Struhl Publications List - 1976-Present
(PDF files for most)
Updated 4/8/2024
1. Struhl, K., Cameron, J.R., and Davis, R.W. (1976). Functional genetic expression of eukaryotic DNA in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 73 1471-1475. Struhl et al, 1976 PNAS.pdf
2. Struhl, K. and Magasanik, B. (1976). Ammonia sensitive mutant of Klebsiella aerogenes. J. Bacteriol. 126 739-742. Struhl & Magasanik, 1976 JBact.pdf
3. Struhl, K. and Davis, R.W. (1976). Genetic selections and the cloning of prokaryotic and eukaryotic genes. ICN-UCLA Symp. Mol. and Cell. Biol. 5 495 506. Struhl & Davis, 1976 ICN-UCLA Symp.pdf
4. Struhl, K. and Davis, R.W. (1977). Production of a functional eukaryotic enzyme in E.coli: Cloning and expression of the yeast structural gene for imidazoleglycerol-phosphate dehydratase (his3). Proc. Natl. Acad. Sci. U.S.A. 74 5255-5259. Struhl & Davis, 1977 PNAS.pdf
5. Struhl, K. and Davis, R.W. (1977). A eukaryotic gene is functionally expressed in E.coli. in Pancreatic Beta Cell Culture, ed. vonWasielewski and Chick, Excerpta Medica, Amsterdam-Oxford. pp. 165-172. Struhl & Davis, 1977, Pancreatic Beta Cell Culture
6. Davis, R.W., Thomas, M., Cameron, J.R., Philippsen, P., Kramer, R., St. John, T., Struhl, K., and Ferguson, J. (1977). Genetic and physical selections of eukaryotic genes cloned in E.coli. in the Molecular Biology of the Mammalian Genetic Apparatus. ed. P.O.P. Ts'O, Elsevier/North Holland Biomedical Press, Amsterdam 2 15-27. Davis et al., 1977 Mol. Biol. of Mammalian Genetic Apparatus.pdf
7. Davis, R.W., Thomas, M., Benton, D., Cameron, J.R., Philippsen, P., Struhl, K., St. John, T., and Kramer, R. (1977). The isolation of particular cloned eukaryotic DNA sequences. in Molecular Cloning of Recombinant DNA. ed. Scott, W.A. and Werner, R. Academic Press, New York pp. 155-160.
8. Struhl, K., Stinchcomb, D.T., Scherer, S., and Davis, R.W. (1979). High frequency transformation of yeast: Autonomous replication of hybrid DNA molecules. Proc. Natl. Acad. Sci. U.S.A. 76 1035-1039. Struhl et al, 1979 PNAS.pdf
9. Struhl, K., Davis, R.W., and Fink, G.R. (1979). Suppression of a yeast amber mutation in E.coli. Nature 279 78-79. Struhl et al, 1979 Nature.pdf
10. Stinchcomb, D.T., Struhl, K., and Davis, R.W. (1979). Isolation and characterization of a yeast chromosomal replicator. Nature 282 39-43. Stinchcomb et al, 1979 Nature.pdf
11. Davis, R.W., Struhl, K., St. John, T., Stinchcomb, D.T., Scherer, S., and McDonell, M. (1979). Structural and functional analysis of the HIS3 gene and galactose inducible sequences in yeast. ICN-UCLA Symp. Mol. and Cell. Biol. 14 51 55.
12. Botstein, D., Falco, S.C., Stewart, S.E., Brennan, M., Scherer, S., Stinchcomb, D.T., Struhl, K., and Davis, R.W. (1979). Sterile host yeasts (SHY): A eukaryotic system of biological containment for recombinant DNA experiments. Gene 8 17-24. Botstein et al, 1979 Gene.pdf
13. Struhl, K., Stinchcomb, D.T., and Davis, R.W. (1980). A physiological study of functional expression in Escherichia coli of the cloned yeast imidazoleglycerolphosphate dehydratase gene. J. Mol. Biol. 136 291-307. Struhl et al, 1980 JMB.pdf
14. Struhl, K. and Davis, R.W. (1980). A physical, genetic, and transcriptional map of the cloned his3 gene region of Saccharomyces cerevisiae. J. Mol. Biol. 136 309 332. Struhl & Davis, 1980 JMB his3.pdf
15. Brennan, M.B. and Struhl, K. (1980). Mechanisms of increasing expression of a yeast gene in E.coli. J. Mol. Biol. 136 333-338. Brennan & Struhl, 1980 JMB.pdf
16. Struhl, K. and Davis, R.W. (1980). Conservation and DNA sequence arrangement of the DNA polymerase I gene region from Klebsiella aerogenes, Klebsiella pneumoniae, and Escherichia coli. J. Mol. Biol. 141 343-368. Struhl & Davis, 1980 JMB Pol.pdf
17. Struhl, K. (1980). Expression of genes cloned in yeast. in Yeast Genetics and Molecular Biology, reports of the Tenth International Conference pp. 51-54.
18. Struhl, K. (1981). Deletion mapping a eukaryotic promoter. Proc. Natl. Acad. Sci. U.S.A. 78 4461-4465. Struhl, 1981 PNAS.pdf
19. Struhl, K. (1981). Deletion, recombination, and gene expression involving the bacteriophage λ attachment site. J. Mol. Biol. 152 517-533. Struhl, 1981 JMB att.pdf
20. Struhl, K. and Davis, R.W. (1981). Transcription of the his3 gene region in Saccharomyces cerevisiae. J. Mol. Biol. 152 535-552. Struhl & Davis, 1981 JMB transcription.pdf
21. Struhl, K. and Davis, R.W. (1981). Promoter mutants of the yeast his3 gene. J. Mol. Biol. 152 553-568. Struhl & Davis, 1981 JMB promoter.pdf
22. Struhl, K. (1981). Position effects in Saccharomyces cerevisiae. J. Mol. Biol. 152 569-575. 
Struhl, 1981 JMB position.pdf
23. Struhl, K. (1982). The yeast his3 promoter contains at least two distinct elements. Proc. Natl. Acad. Sci. U.S.A. 79 7385-7389. Struhl, 1982 PNAS.pdf
24. Struhl, K. (1982). Regulatory sites for his3 gene expression in yeast. Nature 300 284 287. Struhl, 1982 Nature.pdf
25. Struhl, K. (1983). Promoter elements, regulatory elements, and chromatin structure of the yeast his3 gene. Cold Spring Harbor Symp. Quant. Biol. 47 901-910. struhl, 1983 csh symposia.pdf
26. Struhl, K. (1983). The new yeast genetics. Nature 305 391-397. Struhl, 1983 Nature.pdf
27. Struhl, K. (1983). A relationship between chromatin structure and genetic elements at the his3 locus in yeast. Alko Symposium on Yeast Molecular Biology ed. M. Korhola and E. Vaisanen. Foundation for Biotechnical and Industrial Fermentation Research 1 19-29. struhl, 1983 alko yeast symposium.pdf
28. Struhl, K. (1983). Direct selection for gene replacement events in yeast. Gene 26 231 241. Struhl, 1983 Gene.pdf
29. Struhl, K. (1984). Genetic properties and chromatin structure of the yeast GAL regulatory element, an enhancer-like sequence. Proc. Natl. Acad. Sci. U.S.A. 81 7865-7869. Struhl, 1984 PNAS.pdf
30. Oettinger, M.A. and Struhl, K. (1985). Suppressors of promoter mutations lacking the his3 upstream element. Mol. Cell. Biol. 5 1901-1909. oettinger & struhl, 1985 mcb.pdf
31. Struhl, K. (1985). Negative control at a distance mediates catabolite repression in yeast. Nature 317 822-824. struhl, 1985 nature.pdf
32. Hope, I.A. and Struhl, K. (1985). GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences: Implications for general control of amino acid biosynthetic genes in yeast. Cell. 43 177-188. hope & struhl, 1985 cell.pdf
33. Struhl, K. (1985). A rapid method for creating recombinant DNA molecules. BioTechniques 3 452-453. Struhl, 1985 Biotechniques
34. Chen, W. and Struhl, K. (1985). Yeast mRNA initiation sites are determined primarily by specific sequences, not the distance from the TATA element. EMBO J. 4 3273-3280. chen & struhl, 1985 embo.pdf
35. Struhl, K. (1985). Nucleotide sequence and transcriptional mapping of the yeast pet56-his3-ded1 gene region. Nucl. Acids Res. 13 8587-8601. struhl, 1985 nar.pdf
36. Struhl, K. (1985). Naturally occurring poly (dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc. Natl. Acad. Sci. U.S.A. 82 8419 8423. struhl, 1985 pnas.pdf
37. Struhl, K., Chen, W., Hill, D.E., Hope, I.A., and Oettinger, M.A. (1985). Constitutive and coordinately regulated transcription of yeast genes: Promoter elements, positive and negative regulatory sites, and DNA binding proteins. Cold Spring Harbor Symp. Quant. Biol. 50 489-503. struhl et al, 1985 csh symposia.pdf
38. Struhl, K. (1986). Yeast promoters. in From gene to protein: Steps dictating the maximal level of gene expression. ed. J. Davies, Butterworths Publishing Co., Stoneham. pp. 35-78. Struhl, 1986 Yeast Promoters.pdf
39. Oliphant, A., Nussbaum, A.L., and Struhl, K. (1986). Cloning of random-sequence oligodeoxynucleotides. Gene 44 177-183. oliphant et al, 1986 gene.pdf
40. Hope, I.A. and Struhl, K. (1986). Functional dissection of a eukaryotic transcriptional activator protein, GCN4 of yeast. Cell 46 885-894. hope & struhl, 1986 cell.pdf
41. Struhl, K. (1986). Yeast his3 expression in Escherichia coli results from fortuitous homology between prokaryotic and eukaryotic promoter elements. J. Mol. Biol. 191 221-229. struhl, 1986 jmb.pdf
42. Hill, D.E., Hope, I.A., Macke, J.P., and Struhl, K. (1986). Saturation mutagenesis of the yeast his3 regulatory site: Requirements for transcriptional induction and for binding by the GCN4 activator protein. Science 234 451-457. hill et al, 1986 science.pdf
43. Struhl, K. (1986). Constitutive and inducible his3 Promoters: Evidence for distinct molecular mechanisms. Mol. Cell. Biol. 6 3847-3853. struhl, 1986 mcb.pdf
44. Struhl, K. (1986). A complex arrangement of promoter elements mediates independent regulation of the divergently transcribed HIS3 and PET56 genes in yeast. Steenbock Symposium 16 293-302. Struhl, 1986 Steenbock Symposium
45. Hill, D.E. and Struhl, K. (1986). A rapid method to determine tRNA charging levels in vivo: Analysis of yeast mutants defective in the general control of amino acid biosynthesis. Nucl. Acids Res. 14 10045-10051. hill & struhl, 1986 nar.pdf
46. Struhl, K. and Hill, D.E. (1987). Two related regulatory sequences are necessary for maximal his3 induction. Mol. Cell. Biol. 7 104-110. struhl & hill, 1987 mcb.pdf
47. Struhl, K. (1987). Effect of deletion and insertion on double-strand break repair in Saccharomyces cerevisiae. Mol. Cell. Biol. 7 1300-1303. struhl, 1987 mcb.pdf
48. Struhl, K. (1987). Promoters, activator proteins, and the molecular mechanism of transcriptional initiation in yeast. Cell 49 295-297. struhl, 1987 cell minireview.pdf
49. Hill, D.E., Oliphant, A.R., and Struhl, K. (1987). Mutagenesis with degenerate oligonucleotides: An efficient method for saturating a defined DNA region with base pair substitutions. Meth. Enzymol. 155 558-568. hill et al, 1987 meth enz.pdf
50. Oliphant, A.R and Struhl, K. (1987). The use of random-sequence oligonucleotides for determining consensus sequences. Meth. Enzymol. 155 568-582. oliphant & struhl, 1987 meth enz.pdf
51. Hope, I.A. and Struhl, K. (1987). GCN4, a eukaryotic transcriptional activator protein, binds DNA as a dimer. EMBO J. 6 2781-2784. hope & struhl, 1987 embo.pdf
52. Ausubel, F., Brent, R., Kingston, R., Moore, D., Smith, J.A., Seidman, J., and Struhl, K. (1987). Current protocols in molecular biology. Greene Publishing Associates, New York, N.Y.
