Jack F. Greenblatt
  • Faculty, Donnelly Centre and Department of Molecular Genetics, University of Toronto, Canada
Research fields
  • Biochemistry, Microbiology, Molecular Biology
Personal information


Ph.D., Harvard University, 1973

Lab information

Jack Greenblatt lab

Research focus

Combination of genetic, biochemnical, and systems approaches to study regulation of gene expression and its relationships to infectious disease and cancer.



FULL PAPERS (*Corresponding author[s]; Greenblatt lab authors in bold print)

1. Greenblatt, J., Kuchela, K.S. and Sherman, N.K. (1967) "A Digitally Controlled Precision Pulser." Nuc. Inst. Met. 49,86-88.
2. Schleif, R. and Greenblatt, J. (1970) "Transcription in the Lambda-ara Phage." Cold Spring Harbor Symp. Quant. Biol. 35, 369-373.
3. Schleif, R., Greenblatt, J. and Davis, R.W. (1971) "Dual Control of Arabinose Genes in Transducing Phage g dara." J. Mol. Biol. 59, 127-150.
4. Greenblatt, J. and Schleif, R. (1971) "Arabinose C Protein: Regulation of the Arabinose Operon in vitro." Nature New Biol. 233, 166170.
5. Greenblatt, J. (1972) "Positive Control of Endolysin Synthesis in vitroby the Gene N Protein of Phage ." Proc Natl. Acad. Sci. (Wash.) 69, 3606-3610.
6. Greenblatt, J. (1972) "Positive Regulation in E. coli and Phage  ." Ph.D. Thesis, Harvard University, Cambridge, Mass. Thesis approved by Profs. Mario Capecchi, Salvador Luria and Matthew Meselson.
7. Greenblatt, J. and Miller, J.H. (1972) "Cyclic AMP, Catabolite Repression, and Cell-free Enzyme Synthesis." in Experiments in Molecular Genetics, (ed. Miller, J.H.) Cold Spring Harbor Laboratory, New York, pp. 407-429.
8. Greenblatt, J. (1973) "Regulation of the Expression of the N Gene of Bacteriophage Lambda." Proc. Natl. Acad. Sci. (Wash.) 70, 421-424.
9. Kirshbaum, J., Greenblatt, J., Allet, B. and Rochaix, J. (1975) "Studies with a  rif Transducing Phage Carrying the Genes for the ß and ß Subunits of E. coli RNA Polymerase." in RNA Polymerases (ed. Losick, R. and Chamberlin, M.) Cold Spring Harbor Laboratory, New York, pp.503-518.
10. Ahmad-Zadeh, C., Allet, B., Greenblatt, J. and Weil, R. (1976) "Two Forms of Simian-Virus-40-Specific T-Antigen in Abortive and Lytic Infection." Proc,. Natl. Acad. Sci. (Wash.) 73, 1097-1011.
11. Greenblatt, J.F., Allet, B., Weil, R. and Ahmad-Zadeh, C. (1976) "Synthesis of the Tumour Antigen and the Major Capsid Protein of Simian Virus 40 in a Cell-Free System Derived from Escherichia coli." J. Mol. Biol. 108, 361-379.
l2. Marchal, C., Greenblatt, J. and Hofnung, M. (1978) "The Mal B Region in E. coli K-12 = Specialized Transducing Bacteriophages and First Restriction Map." J. Bact. 136,1109-1119.
13. Marchal, C., Greenblatt, J., Mendez, B., Perrin, D. and Hofnung M. (1979) "Construction de Derives du Phage Porteurs du Gene lam B Insere en Aval du Promoteur de l'operon Lactose." C.R. Acad. Sci. Paris, Serie D, 151-154.
14. Greenblatt, J., Malnoe, P. and Li, J. (1980a) "Purification of the Gene N Transcription Anti-Termination Protein of Bacteriophage Lambda." J. Biol. Chem. 255, 1465-1470.
l5. Greenblatt, J., Li, J., Adhya, S., Friedman, D., Baron, L., Redfield, B., Kung, H. and Weissbach, H. (1980b) "L Factor that is required for B-Galactosidase Synthesis is the nusA Gene Product involved in Transcription Termination." Proc. Natl. Acad. Sci. U.S.A. 77, 1991-1994.
16. Greenblatt, J. (1981) "Minireview: Regulation of Transcription Termination by the N Gene Protein of Bacteriophage Lambda." Cell 24, 8-9.
17. Greenblatt, J. and Li, J. (1981a) "The nusA Gene Protein of E. coli: its Identification and a Demonstration that it Interacts with Gene N Transcription Anti-Termination Protein of Bacteriophage Lambda." J. Mol. Biol. 147, 11-23.
18. Greenblatt, J. and Li, J. (1981b) "Interaction of the Sigma Factor and the nusA Gene Protein of E. coli with RNA Polymerase in the Initiation-Termination Cycle of Transcription." Cell 24, 421-428.
19. Greenblatt, J., McLimont, M. and Hanly, S. (1981) "Termination of Transcription by the nusA Gene Protein of Escherichia coli." Nature 292, 215-220.
20. Greenblatt, J. and Li, J. (1982) "Properties of the N Gene Transcription Anti-Termination Protein of Bacteriophage ." J. Biol. Chem. 257, 362-365.
21. Greenblatt, J. (1982) "Antitermination of Transcription by the N Gene Protein of Bacteriophage Lambda: Recent Progress and Remaining Problems." Ann. Microbiol. (Inst. Pasteur) 133A, 225-233.
22. Farnham, P.J., Greenblatt, J. and Platt, T. (1982) "Effects of nusA protein on transcription termination in the tryptophan operon of "E. coli." Cell 29, 945-951.
23. Greenblatt, J., Carthew, R.W. and Sopta, M. (1983) "A model for the regulation of transcriptional events in terminal differentiation and oncogenic transformation by phosphoproteins that bind to RNA polymerase II." In Gene Expression (eds. Hamer, D. and Rosenberg, M.), UCLA Symposia on Molecular and Cellular Biology, New Series, Volume 8 (Alan R.Liss,N.Y.), pp. 283-292.
24. Greenblatt, J. (1984) "The Ayerst Award Lecture 1983: Regulation of transcription termination in Escherichia coli." Can. J. Biochem. Cell Biol. 62, 79-88.
25. Goda, Y. and Greenblatt, J. (1985) "Efficient modification of E. coli RNA polymerase in vitro.by the N gene transcription antitermination protein of bacteriophage lambda." Nucleic Acids Research 13, 2569-2582.
26. Sopta, M., Carthew, R.W. and Greenblatt, J. (1985) "Isolation of three proteins that bind to mammalian RNA polymerase II." J. Biol. Chem. 260, 10353-10360.
27. Greenblatt, J., Horwitz, R., Goda, Y. and Li, J. (1985). "Regulation of transcription termination by the nus gene proteins of Escherichia coli." In Sequence Specificity in Transcription and Translation_(eds. Calendar, R. and Gold, L.), UCLA Symposia on Molecular and Cellular Biology, New Series, Volume 30 (Alan R. Liss, N.Y.), pp. 197-206.
28. Burton, Z.F., Ortolan, L. and Greenblatt, J. (1986) "Proteins that bind to RNA polymerase II are required for accurate initiation of transcription at the adenovirus 2 major late promoter." EMBO J. 5, 2923-2930.
29. Burton, Z.F., Sopta, M., Ortolan, L.G. and Greenblatt, J. (1986) "A transcriptional initiation factor that binds to RNA polymerase II" In Sixteenth Steenbock Symposium: RNA Polymerase and the Regulation of Transcription (Elsevier, New York), pp. 417-420.
30. Greenblatt, J., Horwitz, R.J. and Li, J. (1986) "Genetic and structural analysis of an elongation control particle containing the N protein of bacteriophage lambda" In Sixteenth Steenbock Symposium: RNA Polymerase and the Regulation of Transcription (Elsevier, New York), p. 357-366.
31. Horwitz, R.J., Li, J. and Greenblatt, J. (1987) "An elongation control particle containing the N gene transcriptional antitermination protein of bacteriophage lambda." Cell 51, 631-641.
32. Burton, Z.F., M., Killeen, Sopta, M., Ortolan, L. and Greenblatt, J. (1988) "RAP30/74: A general initiation factor that binds to RNA polymerase II." Mol. Cell. Biol. 8, 1602-1613.
33. Swindle, J., Zylicz, M., Georgopoulos, C.P., Li, J., and Greenblatt, J. (1988) "Purification and properties of the NusB protein of Escherichia coli." J. Biol. Chem. 263, 10229-10235.
34. Flores, O., Maldonado, E., Burton, Z., Greenblatt, J. and Reinberg, D. (1988) "Factors involved in specific transcription by mammalian RNA polymerase II. RNA polymerase II associating protein 30 is an essential component of transcription factor IIF." J. Biol. Chem. 263, 10812-10816.
35. Sopta, M., Burton, Z. and Greenblatt, J. (1989) "Structure and associated DNA helicase activity of a general transcription initiation factor that binds to RNA polymerase II." Nature 341, 410-414.
36. Stringer, K.F., Ingles, C.J. and Greenblatt, J. (1990) "Direct and selective binding of an acidic transcriptional activation domain to TATA-box factor TFIID." Nature 345, 783-786.
37. Ingles, C.J., Shales, M., Cress, W.D., Triezenberg, S.J. and Greenblatt, J. (1991) "Reduced binding of TFIID to transcriptionally compromised mutants of VP16." Nature 351, 588-590.
38. McCracken, S. and Greenblatt, J. (1991) "Related RNA polymerase-binding regions in human RAP30/74 and Escherichia coli s70." Science 253, 900-902.
39. Buratowski, S., Sopta, M., Greenblatt, J. and Sharp, P.A. (1991) "RNA polymerase II associated proteins are required for a DNA conformation change in the transcription initiation complex." Proc. Natl. Acad. Sci. USA 88, 7509-7513.
40. Mason, S.W. and Greenblatt, J. (1991) "Assembly of transcription elongation complexes containing the N protein of phage  and the Escherichia coli elongation factors NusA, NusB, NusG and S10." Genes Dev. 5, 1504-1512.
