Publications 1976-Present


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. icon Struhl et al, 1976 PNAS.pdf

2. Struhl, K. and Magasanik, B. (1976). Ammonia sensitive mutant of Klebsiella aerogenes. J. Bacteriol. 126 739-742. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon Struhl & Davis, 1981 JMB promoter.pdf

22. Struhl, K. (1981). Position effects in Saccharomyces cerevisiae. J. Mol. Biol. 152 569-575. icon 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. icon Struhl, 1982 PNAS.pdf

24. Struhl, K. (1982). Regulatory sites for his3 gene expression in yeast. Nature 300 284 287. icon 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. icon struhl, 1983 csh symposia.pdf

26. Struhl, K. (1983). The new yeast genetics. Nature 305 391-397. icon 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. icon struhl, 1983 alko yeast symposium.pdf

28. Struhl, K. (1983). Direct selection for gene replacement events in yeast. Gene 26 231 241. icon 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. icon 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. icon oettinger & struhl, 1985 mcb.pdf

31. Struhl, K. (1985). Negative control at a distance mediates catabolite repression in yeast. Nature 317 822-824. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon struhl, 1987 mcb.pdf

48. Struhl, K. (1987). Promoters, activator proteins, and the molecular mechanism of transcriptional initiation in yeast. Cell 49 295-297. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon Struhl, 1989 TIBS.pdf

66. Struhl, K. (1989). Molecular mechanisms of transcriptional regulation in yeast. Ann. Rev. Biochem. 58 1051-1077. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon Struhl 1991 Curr Biol.pdf

88. Struhl, K. (1991). Mechanisms for diversity in gene regulatory patterns. Neuron 7 177 181. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon Collart & Struhl, 1993 EMBO.pdf

103. Struhl, K. (1993). Chromatin and transcription factors: Who's on first? Current Biol. 3 220-222. icon 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. icon Kim et al, 1993 PNAS.pdf

105. Struhl, K. (1993). Yeast transcription factors. Curr. Opin. Cell Biol. 5 513-520. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon iyer & struhl, 1995 mcb.pdf

125. Struhl, K. (1995). Yeast transcriptional regulatory mechanisms. Ann. Rev. Genet. 29 651-674. icon struhl, 1995 ann rev genetics.pdf

126. Struhl, K. (1996). Chromatin structure and RNA polymerase II connection: Implications for transcription. Cell 88 179-182. icon 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. icon 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. icon 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. icon 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. icon moqtaderi et al, 1996 nature.pdf

131. Struhl, K. (1996). Transcriptional enhancement by acidic activators. BBA (Reviews on Cancer) 1288 O15-O17. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon fernandes et al, 1997 mcb.pdf

141. Struhl, K. (1998). Histone acetylation and transcriptional regulatory mechanisms. Genes & Dev. 12 599-606. icon 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. icon 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. icon keaveney & struhl, 1998 mol cell.pdf

144. Struhl, K. and Moqtaderi, Z. (1998). The TAFs in the HAT. Cell 94 1-4. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon kuras & struhl, 1999 nature.pdf

155. Struhl, K. (1999). Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98 1-4. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon kulish & struhl, 2001 mcb.pdf

171. Struhl, K. (2001). Gene regulation: a paradigm for precision. Science 293 1054-1055. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon grainger et al, 2004 jbact.pdf

197. ENCODE project consortium. (2004). The ENCODE (ENCyclopedia of DNA Elements) project. Science 304 636-640. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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.icon 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. icon 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.icon 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.icon 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. icon 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 icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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. icon 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

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 Dev25 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.A109 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. Biol20 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 Res23 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. Cell54 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.A111 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.A112 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.A116 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