53. Struhl, K. (1987). Subcloning of DNA fragments. Curr. Protoc. Mol. Biol. Chapter 3: Unit 3.16
54. Greene, J.M. and Struhl, K. (1987). S1 analysis of messenger RNA using single-stranded DNA probes. Curr. Protoc. Mol. Biol. Chapter 4: Unit 4.6
55. Struhl, K. (1987). The DNA-binding domains of the jun oncoprotein and the yeast GCN4 transcriptional activator protein are functionally homologous. Cell 50 841-846. struhl, 1987 cell.pdf
56. Chen, W., Tabor, S., and Struhl, K. (1987). Distinguishing between mechanisms of eukaryotic transcriptional activation with bacteriophage T7 RNA polymerase. Cell 50 1047-1055. chen et al, 1987 cell.pdf
57. Kanazawa, S., Driscoll, M., and Struhl, K. (1988). ATR1, a Saccharomyces cerevisiae gene encoding a transmembrane protein required for aminotriazole resistance. Mol. Cell. Biol. 8 664-673. kanazawa et al, 1988 mcb.pdf
58. Struhl, K. (1988). The jun oncogene, a vertebrate transcription factor, activates transcription in yeast. Nature 332 649-650. struhl, 1988 nature.pdf
59. Chen, W. and Struhl, K. (1988). Saturation mutagenesis of a yeast his3 TATA element: Genetic evidence for a specific TATA-binding protein. Proc. Natl. Acad. Sci. U.S.A. 85 2691-2695. chen & struhl, 1988 pnas.pdf
60. Hope, I.A. Mahadevan, S., and Struhl, K. (1988). Structural and functional characterization of the short acidic transcriptional activation region of yeast GCN4 protein. Nature 333 635-640. hope et al, 1988 nature.pdf
61. Oliphant, A.R. and Struhl, K. (1988). Defining the consensus sequences of E.coli promoter elements by random selection. Nucl. Acids Res. 16 7673-7683. oliphant & struhl, 1988 nar.pdf
62. Hill, D.E. and Struhl, K. (1988). Molecular characterization of GCD1, a yeast gene involved in general control of amino acid biosynthesis and cell cycle initiation. Nucl. Acids Res. 16 9253-9265. hill & struhl, 1988 nar.pdf
63. Struhl, K, Brandl, C.J., Chen, W., Harbury, P.A.B., Hope, I.A., and Mahadevan, S. (1988). Transcriptional activation by yeast GCN4, a functional homologue to the jun oncoprotein. Cold Spring Harbor Symp. Quant. Biol. 53 701-709. Struhl et al., 1988 CSH Symp. Quant. Biol.pdf
64. Chen, W. and Struhl, K. (1989). Yeast upstream activator protein GCN4 can stimulate transcription when its binding site replaces the TATA element. EMBO J. 8 261-268. chen & struhl, 1989 embo.pdf
65. Struhl, K. (1989). Helix-turn-helix, zinc finger, and leucine zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem. Sci. 14 137-140. Struhl, 1989 TIBS.pdf
66. Struhl, K. (1989). Molecular mechanisms of transcriptional regulation in yeast. Ann. Rev. Biochem. 58 1051-1077. struhl, 1989 ann rev biochem.pdf
67. Brandl, C.J. and Struhl, K. (1989). Yeast GCN4 transcriptional activator protein interacts with RNA polymerase II in vitro. Proc. Natl. Acad. Sci. U.S.A. 86 2652 2656. brandl & struhl 1989 pnas.pdf
68. Struhl, G., Struhl, K., and Macdonald, P.M. (1989). The gradient morphogen bicoid is a concentration-dependent transcriptional activator. Cell 57 1259-1273. struhl et al, 1989 cell.pdf
69. Oliphant, A.R, Brandl, C.J., and Struhl, K. (1989). Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: Analysis of yeast GCN4 protein. Mol. Cell. Biol. 9 2944-2949. oliphant et al, 1989 mcb.pdf
70. Sellers, J.W. and Struhl, K. (1989). Changing Fos oncoprotein to a Jun-independent DNA-binding protein with GCN4 dimerization specificity by swapping "leucine zippers". Nature 341 74-76. sellers & struhl, 1989 nature.pdf
71. Struhl K. (1989). Synthesizing proteins in vitro by transcription and translation of cloned genes. Curr Protoc. Mol. Biol. Chapter 10, Unit 10.17.