41. Greenblatt, J. (1991) "Minireview: Roles of TFIID in transcriptional initiation by RNA polymerase II." Cell 66, 1067-1070.
42. Greenblatt, J. (1991) "RNA polymerase associated transcription factors." TIBS 16, 408-411.
43. Flores, O., Lu, H., Killeen, M., Greenblatt, J., Burton, Z.F. and Reinberg, D. (1991) "The small subunit of transcription factor IIF recruits RNA polymerase II into the preinitiation complex." Proc. Natl. Acad. Sci. USA 88, 9999-10003.
44. Nodwell, J.R. and Greenblatt, J. (1991) "The nut site of bacteriophage  is made of RNA and is bound by transcription antitermination factors on the surface of RNA polymerase." Genes Dev. 5, 2141-2151.
45. Mason, S.W., Li, J. and Greenblatt, J. (1992) "Direct interaction between two Escherichia coli transcription antitermination factors, NusB and ribosomal protein S10." J. Mol. Biol. 223, 55-66.
46. Formosa, T., Barry, J., Alberts, B.M. and Greenblatt, J. (1992) "Using protein affinity chromatography to probe the structure of protein machines." Meth. Enzymol. 208, 24-45.
47. Greenblatt, J. (1992) "Protein-protein interactions as critical determinants of regulated initiation and termination of transcription." in Transcriptional Regulation (Cold Spring Harbor Press) pp. 203-226.
48. Killeen, M.T. and Greenblatt, J. (1992) "The general transcription factor RAP30 binds to RNA polymerase II and prevents it from binding non-specifically to DNA." Mol. Cell. Biol. 12, 30-37.
49. Linn, T. and Greenblatt, J. (1992) "The NusA and NusG proteins of Escherichia coli increase the in vitro readthrough frequency of a transcriptional attenuator preceding the gene for the b subunit of RNA polymerase." J. Biol. Chem. 267, 1449-1454.
50. Finkelstein, A., Kostrub, C.F., Li, J., Charez, D.P., Wang, B.Q., Fang, S.M., Greenblatt, J. and Burton, Z.F. (1992) "A cDNA encoding RAP74, a general initiation factor for transcription by RNA polymerase II." Nature 355, 464-467.
51. Li, J., Horwitz, R., McCracken, S. and Greenblatt, J. (1992) "NusG, a new Escherichia coli elongation factor involved in transcriptional antitermination by the N protein of phage ." J. Biol. Chem. 267, 6012- 6019.
52. Coulombe, B., Killeen, M., Liljelund, P., Honda, B., Xiao, H., Ingles, C.J. and Greenblatt, J. (1992) "Identification of three mammalian proteins that bind to yeast TATA box protein TFIID." Gene Exp. 2, 99-110.
53. Killeen, M., Coulombe, B. and Greenblatt, J. (1992) "Recombinant TBP, transcription factor IIB, and RAP30 are sufficient for promoter recognition by mammalian RNA polymerase II." J. Biol. Chem. 267, 9463-9466.
54. Mason, S.W., Li, J. and Greenblatt, J. (1992) "Host factor requirements for processive antitermination of transcription and suppression of pausing by the N protein of bacteriophage l." J. Biol. Chem. 267, 19418-19426.
55. Greenblatt, J. (1992) "News and Views: Riding high on the TATA-box." Nature 360, 16-17.
56. Li, J., Mason, S.W. and Greenblatt, J. (1993) "Elongation factor NusG interacts with termination factor p to regulate termination and antitermination of transcription." Genes Dev. 7, 161-172.
57. Nodwell, J.R. and Greenblatt, J. (1993) "Recognition of boxA antiterminator RNA by the E. coli antitermination factors, NusB and ribosomal protein S10." Cell 72, 261-268.
58. Squires, C.L., Greenblatt, J., Li, J., Condon, C. and Squires, C. (1993) "Ribosomal RNA antitermination factors: in vitro: Requirement for Nus factors and one or more unidentified cellular components." Proc. Natl. Acad. Sci. USA 90, 970-974.
59. Truant, R., Xiao, H., Ingles, C.J. and Greenblatt, J. (1993) "Direct interaction between the transcriptional activation domain of human p53 and the TATA box-binding protein." J. Biol. Chem. 268, 2284-2287.
60. He, Z., Brinton, B.T., Greenblatt, J., Hassell, J.A., and Ingles, C.J. (1993) "The transactivator proteins pVP16 and GAL4 bind replication factor A." Cell 73, 1223-1232.
61. Greenblatt, J., Nodwell, J.R. and Mason, S.W. (1993) "Review Article: Transcriptional antitermination." Nature 364, 401-406.
62. Liljelund, P., Ingles, C.J. and Greenblatt, J. (1993) "Altered promoter binding of the TATA box-binding factor induced by the transcriptional activation domain of VP16 and suppressed by TFIIA." Mol. Gen. Genet. 241, 694-699.
63. Kephart, D.D., Price, M.P., Burton, Z.F., Finkelstein, A., Greenblatt, J. and Price, D.H. (1993) "Cloning of a Drosophila cDNA with sequence similarity to human transcription factor RAP74." Nucleic Acids Res. 21, 1319.
64. Heng, H.H.Q., Xiao, H., Shi, X.-M., Greenblatt, J. and Tsui, L.-C. (1994) "Genes encoding general initiation factors for RNA polymerase II transcription are dispersed in the human genome." Human Molec. Genet. 3, 61-64.
65. Emili, A., Greenblatt, J. and Ingles, C.J. (1994) "Species-specific interaction of the glutamine-rich activation domains of Sp1 with the TATA-box binding protein." Mol. Cell Biol. 14, 1582-1593.
66. Xiao, H., Lis, J.T., Xiao, H., Greenblatt, J. and Friesen, J.D. (1994) "The upstream activator CTF/NFI and RNA polymerase II share a common element involved in transcriptional activation." Nucleic Acids Res. 22, 1966-1973.
67. Coulombe, B., Li, J. and Greenblatt, J. (1994) "Topological localization of the human transcription factors IIA, IIB, TBP and RAP30 on a class II promoter." J. Biol. Chem. 269, 19962-19967.
68. Xiao, H., Pearson, A., Coulombe, B., Truant, R., Regier, J.S., Triezenberg, S.J., O. Flores, Reinberg, D., Ingles, C.J. and Greenblatt, J. (1994) "Binding of basal transcription factor TFIIH to the acidic activation domains of VP16 and p53." Mol. Cell. Biol. 14, 7013-7024.
69. Pan, G. and Greenblatt, J. (1994) "Initiation of transcription by RNA polymerase II is limited by melting of the promoter DNA in the region immediately upstream of the initiation site." J. Biol. Chem. 269, 30101-30104.
70. Truant, R., Antunovic, J., Greenblatt, J., Prives, C. and Cromlish, J.A. (1995) "Direct interaction of the hepatitis B virus HBx protein with p53 leads to inhibition by HBx of p53 response element-directed transactivation." J. Virol. 69, 1851-1859.
71. Richardson, J.P. and Greenblatt, J. (1996) "Control of RNA chain elongation and termination" in Escherichia coli and Salmonella Tryphimurium: Cellular and Molecular Biology, Second Edition (American Society for Microbiology, Washington, DC), pp. 822-848.
72. Mogridge, J., Mah, T.-F. and Greenblatt, J. (1995) "A protein-RNA interaction network facilitates the template-independent cooperative assembly on RNA polymerase of a stable antitermination complex containing the  N protein." Genes Dev. 9, 2831-2844.
73. Blau, J., Xiao, H., McCracken, S., O'Hare, P., Greenblatt, J. and Bentley, D. (1996) "Three functional classes of transcriptional activation domain." Mol. Cell. Biol. 16, 2044-2055.
74. Robert, F., Forget, D., Li, J., Greenblatt, J. and Coulombe, B. (1996) "Localization of subunits of transcription factors IIE and IIF immediately upstream of the transcriptional initiation site of the adenovirus major late promoter". J. Biol. Chem. 271, 8517-8520.
75. Greenblatt, J. and Ingles, C.J. (1996) "Interaction between the acidic transcriptional activation domain of herpes simplex virus activator protein VP16 and transcriptional initiation factor IID." Meth. Enzymol. 274, 120-133.
76. Gupta, R., Emili, A., Pan, G., Xiao, H., Shales, M., Greenblatt, J. and Ingles, C.J. (1996) "Characterization of the interaction between the acidic activation domain of VP16 and the RNA polymerase II initiation factor TFIIB." Nucleic Acids Res. 24, 2324-2330.
77. McCracken, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G., Greenblatt, J., Patterson, S.D., Wickens, M. and Bentley, D.L. (1997) "The C-terminal domain of RNA polymerase II couples mRNA processing to transcription." Nature 385, 357-361.
78. Greenblatt, J. (1997) "RNA polymerase II holoenzyme and transcriptional regulation." Curr. Opin. Cell Biol. 9, 310-319.
79. Rao, N.S., Legault, P., Muhandiram, D.R., Greenblatt, J., Battiste, J.L., Williamson, J.R. and Kay, L.E. (1996) "NMR pulse schemes for the sequential assignment of arginine sidechain H protons." J. Mag. Res., Series B, 113, 272-276.
80. Zwahlen, C., Legault, P., Vincent, S., Greenblatt, J., Konrat, R. and Kay, L.E. (1997) "Methods for measurement of intermolecular NOEs by multi-nuclear NMR spectroscopy: application to a bacteriophage lambda N-peptide:boxB RNA complex." J. Am. Chem. Soc. 119, 6711-6721.
81. Forget, D., Robert, F., Grondin, G., Burton, Z.F., Greenblatt, J. and Coulombe, B. (1997) "RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box" Proc. Natl. Acad. Sci. USA 94, 7150-7155.
82. Pearson, A. and Greenblatt, J. (1997) "Modular organization of the E2F1 activation domain and its interaction with general transcription factors TBP and TFIIH." Oncogene 15, 2643-2658.
