-
1
-
-
33747881750
-
The general transcription machinery and general cofactors
-
Thomas,M.C. and Chiang,C.M. (2006) The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol., 41, 105-178.
-
(2006)
Crit. Rev. Biochem. Mol. Biol
, vol.41
, pp. 105-178
-
-
Thomas, M.C.1
Chiang, C.M.2
-
2
-
-
33646843937
-
Core promoter-selective RNA polymerase II transcription
-
Gross,P. and Oelgeschlager,T. (2006) Core promoter-selective RNA polymerase II transcription. Biochem. Soc. Symp., 225-236.
-
(2006)
Biochem. Soc. Symp
, pp. 225-236
-
-
Gross, P.1
Oelgeschlager, T.2
-
3
-
-
33750345805
-
Rational design of a super core promoter that enhances gene expression
-
Juven-Gershon,J., Cheng,S. and Kadonaga,J.T. (2006) Rational design of a super core promoter that enhances gene expression. Nat. Methods, 3, 917-922.
-
(2006)
Nat. Methods
, vol.3
, pp. 917-922
-
-
Juven-Gershon, J.1
Cheng, S.2
Kadonaga, J.T.3
-
4
-
-
33847213513
-
The new core promoter element XCPE1 (X Core Promoter Element 1) directs activator-, mediator-, and TATA-binding protein-dependent but TFIID-independent RNA polymerase II transcription from TATA-less promoters
-
Tokusumi,Y., Ma,Y., Song,X., Jacobson,R.H. and Takada,S. (2007) The new core promoter element XCPE1 (X Core Promoter Element 1) directs activator-, mediator-, and TATA-binding protein-dependent but TFIID-independent RNA polymerase II transcription from TATA-less promoters. Mol. Cell. Biol., 27, 1844-1858.
-
(2007)
Mol. Cell. Biol
, vol.27
, pp. 1844-1858
-
-
Tokusumi, Y.1
Ma, Y.2
Song, X.3
Jacobson, R.H.4
Takada, S.5
-
5
-
-
34248684091
-
Core promoter elements recognized by transcription factor IIB
-
Deng,W. and Roberts,S.G. (2006) Core promoter elements recognized by transcription factor IIB. Biochem. Soc. Trans., 34, 1051-1053.
-
(2006)
Biochem. Soc. Trans
, vol.34
, pp. 1051-1053
-
-
Deng, W.1
Roberts, S.G.2
-
6
-
-
0037195255
-
Responses of four yeast genes to changes in the transcriptional machinery are determined by their promoters
-
Cheng,J.X., Floer,M., Ononaji,P., Bryant,G. and Ptashne,M. (2002) Responses of four yeast genes to changes in the transcriptional machinery are determined by their promoters. Curr. Biol., 12 1828-1832.
-
(2002)
Curr. Biol
, vol.12
, pp. 1828-1832
-
-
Cheng, J.X.1
Floer, M.2
Ononaji, P.3
Bryant, G.4
Ptashne, M.5
-
7
-
-
0037162292
-
Selective recruitment of TAFs by yeast upstream activating sequences. Implications for eukaryotic promoter structure
-
Li,X.Y., Bhaumik,S.R., Zhu,X., Li,L., Shen,W.C., Dixit,B.L. and Green,M.R. (2002) Selective recruitment of TAFs by yeast upstream activating sequences. Implications for eukaryotic promoter structure. Curr. Biol., 12, 1240-1244.
-
(2002)
Curr. Biol
, vol.12
, pp. 1240-1244
-
-
Li, X.Y.1
Bhaumik, S.R.2
Zhu, X.3
Li, L.4
Shen, W.C.5
Dixit, B.L.6
Green, M.R.7
-
8
-
-
0036239962
-
Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast
-
Mencia,M., Moqtaderi,Z., Geisberg,J.V., Kuras,L. and Struhl,K. (2002) Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol. Cell, 9, 823-833.
-
(2002)
Mol. Cell
, vol.9
, pp. 823-833
-
-
Mencia, M.1
Moqtaderi, Z.2
Geisberg, J.V.3
Kuras, L.4
Struhl, K.5
-
9
-
-
0037108159
-
The RNA polymerase II core promoter: A key component in the regulation of gene expression
-
Butler,J.E. and Kadonaga,J.T. (2002) The RNA polymerase II core promoter: A key component in the regulation of gene expression. Genes Dev., 16, 2583-2592.