72. Struhl, K. (1989). Analysis of DNA-protein interactions using proteins synthesized in vitro from cloned genes. Curr. Protoc. Mol. Biol. Chapter 12: Unit 12.9
73. Harbury, P.A.B. and Struhl, K. (1989). Functional distinctions between yeast TATA elements. Mol. Cell. Biol. 9 5298-5304. harbury & struhl, 1989 mcb.pdf
74. Oliphant, A.R and Struhl, K. (1989). An efficient method for generating proteins with altered enzymatic properties: Application to β-lactamase. Proc. Natl. Acad. Sci. U.S.A. 86 9094-9098. oliphant & struhl, 1989 pnas.pdf
75. Struhl, K. (1990). GCN4, the yeast version of the Jun-Fos oncogene family. in Gene regulation and AIDS. ed. Papis, T. Portfolio Publishing Co., Texas, pp. 19-24. Struhl, 1990 in Gene regulation and AIDS.pdf
76. Singer, V.L., Wobbe, C.R., and Struhl, K. (1990). A wide variety of unrelated DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes & Dev. 4 636-645. Singer et al, 1990 GD.pdf
77. Ponticelli, A.S. and Struhl, K. (1990). Analysis of Saccharomyces cerevisiae his3 transcription in vitro: Biochemical support for multiple mechanisms of transcription. Mol. Cell. Biol. 10 2832 2839. Ponticelli & Struhl, 1990 MCB.pdf
78. Wobbe, C.R. and Struhl, K. (1990). Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro. Mol. Cell. Biol. 10 3859-3867. Wobbe & Struhl, 1990 MCB.pdf
79. Brandl, C.J. and Struhl, K. (1990). A nucleosome positioning sequence is required for GCN4 to activate transcription in the absence of a TATA element. Mol. Cell. Biol. 10 4256-4265. Brandl & Struhl, 1990 MCB.pdf
80. Mahadevan, S. and Struhl, K. (1990). TC, an unusual promoter element required for constitutive transcription of the yeast HIS3 gene. Mol. Cell. Biol. 10 4447 4455. Mahadevan & Struhl, 1990 MCB.pdf
81. Sellers, J.W., Vincent, A.C., and Struhl, K. (1990). Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites. Mol. Cell. Biol. 10 5077-5086. Sellers et al, 1990 MCB.pdf
82. Weiss, M.A., Ellenberger, T., Wobbe, C.R., Lee, J.P., Harrison, S.C., and Struhl, K. (1990). Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA. Nature 347 575-578. Weiss et al, 1990 Nature.pdf
83. Struhl, K. (1991). Reverse biochemistry: Methods and applications for synthesizing yeast proteins in vitro. Meth. Enzymol. 194 520-535. Struhl, 1991 Meth Enz.pdf
84. Oliviero, S. and Struhl, K. (1991). Synergistic transcriptional enhancement does not depend on the number of acidic activation regions. Proc. Natl. Acad. Sci. U.S.A. 88 224-228. Oliviero & Struhl, 1991 PNAS.pdf
85. Cormack, B.P., Strubin, M., Ponticelli, A.S., and Struhl, K. (1991). Functional differences between yeast and human TFIID are localized to the highly conserved region. Cell 65 341-348. Cormack et al, 1991 Cell.pdf
86. Struhl, K. (1991). Structural and functional analysis of the DNA-binding domain of yeast GCN4 protein. Mochida Memorial Symposium 2 163-176. Struhl, 1991 Mochida.pdf
87. Struhl, K. (1991). Acid connections. Current Biology 1 188-191. Struhl 1991 Curr Biol.pdf
88. Struhl, K. (1991). Mechanisms for diversity in gene regulatory patterns. Neuron 7 177 181. Struhl, 1991 Neuron.pdf
89. Pu, W.T. and Struhl, K. (1991). The leucine zipper symmetrically positions the adjacent basic regions for specific DNA binding. Proc. Natl. Acad. Sci. U.S.A 88 6901-6905. Pu & Struhl, 1991 PNAS.pdf
90. Pu, W.T. and Struhl, K. (1991). Highly conserved residues in the bZIP domain of yeast GCN4 are not essential for DNA-binding. Mol. Cell. Biol. 11 4918-4926. Pu & Struhl, 1991 MCB.pdf
91. Strubin, M. and Struhl, K. (1992). Yeast and human TFIID with altered DNA-binding specificity for TATA elements. Cell 68 721-730. Strubin & Struhl, 1992 Cell.pdf
92. Kelleher, R.J. III, Flanagan, P.M., Chasman, D.I., Ponticelli, A.S., Struhl, K., and Kornberg, R.D. (1992). Yeast and human TFIIDs are interchangeable for the response to acidic transcriptional activators in vitro. Genes & Dev. 6 296-303. Kelleher et al, 1992 GD.pdf
93. Pu, W.T. and Struhl, K. (1992). Uracil interference, a rapid and general method for defining protein-DNA contacts involving the 5-methyl group of thymines: The GCN4-DNA complex. Nucl. Acids Res. 20 771-775. Pu & Struhl, 1992 NAR.pdf
94. Tzamarias, D., Pu, W.T., and Struhl, K. (1992). Mutations in the bZIP domain of yeast GCN4 that alter DNA-binding specificity. Proc. Natl. Acad. Sci. U.S.A. 89 2007-2011. Tzamarias et al, 1992 PNAS.pdf
95. Cormack, B.P. and Struhl, K. (1992). The TATA-binding protein is required for transcription by all three nuclear RNA polymerases in yeast cells. Cell 69 685-696. Cormack & Struhl, 1992 Cell.pdf
96. van Heeckeren, W.J., Sellers, J.W., and Struhl, K. (1992). Role of the conserved leucines in the leucine zipper dimerization motif of yeast GCN4. Nucl. Acids Res. 20 3721-3724. van Heeckeren et al, 1992 NAR.pdf
97. Oliviero, S., Robinson, G.S., Struhl, K., and Spiegelman, B.M. (1992). Yeast GCN4 as a probe for oncogenesis by AP-1 transcription factors: Transcriptional activation through AP-1 sites is not sufficient for cellular transformation. Genes & Dev. 6 1799 1809. Oliviero et al, 1992 GD.pdf
98. Vincent, A.C. and Struhl, K. (1992). ACR1, a yeast ATF/CREB repressor. Mol. Cell. Biol. 12 5394-5405. Vincent & Struhl, 1992 MCB.pdf
99. Ellenberger, T.E., Brandl, C.J., Struhl, K., and Harrison, S.C. (1992). The GCN4 basic-region-leucine zipper binds DNA as a dimer of uninterrupted α-helices: Crystal structure of the protein-DNA complex. Cell 71 1223-1237. Ellenberger et al 1992 Cell.pdf
100. Struhl, K. (1992). The yeast GCN4 transcriptional activator protein. in Transcriptional Regulation. ed. Yamamoto, K.R. and McKnight, S.L. Cold Spring Harbor Press, New York, pp. 833-859. Struhl, 1992 CSHL Press.pdf
101. Struhl, K. (1992). Altered DNA-binding specificity mutants of GCN4 and TFIID. in Molecular Structure and Life: Molecular recognition of nucleic acids. ed. Kyogoku, Y. and Nishimura Y. Japan Science Society Press, Tokyo, pp. 207-216. Struhl, 1992 Japan.pdf
102. Collart, M.A. and Struhl, K. (1993). CDC39, an essential nuclear protein that negatively regulates transcription and differentially affects the constitutive and inducible HIS3 promoters. EMBO J. 12 177-186. Collart & Struhl, 1993 EMBO.pdf
103. Struhl, K. (1993). Chromatin and transcription factors: Who's on first? Current Biol. 3 220-222. Struhl, 1993 Curr Biol.pdf
104. Kim, J., Tzamarias, D., Ellenberger, T.E., Harrison, S.C., and Struhl, K. (1993). Adaptability at the protein-DNA interface is an important aspect of sequence recognition by bZIP proteins. Proc. Natl. Acad. Sci. U.S.A. 90 4513-4517. Kim et al, 1993 PNAS.pdf
105. Struhl, K. (1993). Yeast transcription factors. Curr. Opin. Cell Biol. 5 513-520. Struhl 1993 COCB.pdf
106. Pu, W.T. and Struhl, K. (1993). Dimerization of leucine zippers analyzed by random selection. Nucl. Acids Res. 21 4348-4355. Pu & Struhl, 1993 NAR.pdf
107. Cormack, B.P. and Struhl, K. (1993). Regional codon randomization: Defining a TATA-binding protein surface required for RNA polymerase III transcription. Science 262 244-248. Cormack & Struhl, 1993 Science.pdf
108. Baldwin, A.S., Oettinger, M.A., and Struhl, K. (1994). Methylation and uracil interference assays for analysis of protein-DNA interactions. Curr. Protoc. Mol. Biol. Chapter 12: Unit 12.3
109. Struhl, K. (1994). Duality of the universal eukaryotic transcription factor, TBP. Science 263 1103-1104. Struhl, 1994 Science.pdf
110. Klein, C. and Struhl, K. (1994). Protein kinase A mediates growth-regulated expression of yeast ribosomal protein genes by modulating RAP1 transcriptional activity. Mol. Cell. Biol. 14 1920-1928. Klein & Struhl, 1994 MCB.pdf
111. Collart, M.A. and Struhl, K. (1994). NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global negative regulator of transcription that differentially affects TATA-element utilization. Genes & Dev. 8 525-537. Collart & Struhl, 1994 GD.pdf
112. Engelberg, D., Klein, C., Martinetto, H., Struhl, K., and Karin, M. (1994). The UV response involving the Ras signaling pathway and AP-1 transcription factors is conserved between yeast and mammals. Cell 77 381-390. Engleberg et al, 1994 Cell.pdf
113. Arndt, K.M., Wobbe, C.R., Ricupero-Hovasse, S., Struhl, K., and Winston, F. (1994). Equivalent mutations in the two repeats in yeast TATA-binding protein confer distinct TATA-recognition specificities. Mol. Cell. Biol. 14 3719-3728. Arndt et al, 1994 MCB.pdf
114. Cormack, B.P., Strubin, M., Stargell, L.A. and Struhl, K. (1994). Conserved and non-conserved functions of yeast and human TATA-binding proteins. Genes & Dev. 8 1335-1343. Cormack et al, 1994 GD.pdf