83. Pan, G., Aso, T. and Greenblatt, J. (1997) "Interaction of elongation factors TFIIS and Elongin A with a human RNA polymerase II holoenzyme capable of promoter-specific initiation and responsive to transcriptional activators." J. Biol. Chem. 272, 24563-24571
84. Archambault, J. Chambers, R.S. Kobor, M.S., Ho, Y., Cartier, M., Bolotin, D., Andrews, B., Kane, C. M. and Greenblatt, J. (1997) "An essential component of a CTD phosphatase that interacts with TFIIF in Saccharomyces cerevisiae." Proc. Natl. Acad. Sci. USA 94, 14300-14305.
85. Mogridge, J., Legault, P., Li, J., van Oene, M., Kay, L.E. and Greenblatt, J. (1998) "Independent ligand induced folding of the RNA binding domain and two functionally distinct antitermination regions in the disordered N protein of bacteriophage ." Molecular Cell 1, 265-275.
86. Xiao, H., Tao, Y., Greenblatt, J. and Roeder, R.G. (1998) "A cofactor, TIP30, specifically enhances HIV-1 Tat-activated Transcription." Proc. Natl. Acad. Sci. USA 95, 2146-2151.
87. Mogridge, J., Mah, T-F. and Greenblatt, J. (1998) "Involvement of boxA nucleotides in the formation of a stable ribonucleoprotein complex containing the bacteriophage  N protein." J. Biol. Chem. 273, 4143 4148.
88. Legault, P., Li, J., Mogridge, J., Kay, L.E. and Greenblatt, J. (1998) "NMR structure of the bacteriophage  N-peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif." Cell 93, 289 299.
89. Mogridge, J. and Greenblatt, J. (1998) "Specific binding of Escherichia coli ribosomal protein S1 to boxA transcriptional antiterminator RNA." J. Bacteriol. 180, 2248-2252.
90. Greenblatt, J., Mah, T.-F., Legault, P., Mogridge, J., Li, J., and Kay, L.E. (1998) "Structure and mechanism in transcriptional antitermination by the bacteriophage lambda N protein." Cold Spring Harbor Symp. Quant. Biol. 63, 327-336.
91. Archambault, J., Pan, G., Dahmus, G.K., Cartier, M., Marshall, N., Zhang, S., Dahmus, M.E. and Greenblatt, J. (1998) "FCP1, the RAP74 interacting subunit of a human protein phosphatase that dephosphorylates the carboxyl-terminal domain of RNA polymerase IIO." J. Biol. Chem. 273, 27593-27601.
92. Robert, F., Douziech, M., Forget, D., Egly, J.-M., Greenblatt, J., Burton, Z.F. and Coulombe, B. (1998) "Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF." Molecular Cell 2, 341-351.
93. Archambault, J., Jansma, D.B., Kawasse, J.H., Arndt, K.T., Greenblatt, J. and Friesen, J.D. (1998) “Stimulation of transcription by mutations affecting conserved regions of RNA polymerase II.” J. Bacteriol. 180, 2590-2598.
94. Hirst, M., Kobor, M.S., Greenblatt, J. and Sadowski, I. (1999) "GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8." Molecular Cell 3, 673-678.
95. Fry, C.J., Pearson, A., Malinowski, E., Bartley, S.M., Greenblatt, J. and Farnham, P.J. (1999) “Activation of the murine dihydrofolare reductase promoter by E2F1: a requirement for CBP recruitment.” J. Biol. Chem. 274, 15883-15891.
96. Douziech, M., Forget, D., Greenblatt, J. and Coulombe, B. (1999) "Topological localization of the carboxy-terminal domain of RNA polymerase II in the initiation complex" J. Biol. Chem. 274, 19868-19873.
97. Kobor, M.S., Archambault, J., Lester, W.K., Holstege, F.C.P., Gileadi, O., Jansma, D.B., Jennings, E.G., Kouyoumdjian, F., Davidson, A.R., Young, R.A., and Greenblatt, J. (1999) "A new type of eukaryotic protein phosphatase required for dephosphorylation of the CTD and transcription by RNA polymerase II in Saccharomyces cerevisiae" Molecular Cell 4, 55-62.
98. Mah, T.-F., Li, J., Davidson, A., and Greenblatt, J. (1999) "Functional importance of regions in E. coli elongation factor NusA that interact with RNA polymerase, the bacteriophage lambda N protein, and RNA."Molecular Microbiology 34, 523-537.
99. McGarvey, T., Rosonina, E., McCracken, S., Li, Q., Arnaout, R., Mientjes, E., Nickerson, J., Awrey, D., Greenblatt, J., Grosveld, G., and Blencowe, B.J. (2000) "The acute myeloid leukemia-associated protein DEK forms a splicing-dependent interaction with exon-product complexes" J. Cell Biol. 150, 309-320.
100. Mah, T.-F., Kuznedelov, K., Mushegian, A., Severinov, K. and Greenblatt, J. (2000) "The alpha subunit of E. coli RNA polymerase activates RNA-binding by NusA" Genes Dev. 14, 2664-2675.
101. Kobor, M.S., Simon, L.D., Omichinski, J., Zhong, G., Archambault, J. and Greenblatt, J. (2000) "A motif shared by TFIIF and TFIIB mediates their interaction with the RNA polymerase II CTD phosphatase Fcp1p in Saccharomyces cerevisiae" Mol. Cell. Biol. 20, 7438-7449.
102. *Edwards, A.M., Arrowsmith, C.H., Christendat, D., Dharamsi, A., Friesen, J.D., Greenblatt, J. and Vedadi, M. (2000) "Protein production: feeding the crystallographers and NMR spectroscopists" Nature Structural Biology 7 (Supplement), 900-902.
103. Zhou, Y., Mah, T.-F., Yu, Y.N., Mogridge, J., Olson, E.R.., Greenblatt, J. and *Friedman, D. I. (2001) " Interactions of an Arg-rich region of transcription elongation protein NusA with  NUT RNA: implications for the order of assembly of the  N antitermination complex in vivo” J. Mol. Biol. 310, 33-49.
104. Krogan, N. and *Greenblatt, J. (2001) "Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae" Mol. Cell. Biol. 21, 8203-8212.
105. Miller, T., Krogan, N.J., Dover, J., Erdjument-Bromage, H., Pillus, L., Tempst, P., Johnston, M., Greenblatt, J. and *Shilatifard, A. (2001) "COMPASS: a complex of proteins associated with a Trithorax-related SET domain protein" Proc. Natl. Acad. Sci. USA 98, 12902-12907.
106. Cho, E.J., Kobor, M.S., Greenblatt, J. and *Buratowski, S. (2001) "Opposing effects of Ctk1 kinase and Fcp1 phosphatase at serine 2 of the RNA polymerase II C-terminal domain" Genes Dev. 15, 3319-3329.
107. Zhou, Y., Mah, T.F., Greenblatt, J. and *Friedman, D.I. (2002) "Evidence that the KH RNA-binding domains influence the action of the E. coli NusA protein" J. Mol. Biol. 318, 1175-1188.
108. Krogan, N.J., Dover, J., Khorrami, S., Greenblatt, J.F., Schneider, J., Johnston, M. and *Shilatifard, A. (2002) “COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression.” J Biol Chem. 277, 10753-10755.

109. Kobor, M. and *Greenblatt, J. (2002) “Regulation of transcription elongation by phosphorylation”. Biochim Biophys Acta. 1577, 261-275.

110. Krogan, N.J., Kim, M., Ahn, S.H., Zhong, G., Kobor, M.S., Cagney, G., Emili, A., Shilatifard, A., Buratowski, S. and *Greenblatt, J.F. (2002) “RNA Polymerase II Elongation Factors of Saccharomyces cerevisiae: a Targeted Proteomics Approach”. Mol. Cell. Biol. 22, 6979-6992.
111. Edwards, A., Kus, B., Jansen, R., Greenbaum, D., Greenblatt, J., *Gerstein, M. (2002) “Bridging structural biology and genomics: assessing protein interaction data with known complexes”. Trends Genet.18, 529-536.
112. Nguyen, B.D., Chen, H., Kobor, M., Grzesiek, S., Greenblatt, J., Legault, P. and *Omichinski, J.G. (2003) Solution structure of the carboxy-terminal domain of RAP74 and NMR characterization of the FCP-binding sites of RAP74 and human TFIIB. Biochemistry 42, 1460-1469.
113. Nguyen, B.D., Abbott, K., Potempta, K., Kobor, M.S., Greenblatt, J., Legault, P. and *Omichinski, J.G. (2003) “NMR structure of a complex containing the TFIIF subunit RAP74 and the RNA polymerase II carboxy-terminal domain phosphatase FCP1”. Proc. Nat. Acad. Sci USA 100, 5688-5693.
114. Wood, A., Krogan, N.J., Dover, J., Schneider, J., Heidt, J., Boateng, M.A., Dean, K., Golshani, A., Zhang, Y., Greenblatt, J., Johnston, M. and *Shilatifard, A. (2003) Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of rad6 at a promoter. Molecular Cell 11, 267-274.
115. Owens, B.M., Zhu, Y., Suen, T., Wang, P.X., Greenblatt, J., Goss, P.E. and *Hawley, R.G. (2003) “Specific homeodomain-DNA interactions are required for HOX11-mediated transformation.” Blood 101, 4966-4974.
116. Krogan, N.J., Dover, J., Wood, A., Schneide, J., Heidt, J., Boateng, M.A., Dean, K., Ryan, O.W., Golshani, A., Johnston, M., Greenblatt, J. and *Shilatifard, A. (2003) “The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation.” Molecular Cell 11, 721-729.
117. Krogan, N.J., Kim, M., Tong, A., Golshani, A., Cagney, G., Richards, D., Canadien, V., Beattie, B., Emili, A., Boone, C., Shilatifard, A., Buratowski, S. and *Greenblatt, J. (2003) “Methylation of histone H3 by Set2 inSaccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.” Mol. Cell. Biol. 23, 4207-4218.
118. Nedea, E., He, X., Kim, M., Pootoolal, J., Zhong, G., Canadien, V., Hughes, T., Buratowski, S., Moore, C.L. and *Greenblatt, J. (2003) “Organization and Function of APT, a Sub-Complex of the Yeast Cleavage and Polyadenylation Factor Involved in the Formation of mRNA and small nucleolar RNA 3’ Ends” J. Biol. Chem. 278, 33000-33010.
