
16
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
An early demonstration that high-throughput sequencing of ChIP samples can be used to identify genome-wide binding sites of site-specific transcription factors
-
Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods 4, 1-7 (2007). An early demonstration that high-throughput sequencing of ChIP samples can be used to identify genome-wide binding sites of site-specific transcription factors.
-
(2007)
Nature Methods
, vol.4
, pp. 1-7
-
-
Robertson, G.1
-
17
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007).
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
18
-
-
40449141957
-
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
-
Rada-Iglesias, A. et al. Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res. 18, 380-392 (2008).
-
(2008)
Genome Res
, vol.18
, pp. 380-392
-
-
Rada-Iglesias, A.1
-
19
-
-
34250791291
-
Detection of in vivo protein-DNA interactions using DamID in mammalian cells
-
Vogel, M. J., Peric-Hupkes, D. & van Steensel, B. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nature Protoc. 2, 1467-1478 (2007).
-
(2007)
Nature Protoc
, vol.2
, pp. 1467-1478
-
-
Vogel, M.J.1
Peric-Hupkes, D.2
van Steensel, B.3
-
20
-
-
50849090969
-
Genome-wide analysis of transcription factor binding sites based on ChIP-seq data
-
Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-seq data. Nature Methods 5, 829-834 (2008).
-
(2008)
Nature Methods
, vol.5
, pp. 829-834
-
-
Valouev, A.1
-
21
-
-
40449126726
-
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
-
Johnson, D. S. et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 18, 393-403 (2008).
-
(2008)
Genome Res
, vol.18
, pp. 393-403
-
-
Johnson, D.S.1
-
22
-
-
33745140886
-
Unbiased location analysis of E2F1 binding sites suggests a widespread role for E2F1 in the human genome
-
A demonstration that some factors bind exclusively to proximal promoters and do not have strict motif requirements for their binding sites
-
Bieda, M., Xu, X., Singer, M., Green, R. & Farnham, P. J. Unbiased location analysis of E2F1 binding sites suggests a widespread role for E2F1 in the human genome. Genome Res. 16, 595-605 (2006). A demonstration that some factors bind exclusively to proximal promoters and do not have strict motif requirements for their binding sites.
-
(2006)
Genome Res
, vol.16
, pp. 595-605
-
-
Bieda, M.1
Xu, X.2
Singer, M.3
Green, R.4
Farnham, P.J.5
-
23
-
-
23844519339
-
A high-resolution map of active promoters in the human genome
-
An early demonstration that high-density oligonucleotide arrays can be used to identify genome-wide binding sites for human transcription factors
-
Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876-880 (2005). An early demonstration that high-density oligonucleotide arrays can be used to identify genome-wide binding sites for human transcription factors.
-
(2005)
Nature
, vol.436
, pp. 876-880
-
-
Kim, T.H.1
-
24
-
-
10744226888
-
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
-
Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499-509 (2004).
-
(2004)
Cell
, vol.116
, pp. 499-509
-
-
Cawley, S.1
-
25
-
-
60849117520
-
Empirical methods for controlling false positives and estimating confidence in ChIP-seq peaks
-
Nix, D. A., Courdy, S. J. & Boucher, K. M. Empirical methods for controlling false positives and estimating confidence in ChIP-seq peaks. BMC Bioinformatics 9, 523 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 523
-
-
Nix, D.A.1
Courdy, S.J.2
Boucher, K.M.3
-
26
-
-
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
-
-
Zhang, Y.1
-
27
-
-
48249140621
-
FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
-
Fejes, A. P. et al. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24, 1729-1730 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 1729-1730
-
-
Fejes, A.P.1
-
28
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky, J. et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotech. 27, 66-75 (2009).
-
(2009)
Nature Biotech
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
-
29
-
-
0028025345
-
Structural and functional characterization of the mouse hepatocyte growth factor gene promoter
-
Liu, Y., Michalopoulos, G. K. & Zarnegar, R. Structural and functional characterization of the mouse hepatocyte growth factor gene promoter. J. Biol. Chem. 269, 4152-4160 (1994).