115. Tzamarias, D. and Struhl, K. (1994). Functional dissection of the yeast Cyc8-Tup1 transcriptional co-repressor complex. Nature 369 758-761. Tzamarias & Struhl, 1994 Nature.pdf
116. Klein, C. and Struhl, K. (1994). Increased recruitment of TATA-binding protein to the promoter by transcriptional activation domains in vivo. Science 266 280-282. Klein & Struhl, 1994 Science.pdf
117. Ponticelli, A.S., Pardee, T.S., and Struhl, K. (1995). The glutamine-rich activation domains of human Sp1 do not stimulate transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 15 983-988. ponticelli et al, 1995 mcb.pdf
118. Tzamarias, D. and Struhl, K. (1995). Distinct TPR motifs of Cyc8 are involved in recruiting the Cyc8-Tup1 co-repressor complex to differentially regulated promoters. Genes & Dev. 9 821-831. Tzamarias & Struhl, 1995 GD.pdf
119. Chatterjee, S. and Struhl, K. (1995). Connecting a promoter-bound protein to TBP bypasses the need for a transcriptional activation domain. Nature 374 820-822. chatterjee & struhl, 1995 nature.pdf
120. Iyer, V. and Struhl, K. (1995). Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 14 2570-2579. iyer & struhl, 1995 embo.pdf
121. Stargell, L.A. and Struhl, K. (1995). The TBP-TFIIA interaction in the response to acidic activators in vivo. Science 269 75-78. stargell & struhl, 1995 science.pdf
122. Kim, J. and Struhl, K. (1995). Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains. Nucl. Acids Res. 23 2531-2537. kim & struhl, 1995 nar.pdf
123. Lee, M. and Struhl, K. (1995). Mutations on the DNA-binding surface of TATA-binding protein can specifically impair the response to acidic activators in vivo. Mol. Cell. Biol. 15 5461-5469. lee & struhl, 1995 mcb.pdf
124. Iyer, V. and Struhl, K. (1995). Mechanism of differential utilization of the his3 TR and TC TATA elements. Mol. Cell. Biol. 15 7059-7066. iyer & struhl, 1995 mcb.pdf
125. Struhl, K. (1995). Yeast transcriptional regulatory mechanisms. Ann. Rev. Genet. 29 651-674. struhl, 1995 ann rev genetics.pdf
126. Struhl, K. (1996). Chromatin structure and RNA polymerase II connection: Implications for transcription. Cell 88 179-182. struhl, 1996 cell.pdf
127. Iyer, V. and Struhl, K. (1996). Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 93 5208-5212. iyer & struhl, 1996 pnas.pdf
128. Stargell, L.A. and Struhl, K. (1996). A new class of activation defective TATA-binding protein mutants: Evidence for two steps of transcriptional activation in vivo. Mol. Cell. Biol. 16 4456-4464. stargell & struhl, 1996 mcb.pdf
129. Stargell, L.A. and Struhl, K. (1996). Mechanisms of transcriptional activation in vivo: Two steps forward. Trends Genet. 12 311-315. stargell & struhl, 1996 trends genet.pdf
130. Moqtaderi, Z., Bai, Y., Poon, D., Weil, A.P., and Struhl, K. (1996). TBP-associated factors are not generally required for transcriptional activation in yeast. Nature 382 188-191. moqtaderi et al, 1996 nature.pdf
131. Struhl, K. (1996). Transcriptional enhancement by acidic activators. BBA (Reviews on Cancer) 1288 O15-O17. struhl, 1996 bba.pdf
132. Moqtaderi, Z., Yale, J.D., Struhl, K., and Buratowski, S. (1996). Yeast homologues of higher eukaryotic TFIID subunits. Proc. Natl. Acad. Sci. U.S.A. 93 14654-14658. moqtaderi et al, 1996 pnas.pdf
133. DeRubertis, F., Kadosh, D., Henchoz, S., Pauli, D., Reuter, G., Struhl, K., and Spierer, P. (1996). The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature 384 589-591. de rubertis et al, 1996 nature.pdf
134. Struhl, K. Selective roles for TAFs in vivo. (1997). Genes Funct. 1 5-9. Struhl, 1997 Genes Funct.pdf
135. Lee, M. and Struhl, K. (1997). A severely defective TATA-binding protein-TFIIB interaction does not preclude transcriptional activation in vivo. Mol. Cell. Biol. 17 1336-1345. lee & struhl, 1997 mcb.pdf
136. Mahadevan, S., Raghunand, T.R., Panicker, S. and Struhl, K. (1997). Characterisation of 3' end formation of the yeast his3 mRNA. Gene 190 69-76. mahadevan et al, 1997 gene.pdf
137. Kadosh, D. and Struhl, K. (1997). Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89 365-371. kadosh & struhl, 1997 cell.pdf
138. Schaffrath, R., Struhl, K., and Stark, M.J.R. (1997). Toxin-mediated cell cycle arrest in yeast: The killer phenomenon of Kluyveromyces lactis. BIOforum International 1 83-85. Schaffrath et al., 1997 BIOforum International.pdf
139. Chou, S. and Struhl, K. (1997). Transcriptional activation by TFIIB mutants that severely impair the interaction with promoter DNA and acidic activation domains. Mol. Cell. Biol. 17 6794-6802. chou & struhl, 1997 mcb.pdf
140. Fernandes, L., Rodrigues-Pousada, C., and Struhl, K. (1997). Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions. Mol. Cell. Biol. 17 6982-6993. fernandes et al, 1997 mcb.pdf
141. Struhl, K. (1998). Histone acetylation and transcriptional regulatory mechanisms. Genes & Dev. 12 599-606. struhl, 1998 gd.pdf
142. Kadosh, D. and Struhl, K. (1998). Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo. Genes & Dev. 12 797-805. kadosh & struhl, 1998 gd.pdf
143. Keaveney, M. and Struhl, K. (1998). Activator-mediated recruitment of the RNA polymerase II machinery is the predominant mechanism for transcriptional activation in yeast. Mol. Cell 1 917-924. keaveney & struhl, 1998 mol cell.pdf
144. Struhl, K. and Moqtaderi, Z. (1998). The TAFs in the HAT. Cell 94 1-4. struhl & moqtaderi, 1998 cell.pdf
145. Kadosh, D. and Struhl, K. (1998). Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell. Biol. 18 5121-5127. kadosh & struhl, 1998 mcb.pdf
146. Benson, J.D., Benson, M., Howley, P.M., and Struhl, K. (1998). Association of distinct yeast Not2 functional domains with components of the Gcn5 histone acetylase and Ccr4 transcriptional regulatory complexes. EMBO J. 17 6714-6722. benson et al, 1998 embo.pdf
147. Moqtaderi, Z., Keaveney, M., and Struhl, K. (1998). The histone H3-like TAF is broadly required for transcription in yeast. Mol. Cell 2 675-682. moqtaderi et al, 1998 mol cell.pdf
148. van Heeckeren, W.J., Dorris, D.R., and Struhl, K. (1998). The mating-type proteins of fission yeast induce meiosis by directly activating mei3 transcription. Mol. Cell. Biol. 18 7317-7326. van heeckeren et al, 1998 mcb.pdf
149. Struhl, K., Kadosh, D., Keaveney, M., Kuras, L., and Moqtaderi, Z. (1998). Activation and repression mechanisms in yeast. Cold Spring Harbor Symp. Quant. Biol. 63 413-421. struhl et al, 1998 csh symposia.pdf
150. Gaudreau, L., Keaveney, M., Nevado, J., Zaman, Z., Bryant, G.O., Struhl, K., and Ptashne, M. (1999). Transcriptional activation by artificial recruitment is influenced by promoter architecture and downstream sequences. Proc. Natl. Acad. Sci. U.S.A. 96 2668-2673. gaudreau et al, 1999 pnas.pdf
151. Keaveney, M. and Struhl, K. (1999). Incorporation of Drosophila TAF110 into the yeast TFIID complex does not permit the Sp1 glutamine-rich activation domain to function in vivo. Genes Cells 4 197-203. keaveney & struhl, 1999 genes cells.pdf
152. Ranallo, R.T., Struhl, K., and Stargell, L.A. (1999). A TBP mutant defective for TFIID complex formation in vivo. Mol. Cell. Biol. 19 3951-3957. ranallo et al, 1999 mcb.pdf
153. Dreyfuss, G. and Struhl, K. (1999). Editorial overview: multiprotein complexes, mechanistic connections and nuclear organization. Curr. Op. Cell. Biol. 11 303-306. dreyfuss & struhl, 1999 cocb.pdf
154. Kuras, L. and Struhl, K. (1999). Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399 609-613. kuras & struhl, 1999 nature.pdf
155. Struhl, K. (1999). Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98 1-4. struhl, 1999 cell.pdf
156. Chou, S., Chatterjee, S., Lee, M., and Struhl, K. (1999). Transcriptional activation in yeast cells lacking transcription factor IIA. Genetics 153 1573-1581. chou et al, 1999 genetics.pdf
157. Geisberg, J.V. and Struhl, K. (2000). TATA-binding protein mutants that increase transcription from enhancerless and repressed promoters in vivo. Mol. Cell. Biol. 20 1478-1488. geisberg & struhl, 2000 mcb.pdf
158. Stargell, L.A., Moqtaderi, Z., Dorris, D.R., Ogg, R.C. and Struhl, K. (2000). TFIIA has activator-dependent and core promoter functions in vivo. J. Biol. Chem. 275 12374-12380. stargell et al, 2000 jbc.pdf
159. Kuras, L., Kosa, P., Mencia, M., and Struhl, K. (2000). TAF-containing and TAF-independent forms of transcriptionally active TBP in vivo. Science 288 1244-1248. kuras et al, 2000 science.pdf