119. Holowaty, M., Zeghouf, M., Greenblatt, J. and *Frappier, L. (2003) “Protein profiling with Epstein-Barr nuclear antigen I reveals a functional interaction with USP7” J. Biol. Chem. 278, 29987-29994.
120. Peng, W.T., Robinson, M.D., Mnaimneh, S., Krogan, N., Cagney, G., Davierwala, A.P., Grigull, J., Yang, X., Zhang, W., Mitsakakis, N., Ryan, O.W., Datta, N., Jojic, V., Pal, C., Morris, Q., Frey, B.J., Canadien, V., Richards, D., Beattie, B., Wu, L.F., Altschuler, S.J., Emili, A., Greenblatt, J. and *Hughes, T.R. (2003) “A panoramic view of yeast non-coding RNA processing” Cell 113, 919-933.
121. Jansen, R., Yu, H., Greenbaum, D., Kluger, Y., Krogan, N.J., Chung, S., Emili, A., Snyder, M., Greenblatt, J. and *Gerstein, M. (2003) “A Bayesian networks approach to predict protein complexes from genomic data” Science 302, 449-453.
122. Hoheisel, S., Kobor, M.S., Pierstorff, E., Greenblatt, J. and *Kane, C.M. (2003) “ Purification and assay of Saccharomyces cerevisiae phosphatase that acts on the C-terminal domain of the largest subunit of RNA polymerase II” Meth. Enzymol. 370, 386-395.
123. Krogan, N.J., Keogh, M., Datta, N., Haw, R.A., Pootoolal1, J., Canadien, V., Richards, D.P., Tong, A., Ding, H., Boone, C., Emili, A., Hughes, T.R., Buratowski, S., and *Greenblatt, J. (2003) A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Molecular Cell 12, 1565-1576.
124. Baetz, K.K., Krogan, N.J., Emili, A., Greenblatt, J. and *Hieter, P. (2004) "ctf13-30/CTF13 genomic haploinsufficiency modifier screen identifies the yeast chromatin remodeling complex RSC which is required for the establishment of sister chromatid cohesion" Mol. Cell. Biol. 24, 1232-1244.
125. Kim, M., Ahn, S.H., Krogan, N., Greenblatt, J. and *Buratowski, S. (2004) “Transitions in RNA polymerase II elongation complexes at the 3’ ends of genes” EMBO J. 23, 354-364.
126. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, *Boone C. (2004) “Global mapping of the yeast genetic interaction network” Science 303, 808-813.
127. Zeghouf, M., Li, J., Butland, G., Borkowska, A., Canadien, V., Richards, D., Beattie, B., Emili, A. and *Greenblatt, J. (2004) “A sequential peptide affinity (SPA) system for the identification of mammalian and bacterial protein complexes” J. Proteome Res. 3, 463-468.
128. Krogan, N.J., Peng, W.T., Cagney, G., Robinson, M.D., Haw, R., Bray, J.E., Lalev, A., Zhong, G., Guo, G., Zheng, X., Canadien, V., Richards, D., Starostine, A., Beattie, B., Grigull, J., Tikuisis, A., Hughes, T.R., Emili, E. and *Greenblatt, J. (2004) “High-definition macromolecular composition of yeast RNA processing complexes” Molecular Cell 13, 225-239.
129. Jeronimo, C., Langelier, M.F., Zeghouf, M., Cojocaru, M., Bergeron, D., Baali, D., Forget, D., Mnaimneh, S., Davierwala, A.P., Pootoolal, J., Chandy, M., Canadien, V., Beattie, B.K., Richards, D.P., Workman, J.L., Hughes, T.R., Greenblatt, J. and *Coulombe, B.(2004) « RPAP1, a Novel Human RNA Polymerase II-Associated Protein Affinity Purified with Recombinant Wild-Type and Mutated Polymerase Subunits” Mol. Cell. Biol. 24, 7043-7058.
130. Mnaimneh, S., Davierwala, A.P., Haynes, J., Moffat, J., Peng, W.T., Zhang, W., Stuart Yang, S., Pootoolal, J., Chua, G., Lopez, A., Krogan, N.J., Hiley, S.L., Li, Z., .Morris, Q., Grigull, J., Trochesset, M,. Mitsakakis, N., Roberts, C.J., Greenblatt, J.F., Morse, D., Kaiser4, C.A., Andrews, B.J., and *Hughes, T.R. (2004) “Exploration of essential gene functions via titratable promoter alleles” Cell 118, 31-44.
131. Sawa, C., Nedea, E., Krogan, N., Wada, T., Handa, H., Greenblatt, J. and *Buratowski, S. (2004) “Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2” Mol. Cell. Biol. 24, 4734-4742.
132. Peng, W.T., Krogan, N.J., Richards, D.P., Greenblatt, J.F. and *Hughes, T.R. (2004) “ESF1 is required for rRNA synthesis in Saccharomyces cerevisiae” Nucleic Acids Res. 32, 1993-1999.
133. Fath, S., Kobor, M.S., Philippi, A., Greenblatt, J. and *Tschochner, H. (2004) “Dephosphorylation of RNA polymerase I by Fcp1p is required for efficient rRNA synthesis” J. Biol. Chem. 279, 25251-25259.
134. Krogan, N.J., Lam, M.H.Y., Fillingham, J., Keogh, M.-C., Gebbia, M., Li, J., Datta, N., Wu, X., Cagney, G., *Emili, A. and *Greenblatt, J.F. (2004) “Proteasome involvement in the repair of DNA double strand breaks” Mol. Cell 16, 1027-1034.
135. Krogan, N.J., Baetz, K., Keogh, M.C., Datta, N., Sawa, C., Kwok, T.C.Y., Thompson, N.J., Davey, M.G., Pootoolal, J., Hughes, T.R., Emili, A., Buratowski, S., Hieter, P. and *Greenblatt, J.F. (2004) “Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex and the histone acetyltransferase NuA4” Proc. Nat. Acad Sci. USA 101, 13513-13518.
136. Butland, G., Peregrin-Alvarez, J.M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., *Greenblatt, J. and *Emili, A. (2005) “Interaction network containing conserved and essential protein complexes in Escherichia coli” Nature 433, 531-537.
137. Kim, M., Krogan, N.J., Rando, O.J., Nedea, E., Greenblatt, J.F. and *Buratowski, S. (2004) “The Rat1 exonuclease promotes transcription termination by RNA polymerase II” Nature 432, 517-522.
138. Abbott, K.L., Archambault, J., Xiao, H., Nguyen, B.D., Roeder, R.G., Greenblatt, J., Omichinski, J.G., and *Legault, P. (2005) “Interactions of the HIV-1 Tat and RAP74 proteins with the RNA polymerase II CTD phosphatase FCP1” Biochemistry 44, 2716-2731..
139. Hoang, T., Peng, W.-T., Vanrobays, E., Krogan, N.J., Hiley, S., Greenblatt, J., Hughes, T.R. and *Lafontaine, L.J. (2005) “Esf2p, a U3-associated factor required for the initial steps of small ribosomal subunit synthesis” Mol. Cell. Biol. 25, 5523-5534.
140. Morrison, A.J., Highland, J., Krogan, N.J., Arbel-Eden, A., Greenblatt, J.F., Haber, J.E. and *Shen, X. (2004) “INO80 and γ-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair” Cell 119, 767-775.
141. Zhang, J.W., Butland, G., Greenblatt, J.F., Emili, A. and *Zamble, D.B. (2005) “A Role for SlyD in the Escherichia coli Hydrogenase Biosynthetic Pathway” J. Biol. Chem. 280, 4360-4366.
142. Ingvarsdottir, K., Krogan, N.J., Tolga Emre, N.C., Wyce, A., Thompson, N.J., Emili, A., Hughes, T.R., Greenblatt, J. and *Berger, S.L. (2005) “H2B ubiquitin protease Ubp8 and Sgf11 constitute a distinct functional module within the S. cerevisiae SAGA complex” Mol. Cell. Biol. 25, 1162-1172.
143. Xiao, T., Kao, C.-F., Krogan, N.J., Sun, Z.-W., Greenblatt, J.F., Osley, M.A. and *Strahl, B.D. (2005) “Histone H2B ubiquitylation is associated with elongating RNA polymerase II” Mol. Cell. Biol. 25, 637-651.
144. Kong, S.E., Kobor, M.S., Krogan, N.J., Somesh, B., Sogaard, T.M.M., Greenblatt, J.F. and *Svejstrup, J.Q. (2005) “Fcp1 phosphatase: interaction with elongating RNA polymerase II holoenzyme, enzymatic mechanism of action, and genetic interaction with elongator” J. Biol. Chem. 280, 4299-4306.
145. Zhao, R., Davey, M., Hsu, Y.-C., Kaplanek, P., Tong, A., Parsons, A.B., Krogan, N.J., Cagney, G., Mai, D., Greenblatt, J., Boone, C., Emili, A.. and *Houry, W.A. (2005) “Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the Hsp90 chaperone” Cell 120, 715-727.
146. Zhang, W.*, Morris, Q.D.*, Chang, R., Shai, O., Bakowski, M.A., Mitsakakis, N., Mohammad, N., Robinson, M.D., Zirnglibl, R., Somogyi, E., Laurin, N., Eftekharpour, E., Sat, E., Grigull, J., Pan, Q., Peng, W.-T., Krogan, N., Greenblatt, J., Fehlings, M., van der Kooy, D., Aubin, J., Bruneau, B.G., Rossant, J., Blencowe, B.J., Frey, B.J., and *Hughes, T.R. (2004) “The functional landscape of mouse gene expression” J. Biol. 3, 21.
147. Emre, N.C., Ingvarsdottir, K., Wyce, A., Wood, A., Krogan, N.J., Henry, K.W., Li, K., Greenblatt, J.F., Marmorstein, R., Shilatifard, A. and *Berger, S.L. (2005) “Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere proximal Sir2 association and gene silencing” Molecular Cell 17, 585-594.
