-
1
-
-
0023948705
-
Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene
-
Solomon, M.J., Larsen, P.L. & Varshavsky, A. Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene. Cell 53, 937-947 (1988).
-
(1988)
Cell
, vol.53
, pp. 937-947
-
-
Solomon, M.J.1
Larsen, P.L.2
Varshavsky, A.3
-
2
-
-
0025978212
-
Formaldehyde cross-linking and immunoprecipitation demonstrate developmental changes in H1 association with transcriptionally active genes
-
Dedon, P.C., Soults, J.A., Allis, C.D. & Gorovsky, M.A. Formaldehyde cross-linking and immunoprecipitation demonstrate developmental changes in H1 association with transcriptionally active genes. Mol. Cell. Biol 11, 1729-1733 (1991).
-
(1991)
Mol. Cell. Biol
, vol.11
, pp. 1729-1733
-
-
Dedon, P.C.1
Soults, J.A.2
Allis, C.D.3
Gorovsky, M.A.4
-
3
-
-
0027139910
-
Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin
-
Orlando, V. & Paro, R. Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell 75, 1187-1198 (1993).
-
(1993)
Cell
, vol.75
, pp. 1187-1198
-
-
Orlando, V.1
Paro, R.2
-
4
-
-
0034515772
-
Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase
-
Reid, J.L., Iyer, V.R., Brown, P.O. & Struhl, K. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol. Cell 6, 1297-1307 (2000).
-
(2000)
Mol. Cell
, vol.6
, pp. 1297-1307
-
-
Reid, J.L.1
Iyer, V.R.2
Brown, P.O.3
Struhl, K.4
-
5
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000).
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
-
6
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
Iyer, V.R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533-538 (2001).
-
(2001)
Nature
, vol.409
, pp. 533-538
-
-
Iyer, V.R.1
-
7
-
-
0034934774
-
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
-
Lieb, J.D. Liu, X., Botstein, D. & Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nature Genet. 28, 327-334 (2001).
-
(2001)
Nature Genet
, vol.28
, pp. 327-334
-
-
Lieb, J.D.1
Liu, X.2
Botstein, D.3
Brown, P.O.4
-
8
-
-
0036649756
-
Genome-wide binding map of the histone deacetylase Rpd3 in yeast
-
Kurdistani, S.K., Robyr, D., Tavazoie, S. & Grunstein, M. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nature Genet. 31, 248-254 (2002).
-
(2002)
Nature Genet
, vol.31
, pp. 248-254
-
-
Kurdistani, S.K.1
Robyr, D.2
Tavazoie, S.3
Grunstein, M.4
-
9
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
-
10
-
-
0037080483
-
E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints
-
Ren, B. et al. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev. 16, 245-256 (2002).
-
(2002)
Genes Dev
, vol.16
, pp. 245-256
-
-
Ren, B.1
-
11
-
-
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. & 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.4
Farnham, P.J.5
-
12
-
-
23844519339
-
A high-resolution map of active promoters in the human genome
-
Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876-880 (2005).
-
(2005)
Nature
, vol.436
, pp. 876-880
-
-
Kim, T.H.1
-
13
-
-
23944462969
-
Genome-wide map of nucleosome acetylation and methylation in yeast
-
Pokholok, D.K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517-527 (2005).
-
(2005)
Cell
, vol.122
, pp. 517-527
-
-
Pokholok, D.K.1
-
14
-
-
33646865180
-
Control of developmental regulators by Polycomb in human embryonic stem cells
-
Lee, T.I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301-313 (2006).
-
(2006)
Cell
, vol.125
, pp. 301-313
-
-
Lee, T.I.1
-
15
-
-
0034984305
-
Location analysis of DNA-bound proteins at the whole-genome level: Untangling transcriptional regulatory networks
-
Nal, B., Mohr, E. & Ferrier, P. Location analysis of DNA-bound proteins at the whole-genome level: Untangling transcriptional regulatory networks. Bioessays 23, 473-476 (2001).