160. Garcia-Gimeno, M.A. and Struhl, K. (2000). Aca1 and Aca2, ATF/CREB activators in Saccharomyces cerevisiae, are important for carbon-source utilization but not the response to stress. Mol. Cell. Biol. 20 4340-4349. garcia-gimeno & struhl,2000 mcb.pdf
161. Dorris, D.R. and Struhl, K. (2000). Artificial recruitment of TFIID, but not RNA polymerase II holoenzyme, activates transcription in mammalian cells. Mol. Cell. Biol. 20 4350-4358. dorris & struhl, 2000 mcb.pdf
162. Lee, M., Chatterjee, S., and Struhl, K. (2000). Genetic analysis of the role of Pol II holoenzyme components in repression by the Cyc8-Tup1 complex. Genetics 155 1535-1542. lee et al, 2000 genetics.pdf
163. Mai, X., Chou, S. and Struhl, K. (2000). Preferential accessibility of the yeast his3 promoter region is determined by a general property of the DNA sequence, not by specific elements. Mol. Cell. Biol. 20 6668-6676. mai et al, 2000 mcb.pdf
164. Reid, J.L., Iyer, V.R., Brown, P.O., and Struhl, K. (2000). Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol. Cell 6 1297-1307. reid et al, 2000 mol cell.pdf
165. Kuo, M.-H., vom Baur, E., Struhl, K., and Allis, C.D. (2000). Gcn4 activator targets Gcn5 histone acetyltransferase to specific promoters independently of transcription. Mol. Cell 6 1309-1320. kuo et al, 2000 mol cell.pdf
166. Mencia, M. and Struhl, K. (2001). Region of yeast TAF130 required for association of the TFIID complex with promoters. Mol. Cell. Biol. 21 1145-1154. mencia & struhl, 2001 mcb.pdf
167. Deckert, J. and Struhl, K. (2001). Histone acetylation at promoters is differentially affected by specific activators and repressors. Mol. Cell. Biol. 21 2726-2735. deckert & struhl, 2001 mcb.pdf
168. Geisberg, J.V., Holstege, F.C., Young, R.A., and Struhl, K. (2001). Yeast NC2 associates with the RNA polymerase II preinitiation complex and selectively affects transcription in vivo. Mol. Cell. Biol. 21 2736-2742. geisberg et al, 2001 mcb.pdf
169. Lee, M. and Struhl, K. (2001). Multiple functions of the nonconserved N-terminal domain of yeast TATA-binding protein. Genetics 158 87-93. lee & struhl, 2001 genetics.pdf
170. Kulish, D. and Struhl, K. (2001). TFIIS enhances transcriptional elongation through an artificial arrest site in vivo. Mol. Cell. Biol. 21 4162-4168. kulish & struhl, 2001 mcb.pdf
171. Struhl, K. (2001). Gene regulation: a paradigm for precision. Science 293 1054-1055. struhl, 2001 science.pdf
172. Struhl, K. (2001). Book review. The recombinant DNA controversy- a memoir- Science, politics, and the public interest 1974-1981 by Donald S. Fredrickson. N. Engl. J. Med. 345 1431. Struhl, 2001 NEJM.pdf
173. Katan-Khaykovich, Y. and Struhl, K. (2002). Dynamics of global histone acetylation and deacetylation in vivo: Rapid restoration of normal histone acetylation status upon removal of activator and repressors. Genes & Dev. 16 743-752. katan-khaykovich & struhl, 2002, gd.pdf
174. Ng, H.H., Robert, F., Young, R.A., and Struhl, K. (2002). Genome-wide location and regulated recruitment of the RSC nucleosome remodeling complex. Genes & Dev. 16 806-819. ng et al, 2002 gd-rsc.pdf
175. 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. mencia et al, 2002 mol cell.pdf
176. Struhl, K. (2002). From E.coli to elephants. Book review. Genes & Signals by Mark Ptashne and Alexander Gann. Nature 417 22-23. struhl, 2002 nature.pdf
177. Strasser, K. Masuda, S., Mason, P., Pfannstiel, J., Oppizzi, M., Rodriguez-Navarro, S., Rondon, A.G., Aguilera, A.A., Struhl, K., Reed, R., and Hurt, E. (2002). TREX is a conserved complex coupling transcription with mRNA export. Nature 417 304-307. strasser et al, 2002 nature.pdf
178. Ng, H.H., Feng, Q., Wang. H., Erdjument-Bromage, H., Tempst, P., Zhang, Y., and Struhl, K. (2002). Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes & Dev. 16 1518-1527. ng et al, 2002 gd-k79.pdf
179. Proft, M. and Struhl, K. (2002). Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol. Cell. 9 1307-1317. proft & struhl, 2002 mol cell.pdf
180. Feng, Q., Wang, H., Ng, H.H., Erdjment-Bromage, H., Tempst, P., Struhl, K., and Zhang, Y. (2002). Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12 1052-1058. feng et al, 2002 curr biol.pdf Supplementary Material
181. Deckert, J. and Struhl, K. (2002). Targeted recruitment of Rpd3 histone deacetylase represses transcription by inhibiting recruitment of Swi/Snf, SAGA, and TATA-binding protein. Mol. Cell. Biol. 22 6458-6470. deckert & struhl, 2002, mcb.pdf
182. Ng, H.H., Xu, R.M., Zhang, Y., and Struhl, K. (2002). Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J. Biol. Chem. 277 34655-34657. ng et al, 2002 jbc.pdf
183. Hall, D.B. and Struhl, K. (2002). The VP16 activation domain interacts with multiple transcriptional components as determined by protein-protein crosslinking in vivo. J. Biol. Chem. 277 46043-46050. hall and struhl, 2002 jbc.pdf
184. Geisberg, J.V., Moqtaderi, Z., Kuras, L., and Struhl, K. (2002). Mot1 associates with transcriptionally active promoters and inhibits the association of NC2 in Saccharomyces cerevisiae. Mol. Cell. Biol. 22 8122-8134. geisberg et al, 2002 mcb.pdf
185. Ng, H.H., Ciccone, D.N., Morshead, K.B., Oettinger, M.A., and Struhl, K. (2003). Methylation of lysine 79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc. Natl. Acad. Sci. U.S.A. 100 1820-1825. ng. et al, 2003, pnas.pdf
186. Ng, H.H., Robert, F., Young, R.A., and Struhl, K. (2003). Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell 11 709-719. ng et al, 2003, mol cell.pdf Supplementary Material - Oligos
187. Ng. H.H., Dole, S., and Struhl, K. (2003). The Rtf1 component of the Paf1 transcriptional elongation complex is required for ubiquitination of histone H2B. J. Biol. Chem. 278 33625-33628. ng et al, 2003 jbc.pdf
188. Mason, P.B. and Struhl, K. (2003). The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol. Cell. Biol. 23 8323-8333. mason & struhl, 2003 mcb.pdf
189. Reid, J.L., Moqtaderi, Z., and Struhl, K. (2004). Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae. Mol. Cell. Biol. 24 757-764. reid et al, 2004 mcb.pdf
190. Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A., Wheeler, R., Wong, B., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Helt, G., Struhl, K. and Gingeras, T. R. (2004). Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of non-coding RNAs. Cell 116 499-509. cawley et al, 2004.pdf
191. Moqtaderi, Z. and Struhl, K. (2004). Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol. Cell. Biol. 24 4118-4127. moqtaderi & struhl, 2004 mcb.pdf
192. Geisberg, J.V. and Struhl, K. (2004). Cellular stress alters the transcriptional properties of promoter-bound Mot1-TBP complexes. Mol. Cell 14 479-489. geisberg & struhl 2004 mol cell.pdf
193. Bourbon, H.-M. et al. (2004). A unified nomenclature for protein subunits of Mediator complexes linking transcriptional regulators to RNA polymerase II. Mol. Cell 14 553-557. bourbon et al, 2004 mol cell.pdf
194. Proft, M. and Struhl, K. (2004). MAP kinase-mediated stress relief that precedes and regulates the timing of transcriptional induction. Cell 118 351-361. proft & struhl, 2004 cell.pdf
195. Moqtaderi, Z. and Struhl, K. (2004). Defining in vivo targets of nuclear proteins by chromatin immunoprecipitation and microarray analysis. Curr. Protoc. Mol. Biol. Chapter 21: Unit 21.9
196. Grainger, D.C., Overton, T.W., Reppas, N., Wade, J.T., Tamai, E., Hobman, J.L., Constantinidou, C., Struhl, K., Church, G.M., and Busby, S.J.W. (2004). Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J. Bacteriol. 186 6938-6943. grainger et al, 2004 jbact.pdf
197. ENCODE project consortium. (2004). The ENCODE (ENCyclopedia of DNA Elements) project. Science 304 636-640. encode 2004, science.pdf
198. Geisberg, J.V. and Struhl, K. (2004). Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo. Nucl. Acids Res. 32 e151. geisberg & struhl, 2004 nar.pdf
199. Schwabish, M.A. and Struhl, K. (2004). Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 24 10111-10117. schwabish & struhl, 2004 mcb.pdf
200. Wade, J.T. and Struhl, K. (2004). Association of RNA polymerase with transcribed regions in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 101 17777-17782. wade & struhl, 2004 pnas.pdf
201. Wade, J.T., Hall, D.B., and Struhl, K. (2004). The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 432 1054-1058. wade et al, 2004 nature.pdf
202. Aparicio, O.M., Geisberg, J.V., Sekinger, E.A., Yang, A., Moqtaderi, Z., and Struhl, K. (2005). Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr. Protoc. Mol. Biol. Chapter 21: Unit 21.3201. Struhl, K. (2005).