-
(2002)
Genes Dev
, vol.16
, pp. 2583-2592
-
-
Butler, J.E.1
Kadonaga, J.T.2
-
10
-
-
34447522202
-
New problems in RNA polymerase II transcription initiation: Matching the diversity of core promoters with a variety of promoter recognition factors
-
Muller,F., Demeny,M.A. and Tora,L. (2007) New problems in RNA polymerase II transcription initiation: Matching the diversity of core promoters with a variety of promoter recognition factors. J. Biol. Chem, 282, 14685-14689.
-
(2007)
J. Biol. Chem
, vol.282
, pp. 14685-14689
-
-
Muller, F.1
Demeny, M.A.2
Tora, L.3
-
11
-
-
0035477093
-
Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs
-
Butler,J.E. and Kadonaga,J.T. (2001) Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev., 15 2515-2519.
-
(2001)
Genes Dev
, vol.15
, pp. 2515-2519
-
-
Butler, J.E.1
Kadonaga, J.T.2
-
12
-
-
0342680080
-
Developmental change in TATA-box utilization during preimplantation mouse development
-
Davis,W. Jr and Schultz,R.M. (2000) Developmental change in TATA-box utilization during preimplantation mouse development, Dev. Biol., 218, 275-283.
-
(2000)
Dev. Biol
, vol.218
, pp. 275-283
-
-
Davis Jr, W.1
Schultz, R.M.2
-
13
-
-
0028231941
-
TATA-dependent enhancer stimulation of promoter activity in mice is developmentally acquired
-
Majumder,S. and DePamphilis,M.L. (1994) TATA-dependent enhancer stimulation of promoter activity in mice is developmentally acquired. Mol. Cell. Biol., 14, 4258-4268.
-
(1994)
Mol. Cell. Biol
, vol.14
, pp. 4258-4268
-
-
Majumder, S.1
DePamphilis, M.L.2
-
14
-
-
0037117575
-
Developmental specificity of recruitment of TBP to the TATA box of the human gamma-globin gene
-
Duan,Z.J., Fang,X., Rohde,A., Han,H., Stamatoyannopoulos,G. and Li,Q. (2002) Developmental specificity of recruitment of TBP to the TATA box of the human gamma-globin gene. Proc. Natl. Acad. Sci. USA, 99 5509-5514.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5509-5514
-
-
Duan, Z.J.1
Fang, X.2
Rohde, A.3
Han, H.4
Stamatoyannopoulos, G.5
Li, Q.6
-
15
-
-
0029119404
-
TAFs and TFIIA mediate differential utilization of the tandem Adh promoters
-
Hansen,S.K. and Tjian,R. (1995) TAFs and TFIIA mediate differential utilization of the tandem Adh promoters. Cell, 82, 565-575.
-
(1995)
Cell
, vol.82
, pp. 565-575
-
-
Hansen, S.K.1
Tjian, R.2
-
16
-
-
0038303112
-
Distinct transcriptional pathways regulate basal and activated major histocompatibility complex class I expression
-
Howcroft,T.K., Raval,A., Weissman,J.D., Gegonne,A. and Singer,D.S. (2003) Distinct transcriptional pathways regulate basal and activated major histocompatibility complex class I expression. Mol. Cell. Biol. 23, 3377-3391.
-
(2003)
Mol. Cell. Biol
, vol.23
, pp. 3377-3391
-
-
Howcroft, T.K.1
Raval, A.2
Weissman, J.D.3
Gegonne, A.4
Singer, D.S.5
-
17
-
-
0141682029
-
Promoter-specific function of the TATA element in undifferentiated P19 cells
-
Kobayashi,A., Kokubo,T., Ota,Y. and Yokoyama,S. (2003) Promoter-specific function of the TATA element in undifferentiated P19 cells. Biochem. Biophys. Res. Commun., 310, 458-463.