-
(1994)
J. Biol. Chem
, vol.269
, pp. 4152-4160
-
-
Liu, Y.1
Michalopoulos, G.K.2
Zarnegar, R.3
-
30
-
-
0036813346
-
Analysis of tissue-specific and PPAR?-dependent induction of FABP gene expression in the mouse liver by an in vivo DNA electroporation method
-
Fujishiro, K. et al. Analysis of tissue-specific and PPAR?-dependent induction of FABP gene expression in the mouse liver by an in vivo DNA electroporation method. Mol. Cell. Biochem. 239, 165-172 (2002).
-
(2002)
Mol. Cell. Biochem
, vol.239
, pp. 165-172
-
-
Fujishiro, K.1
-
31
-
-
0037080674
-
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis
-
Weinmann, A. S., Yan, P. S., Oberley, M. J., Huang, T. H.-M. & Farnham, P. J. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 16, 235-244 (2002).
-
(2002)
Genes Dev
, vol.16
, pp. 235-244
-
-
Weinmann, A.S.1
Yan, P.S.2
Oberley, M.J.3
Huang, T.H.-M.4
Farnham, P.J.5
-
32
-
-
0038492517
-
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells
-
Li, Z. et al. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc. Natl Acad. Sci. USA 100, 8164-8169 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 8164-8169
-
-
Li, Z.1
-
33
-
-
0037080483
-
2/M checkpoints
-
2/M checkpoints. Genes Dev. 16, 245-256 (2002).
-
(2002)
Genes Dev
, vol.16
, pp. 245-256
-
-
Ren, B.1
-
34
-
-
10744227070
-
Control of pancreas and liver gene expression by HNF transcription factors
-
Odom, D. T. et al. Control of pancreas and liver gene expression by HNF transcription factors. Science 303, 1378-1381 (2004).
-
(2004)
Science
, vol.303
, pp. 1378-1381
-
-
Odom, D.T.1
-
35
-
-
7444260846
-
-
Consortium, T. E. P. The ENCODE (ENCyclopedia of DNA Elements) Project. Science 306, 636-640 (2004).
-
Consortium, T. E. P. The ENCODE (ENCyclopedia of DNA Elements) Project. Science 306, 636-640 (2004).
-
-
-
-
36
-
-
22144486551
-
Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1
-
Carroll, J. S. et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122, 33-43 (2005).
-
(2005)
Cell
, vol.122
, pp. 33-43
-
-
Carroll, J.S.1
-
37
-
-
33847057887
-
Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells
-
Yang, A. et al. Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol. Cell 24, 593-602 (2006).
-
(2006)
Mol. Cell
, vol.24
, pp. 593-602
-
-
Yang, A.1
-
38
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117 (2008).
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
-
39
-
-
0036777881
-
Molecular mechanisms of selector gene function and evolution
-
Mann, R. S. & Carroll, S. B. Molecular mechanisms of selector gene function and evolution. Curr. Opin. Genet. Dev. 12, 592-600 (2002).
-
(2002)
Curr. Opin. Genet. Dev
, vol.12
, pp. 592-600
-
-
Mann, R.S.1
Carroll, S.B.2
-
40
-
-
33747072322
-
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster
-
This demonstrates clustering of transcription factors throughout the D. melanogaster genome
-
Moorman, C. et al. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc. Natl Acad. Sci. USA 103, 12027-12032 (2006). This demonstrates clustering of transcription factors throughout the D. melanogaster genome.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 12027-12032
-
-
Moorman, C.1
-
41
-
-
33845341455
-
Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
-
Elnitski, L., Jin, V. X., Farnham, P. J. & Jones, S. J. M. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res. 16, 1455-1464 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 1455-1464
-
-
Elnitski, L.1
Jin, V.X.2
Farnham, P.J.3
Jones, S.J.M.4
-
43
-
-
0032458247
-
Structure and function of the interferon-β enhanceosome
-
Maniatis, T. et al. Structure and function of the interferon-β enhanceosome. Cold Spring Harb. Symp. Quant. Biol. 63, 609-620 (1998).
-
(1998)
Cold Spring Harb. Symp. Quant. Biol
, vol.63
, pp. 609-620
-
-
Maniatis, T.1
-
44
-
-
29444448047
-
On a chromosome far, far away: LCRs and gene expression
-
Dean, A. On a chromosome far, far away: LCRs and gene expression. Trends Genet. 22, 38-45 (2006).