203. Struhl, K. (2005). Transcriptional activation: Mediator can act after preinitiation complex formation. Mol. Cell 17 752-754. struhl 2005 mol. cell.pdf
204. Mason, P.B. and Struhl, K. (2005). Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell. 17 831-840. mason & struhl, 2005 mol. cell.pdf
205. Sekinger, E.A., Moqtaderi, Z., and Struhl, K. (2005). Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol. Cell. 18 735-748. sekinger et al, 2005, mol. cell.pdf Supplementary Data Supplementary Material - Oligos
206. Katan-Khaykovich, Y. and Struhl, K. (2005). Heterochromatin formation involves changes in histone modifications over multiple cell generations. EMBO J. 24 2138-2149. katan-khaykovich & struhl, 2005, embo j.pdf Supplementary Figure 1 Supplementary Figure 2 Supplementary Figure 3 Supplementary Figure Legends
207. Proft, M., Gibbons, F.D., Copeland, M., Roth, R.P., and Struhl, K. (2005). Genome-wide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae. Eukaryot. Cell 4 1343-1352. proft et al 2005 eukaryot. cell.pdf
208. Wade, J.T., Reppas, N.B., Church, G.M., and Struhl, K. (2005). Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes & Dev. 19 2619-2630. wade et al 2005.pdf
209. Gibbons, F.D., Proft, M., Struhl, K., and Roth, F.P. (2005). Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. Genome Biol. 6R96 Gibbons et al, 2005 Genome Biol Data File 1 Data File 2 Data File 3 Data File 4 Data File 5 Data File 6
210. Joshi, A.A. and Struhl, K. (2005). Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol. Cell 20 971-978. joshi & struhl, 2005 mol. cell.pdf
211. Fan, X., Chou, D. and Struhl, K. (2006). Activator-specific recruitment of Mediator in vivo. Nat. Struct. Mol. Biol. 13 117-120. fan et al, 2006 nsmb.pdf Supplementary Figure 1 Supplementary Figure 2
212. Hall, D.B., Wade, J.T., and Struhl, K. (2006). An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol. Cell. Biol. 26 3672-3679. hall et al, 2006 mcb.pdf
213. Schwabish, M.A. and Struhl, K. (2006). Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II. Mol. Cell. 22 415-422. schwabish & struhl,2006 mol. cell.pdf Supplementary Figures
214. Proft, M., Mas, G., de Nadal, E., Vendrell, A., Noriega, N., Struhl, K., and Posas, F. (2006). The stress-activated Hog1 kinase is a selective transcriptional elongation factor for genes responding to osmotic stress. Mol. Cell. 23 241-250. Proft et al, 2006 Mol. Cell.pdf Supplemental Data
215. Miotto, B. and Struhl, K. (2006). Differential gene regulation by selective association of transcriptional co-activators and bZIP DNA-binding domains. Mol. Cell. Biol. 26 5969-5982. Miotto & Struhl, 2006 MCB.pdf Supplemental Methods Supplemental Figures
216. Wade, J.T., Roa, D.C., Grainger, D.C., Hurd, D., Busby, S.J.W., Struhl, K., and Nudler, E. (2006). Extensive functional overlap among σ factors in Escherichia coli. Nat. Struct. Mol. Biol. 13 806-814. wade et al 2006 nature str & mol biol.pdf Supplementary Fig. 1 Supplementary Fig. 2 Supplementary Fig. 3 Supplementary Fig. 4 Supplementary Table 1 Supplementary Data
217. Pascual-Ahuir, A., Struhl, K., and Proft, M. (2006). Genome-wide location analysis of the stress-activated MAP kinase Hog1 in yeast. Methods 40 272-278. pascual-ahuir et al 2006 methods.pdf
218. Ghosh, S., Hirsch, H.A., Sekinger, E.A. Struhl, K., and Gingeras, T.R. (2006). Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments. BMC Bioinformatics 7 434. Ghosh et al 2006 BMC Bioinfo.pdf
219. Yang, A., Zhu, Z., Kapranov, P., McKeon, F., Church, G.M., Gingeras, T.R., and Struhl, K. (2006) Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol. Cell. 24 593-602. yang et al 2006 mol cell.pdf Supplementary Table S1 Supplementary Table S5
220. Reppas, N.B., Wade, J.T., Church, G.M., and Struhl, K. (2006). The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate-limiting. Mol. Cell. 24 747-757. Reppas et al, 2006 Mol. Cell.pdf Supplemental Data Document 1 Supplemental Data Document 2
221. Struhl, K. (2007). Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat. Struct. Mol. Biol. 14 103-105. Struhl, 2007 NSMB.pdf
222. ENCODE Project Consortium. (2007). The ENCODE pilot project: Identification and analysis of functional elements in 1% of the human genome. Nature 447 799-816. ENCODE 2007, Nature.pdf Supplementary Information 1 Supplementary Information 2
223. Wade, J.T., Struhl, K., Busby, S.J.W., and Grainger, D.C. (2007). Genomic analysis of protein-DNA interactions in bacteria: Insights into transcription and chromosome organization. Mol. Microbiol. 65 21-26. Wade et al, 2007 Mol. Micro.pdf
224. Peckham, H.E., Thurman, R.E., Fu, Y., Stamatoyannopoulos, J.A., Noble, W.S., Struhl, K., and Weng, Z. (2007). Nucleosome positioning signals in genomic DNA. Genome Res. epub July 9. peckham et al. 2007 genome res.pdf Data File 1 Data File 2 Data File 3
225. Miotto, B. and Struhl, K. (2007). Histone H4 lysine 16 acetylation: from genome regulation to tumoral progression. Med. Sci. (Paris). 23 735-740 Miotto & Struhl, 2007 Med Sci.pdf
226. Schwabish, M.A. and Struhl, K. (2007). The Swi/Snf complex is important for histone eviction during transcriptional activation and RNA polymerase II elongation in vivo. Mol. Cell. Biol. 27 6987-6995. Schwabish & Struhl, 2007 MCB.pdf
227. Ghosh, S., Hirsch, H.A., Sekinger, E.A., Kapranov, P., Struhl, K., and Gingeras, T.R. (2007). Differential analysis for high density tiling microarray data. BMC Bioinformatics 8 359. Ghosh et al, 2007 BMC Bioinformatics.pdf Supplementary Information: Additional File 1 is a file archive comprised of prototype R code for gSAM implementation including readme and examples. This can be downloaded from http://www.biomedcentral.com.
228. Struhl, K. (2007). Interpreting chromatin immunoprecipitation experiments. In Evaluating Techniques in Biochemical Research, D. Zuk, ed. (Cambridge, MA; Cell Press) pp. 29-33. Struhl, 2008 ChIP.pdf
229. Struhl, K. (2008). Kevin Struhl. Curr. Biol. 18 R7-R9. Struhl, 2008 Curr. Biol.pdf
230. Johnson, D.S. et al. (2008). Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 18 393-403. Johnson et al, 2008, Genome Res.pdf Supplemental Figures and Tables Supplemental Methods Supplemental Data Table for Fig 2
231. Moqtaderi, Z. and Struhl, K. (2008). Expanding the repertoire of plasmids for PCR-mediated epitope tagging in yeast. Yeast 25 287-292. Moqtaderi & Struhl, 2007, Yeast.pdf
232. Thakur, J.K., Arthanari, H., Yang, F., Pan, S.-J., Fan, X., Breger, J., Frueh, D.P., Gulshan, K., Li, D., Mylonakis, E., Struhl, K., Moye-Rowley, W.S., Cormack, B.P., Wagner, G., and Naar, A.M. (2008). A nuclear receptor-like pathway regulating multidrug resistance in fungi. Nature 452 602-611. Thakur et al, 2008, Nature.pdf Supplementary Figures and Tables
233. Wade, J.T. and Struhl, K. (2008). The transition between transcriptional initiation and elongation. Curr. Opin. Genet. Dev. 18 130-136. Wade & Struhl, 2008, Curr. Opin. Genet. Dev.pdf
234. Fan, X., Lamarre-Vincent, N., Wang, Q., and Struhl, K. (2008). Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucl. Acids Res. 36 e125. Fan et al, 2008, NAR
235. Miotto, B. and Struhl, K. (2008). HBO1 histone acetylase is a co-activator of the replication licensing factor Cdt1. Genes & Dev. 22 2633-2638 Miotto & Struhl, 2008, GD Supplemental material
236. Madhani, H.D., Francis, N.J., Kingston, R.E., Kornberg, R.D., Moazed, D., Narlikar, G.J., Panning, B., and Struhl, K. (2008). Epigenomics: A roadmap, but to where. Science 322 43-44. Madhani et al., 2008, Science
237. Struhl, K. (2008). The hisB463 mutation and expression of a eukaryotic protein in E. coli. Genetics 180 709-714. Struhl, 2008, Genetics
238. Fan, X. and Struhl, K. (2009). Where does Mediator bind in vivo? PLoS ONE 4 e5029. Fan & Struhl, 2009, PLoS ONE
239. Zhang, Y., Moqtaderi, Z., Rattner, B.P., Euskirchen, G., Snyder, M., Kadonaga, J.T., Liu, X.S., and Struhl, K. (2009). Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat. Struct Mol. Biol. 16 847-852. Zhang et al., 2009, Nat. Struct. Mol. Biol. Supplementary Text and Figures
240. Auerbach, R.K., Euskirchen, G., Rozofsky, J., Lamarre-Vincent, N., Moqtaderi, Z., LeFrancois, P., Struhl, K., Gerstein, M., and Snyder, M. (2009). Mapping accessible chromatin regions using Sono-Seq. Proc. Natl. Acad. Sci. U.S.A. 106 14926-14931.Auerbach et al., 2009, Proc. Natl. Acad. Sci.
241. Hirsch, H.A., Iliopoulos, D., Tsichlis, P.N., and Struhl, K. (2009). Metformin selectively targets cancer stem cells, and acts together with chemotherapy to block tumor growth and prolong remission. Cancer Res. 69 7507-7511. Hirsch et al., 2009, Cancer Res.