-
(2003)
Biochem. Biophys. Res. Commun
, vol.310
, pp. 458-463
-
-
Kobayashi, A.1
Kokubo, T.2
Ota, Y.3
Yokoyama, S.4
-
18
-
-
0037100669
-
Functional interaction between TATA and upstream CACGTG elements regulates the temporally specific expression of Otx mRNAs during early embryogenesis of the sea urchin, Hemicentrotus pulcherrimus
-
Kobayashi,A., Akasaka,K., Kawaichi,M. and Kokubo,T. (2002) Functional interaction between TATA and upstream CACGTG elements regulates the temporally specific expression of Otx mRNAs during early embryogenesis of the sea urchin, Hemicentrotus pulcherrimus. Nucleic Acids Res., 30, 3034-3044.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3034-3044
-
-
Kobayashi, A.1
Akasaka, K.2
Kawaichi, M.3
Kokubo, T.4
-
19
-
-
0023613953
-
Rapid and efficient site-specific mutagenesis without phenotypic selection
-
Kunkel,T.A., Roberts,J.D. and Zakour,R.A. (1987) Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol., 154, 367-382.
-
(1987)
Methods Enzymol
, vol.154
, pp. 367-382
-
-
Kunkel, T.A.1
Roberts, J.D.2
Zakour, R.A.3
-
20
-
-
0033155772
-
Upstream element of the sea urchin arylsulfatase gene serves as an insulator
-
Akasaka,K., Nishimura,A., Takata,K., Mitsunaga,K., Mibuka,F., Ueda,H., Hirose,S:, Tsutsui,K. and Shimada,H. (1999) Upstream element of the sea urchin arylsulfatase gene serves as an insulator. Cell. Mol. Biol. (Noisy-le-grand), 45, 555-565.
-
(1999)
Cell. Mol. Biol. (Noisy-le-grand)
, vol.45
, pp. 555-565
-
-
Akasaka, K.1
Nishimura, A.2
Takata, K.3
Mitsunaga, K.4
Mibuka, F.5
Ueda, H.6
Hirose, S.7
Tsutsui, K.8
Shimada, H.9
-
21
-
-
34047105274
-
Ars insulator protects transgenes from long-term silencing in sea urchin larva
-
Yajima,M., Kiyomoto,M. and Akasaka,K. (2007) Ars insulator protects transgenes from long-term silencing in sea urchin larva. Dev. Genes. Evol., 217, 331-336.
-
(2007)
Dev. Genes. Evol
, vol.217
, pp. 331-336
-
-
Yajima, M.1
Kiyomoto, M.2
Akasaka, K.3
-
22
-
-
0037295330
-
Utilization of a particle gun DNA introduction system for the analysis of cis-regulatory elements controlling the spatial expression pattern of the arylsulfatase gene (HpArs) in sea urchin embryos
-
Kurita,M., Kondoh,H., Mitsunaga-Nakatsubo,K., Shimotori,T., Sakamoto,N., Yamamoto,T., Shimada,H., Takata,K. and Akasaka,K. (2003) Utilization of a particle gun DNA introduction system for the analysis of cis-regulatory elements controlling the spatial expression pattern of the arylsulfatase gene (HpArs) in sea urchin embryos. Dev. Genes. Evol., 213, 44-49.
-
(2003)
Dev. Genes. Evol
, vol.213
, pp. 44-49
-
-
Kurita, M.1
Kondoh, H.2
Mitsunaga-Nakatsubo, K.3
Shimotori, T.4
Sakamoto, N.5
Yamamoto, T.6
Shimada, H.7
Takata, K.8
Akasaka, K.9
-
23
-
-
0031568327
-
Two isoforms of orthodenticle-related proteins (HpOtx) bind to the enhancer element of sea urchin arylsulfatase gene
-
Sakamoto,N., Akasaka,K., Mitsunaga-Nakatsubo,K., Takata,K., Nishitani,T. and Shimada,H. (1997) Two isoforms of orthodenticle-related proteins (HpOtx) bind to the enhancer element of sea urchin arylsulfatase gene. Dev. Biol., 181, 284-295.
-
(1997)
Dev. Biol
, vol.181
, pp. 284-295
-
-
Sakamoto, N.1
Akasaka, K.2
Mitsunaga-Nakatsubo, K.3
Takata, K.4
Nishitani, T.5
Shimada, H.6
-
24
-
-
0036158094
-
Molecular patterning along the sea urchin animal-vegetal axis
-
Brandhorst,B.P. and Klein,W.H. (2002) Molecular patterning along the sea urchin animal-vegetal axis. Int. Rev. Cytol., 213, 183-232.