148. Savchenko, A., Krogan, N., Cort, J.R., Evdokimova, E., Lew, J.M., Yee, A.A., Sánchez-Pulido, L., Andrade, M.A., Bochkarev, A., Watson, J.D., Kennedy, M.A., Greenblatt, J., Hughes, T., Arrowsmith, C.H. Rommens, J. and *Edwards, A.M. (2005) “The Shwachman-Bodian-Diamond Syndrome protein family is involved in RNA metabolism” J. Biol Chem. 280, 19213-19220.
149. Langelier, M.-F., Baali, D., Trinh, V., Greenblatt, J., Archambault, J. and *Coulombe, B. (2005) “The highly conserved glutamic acid 791 of Rpb2 is involved in binding of NTP and Mg(B) in the active center of human RNA polymerase II” Nucleic Acids Res. 33, 2629-2639.
150. Keogh, M.-C., Kurdistani, S.K., Ahn, S.H., Collins, S.R., Podolny, V., Chin, K., Boone, C., Morris, S.A., Strahl, B.D., Emili, A., Weissman, J.S., Hughes, T.R., Grunstein, M., *Greenblatt, J.F., *Buratowski, S., and Krogan, N.J., (2005) “Co-transcriptional Set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex” Cell 123, 593-605.
151. Laribee, R.N., Krogan, N.J., Xiao, T., Shibata, Y., Hughes, T.R., Greenblatt, J.F. and *Strahl, B.D. (2005) “BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex” Current Biology 15, 1487-1493.
152. Schuldiner, M., Collins, S.R., Thompson, N.J., Denic, V., Bhamidipati, A., Punna, T., Ihmels, J., Andrews, B.J., Boone, C., Greenblatt, J.F., *Weissman, J. and Krogan, N.J., (2005) “Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile” Cell 123, 507-519.
153. Downey, M.S., Houlsworth, R., Rollie, A., Brehme, M., Galicia, S., Guillard, S., Zubko, M.K., Krogan, N.J., Emili, A., Greenblatt, J.F., Harrington, L., Lydall, D. and *Durocher, D. (2006) “A genome wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator” Cell 124, 1155-1168.
154. Prather, D., Krogan, N.J., Emili, A., Greenblatt, J.F. and *Winston, F. (2005) “Identification and characterization of Elf1, a conserved transcription elongation factor in S. cerevisiae” Mol. Cell. Biol. 25, 10122-10135.
155. Keogh, M.C., Kim, J.A., Downey, M., Fillingham, J., Chowdhury, D., Harrison, J.C., Onishi, M., Galicia, S., Emili, A., Lieberman, J., Shen, X., Buratowski, S., Haber, J.E., *Durocher, D., *Greenblatt, J.F. and Krogan, N.J. (2006) “A phosphatase complex that dephosphorylates H2A.X regulates DNA damage checkpoint recovery ” Nature 439, 497-501.
156. Keogh, M.C., Mennella, T.A., Sawa, C., Berthelet, S., Krogan, N.J., Wolek, A., Podolny, V., Carpenter, L.R., Greenblatt, J.F., Baetz, K. and *Buratowski, S. (2006) “The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4” Genes Dev. 20, 660-665.
157. Maciag, K., Altschuler, S.J., Slack, M.D., Krogan, N.J., Emili, A., Greenblatt, J.F., Maniatis, T. and *Wu, L.F. (2006) “Systems-level analyses identify extensive coupling among gene expression machines” Molecular Systems Biol. 2:2006.0003.
158. Snider, J., Gutsche, I., Lin, M., Baby, S., Cox, B., Butland, G., Greenblatt, J., Emili, A. and *Houry, W.A. (2006) “Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase” J Biol Chem. 281, 1532-1546.
159. Butland, G., Zhang, J.W., Yang, W., Sheung, A., Wong, P., Greenblatt, J.F., Emili, A. and *Zamble, D.B. (2006) “Interactions of the Escherichia coli hydrogenase biosynthetic proteins: HybG complex formation” FEBS Lett. 580, 677-681.
160. Krogan, N.J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A.P., Punna, T., Peregrín-Alvarez, J.M., Shales, M., Zhang, X., Davey, M., Wong, P., Starostine, A., Robinson, M., Paccanaro, A., Sheung, A., Beattie, B., Richards, D.P., Canadien, V., Lalev, A., Mena, F., Canete, M.M., Vlasblom, J., Wu, S., Orsi, C., Haw, R., Rilstone, J., Gandi, K., Thompson, N.J., Musso, G., St. Onge, P., Ghanny, S., Lam, M.H.Y., Butland, G., Altaf, A., Kanaya, S., Shilatifard, A., O’Shea, E., Weissman, J.S., Ingles, C.J., Hughes, T.R., Parkinson, J., Gerstein, M., Wodak, S.J., *Emili, A. and *Greenblatt, J.F. (2006) “Global landscape of protein complexes in the yeast Saccharomyces cerevisiae” Nature 440, 637-643.
161. Pitre, S., Dehne, F., Chan, A., Cheetham, J., Duong, A., Emili, A., Gebbia, M., Greenblatt, J., Jessulat, M., Krogan, N.J., Luo, X. and *Golshani, A. (2006) “PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs” BMC Bioinformatics 7:365.
162. Butland, G., Krogan, N.J., Xu, J., Yang, W.H., Aoki, H., Li, J.S., Menendez, J., Cagney, G., Kiani, G.C., Jessulat, M.G., Datta, N., Ivanov, I., Abouhaidar, M.G., Emili, A., Greenblatt, J., Ganoza, M.C. and *Golshani, A. (2006) “Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs” J Cell Biochem. 100: 642-652.
163. Orchard, S., Salwinski, L., Kerrien, S., Montecchi-Palazzi, L., Oesterheld, M., Stumpflen, V., Ceol, A., Chatr-aryamontri, A., Armstrong, J., Woollard, P., Salama, J., Moore, S., Wojcik, J., Bader, G.D., Vidal, M., Cusick, M., Gerstein, M., Gavin, A.C., Superti-Furga, G., Greenblatt, J., Bader, J., Uetz, P., Tyers, M., Legrain, P., Fields, S., The GO Consortium, Gilson, M., Hogue, C., Mewes, H.W., Apweiler, R., Xenarios, I., Eisenberg, D., Cesareni, G. and Hermjakob, H. (2007) “The Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx)” Nature Biotech. 25: 894-898.
164. Collins, S.R., Miller, K.M., Maas, N.L., Roguev, Fillingham, J., Chu, C.S., Schuldiner, M., Gebbia, M., Recht, J., Shales, M., Ding, H., Xu, H., Han, J., Invarsdottir, I., Cheng, B., Andrews, B., Boone, C., Berger, S.L., Hieter, P., Zhang, Z., Brown, G.W., Ingles, C.J., Emili, A., Allis, C.D., Toczyski, D.P., *Weissman, J.S., *Greenblatt, J.F. and *Krogan, N.J. (2007) “Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map” Nature 446: 806-810.
165. Collins, S.R., Kemmeren, P., Zhao, X.C., Spencer, F., Greenblatt, J.F., Holstege, F.C.P., *Weissman, J. and *Krogan, N.J. (2007) “Towards a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae” Mol. Cell. Proteomics 6: 439-450.
166. Pu, S., Vlasblom, J., Emili, A., Greenblatt, J. and Wodak, S.J. (2007) “Identifying functional modules in the physical interactome of Saccharomyces cerevisiae” Proteomics 7: 944-960.
167. Xiao, T., Shibata, Y., Rao, B., Laribee, N., O’Rourke, R., Buck, M.J., Greenblatt, J.F., Krogan, N.J., Lieb, J.D. and *Strahl, B.D. (2007) “The RNA PolII kinase Ctk1 regulates positioning of a 5’ histone methylation boundary along genes” Mol. Cell. Biol. 27: 721-731.
168. Jeronimo, C., Forget, D., Bouchard, A., Li , Q., Chua, G., Poitras, C., Thérien, C., Bergeron, D., Bourassa, S., Greenblatt, J., Chabot, B., Poirier, G.G., Hughes, T.R. Blanchette, M., Price, D. and *Coulombe, B. (2007) “Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme” Molecular Cell 27: 262-274.
169. Suter, B., Fetchko, M.J., Imhof, R., Graham, C., Stoffel-Studer, I., Zbinden, C., Raghavan, M., Benetti, L., Hort, J., Fillingham, J., Greenblatt, J.F., Giaever, G.N., Nislow, C. and *Stagljar, I. (2007) “Examining protein-protein interactions and protein modifications using endogenously tagged yeast arrays: the Cross-and-Capture system“ Genome Res. 17: 1774-1782.
170. Cojocaru, M., Jeronimo, C., Forget, D., Bouchard, A., Bergeron, D., Côte, P., Poirier, G.G., Greenblatt, J. and *Coulombe, B. (2008) Genomic location of the human RNA polymerase II general machinery: Evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription. Biochem. J. 409:139-147.
171. Suter, B., Pogoutse, O., Guo, X., Krogan, N.J., Lewis, P., Greenblatt, J.F., Rine, J. and *Emili, A. (2007) “Association with the Origin Recognition Complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p” BMC Biology 5:38.
172. McKinnell, I.W., Ishibashi, J., Le Grand, F., Punch, V.J.G., Addicks, G.C., Greenblatt, J.F., Dilworth, F.J. and *Rudnicki, M.A. (2008) “Pax7 activates myogenic genes by recruitment of a histone methyltransferase complex” Nature Cell Biology 10:77-84.
173. Jessulat, M., Alamgir, M., Salsali, H., Greenblatt, J., Xu, J. and *Golshani, A. (2008) “Interacting proteins Vps75 and Rtt109 affect the efficiency of non-homologous end-joining in Saccharomyces cerevisiae” Arch. Biochem. Biophys. 469: 157-164.
174. Nedea, E., Nalbant, D., Xia, D., Theoharis, N.T., Suter, B., Richardson, C., Tatchell, K., Kislinger, T., Greenblatt, J.F. and *Nagy, P.L. (2007) “The Glc7 phosphatase subunit of the cleavage and polyadenylation factor is essential for transcription termination on snoRNA genes“ Molecular Cell 29:577-587.
175. Babu, M., Butland, G., Pogoutse, O., Li, J., Greenblatt, J.F. and *Emili, A. (2008) “Sequential peptide affinity (SPA) system for the systematic isolation and identification of protein complexes from Escherichia coli” Meth. Mol. Biol. 564: 373-400.