242. Iliopoulos, D., Polytarchou, C., Hatziapostolou, M., Maroulakou, I.G., Struhl, K., and Tsichlis, P.N. (2009). MicroRNAs differentially regulated by Akt isoforms control EMT and stem cell renewal in cancer cells. Sci. Signal. 2 ra62. Iliopoulos et al., 2009, Sci. Signal Supplementary Materials
243. Iliopoulos, D., Hirsch, H.A., and Struhl, K. (2009). An epigenetic switch involving NF-kB, Lin28, Let-7 microRNA, and interleukin 6 that links inflammation to cellular transformation. Cell 139 693-706. Iliopoulos et al, 2009, Cell Supplemental Data
244. Miotto, B. and Struhl, K. (2010). HBO1 histone acetylase activity is essential for replication licensing and inhibited by Geminin. Mol. Cell. 37 57-66. Miotto & Struhl, 2010, Mol. Cell Supplemental Data
245. Raha, D., Wang, Z., Moqtaderi, Z., Wu, L, Zhong, G., Gerstein, M., Struhl, K., and Snyder, M. (2010). Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc. Natl. Acad. Sci. U.S.A. 1073639-3644.Raha et al, 2010, PNAS
246. Hirsch, H.A., Iliopoulos, D., Joshi, A., Zhong, Y., Jaeger, S.A., Bulyk, M., Tsichlis, P.N., Liu, X.S., and Struhl, K. A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases. Cancer Cell 317 348-361. Hirsch et al, 2010, Cancer Cell Document S1 Table S1 Table S2 Table S4 Table S7 Table S8
247. Moqtaderi, Z., Wang, J., Raha, D., White, R.J., Snyder, M., Weng, Z., and Struhl, K. (2010). Genome-wide binding profiles of functional distinct RNA polymerase III transcription complexes in human cells. Nat. Struct. Mol. Biol. 17 635-640. Moqtaderi et al, 2010, NSMB Supplementary Figure 1 Supplementary Data 1 Supplementary Data 2 Supplementary Data 3
248. Yang, A., Zhu, Z., Kettenbach, A., Kapranov, P., McKeon, F., Gingeras, T.R., and Struhl, K. (2010). Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar DNA-binding profiles in vivo. PLoS ONE 5 e11572. Yang et al, 2010, PLoS ONE Supplementary Table 1 Supplementary Table 2 Supplementary Fig. S1
249. Zhang, Y., Moqtaderi, Z., Rattner, B.P., Euskirchen, G., Snyder, M., Kadonaga, J.T., Liu, X.S., and Struhl, K. (2010). Evidence against a genomic code for nucleosome positioning. Nat. Struct. Mol. Biol. 17 920-923. Zhang et al, 2010, NSMB (Correspondence)
250. Iliopoulos, D., Jaeger, S.A., Hirsch, H.A., Bulyk, M.L., and Struhl, K. (2010). STAT3 activation of miR-21 and miR-181b, via PTEN and CYLD, are part of the epigenetic switch linking inflammation to cancer. Mol. Cell. 39 493-506. Iliopoulos et al, 2010, Mol Cell STAT3 Document S1 (Experimental Procedures, 5 Figures) Table S1 Table S2 Table S3 Table S4 Table S5 Table S6 Table S7
251. Iliopoulos, D., Lindahl-Allen, M., Polytarchou, C., Hirsch, H.A., Tsichlis, P.N., and Struhl, K. (2010). Loss of miR-200 inhibition of Suz12 leads to Polycomb-mediated repression required for the formation and maintenance of cancer stem cells. Mol. Cell. 39761-772. Iliopoulos et al, 2010, Mol Cell miR-200 Supplemental Information
252. Fan, X., Moqtaderi, Z., Jin, Y., Zhang, Y., Liu, X.S., and Struhl, K. (2010). Nucleosome depletion in yeast terminator regions is not intrinsic and can occur by a transcriptional mechanism linked to 3’ end formation. Proc. Natl. Acad. Sci. U.S.A. 107 17945-17950. Fan et al, 2010, PNAS
253. Locke, G., Tolkunov, D., Moqtaderi, Z., Struhl, K., and Morozov, A.V. (2010). High throughput sequencing reveals a simple model of nucleosome energetics. Proc. Natl. Acad. Sci. U.S.A. 107 20998-21003. Locke et al, 2010, PNAS
254. Katan-Khaykovich, Y. and Struhl, K. (2011). Splitting of H3-H4 tetramers at transcriptionally active genes undergoing dynamic histone exchange. Proc. Natl. Acad. Sci. U.S.A. 108 1296-1301. Katan-Khaykovich & Struhl, 2011, PNAS
255.Iliopoulos, D., Hirsch, H.A., and Struhl, K. (2011). Inducible formation of cancer stem cells, and their dynamic equilibrium with non-stem cancer cells via IL6 secretion.Proc. Natl. Acad. Sci. U.S.A.1081397-1402. Iliopoulos et al, 2011, PNAS Supporting Information
256.ENCODE project consortium. (2011). A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9 e1001046. ENCODE, 2011, PLoS Biol. Figure S1 Figure S2 Table S1
257. Iliopoulos, D., Hirsch, H.A., and Struhl, K (2011). Metformin decreases the dose of chemotherapy for prolonging tumor remission in mouse xenografts involving multiple cancer cell types. Cancer Res. 71 3196-3201. Iliopoulos et al, 2011, CancerResearch metformin
258. Esberg, A., Moqtaderi, Z., Fan, X., Lu, J., Struhl, K., and Bystrom, A. (2011). Iwr1 protein is important for preinitiation complex formation by all three nuclear RNA polymerases in Saccharomyces cerevisiae. PLoS ONE 6 e20829. Esberg et al, 2011, PLoSONE Supplementary Methods
259. Polytarchou, C., Iliopoulos, D., Hatziapostolou, M., Kottakis, F., Maroulakou, I., Struhl, K., and Tsichlis, P.N. (2011).Akt2 regulates all Akt isoforms and promotes resistance to hypoxia through induction of miR-21 upon oxygen deprivation.Cancer Res. 71 4720-4731. Polytarchou et al., 2011 Cancer Res.pdf Supplementary Data (Supp. Figs. 1-18, Methods)
260. Iliopoulos, D., Rotem, A., and Struhl, K. Inhibition of miR-193a expression by Max and RXRa activates K-Ras and PLAU to mediate distinct aspects of cellular transformation. (2011). Cancer Res. 71 5144-5153.Iliopoulos et al., 2011 Cancer Res. miR-193a.pdf Supplementary Figures 1-2
261.Tirosh, I., Wong, K.H., Barkai, N., and Struhl, K. (2011).Extensive divergence of the yeast stress response through transitions between induced and constitutive activation.Proc. Natl. Acad. Sci. U.S.A.10816693-16698. Tirosh et al., 2011 PNAS.pdf Supporting Information
262.Miotto, B. and Struhl, K. (2011).JNK1 phosphorylation of Cdt1 inhibits recruitment of HBO1 histone acetylase and blocks replication licensing in response to stress.Mol. Cell.4462-71. Miotto & Struhl, 2011 Mol. Cell.pdf Supplemental Information (7 Figures)
263. Krebs, A.R., Karmodiya, K., Lindahl-Allen, M., Struhl, K., and Tora, L. (2011). SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a novel class of p300-independent enhancers. Mol. Cell 44 410-423. Krebs et al., 2001 Mol. Cell.pdf Document S1 Table S1 (Primers used for ChIP qPCR)
264. Wong, K.H. and Struhl, K. (2011). The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein. Genes Dev. 25 2525-2539. Wong & Struhl, 2011 Genes Dev.pdf
265. Hatziapostolou, M., Polytarchou, C., Aggelidou, E., Drakaki, A., Poultsides, G.A., Jaeger, S.A., Ogata, H., Karin, M., Struhl, K., Hadzopoulou-Cladaras, M., and Iliopoulos, D. (2011). An HNF4a -miRNA inflammatory feedback circuit regulates hepatocellular oncogenesis. Cell 147 1233-1247. Hatziapostolou et al., 2011 Cell.pdf (with supplemental figures and extended experimental procedures)
266. Yuan, C.C., Matthews, A.G.W., Jin, Y., Chen, C.F., Chapman, B.A., Ohsumi, T.K., Glass, K.C., Kutateladze, T.G., Borowsky, M.L., Struhl, K., and Oettinger, M.A. (2012). Histone H3-R2 symmetric dimethylation and histone H3-K4 trimethylation are tightly correlated in eukaryotic genomes. Cell Reports 1 83-90. Yuan et al., 2012 Cell Report Supplemental Information
267. Barber, M.F., Michishita-Kioi, E., Xi, Y., Tasseli, L., Kioi, M., Moqtaderi, Z., Tennen, R.I., Paredes, S., Young, N.L., Chen, K., Struhl, K., Garcia, B.A., Gozani, O., Li, W., and Chua, K.F. (2012), SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature 487 114-118. Barber et al., 2012 Nature
268. Lee, J.-J., Drakaki, A., Iliopoulos, D., and Struhl, K. (2012). MiR-27b targets PPARg to inhibit growth, tumor progression, and the inflammatory response in neuroblastoma cells. Oncogene 31 3818-3825. Lee et al., 2012 Oncogene Supplementary Figures Supplementary Table
269. Polytarchou, C., Iliopoulos, D., and Struhl, K. (2012). An integrated transcriptional regulatory circuit that reinforces the breast cancer stem cell state. Proc. Natl. Acad. Sci. U.S.A. 109 14470-14475. Polytarchou et al., 2012 PNAS Supporting Information
270. ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489 57-74. ENCODE Project Consortium, 2012 Nature Supplementary Information 1 Supplementary Information 2
271. Hughes, A., Jin, Y., Rando, O.J., and Struhl, K. (2012). A functional evolutionary approach to identify determinants of nucleosome positioning: A unifying model for establishing the genome-wide pattern. Mol. Cell 48 5-15. Hughes et al., 2012 Mol. Cell Supplemental Information
272. Hirsch, H.A., Iliopoulos, D., and Struhl, K. (2013). Metformin inhibits the inflammatory response associated with cellular transformation and cancer stem cell growth. Proc. Natl. Acad. Sci. US.A. 110 972-979 Hirsch et al., 2013 PNAS Supporting Information
273. Struhl, K. and Segal, E. (2013). Determinants of nucleosome positioning. Nat. Struct. Mol. Biol. 20 267-273. Struhl & Segal, 2013 NSMB
274. Moqtaderi, Z., Geisberg, J.V., Jin, Y., Fan, X., and Struhl, K. (2013). Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts. Proc. Natl. Acad. Sci. U.S.A. 109 11073-11078. Moqtaderi et al., 2013 PNAS Supporting Information
275. Fleming, J.D., Pavesi, G., Benatti, P., Imbriano, C., Mantovani, R., and Struhl, K. (2013). NF-Y co-associates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. Genome Res. 23 1195-1209. Fleming et al., 2013 Genome Res. Supplemental Figures 1-15 Supplemental Methods & Figure Legends Supplemental Tables
276. Geisberg, J.V., Moqtaderi, Z., Fan, X., Ozsolak, F., and Struhl, K. (2014). Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast. Cell 156 812-824. Geisberg et al., 2014 Cell (with Supplemental Information)
277. Struhl, K. (2014). Is DNA methylation of tumor suppressor genes epigenetic? eLife 3 e02475. Struhl, 2014 eLife
278. Moqtaderi, Z., Geisberg, J.V., and Struhl, K. (2014). Secondary structures involving the poly(A) tail and other 3’ sequences are major determinants of mRNA isoform stability in yeast. Microbial Cell 1 137-139. Moqtaderi et al., 2014 Microbial Cell
279. Wong, K.H., Jin, Y., and Struhl, K. (2014). TFIIH phosphorylation of the Pol II CTD stimulates Mediator dissociation from the preinitiation complex and promoter escape. Mol. Cell. 54 601-612. Wong et al., 2014 Molecular Cell Supplemental Information Supplemental Table S1
280. Janzer, A., German, N.J., Gonzalez-Herrera, K.N., Asara, J.M., Haigis, M.C., and Struhl, K. (2014). Metformin and phenformin deplete tricarboxylic acid cycle and glycolytic intermediates during cell transformation and NTPs in cancer stem cells. Proc. Natl. Acad. Sci. U.S.A. 111 10574-10579. Janzer et al., 2014 PNAS Supporting Information
281. Fleming, J.D., Giresi, P.G., Lindahl-Allen, M., Krall, E.B., Lieb, J.D., and Struhl, K. (2015). STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer. Epigenet Chromatin 8 Fleming et al, 2015 EC Additional Files 1 through 18: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
282. Jin, Y., Geisberg, J.V., Moqtaderi, Z., Ji, Z., Hoque, M., Tian, B., and Struhl, K. (2015). Mapping 3’ mRNA isoforms on a genomic scale. Curr. Protoc. Mol. Biol. Chapter 4: Unit 4.23
283. Rotem, A., Janzer, A., Izar, B., Ji, Z., Doench, J.G., Garraway, L.A., and Struhl, K. (2015). Alternative to the soft-agar assay that permits high-throughput drug and genetic screens for cellular transformation. Proc. Natl. Acad. Sci. U.S.A. 112 5708-5713. Rotem et al., 2015 PNAS Supporting Information
284. Ji, Z., Song, R., Regev, A., and Struhl, K. (2015). Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins. eLife 4 e08890. Ji et al., 2015 eLife Ji et al., 2015 eLife supplemental
285. Ji, Z., Song, R., Huang, H., Regev, A., and Struhl, K. (2016). Transcriptome-scale RNase-footprinting of RNA-protein complexes. Nat. Biotechnol. 34 410-413. Ji et al., 2016 Nat. Biotechnol.