-
(2002)
Int. Rev. Cytol
, vol.213
, pp. 183-232
-
-
Brandhorst, B.P.1
Klein, W.H.2
-
25
-
-
0026323133
-
Sea urchin USF: A helix-loop-helix protein active in embryonic ectoderm cells
-
Kozlowski,M.T., Gan,L., Venuti,J.M., Sawadogo,M. and Klein,W.H. (1991) Sea urchin USF: A helix-loop-helix protein active in embryonic ectoderm cells. Dev. Mol., 148, 625-630.
-
(1991)
Dev. Mol
, vol.148
, pp. 625-630
-
-
Kozlowski, M.T.1
Gan, L.2
Venuti, J.M.3
Sawadogo, M.4
Klein, W.H.5
-
26
-
-
0023777673
-
Mosaic incorporation and regulated expression of an exogenous gene in the sea-urchin embryo
-
Hough-Evans,B.R., Britten,R.J. and Davidson,E.H. (1988) Mosaic incorporation and regulated expression of an exogenous gene in the sea-urchin embryo. Dev. Biol., 129, 198-208.
-
(1988)
Dev. Biol
, vol.129
, pp. 198-208
-
-
Hough-Evans, B.R.1
Britten, R.J.2
Davidson, E.H.3
-
27
-
-
0024278916
-
Spec2 genes of Strongylocentrotus purpuratus. Structure and differential expression in embryonic aboral ectoderm cells
-
Hardin,P.E., Angerer,L.M., Hardin,S.H., Angerer,R.C. and Klein,W.H. (1988) Spec2 genes of Strongylocentrotus purpuratus. Structure and differential expression in embryonic aboral ectoderm cells. J. Mol. Biol., 202, 417-431.
-
(1988)
J. Mol. Biol
, vol.202
, pp. 417-431
-
-
Hardin, P.E.1
Angerer, L.M.2
Hardin, S.H.3
Angerer, R.C.4
Klein, W.H.5
-
28
-
-
1642295844
-
The Otx binding site is required for the activation of HpOtxL mRNA expression in the sea urchin,Hemicentrotus pulcherrimus
-
Hayashibara,Y., Mitsunaga-Nakatsubo,K., Sakamoto,N., Shimotori,J., Akasaka,K. and Yamamoto,T. (2004) The Otx binding site is required for the activation of HpOtxL mRNA expression in the sea urchin,Hemicentrotus pulcherrimus. Dev. Growth. Differ., 46, 61-67.
-
(2004)
Dev. Growth. Differ
, vol.46
, pp. 61-67
-
-
Hayashibara, Y.1
Mitsunaga-Nakatsubo, K.2
Sakamoto, N.3
Shimotori, J.4
Akasaka, K.5
Yamamoto, T.6
-
29
-
-
15544371346
-
Gene regulation at the single-cell level
-
Rosenfeld,N., Young,J.W., Alon,U., Swain,P.S. and Elowitz,M.B. (2005) Gene regulation at the single-cell level. Science, 307, 1962-1965.
-
(2005)
Science
, vol.307
, pp. 1962-1965
-
-
Rosenfeld, N.1
Young, J.W.2
Alon, U.3
Swain, P.S.4
Elowitz, M.B.5
-
30
-
-
0037119587
-
Stochastic gene expression in a single cell
-
Elowitz,M.B., Levine,A.J., Siggia,E.D. and Swain,P.S. (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186.
-
(2002)
Science
, vol.297
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
31
-
-
0036790975
-
Intrinsic and extrinsic contributions to stochasticity in gene expression
-
Swain,P.S., Elowitz,M.B. and Siggia,E.D. (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. USA, 99, 12795-12800.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12795-12800
-
-
Swain, P.S.1
Elowitz, M.B.2
Siggia, E.D.3
-
32
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
Raser,J.M. and O'Shea,E.K. (2004) Control of stochasticity in eukaryotic gene expression. Science, 304, 1811-1814.
-
(2004)
Science
, vol.304
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
33
-
-
26944476331
-
Regulated cell-to-cell variation in a cell-fate decision system
-
Colman-Lerner,A., Gordon,A., Serra,E., Chin,T., Resnekov,O., Endy,D., Pesce,C.G. and Brent,R. (2005) Regulated cell-to-cell variation in a cell-fate decision system. Nature, 437, 699-706.