-
(2001)
Bioessays
, vol.23
, pp. 473-476
-
-
Nal, B.1
Mohr, E.2
Ferrier, P.3
-
16
-
-
8644232564
-
Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays
-
Hanlon, S.E. & Lieb, J.D. Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. Curr. Opin. Genet. Dev. 14, 697-705 (2004).
-
(2004)
Curr. Opin. Genet. Dev
, vol.14
, pp. 697-705
-
-
Hanlon, S.E.1
Lieb, J.D.2
-
17
-
-
22344449669
-
Constructing transcriptional regulatory networks
-
Blais, A. & Dynlacht, B.D. Constructing transcriptional regulatory networks. Genes Dev. 19, 1499-1511 (2005).
-
(2005)
Genes Dev
, vol.19
, pp. 1499-1511
-
-
Blais, A.1
Dynlacht, B.D.2
-
18
-
-
13444278955
-
Genomic studies of transcription factor-DNA interactions
-
Sikder, D. & Kodadek, T. Genomic studies of transcription factor-DNA interactions. Curr. Opin. Chem. Biol. 9, 38-45 (2005).
-
(2005)
Curr. Opin. Chem. Biol
, vol.9
, pp. 38-45
-
-
Sikder, D.1
Kodadek, T.2
-
19
-
-
5444250990
-
Applications of genomic microarrays to explore human chromosome structure and function
-
Carter, N.P. & Vetrie, D. Applications of genomic microarrays to explore human chromosome structure and function. Hum. Mol. Genet. 13 (Spec No 2), R297-R302 (2004).
-
(2004)
Hum. Mol. Genet
, vol.13
, Issue.SPEC 2
-
-
Carter, N.P.1
Vetrie, D.2
-
20
-
-
0042736137
-
Epigenomic profiling using microarrays
-
van Steensel, B. & Henikoff, S. Epigenomic profiling using microarrays. Biotechniques 35, 346-357 (2003).
-
(2003)
Biotechniques
, vol.35
, pp. 346-357
-
-
van Steensel, B.1
Henikoff, S.2
-
21
-
-
23444434202
-
A genomic view of eukaryotic DNA replication
-
MacAlpine, D.M. & Bell, S.P. A genomic view of eukaryotic DNA replication. Chromosome Res. 13, 309-326 (2005).
-
(2005)
Chromosome Res
, vol.13
, pp. 309-326
-
-
MacAlpine, D.M.1
Bell, S.P.2
-
22
-
-
23444451289
-
Investigating chromosome organization with genomic microarrays
-
Woodfine, K., Carter, N.P., Dunham, I. & Fiegler, H. Investigating chromosome organization with genomic microarrays. Chromosome Res. 13, 249-257 (2005).
-
(2005)
Chromosome Res
, vol.13
, pp. 249-257
-
-
Woodfine, K.1
Carter, N.P.2
Dunham, I.3
Fiegler, H.4
-
23
-
-
0035878119
-
Messenger RNAs are recruited for nuclear export during transcription
-
Lei, E.P., Krebber, H. & Silver, P.A. Messenger RNAs are recruited for nuclear export during transcription. Genes Dev. 15, 1771-1782 (2001).
-
(2001)
Genes Dev
, vol.15
, pp. 1771-1782
-
-
Lei, E.P.1
Krebber, H.2
Silver, P.A.3
-
24
-
-
0037205232
-
Chromatin boundaries in budding yeast: The nuclear pore connection
-
Ishii, K., Arib, G., Lin, C., Van Houwe, G. & Laemmli, U.K. Chromatin boundaries in budding yeast: The nuclear pore connection. Cell 109, 551-562 (2002).
-
(2002)
Cell
, vol.109
, pp. 551-562
-
-
Ishii, K.1
Arib, G.2
Lin, C.3
Van Houwe, G.4
Laemmli, U.K.5
-
25
-
-
10744233477
-
Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery
-
Rodriguez-Navarro, S. et al. Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery. Cell 116, 75-86 (2004).
-
(2004)
Cell
, vol.116
, pp. 75-86
-
-
Rodriguez-Navarro, S.1
-
26
-
-
0034644626
-
Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier
-
Takizawa, P.A., DeRisi, J.L., Wilhelm, J.E. & Vale, R.D. Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier. Science 290, 341-344 (2000).