286. Miotto, B. Ji, Z., and Struhl, K. (2016). Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers. Proc. Natl. Acad. Sci. U.S.A. 113 E4810-E4819. Miotto et al., 2016 PNAS Supplemental information MacAlpine commentary
287. Petrenko, N., Jin, Y., Wong, K.H., and Struhl, K. (2016). Mediator undergoes a compositional change during transcriptional activation. Mol. Cell. 64 443-454. Petrenko et al., 2016 Mol. Cell Preview
288. Henry, W.S., Hendrickson, D.G., Beca, F., Glass, B., Lindahl-Allen, M., He, L., Ji, Z., Struhl, K., Beck, A.H., Rinn, J.L., and Toker, A. (2016). LINC00520 is induced by Src, STAT3, and PI3K and plays a functional role in breast cancer. Oncotarget 7 81981-81994. Henry et al., 2016 Oncotarget
289. Rotem, A., Garraway, L., Su, M.J., Basu, A., Regev, A., and Struhl, K. (2017). Miniaturizing 3D assay for high-throughput drug and genetic screens for small patient-derived tumor samples. in Visualizing and quantifying drug distribution in tissue. Proceedings of SPIE 10046 UNSP 100460H
290. Petrenko, N., Jin, Y., Wong, K.H., and Struhl, K. (2017). Evidence that Mediator is essential for Pol II transcription, but is not a required component of the preinitiation complex in vivo. eLife 6 e28447. Petrenko et al., 2017 eLife Supplemental figures
291. Jin, Y., Eser, U., Struhl, K., and Churchman, L.S. (2017). The ground state and evolution of promoter region directionality. Cell 170 889-898. Jin et al., 2017 Cell Supplemental information
292. Ji, Z., He, L., Rotem, A., Janzer, A., Cheng, C.S., Regev, A., and Struhl, K. (2018). Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. Nat. Commun. 9 2068. Ji et al., 2018 Nat. Commun Supplemental information
293. Gameiro, P.A. and Struhl, K. (2018). Nutrient deprivation elicits a transcriptional and translational inflammatory response coupled to decreased protein synthesis. Cell Rep. 24 1415-1424. Gameiro & Struhl, 2018 Cell Rep Commentary
294. Li, B.B., Qian, C., Gameiro, P.A., Liu, C.C., Jiang, T., Roberts, T.M., Struhl, K., and Zhao J.J. (2018). Targeted profiling of RNA translation reveals mTOR-4EBP1/2-independent translational regulation of mRNAs encoding ribosomal proteins. Proc. Natl. Acad. Sci. U.S.A. 115 E9325-E9332. Li et al., 2018 PNAS Supplemental information
295. Moqtaderi, Z., Geisberg, J.V., and Struhl, K. (2018). Extensive structural differences of closely related 3’ mRNA isoforms: links to Pab1 binding and mRNA stability. Mol. Cell. 72 849-861. Moqtaderi et al., 2018 Mol. Cell Supplemental information
296. Petrenko, N., Jin, Y, Dong, L., Wong, K.H., and Struhl, K. (2019). Requirements for RNA polymerase II preinitiation complex formation in vivo. eLife 8 e43654. Petrenko et al., 2019 eLife Supplemental information
297. Ji, Z., He, L., Regev, A., and Struhl, K. (2019). Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers. Proc. Natl. Acad. Sci. U.S.A. 116 9453-9462. Ji et al., 2019 PNAS SI Appendix
298. Koutsioumpa, M., Hatziapostolou, M., Polytarchou, C., Tolosa, E.J., Almada, L.L., Mahurkar-Joshi, S., Williams, J., Tirado-Rodriguez, B., Huerta-Yepez, S., Karavias, D., Kourea, H., Poultsides, G.A., Struhl, K., Dawson, D.W., Donahue, T.R., Fernandez-Zapico, M.E., and Iliopoulos, D. (2019). Lysine methyltransferase 2D regulates pancreatic carcinogenesis through metabolic reprogramming. Gut 68 1271-1286. Koutsioumpa et al., 2019 Gut
299. Hasegawa, Y. and Struhl, K. (2019). Promoter-specific dynamics of TATA-binding protein association with the human genome. Genome Res. 29 1939-1950. Hasagawa & Struhl, 2019 Genome Res Supplemental information
300. Geisberg, J.V., Moqtaderi, Z., and Struhl, K. (2020). The transcriptional elongation rate regulates alternative polyadenylation in yeast. eLife 9 e59810. Geisberg et al., 2020 eLife Supplemental information
301. Darwiche, R., and Struhl, K. (2020). Pheno-RNA, a method to associate genes with a specific phenotype, identifies genes linked to cellular transformation. Proc. Natl. Acad. Sci. U.S.A. 117 28925-28929. Darwiche & Struhl, 2020 PNAS
302. Song, R. and Struhl, K. (2021). S100A8/S100A9 cytokine acts as a transcriptional coactivator during breast cellular transformation. Sci. Adv. 7 eabe5357. Song & Struhl, 2021 Sci Adv Supplemental
303. He, L., Pratt, H. Wei, F., Gao, M., Weng, Z., and Struhl, K. (2021). YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation. eLife 10 e67312. He et al., 2021 eLife
304. Petrenko, N. and Struhl, K. (2021). Comparison of transcriptional initiation by RNA polymerase II across eukaryotic species. eLife 10 e67964. Petrenko & Struhl, 2021 eLife
305. Hasegawa, Y. and Struhl, K. (2021). Different SP1 binding dynamics at individual genomic loci in human cells. Proc. Natl. Acad. Sci. U.S.A. 118 e2113579118. Hasegawa & Struhl, 2021 PNAS SI Appendix
306. Moqtaderi, Z., Geisberg, J.V., and Struhl, K. (2022). A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast. Proc. Natl. Acad. Sci. U.S.A. 119 e2121488119. Moqtaderi et al., 2022 PNAS
307. He, L., Gao, M., Pratt, H. Weng, Z., and Struhl, K. (2022). MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles. PLOS ONE 17 e0264799. He et al., 2022 PLOS ONE
308. Lui, K.H., Geisberg, J.V., Moqtaderi, Z., and Struhl, K. (2022). 3’ untranslated regions are modular entities that determine polyadenylation profiles. Mol. Cell. Biol. 42 e0024422. Lui et al., 2022 MCB
309. Geisberg, J.V., Moqtaderi, Z., Fong, N., Erickson, B., Bentley, D.L. and Struhl, K. (2022). Nucleotide-level linkage of transcriptional elongation and polyadenylation. eLife 11 e83153. Geisberg et al., 2022 eLife
310. Geisberg, J.V., Moqtaderi, Z., and Struhl, K. (2023). Condition-specific 3’ mRNA isoform half-lives and stability elements in yeast. Proc. Natl. Acad. Sci. U.S.A. 120 e2301117120. Geisberg et al., 2023 PNAS
311. Gvozdenov, Z., Barcutean, Z., and Struhl, K. (2023). Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast. Mol. Cell. 83 1786-1797. Gvozdenov et al., 2023 Mol. Cell
312. Khitun, A., Brion, C., Moqtaderi, Z., Geisberg, J.V., Churchman, L.S., and Struhl, K. (2023). Elongation rate of RNA polymerase II affects pausing patterns across 3’UTRs. J. Biol. Chem. 299 105289. Khitun et al., 2023 JBC
313. Struhl, K. (2024). How is polyadenylation restricted to 3’ untranslated regions? Yeast 40 186-191. Struhl, 2024 Yeast
314. Struhl, K. (2024). Intrinsically disordered regions (IDRs): a vague and confusing concept for protein function. Mol. Cell. 84 1186-1187. Struhl, 2024 Mol. Cell