-
(2005)
Nature
, vol.437
, pp. 699-706
-
-
Colman-Lerner, A.1
Gordon, A.2
Serra, E.3
Chin, T.4
Resnekov, O.5
Endy, D.6
Pesce, C.G.7
Brent, R.8
-
34
-
-
0038185273
-
Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness
-
Conkright,M.D., Guzman,E., Flechner,L., Su,A.I., Hogenesch,J.B. and Montminy,M. (2003) Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Mol. Cell, 11, 1101-1108.
-
(2003)
Mol. Cell
, vol.11
, pp. 1101-1108
-
-
Conkright, M.D.1
Guzman, E.2
Flechner, L.3
Su, A.I.4
Hogenesch, J.B.5
Montminy, M.6
-
35
-
-
0035477896
-
Core promoters: Active contributors to combinatorial gene regulation
-
Smale,S.T. (2001) Core promoters: Active contributors to combinatorial gene regulation. Genes Dev., 15, 2503-2508.
-
(2001)
Genes Dev
, vol.15
, pp. 2503-2508
-
-
Smale, S.T.1
-
36
-
-
0024284087
-
Definition of multiple, functionally distinct TATA elements, one of which is a target in the hsp70 promoter for E1A regulation
-
Simon,M.C., Fisch,T.M., Benecke,B.J., Nevins,J.R. and Heintz,N. (1988) Definition of multiple, functionally distinct TATA elements, one of which is a target in the hsp70 promoter for E1A regulation. Cell, 52, 723-729.
-
(1988)
Cell
, vol.52
, pp. 723-729
-
-
Simon, M.C.1
Fisch, T.M.2
Benecke, B.J.3
Nevins, J.R.4
Heintz, N.5
-
37
-
-
0025234468
-
Functional heterogeneity of mammalian TATA-box sequences revealed by interaction with a cell-specific enhancer
-
Wefald,F.C., Devlin,B.H. and Williams,R.S. (1990) Functional heterogeneity of mammalian TATA-box sequences revealed by interaction with a cell-specific enhancer. Nature, 344, 260-262.
-
(1990)
Nature
, vol.344
, pp. 260-262
-
-
Wefald, F.C.1
Devlin, B.H.2
Williams, R.S.3
-
38
-
-
0034614612
-
The TATA motif specifies the differential activation of minimal promoters by varicella zoster virus immediate-early regulatory protein IE62
-
Perera,L.P. (2000) The TATA motif specifies the differential activation of minimal promoters by varicella zoster virus immediate-early regulatory protein IE62. J. Biol. Chem., 275, 487-496.
-
(2000)
J. Biol. Chem
, vol.275
, pp. 487-496
-
-
Perera, L.P.1
-
39
-
-
17044396348
-
Logic functions of the genomic cis-regulatory code
-
Istrail,S. and Davidson,E.H. (2005) Logic functions of the genomic cis-regulatory code. Proc. Natl Acad. Sci. USA, 102, 4954-4959.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4954-4959
-
-
Istrail, S.1
Davidson, E.H.2
-
40
-
-
34547634659
-
High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution
-
Howard-Ashby,M., Materna,S.C., Brown,C.T., Tu,Q., Oliveri,P., Cameron,R.A. and Davidson,E.H. (2006) High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution. Dev. Biol., 300, 27-34.
-
(2006)
Dev. Biol
, vol.300
, pp. 27-34
-
-
Howard-Ashby, M.1
Materna, S.C.2
Brown, C.T.3
Tu, Q.4
Oliveri, P.5
Cameron, R.A.6
Davidson, E.H.7
-
41
-
-
33750995860
-
The genome of the sea urchin Strongylocentratus purpuratus
-
Sodergren,E., Weinstock,G.M., Davidson,E.H., Cameron,R.A., Gibbs,R.A., Angerer,R.C., Angerer,L.M., Arnone,M.I., Burgess,D.R. et al. (2006) The genome of the sea urchin Strongylocentratus purpuratus. Science, 314, 941-952.
-
(2006)
Science
, vol.314
, pp. 941-952
-
-
Sodergren, E.1
Weinstock, G.M.2
Davidson, E.H.3
Cameron, R.A.4
Gibbs, R.A.5
Angerer, R.C.6
Angerer, L.M.7
Arnone, M.I.8
Burgess, D.R.9
|