176. Babu, M., Krogan, N.J., Awrey, D.E., Emili, A. and *Greenblatt, J.F. (2008) “Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry” Meth. Mol. Biol. 548: 187-207.
177. *Greenblatt, J.F. (2008) “Preview: Transcription: Pulling out all the stops” Cell 132: 917-918.
178. Fillingham, J., Recht, J., Silva, A.C., Suter, B., Emili, A., Stagljar, I., Krogan, N.J., Allis, C.D., Keogh, M.C. and *Greenblatt, J.F. (2008) “Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109” Mol. Cell. Biol. 28: 4342-4353.
179. Butland, G., Babu, M., Diaz-Mejia, J.J., Bohdana, F., Phanse, S., Gold, B., Yang, W., Li, J., Gagarinova, A.G., Pogoutse, O., Mori, H., Wanner, B.L., Lo, H., Wasniewski, J., Christopolous, C., Venn, P., Safavi-Naini, A., Sourour, N., Caron, S., Choi, J.-Y., Laigle, L., Navarians-Armsavil, A., Deshpande, A., Joe, S., Datsenko, K.A., Yamamoto, N., Andrews, B.J., Boone, C., Ding, H., Sheikh, B., Moreno-Hagelseib, G., *Greenblatt, J.F. and *Emili, A. (2008) “eSGA: E. coli Synthetic Genetic Array analysis” Nature Methods 5: 789-795.
180. Fillingham, J. and *Greenblatt, J.F. (2008) “Preview: A histone code for chromatin assembly” Cell 134: 206-208.
181. Luke, I., Butland, G., Moore, K., Buchanan, G., Lyall, V., Fairhurst, S.A., Greenblatt, J.F., Emili, A., Palmer, T. and *Sargent, F. (2008) “Biosynthesis of the respiratory formate dehydrogenases from Escherichia coli: characterization of the FdhE protein” Arch. Microbiol. 190: 685-696.
182. Pu, S., Ronen, K., Vlasblom, J., Greenblatt, J.F. and *Wodak, S. (2008) “Local coherence in genetic interaction patterns reveals prevalent functional versatility” Bioinformatics 24: 2376-2383.
183. Zhou, K., Kuo, W.H.W., Fillingham, J. and *Greenblatt, J.F. (2008) “Control of Transcriptional Elongation and Co-transcriptional Histone Modification by the Yeast BUR Kinase Substrate Spt5” PNAS 106: 6956-6961.
184. Lam, M.H.Y., Urban-Grimal, D., Bugnicourt, A., Greenblatt, J.F., Haguenauer-Tsapis, R. and *Emili, A. (2009) “Interaction of the deubiquitinating enzyme Ubp2 and the E3 ligase Rsp5 is required for transporter/receptor sorting in the multivesicular body pathway” PLoS ONE 4: e4259.
185. Hu, P., Janga, S.C., Babu, M., Diaz-Mejia, J.J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., Chandran, S., Christopoulos, C., Nazarians-Armavil, A., Nasseri, N.K., Musso, G., Ali, M., Nazemof, N., Eroukova, V., Golshani, A., Paccanaro, A., Greenblatt, J.F., *Moreno-Hagelsieb, G. and *Emili, A. (2009) “Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins” PLoS Biology 7: e96.
186. Cochrane, .A, Murley, L.L., Gao, M., Wong, R., Clayton, K., Brufatto, N., Canadien, V., Mamelak, D., Chen, T., Richards, D., Zeghouf, M., Greenblatt, J., Burks, C. and *Frappier, L. (2009) “Stable complex formation between HIV Rev and the nucleosome assembly protein, NAP1, affects Rev function” Virology 388: 101-111.
187. Handford, J.I., Ize, B., Buchanan, G., Butland, G.P., Greenblatt, J., Emili, A. and *Palmer, T. (2009) “Conserved network of proteins essential for bacterial viability” .J. Bacteriol. 191: 4732-4749.
188. Fillingham, J., Kainth, P., Lambert, J.-P., van Bakel, H., Tsui, K., Pena-Castillo, L., Nislow, C., Figeys, D., Hughes, T.R., Greenblatt, J.F. and *Andrews, B.J. (2009) “A two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene expression” Molecular Cell 35: 340-351.
189. Gong, Y., Kakihara, Y., Krogan, N., Greenblatt, J., Emili, A., Zhang, Z. and Houry, W.A. (2009) “An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell” Mol. Systems Biol. 5: 275.
190. Kim, H.-S., Vanoosthuyse, V., Fillingham, J., Watt, S., Roguev, A., Kislinger, T., Hardwick, K., Greenblatt, J.F., Krogan, N.J., Bahler, J. and *Keogh, M.C. (2009) “An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe” Nature Struct. Mol. Biol. 16: 1286-1293.
191. Khanna, M., Van Bakel, H., Tang, X., Calarco, J., Babak, T., Guo, X., Emili, A., Greenblatt, J., Hughes, T.R., Krogan, N.J. and Blencowe, B.J. (2009) “A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300” RNA 15:2174-2185.
192. Babu, M., Musso, G., Diaz-Mejia, J.J., Butland, G. Greenblatt, J.F. and *Emili, A. (2009) “Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes” Mol. Biosyst. 5: 1439-1455.
193. On, T., Xiong, X., Pu, S., Turinsky, A., Gong, Y., Zhang, Z., Greenblatt, J., Wodak, S.J. and *Parkinson, J. (2010) “The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions and losses” Proteins 78: 2075-2089.
194. Mak, A.B., Ni, Z., Hewel, J., Chen, G.I., Zhong, G., Karamboulas, K., Blakely, K., Smiley, S., Marcon, E., Roudeva, D., Li, J., Olsen, J.B., Punna, T., Isserlin, R., Chetyrkin, S., Gingras, A.C., *Emili, A., *Greenblatt, J. and *Moffat, J. (2010) “A lentiviral-based functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency” Mol. Cell. Proteomics 9: 811-823.
195. Babu, M., Greenblatt, J.F., Emili, A., Strynadka, N.C.J., Reithmeier, R.A.F. and *Moraes, T.F. (2010) “Structure of a SLC26A Anion Transporter STAS Domain in Complex with Acyl Carrier Protein: Implications for E.coli YchM in Fatty Acid Metabolism” Structure 18: 1450-1462.
196. Campos, E.I., Fillingham, J., Li, G., Zheng, H., Voigt, P., Kuo, W.H.W., Seepany, H., Gao, Z., Day, L.A., Greenblatt, J.F. and *Reinberg, D. (2010) “The program for processing replicative histones H3.1 and H4: from the cytoplasm to the nucleus” Nature Struct. Mol. Biol. 17: 1343-1351.
197. Zheng, J., Benschop, J.J., Shales, M., Kemmeren, P., Greenblatt, J.F., Cagney, G., Holstege, F., Li, H. and *Krogan, N.J. (2010) “Epistatic relationships reveal the global and local regulatory organization of the yeast transcriptional factors” Molecular Systems Biology 6: 420.
198. Turinsky, A.L., Turner, B., Borja, R.C., Glreeson, J.A., Heath, M., Pu, S., Switzer, T., Dong, D., Gong, Y., On, T., Xiong, X., Emili, A., Greenblatt, J., Parkinson, J., Zhang, Z. and *Wodak, S.J. (2010) “DAnCER: disease-annotated chromatin epigenetics resource” Nucleic Acids Res. D889-894.
199. Ni, Z., Olsen, J.B., Emili, A. and *Greenblatt, J. (2011) “Identification of mammalian protein complexes by lentiviral-based affinity purification and mass spectrometry” Methods Mol. Biol, 781: 31-45.
200. Lambert, J.-P., Fillingham, J., Siahbazi, M., Greenblatt, J.F., Baetz, K and *Figeys, D. (2010) “Defining the budding yeast chromatin associated interactome” Mol. Systems Biol. 6: 448.
201. Babu, M., Beloglazova, N., Flick, R., Graham, C., Brown, G., Gagarinova, A., Phanse, S., Hu, P., Vizeacoumar, F., *Emili, A., *Greenblatt, J., *Edwards, A. and *Yakunin, A. (2011) “A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair” Molecular Microbiol. 79: 484-502.
202. Hao, Y., Merkoulovitch, A., Vlasblom, J., Pu, S., Turinsky, A.L., Roudeva, D., Turner, B., Greenblatt, J. and *Wodak, S.J. (2011) “OrthoNets: Simultaneous Visual Analysis of Orthologs and their Interaction Neighborhoods across Different Organisms” Bioinformatics 27: 883-884.
203. Pu, S., Turinsky, A., Vlasblom, J., On, T., Xiong, X., Emili, A., Zhang, Z., Greenblatt, J., Parkinson, J. and *Wodak, S.J. (2010) “Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human” PLoS ONE 5:e14112.
204. Babu, M., Aoki, H., Chowdhury, W.Q., Gagarinova, A., Graham, C., Phanse, S., Laliberte, B., Sunba, N., Jessulat, M., Golshani, A., Emili, A., Greenblatt, J.F. and *Ganoza, M.C. (2011) “Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichis coli to modulate protein synthesis and oxidative phosphorylation” PLoS ONE 6: e18510.
205. Babu, M., Gagarinova, A., Greenblatt, J., and *Emili, A. (2011) “Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli” Methods Mol. Biol. 765: 125-153.
206. Ni, Z., Olsen, J., Guo, X., Zhong, G., Ruan, D.R., Marcon, E., Young, P., Guo, H., Li, J., Moffat, J., Emili, A., and *Greenblatt, J.F. (2011) “Control of the RNA polymerase II phosphorylation state by CTD interaction domain-containing proteins RPRD1A and RPRD1B” Transcription 2: 237-242.
207. Babu, M., Diaz-Mejia, J., Vlasblom, J., Gagarinova, A., Phanse, S., Graham, C., Arnold, R., Yousif, F., Ding, H., Xiong, X., Nazarians-Armavil, A., Alamgir, M., Ali, M., Pogoutse, O., Pe’er, A., Parkinson, J., Golshani, A., Whitfield, C., Wodak, S.J., Moreno-Hagelsieb, G., Greenblatt, J.F. and *Emili, A. (2011) “Genetic interaction maps in Escherichia coli reveal condition-dependent functional crosstalk among cell envelope biogenesis pathways” PLoS Genetics 7: e1002377.