-
(2006)
Trends Genet
, vol.22
, pp. 38-45
-
-
Dean, A.1
-
45
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
This identifies specific histone modifications that are associated with cell-type-specific transcriptional regulation
-
Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108-112 (2009). This identifies specific histone modifications that are associated with cell-type-specific transcriptional regulation.
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
-
46
-
-
33847334699
-
Distinct predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman, N. D. et al. Distinct predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet. 39, 311-318 (2007).
-
(2007)
Nature Genet
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
-
47
-
-
0027528993
-
CASTing for multicomponent DNA-binding components
-
Wright, W. E. & Funk, W. D. CASTing for multicomponent DNA-binding components. Trends Biochem. Sci. 18, 77-80 (1993).
-
(1993)
Trends Biochem. Sci
, vol.18
, pp. 77-80
-
-
Wright, W.E.1
Funk, W.D.2
-
48
-
-
38549158519
-
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining
-
Morgan, X. C., Ni, S., Miranker, D. P. & Iyer, V. R. Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. BMC Bioinformatics 8, 445 (2007).
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 445
-
-
Morgan, X.C.1
Ni, S.2
Miranker, D.P.3
Iyer, V.R.4
-
49
-
-
55549103719
-
-
Rabinovich, A., Jin, V. X., Rabinovich, R., Xu, X. & Farnham, P. J. E2F in vivo binding specificity: comparison of consensus versus non-consensus binding sites. Genome Res. 18, 1763-1777 (2008).
-
Rabinovich, A., Jin, V. X., Rabinovich, R., Xu, X. & Farnham, P. J. E2F in vivo binding specificity: comparison of consensus versus non-consensus binding sites. Genome Res. 18, 1763-1777 (2008).
-
-
-
-
50
-
-
0035816691
-
Differential usage of signal transduction pathways defines two types of serum response factor target gene
-
Gineitis, D. & Treisman, R. Differential usage of signal transduction pathways defines two types of serum response factor target gene. J. Biol. Chem. 276, 24531-24539 (2001).
-
(2001)
J. Biol. Chem
, vol.276
, pp. 24531-24539
-
-
Gineitis, D.1
Treisman, R.2
-
51
-
-
33846890433
-
Serum response factor binding sites differ in three human cell types
-
Cooper, S. J., Trinklein, N. D., Nguyen, L. & Myers, R. M. Serum response factor binding sites differ in three human cell types. Genome Res. 17, 136-144 (2009).
-
(2009)
Genome Res
, vol.17
, pp. 136-144
-
-
Cooper, S.J.1
Trinklein, N.D.2
Nguyen, L.3
Myers, R.M.4
-
52
-
-
34250369235
-
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
-
Jin, V. X., O'Geen, H., Iyengar, S., Green, R. & Farnham, P. J. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res. 17, 807-817 (2007).
-
(2007)
Genome Res
, vol.17
, pp. 807-817
-
-
Jin, V.X.1
O'Geen, H.2
Iyengar, S.3
Green, R.4
Farnham, P.J.5
-
53
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
Li, X.-Y. et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 6, e27 (2008).
-
(2008)
PLoS Biol
, vol.6
-
-
Li, X.-Y.1
-
54
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis, G. et al. Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720-1723 (2009).
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
-
55
-
-
33745809637
-
Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF
-
Li, H. et al. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442, 91-95 (2006).
-
(2006)
Nature
, vol.442
, pp. 91-95
-
-
Li, H.1
-
56
-
-
33745818717
-
Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2
-
Pena, P. V. et al. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 442, 100-103 (2006).
-
(2006)
Nature
, vol.442
, pp. 100-103
-
-
Pena, P.V.1
-
57
-
-
34047248383
-
Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36
-
Shi, X. et al. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J. Biol. Chem. 282, 2450-2455 (2007).
-
(2007)
J. Biol. Chem
, vol.282
, pp. 2450-2455
-
-
Shi, X.1
-
58
-
-
34848911602
-
Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4
-
Vermeulen, M. et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 58-69 (2007).