-
(2000)
Science
, vol.290
, pp. 341-344
-
-
Takizawa, P.A.1
DeRisi, J.L.2
Wilhelm, J.E.3
Vale, R.D.4
-
27
-
-
0034687794
-
Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays
-
Tenenbaum, S.A., Carson, C.C., Lager, P.J. & Keene, J.D. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc. Natl. Acad. Sci. USA 97, 14085-14090 (2000).
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 14085-14090
-
-
Tenenbaum, S.A.1
Carson, C.C.2
Lager, P.J.3
Keene, J.D.4
-
28
-
-
18044379515
-
Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome
-
Brown, V. et al. Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107, 477-487 (2001).
-
(2001)
Cell
, vol.107
, pp. 477-487
-
-
Brown, V.1
-
29
-
-
0037313537
-
Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery
-
Hieronymus, H. & Silver, P.A. Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nature Genet. 33, 155-161 (2003).
-
(2003)
Nature Genet
, vol.33
, pp. 155-161
-
-
Hieronymus, H.1
Silver, P.A.2
-
30
-
-
0141482078
-
Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts using DNA microarray analysis
-
Shepard, K.A. et al. Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts using DNA microarray analysis. Proc. Natl Acad. Sci. USA 100, 11429-11434 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 11429-11434
-
-
Shepard, K.A.1
-
31
-
-
33644514069
-
Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax
-
Sanchez-Elsner, T., Gou, D., Kremmer, E. & Sauer, F. Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 311, 1118-1123 (2006).
-
(2006)
Science
, vol.311
, pp. 1118-1123
-
-
Sanchez-Elsner, T.1
Gou, D.2
Kremmer, E.3
Sauer, F.4
-
32
-
-
0031080378
-
Analysis of chromatin structure by in vivo formaldehyde cross-linking
-
Orlando, V., Strutt, H. & Paro, R. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11, 205-214 (1997).
-
(1997)
Methods
, vol.11
, pp. 205-214
-
-
Orlando, V.1
Strutt, H.2
Paro, R.3
-
33
-
-
0033388858
-
In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment
-
Kuo, M.H. & Allis, C.D. In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 19, 425-433 (1999).
-
(1999)
Methods
, vol.19
, pp. 425-433
-
-
Kuo, M.H.1
Allis, C.D.2
-
34
-
-
1242316281
-
ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
-
Buck, M.J. & Lieb, J.D. ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83, 349-360 (2004).
-
(2004)
Genomics
, vol.83
, pp. 349-360
-
-
Buck, M.J.1
Lieb, J.D.2
-
35
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
Boyer, L.A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956 (2005).
-
(2005)
Cell
, vol.122
, pp. 947-956
-
-
Boyer, L.A.1
-
36
-
-
33646882068
-
Polycomb complexes repress developmental regulators in murine embryonic stem cells
-
Boyer, L.A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349-353 (2006).
-
(2006)
Nature
, vol.441
, pp. 349-353
-
-
Boyer, L.A.1
-
37
-
-
1242311783
-
Genome-wide mapping of protein-DNA interactions by chromatin immunoprecipitation and DNA microarray hybridization
-
Lieb, J.D. Genome-wide mapping of protein-DNA interactions by chromatin immunoprecipitation and DNA microarray hybridization. Methods Mol. Biol. 224, 99-109 (2003).
-
(2003)
Methods Mol. Biol
, vol.224
, pp. 99-109
-
-
Lieb, J.D.1
-
38
-
-
0348166011
-
Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins
-
Oberley, M.J. & Farnham, P.J. Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol. 371, 577-596 (2003).
-
(2003)
Methods Enzymol
, vol.371
, pp. 577-596
-
-
Oberley, M.J.1
Farnham, P.J.2
-
39
-
-
1042300237
-
Histone methylation: Recognizing the methyl mark
-
Bannister, A.J. & Kouzarides, T. Histone methylation: Recognizing the methyl mark. Methods Enzymol. 376, 269-288 (2004).