208. Babu, M., Vlasblom, J., Shuye Pu, S., Guo, X., Graham, C., Vizeacoumar, F.J., Phanse, S., Fong, V., Bean, B.D.M. Davey, M., Snider, J., Hnatshak, O., Bajaj, N., Chandran, S., Punna, T., Wong, V., Zhong, G., Li, J., Stagljar, I., *Conibear, E., *Wodak, S.J., *Emili, A. and *Greenblatt, J.F. (2012) “Interaction Landscape of Membrane Protein Complexes in Saccharomyces cerevisiae” Nature 489: 585-589.
209. Makhnevych, T., Wong, P., Pogoutse, O., Vizeacoumar, F.J., Greenblatt, J.F., *Emili, A., and *Houry, W.A. (2012) “Hsp110 is needed for spindle length control” J. Cell Biol. 198: 623-636.
210. Radovani, E., Cadorin, M., Shams, T., El-Rass, S., Karsou, A.R., Kim, H.S., Kurat, C., Keogh, M.-C., Greenblatt, J.F. and *Fillingham, J.S. (2013) “The carboxy-terminus of Rtt109 functions in chaperone control of histone acetylation” Eukaryotic Cell 12: 654-664.
211. James, L.I., Barsyte-Lovejoy, D., Zhong, N., Krichevsky, L., Korboukh, V.K., Herold, J.M., MacNevin, C.J., Norris, J.L., Sagum, C.C., Tempel, W., Marcon, E., Guo, H., Gao, C., Huang, X.-P., Kireev, D.B., Jin, J., Emili, A., Greenblatt, J.F., Roth, B., Janzen, W.P., Brown, P.J., Bedford, M.T., *Arrowsmith, C.H. and *Frye, S.V. (2013) “Discovery of a chemical probe for a methyl-lysine reader domain: L3MBTL3” Nature Chem. Biol. 9:184-191.
212. Gagarinova, A., Babu, M., Greenblatt, J. and *Emili, A. (2012) “Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays.” J Vis Exp. 69. doi:pii: 4056. 10.3791/4056.
213. Li, Y., Zhao, D., Greenblatt, J. and *Zhang, Z. (2013) “RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments” Nucleic Acids Res. 41: e94.
214. Babu, M., Kagan, O., Guo, H., Greenblatt, J. and *Emili, A. (2012) “Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry.” J Vis Exp. 69. doi:pii: 4057. 10.3791/4057.
215. Snider, J., Hanif, A., Lee, M.E., Jin, K., Yu, A.R., Chuk, M., Damjanovic, D., Graham, C., Wierzbicka, M., Tang, P., Balderes, B., Wong, V., San Luis, B., Shevelev, I., Sturley, S.L., Boone, C., Greenblatt, J.F., Babu, M., Zhang, Z., Paumi, C.M., Park, H., Michaelis, S. and *Stagljar, I. (2013) “A global analysis of the Saccharomyces cerevisiae ABC transporter interaction network: towards a greater understanding of membrane transport” Nature Chem. Biol. 9:565-572.
216. Marcon, E., Smiley, S., Turinsky, A.L. and *Greenblatt, J. (2013) “Networks of histone demethylases and their relevance to the regulation of chromatin structure and dynamics” in Systems Analysis of Chromatin-Related Protein Complexes in Cancer (Emili, A., Greenblatt, J. and Wodak, S., Eds), Springer
217. Olsen, J.B., Greenblatt, J. and *Emili, A. (2013) “Histone methyltransferase complexes in transcription, development, and cancer” in Systems Analysis of Chromatin-Related Protein Complexes in Cancer (Emili, A., Greenblatt, J. and Wodak, S., Eds), Springer
218. Zhao, D.Y., Li, Y., Greenblatt, J. and *Zhang, Z. (2013) “ncRNA-protein interactions in development and disease from the perspective of high-throughput studies” in Systems Analysis of Chromatin-Related Protein Complexes in Cancer (Emili, A., Greenblatt, J. and Wodak, S., Eds), Springer
219. De Boer, C.G., van Bakel, H., Tsui, K., Li, J., Morris, Q.D., Nislow, C., Greenblatt, J.F. and *Hughes, T.R. (2014) “A unified model for yeast transcript definition” Genome Res. 24:154-166, 2014.
220. *Babu, M., Arnold, R., Bundalovic-Torm, C., Gagarinova, Wong, K.S., Phanse, S., Kumar, A., Wagih, O., Lad, K., Samanfar, B., Stewart, G., Graham, C., Aoki, H., Brown, E., Golshani, A., Kim, P., Moreno-Hagelsieb, G., Greenblatt, J., Houry, W.A., Parkinson, J. and *Emili, A. (2014) “Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic relationships of Soluble Protein Complexes in Escherichia coli” PLoS Genetics 10: e1004120.
221. Kim, H.-S., Mukhopadhyay, R., Rothbart, S.B., Silva, A.C., Vanoosthuyse, V., Radovani, E., Kislinger, T., Roguev, A., Ryan, C.J., Xu, J., Jahari, H., Hardwick, K.G., Greenblatt, J.F., Krogan, N.J., Fillingham, J.S., Strahl, B.D., Bouhassira, E.E., Edelmann, W. and *Keogh, M.-C. (2014) “Identification of a novel Bromodomain / Casein Kinase II / TAF-containing complex as a regulator of mitotic condensin function” Cell Reports 13: 892-905.
222. Wong, K.S., Snider, J.D., Graham, C., Greenblatt, J.F., Emili, A., Babu, M. and *Houry, W.A. (2014) "The MoxR ATPase RavA and its Cofactor ViaA are Involved in Fe-S Cluster Assembly Pathways in Escherichia coli" PLoS One 9: e85529.
223. Ni, Z., Xu, C., Guo, X., Tempel, W., Marcon, E., Zhong, G., Guo, H., Kuo, W., Li, J., Young, P., Olsen, J.B., Wan, C., Loppnau, P., El Bakkouri, M., Senisterra, G., He, H., Huang, H.-M., Sidhu, S., Emili, A., Arrowsmith, C., Min, J. and Greenblatt, J.F. (2014) “RPRD1A and RPRD1B Are Human RNA Polymerase II C-Terminal Domain Scaffolds for Ser5 Dephosphorylation” Nat. Struct. Mol. Biol. 21: 686-695.
224. Paladino, P., Marcon, E., Greenblatt, J. and *Frappier, L. (2014) “Identification of Herpesvirus proteins that contribute to G1 arrest” J. Virol. 88:4480-4492.
225. Marcon, E., Ni, Z., Pu, P., Turinsky, A., Trimble, S.S., Phanse, S., Silverman-Gavrila, R., Silverman-Gavrila, L., Olsen, J., Guo, H., Zhong, G., Guo, X., Young, P., Roudeva, D., Zhao, D., Hewel, J., Li, J., Graslund, S., Paduch, M., Kossiakoff, A.A., Emili, A., Wodak, S.J., and *Greenblatt, J.F. (2014) “Protein interactions for the human chromatin-related proteins identify a demethylase complex required for chromosome segregation” Cell Reports 8: 297-310.
226. Marcon, E., Jain, H., Bhattacharya, A., Guo, H., Phanse, S., Pu, S., Byram, G., Collins, B.C., Dowdell, E., Fenner, M., Guo, X., Hutchinson, A., Kennedy, J.J., Krastins, B., Larsen, B., Lin, Z.Y., Lopez, M.F., Loppnau, P., Miersch, S., Nguyen, T., Olsen, J.B., Paduch, M., Ravichandran, M., Seitova, A., Vadali, G., Vogelsang, M., Whiteaker, J.R., Zhong, G., Zhong, N., Zhao, L., Aebersold, R., Arrowsmith, C.H., Emili, A., Frappier, L.D., Gingras, A.C., Gstaiger, M., Paulovitch, A.G., Koide, S., Kossiakoff, T., Sidhu, S., Wodak, S.F., Graslund, S., Greenblatt, J.F. and *Edwards, A.M. (2015) “A method to characterize antibody selectivity and specificity for use in immunoprecipitation” Nature Methods 12: 725-731.
227. Vlasblom, J., Zuberi, K., Rodriguez, H., Arnold, R., Gagarinova, A., Deineko, V., Leung, E., Samanfar, B., Chang, L., Phanse, S., Golshani, A., Greenblatt, J.F., Houry, W., Emili, A., Morris, Q., *Bader, G. and *Babu, M. (2015) “Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli” Bioinformatics 31: 306-310.
228. Najafabadi, H.S., Mnaimneh, S., Schmitges, F.W., Garton, M., Lam, K.N., Yang, A., Albu, M., Weirauch, M.T., Radovani, E., Kim, P.M., Greenblatt, J.F., Frey, B.J. and *Hughes, T.R. (2015) “C2H2 zinc fingers greatly expand the human regulatory lexicon” Nature Biotechnology 33:555-562.
229. Pu, S., Vlasblom, J., Turinsky, A., Marcon, E., Phanse, S., Trimble, S.S., Olsen, J., Greenblatt, J., Emili, A. and *Wodak, S.J. (2015) “Extracting high confidence protein interactions from affinity purification data: at the crossroads” J. Proteomics 118:63-80.
230. Wan, C., Borgeson, B., Phanse, S., Tu, F., Drew K., Clark, G., Xiong, X., Kagan, O., Kwan, J., Chessman, K., Berzginov, A., Pal, S., Cromar, G., Papoulas, O., Ni, Z., Boutz, D.R., Malty, R.H., Greenblatt, J.F., Sarov, M., Babu, M., Derry, B., Tillier, E., Wallingford, J.B., Parkinson, J., *Marcotte, E.M. and *Emili, A. (2015) “Panorama of ancient metazoan macromolecular complexes” Nature 525: 339-344.