-
(2007)
Cell
, vol.131
, pp. 58-69
-
-
Vermeulen, M.1
-
59
-
-
0035827560
-
The chromatin structure of the dual c-myc promoter P1/P2 is regulated by separate elements
-
Albert, T. et al. The chromatin structure of the dual c-myc promoter P1/P2 is regulated by separate elements. J. Biol. Chem. 276, 20482-20490 (2001).
-
(2001)
J. Biol. Chem
, vol.276
, pp. 20482-20490
-
-
Albert, T.1
-
60
-
-
33845290262
-
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data - a case study using E2F1
-
Jin, V. X., Rabinovich, A., Squazzo, S. L., Green, R. & Farnham, P. J. A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data - a case study using E2F1. Genome Res. 16, 1585-1595 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 1585-1595
-
-
Jin, V.X.1
Rabinovich, A.2
Squazzo, S.L.3
Green, R.4
Farnham, P.J.5
-
61
-
-
34248198548
-
Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays
-
Krig, S. R. et al. Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. J. Biol. Chem. 282, 9703-9712 (2007).
-
(2007)
J. Biol. Chem
, vol.282
, pp. 9703-9712
-
-
Krig, S.R.1
-
62
-
-
0142027777
-
Distribution of NF-κB-binding sites across human chromosome 22
-
Martone, R. et al. Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl Acad. Sci. USA 100, 12247-12252 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 12247-12252
-
-
Martone, R.1
-
63
-
-
55049107572
-
Unique ER? cistromes control cell type-specific gene regulation
-
Krum, S. A. et al. Unique ER? cistromes control cell type-specific gene regulation. Mol. Endocrinol. 22, 2393-2406 (2008).
-
(2008)
Mol. Endocrinol
, vol.22
, pp. 2393-2406
-
-
Krum, S.A.1
-
64
-
-
53449085707
-
Visualizing chromatin dynamics in intact cells
-
Voss, T. C. & Hager, G. L. Visualizing chromatin dynamics in intact cells. Biochem. Biophys. Acta 1783, 2044-2051 (2008).
-
(2008)
Biochem. Biophys. Acta
, vol.1783
, pp. 2044-2051
-
-
Voss, T.C.1
Hager, G.L.2
-
65
-
-
5444243359
-
Active genes dynamically colocalize to shared sites of ongoing transcription
-
Osborne, C. S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nature Genet. 36, 1065-1071 (2004).
-
(2004)
Nature Genet
, vol.36
, pp. 1065-1071
-
-
Osborne, C.S.1
-
66
-
-
33646835742
-
Specialized transcription factories
-
Bartlett, J. et al. Specialized transcription factories. Biochem. Soc. Symp. 73, 67-75 (2006).
-
(2006)
Biochem. Soc. Symp
, vol.73
, pp. 67-75
-
-
Bartlett, J.1
-
67
-
-
0037083376
-
Capturing chromosome conformation
-
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306-1311 (2002).
-
(2002)
Science
, vol.295
, pp. 1306-1311
-
-
Dekker, J.1
Rippe, K.2
Dekker, M.3
Kleckner, N.4
-
68
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
This study demonstrates that using ChIP-seq to identify binding sites for p300 is a highly accurate method for identifying enhancers that can be shown, using follow-up assays in transgenic mice, to function in a tissue-specific manner
-
Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009). This study demonstrates that using ChIP-seq to identify binding sites for p300 is a highly accurate method for identifying enhancers that can be shown, using follow-up assays in transgenic mice, to function in a tissue-specific manner.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
-
69
-
-
46749149696
-
Critical parameters for genome editing using zinc finger nucleases
-
Camenisch, T. D., Brilliant, M. H. & Segal, D. J. Critical parameters for genome editing using zinc finger nucleases. Mini Rev. Med. Chem. 8, 669-676 (2008).
-
(2008)
Mini Rev. Med. Chem
, vol.8
, pp. 669-676
-
-
Camenisch, T.D.1
Brilliant, M.H.2
Segal, D.J.3
-
70
-
-
33746111884
-
Interrogating genomes with combinatorial artificial transcription factor libraries: Asking zinc finger questions
-
Bletran, A., Liu, Y., Parikh, S., Temple, B. & Blancafort, P. Interrogating genomes with combinatorial artificial transcription factor libraries: asking zinc finger questions. Assay Drug Dev. Technol. 4, 317-331 (2006).