-
(2004)
Methods Enzymol
, vol.376
, pp. 269-288
-
-
Bannister, A.J.1
Kouzarides, T.2
-
40
-
-
1042265480
-
The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications
-
Bernstein, B.E., Humphrey, E.L., Liu, C.L. & Schreiber, S.L. The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. Methods Enzymol. 376, 349-360 (2004).
-
(2004)
Methods Enzymol
, vol.376
, pp. 349-360
-
-
Bernstein, B.E.1
Humphrey, E.L.2
Liu, C.L.3
Schreiber, S.L.4
-
41
-
-
1042265482
-
Sequential chromatin immunoprecipitation from animal tissues
-
Chaya, D. & Zaret, K.S. Sequential chromatin immunoprecipitation from animal tissues. Methods Enzymol. 376, 361-372 (2004).
-
(2004)
Methods Enzymol
, vol.376
, pp. 361-372
-
-
Chaya, D.1
Zaret, K.S.2
-
42
-
-
1042300232
-
Chromatin immunoprecipitation in the analysis of large chromatin domains across murine antigen receptor loci
-
Ciccone, D.N., Morshead, K.B. & Oettinger, M.A. Chromatin immunoprecipitation in the analysis of large chromatin domains across murine antigen receptor loci. Methods Enzymol. 376, 334-348 (2004).
-
(2004)
Methods Enzymol
, vol.376
, pp. 334-348
-
-
Ciccone, D.N.1
Morshead, K.B.2
Oettinger, M.A.3
-
43
-
-
1042276978
-
High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays
-
Oberley, M.J., Tsao, J., Yau, P. & Farnham, P.J. High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods Enzymol. 376, 315-334 (2004).
-
(2004)
Methods Enzymol
, vol.376
, pp. 315-334
-
-
Oberley, M.J.1
Tsao, J.2
Yau, P.3
Farnham, P.J.4
-
44
-
-
1042288539
-
Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors
-
Ren, B. & Dynlacht, B.D. Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol. 376, 304-315 (2004).
-
(2004)
Methods Enzymol
, vol.376
, pp. 304-315
-
-
Ren, B.1
Dynlacht, B.D.2
-
45
-
-
8444245244
-
Global nucleosome occupancy in yeast
-
Bernstein, B.E., Liu, C.L., Humphrey, E.L., Perlstein, E.O. & Schreiber, S.L. Global nucleosome occupancy in yeast. Genome Biol. 5, R62 (2004).
-
(2004)
Genome Biol
, vol.5
-
-
Bernstein, B.E.1
Liu, C.L.2
Humphrey, E.L.3
Perlstein, E.O.4
Schreiber, S.L.5
-
46
-
-
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
-
47
-
-
26444508841
-
Single-nucleosome mapping of histone modifications in S. cerevisiae
-
Liu, C.L. et al. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol 3, e328 (2005).
-
(2005)
PLoS Biol
, vol.3
-
-
Liu, C.L.1
-
48
-
-
27944435825
-
Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays
-
Rada-Iglesias, A. et al. Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays. Hum. Mol. Genet. 14, 3435-3447 (2005).
-
(2005)
Hum. Mol. Genet
, vol.14
, pp. 3435-3447
-
-
Rada-Iglesias, A.1
-
49
-
-
27144458417
-
Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide
-
Rao, B., Shibata, Y., Strahl, B.D. & Lieb, J.D. Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol. Cell. Biol. 25, 9447-9459 (2005).
-
(2005)
Mol. Cell. Biol
, vol.25
, pp. 9447-9459
-
-
Rao, B.1
Shibata, Y.2
Strahl, B.D.3
Lieb, J.D.4
-
50
-
-
22744432660
-
Genome-scale identification of nucleosome positions in S. cerevisiae
-
Yuan, G.C. et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309, 626-630 (2005).
-
(2005)
Science
, vol.309
, pp. 626-630
-
-
Yuan, G.C.1
-
51
-
-
33745140886
-
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
-
Bieda, M., Xu, X., Singer, M.A., 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).
-
(2006)
Genome Res
, vol.16
, pp. 595-605
-
-
Bieda, M.1
Xu, X.2
Singer, M.A.3
Green, R.4
Farnham, P.J.5
-
52
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
|