-
(2006)
Assay Drug Dev. Technol
, vol.4
, pp. 317-331
-
-
Bletran, A.1
Liu, Y.2
Parikh, S.3
Temple, B.4
Blancafort, P.5
-
71
-
-
0032539707
-
Peptide nucleic acid-targeted mutagenesis of a chromosomal gene in mouse cells
-
Faruqi, A. F., Egholm, M. & Glazer, P. M. Peptide nucleic acid-targeted mutagenesis of a chromosomal gene in mouse cells. Proc. Natl Acad. Sci. USA 95, 1398-1403 (1998).
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 1398-1403
-
-
Faruqi, A.F.1
Egholm, M.2
Glazer, P.M.3
-
72
-
-
33746795976
-
DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA-TCC repeats in Friedreich's ataxia
-
Burnett, R. et al. DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA-TCC repeats in Friedreich's ataxia. Proc. Natl Acad. Sci. USA 103, 11497-11502 (2006).
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 11497-11502
-
-
Burnett, R.1
-
73
-
-
34447098370
-
-
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77-88 (2007).
-
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77-88 (2007).
-
-
-
-
74
-
-
36549061004
-
RNA polymerase is poised for activation across the genome
-
Muse, G. W. et al. RNA polymerase is poised for activation across the genome. Nature Genet. 39, 1507-1511 (2007).
-
(2007)
Nature Genet
, vol.39
, pp. 1507-1511
-
-
Muse, G.W.1
-
75
-
-
41649121741
-
Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
-
Komashko, V. M. et al. Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res. 18, 521-532 (2008).
-
(2008)
Genome Res
, vol.18
, pp. 521-532
-
-
Komashko, V.M.1
-
76
-
-
37349081961
-
Genome-scale ChIP-chip analysis using 10,000 human cells
-
Acevedo, L. G. et al. Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques 43, 791-797 (2007).
-
(2007)
Biotechniques
, vol.43
, pp. 791-797
-
-
Acevedo, L.G.1
-
77
-
-
33745549658
-
Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations
-
O'Neill, L. P., VerMilyea, M. D. & Turner, B. M. Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nature Genet. 38, 835-841 (2006).
-
(2006)
Nature Genet
, vol.38
, pp. 835-841
-
-
O'Neill, L.P.1
VerMilyea, M.D.2
Turner, B.M.3
-
78
-
-
34147171123
-
-
Dahl, J. A. & Collas, P. Q2ChIP, a quick and quantitative chromatin immunoprecipitation assay, unravels epigenetic dynamics of developmentally regulated genes in human carcinoma cells. Stem Cells 25, 1037-1046 (2007).
-
Dahl, J. A. & Collas, P. Q2ChIP, a quick and quantitative chromatin immunoprecipitation assay, unravels epigenetic dynamics of developmentally regulated genes in human carcinoma cells. Stem Cells 25, 1037-1046 (2007).
-
-
-
-
79
-
-
34547635995
-
Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis
-
Attema, J. L. et al. Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc. Natl Acad. Sci. USA 104, 12371-12376 (2007).
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 12371-12376
-
-
Attema, J.L.1
-
80
-
-
53749092745
-
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
-
Xu, H., Wei, C.-L., Lin, F. & Sung, W.-K. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 24, 2344-2349 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 2344-2349
-
-
Xu, H.1
Wei, C.-L.2
Lin, F.3
Sung, W.-K.4
-
81
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-seq data
-
Jothi, R., Cuddapah, S., Barski, A., Cui, K. & Zhao, K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-seq data. Nucleic Acids Res. 36, 5221-5231 (2008).
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
Cui, K.4
Zhao, K.5
-
82
-
-
67649453965
-
Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing
-
Hoffman, B. G. & Jones, S. J. Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. J. Endocrinol. 201, 1-13 (2009).
-
(2009)
J. Endocrinol
, vol.201
, pp. 1-13
-
-
Hoffman, B.G.1
Jones, S.J.2
|