231. Zhong, N., Loppnau, P., Seitova,A., Ravichandran, M., Fenner, M., Jain, H., Bhattacharya, A., Hutchinson, A., Paduch, M., Lu, V., Olszewski, M., Kossiakoff, A.A., Koide, A., Dowdell, E., Koide, S., Huang, H., Nadeem, V., Sidhu, S., Ngyuen, T., Frappier, L., Greenblatt, J., Marcon, E., Arrowsmith, C., Edwards, A.M. and Gräslund, S. (2015) “Optimizing production of antigens and Fabs in the context of generating recombinant antibodies to human proteins” PLoS One 10: e0139695.
232. Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A. (2015) “Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes” Data in Brief 6: 715-721.
233. Zhao, D.Y., Gish, G., Li, Y., Zhong, G., Min, J., Vedadi, M., Moffat, J., Pawson, T., and *Greenblatt, J.F. (2016) “SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination” Nature 529: 48-53.
234. Gorelik, M., Orlicky, S., Sartori, M.A., Tang, X., Marcon, E., Kurinov, I., Greenblatt, J.F., Tyers, M., Moffat, J., Sicheri, F. and Sidhu, S.S. (2016) “Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1–F-box interface” Proc. Natl. Acad. Sci. (USA) 113:3527-3532.
235. Olsen, J.B., Wong, L., Deimling, S., Miles, A., Guo, H., Li, Y., Zhang, Z., Greenblatt, J.F., Emili, A. and Tropepe, V. (2016) “G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis.” Stem Cell Reports 7: 454-470.
236. Schmitges, F.W., Radovani, E., Najafabadi, H.S., Barazandeh, M., Campitelli, L.F., Zhong, G., Guo, H., Kanagalingam, T., Dai, W.F., Emili, A., *Greenblatt, J.F. and *Hughes, T.R. (2016) “Multiparameter functional diversity of human C2H2 zinc finger proteins” Genome Res. 26:1742-1752.
237. Han, H., Braunschweig, U., Gonatopoulos-Pournatzis, T., Weatheritt, R.J., Hirsch, C.L., Ha, K.C.H., Radovani, E., Wang, J., O’Hanlon, D., Pan, Q., Ray, D., Vizeacoumar, F., Datti, A., Morris, Q., Hughes, T.R., Greenblatt, J.F., Wrana, J.L., Moffat, J., and *Blencowe, B.J. (2017) "Multilayered control of alternative splicing regulatory networks by transcription factors" Molecular Cell 65:539-553.
238. Babu, M., Bundalovic-Torma, C., Calmettes, C., Phanse, S., Zhang, Q., Jiang, Y., Minic, Z., Kim, S., Mehla, J., Gagarinova, A., Rodionova, I., Kumar, A., Guo, H., Kagan, O., Pogoutse, O., Aoki, H., Deineko, V., Caufield, H., Holtzapple, E., Zhang, Z., Vastermark, A., Pandya, Y., Chieh-lin Lai, C.C., El Bakkouri, M., Hooda, Y., Shah, M., Burnside, D., Hooshyar, M., Vlasblom, J., Rajagopala, S., Golshani, A., Wuchty, S., Greenblatt, J., Saier, M., Uetz, P., Moraes, T., Parkinson, J., and Emili, A. (2018) “Global landscape of cell envelope protein complexes in Escherichia coli” Nature Biotech. 36: 103-112.
239. Ho, T.-H., Sitz, J., Shen, Q., Leblanc-Lacroix, A., Campos, E., Borozan, I., Marcon, E., Greenblatt, J., Fradet-Turcotte, A., Jin, D.-Y., and *Frappier, L. (2018) “A Screen for Epstein-Barr Virus Proteins that Inhibit the DNA Damage Response Reveals a Novel Histone Binding Protein” (2018) J. Virol. 92: pii:e00262-18.
240. Georges, A., Marcon, E., Greenblatt, J., and *Frappier, L. (2018) “Identification and characterization of USP7 targets in cancer cells” Scientific Reports 8: 15833.
241. Ivanochko, D., Halabelian, L., Henderson, E., Savitsky, P., Jain, H., Marcon, E., Duan, S., Hutchinson, A., Seitova, A., Barsyte-Lovejoy, D., Filippakopoulos, P., Greenblatt, J., Lima-Fernandes, E., and *Arrowsmith, C.H. (2018) “Direct interaction between the PRDM3 and PRDM16 tumour suppressors and the NuRD chromatin remodelling complex” Nucleic Acids Res. 47: 1225-1238.
242. Georges, A,. Coyaud, E., Marcon, E., Greenblatt, J., Raught, B., and *Frappier, L. (2019) “USP7 regulates cytokinesis through FBXO38 and KIF20B” Scientific Reports 9: 2724.
243. Cheng, A.Z., Yockteng-Melgar, J., Jarvis, M.C., Malik-Soni, N., Borozan, I., Carpenter, M.A., McCann, J.L., Ibrahimi, D., Shaban, N.M., Marcon, E., Greenblatt, J., Brown, W.L., Frappier, L., and *Harris, R.S. (2019) “Epstein-Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity” Nature Microbiol. 4: 78-88.
244. Ali, I., Ruiz, D.G., Ni, Z., Johnson, J., Zhang, H., Li, P.-C., Khalid, M.M., Conrad, R.J., Guo, X., Min, J., Greenblatt, J., Jacobson, M., Krogan, N., and *Ott, M. (2019) “Crosstalk between RNA PolII C-terminal domain acetylation and phosphorylation via RPRD1 proteins” Mol. Cell 74: 1164-1174.
245. Garg, J., Saettone, A., Nabeel-Shah, S., Cadorin, M., Ponce, M., Marquez, S., Pu, P., Greenblatt, J., Lambert, J.-P., Pearlman, R., and *Fillingham, J. (2019) “The MED31 conserved component of the divergent Mediator complex in Tetrahymena thermophila participates in developmental regulation” Current Biol. 29: 2371-2379.
246. Siddiqui, U., Vaidya, A., Li, X., Marcon, E., Tsao, S.W., Greenblatt, J., and *Frappier, L. (2019) “Identification of ARKL1 as a negative regulator of Epstein-Barr virus reactivation ” J. Virol. 93: pii: e00989-19.
247. Salamun, S.G., Sitz, J., De La Cruz-Herrera, C.F., Marcon, E., Greenblatt, J., Fradet-Turcotte, A. and Frappier, L. (2019) “The Epstein-Barr Virus BMRF1 Protein Activates Transcription and Inhibits the DNA Damage Response by Binding NuRD” J. Virol. 93: pii: e01070-19.
248. Lee, K.Y., Chopra, A., Burke, G., Greenblatt, J., Biggar, K., and *Meneghini, M.D. (2020) “A crucial RNA-binding lysine residue in the Nab3 RRM domain undergoes SET1 and SET3-responsive methylation” Nucleic Acids Res. 48: 2897-2911.
249. Wolf, E.J., Miles, A., Lee, E.S., Nabeel-Shah, S., Greenblatt, J.F., Palazzo, A.F., Tropepe, V. and *Emili, A. (2020) “MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development” Cell Reports 31: 107693.
250. Abraham, K..J., Khosraviani, N., Chan, J.N.Y., Gorthi, A., Samman, A., Zhao, D.Y., Wang, M., Singhania, R., Ostrowski, L.A., Oshidari, R., Pietrobon, V., Bokros, M.H., Vidya, E., Liu, Y., Hakem, R., Dickson, B.C., De Carvalho, D.D., Greenblatt, J.F., Lee, S., Bishop, A.J.R. and *Mekhail, K. (2020) “Nucleolar RNA polymerase II drives ribosome biogenesis” Nature 585: 298-302.
251. ENCODE Project Consortium (2020) “Perspectives on ENCODE” Nature 583: 693-698.
252. ENCODE Project Consortium (2020) "Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes" Nature 583: 699-710.
253. Dilworth, D., Hanley, R., Ferreira de Freitas, R., Allali-Hassani, A., Zhou, M., Mehta, N., Marunde, M.R., Ackloo, S., Machado, R.A.M., Yazdi, A.K., Owens, D., Vu, V., Nie, D., Alqazzaz, M., Marcon, E., Li, F., Chau, I., Bolotokova, A., Qin, S., Liu, Y., Szewczyk, M.M., Kazemzadeh, S., Abramyan, T., Popova, I.K., Hall, N.W., Meiners, M.J., Cheek, M.A., Kireev, D., Greenblatt, J.F., Keogh, M.-C., Min, J., Brown, P.J., Vedadi, M., Arrowsmith, C.H., *Barsyte-Lovejoy, D., *James, L.I. and *Schapira, M. (2022) “A chemical probe targeting the PWWP domain alters NSD2 nucleolar localization” Nature Chem. Biol. 18: 56-63.
254. Nabeel-Shah, S., Garg, J., Saettone, A., Ashraf, K., Lee, H., Wahab, S., Ahmed, N., Fine, J., Derynck, J., Ponce, M., Marcon, E., Zhang, Z., Greenblatt, J.F., Pearlman, R.E., *Lambert, J.-P. and *Fillingham, J. (2021) “Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of RBBP4/7 ortholog in Tetrahymena thermophila” Nucleic Acids Res. 49, 6196-6212.
255. Shire, K., Marcon, E., Greenblatt, J. and *Frappier, L. (2021) “Characterization of a cancer-associated Epstein-Barr virus EBNA1 variant reveals a novel interaction with PLOD1 and PLOD3. ” Virology 562, 103-109.
256. Nabeel-Shah, S., Lee, H., Ahmed, N., Burke, G.L., Farhangmehr, S., Ashraf, K., Pu, S., Braunschweig, U., Zhong, G., Wei, H., Tang, H., Yang, J., Marcon , E., Blencowe, B.J., Zhang, Z. and *Greenblatt, J.F. (2022) “SARS-CoV-2 nucleocapsid protein attenuates stress granule formation and interacts directly with mRNAs to impair host stress response” iScience 25: 103562.
257. Campbell, A.M., Herrera, C.D.L.C., Marcon, E., Greenblatt, J. and Frappier, L. (2022) “Epstein-Barr virus BGLF2 commandeers RISC to interfere with miRNA function” PLoS Pathogens 18: e1010235.
258. Chan, K., Farias, A.G., Lee, H., Guvenc, F., Mero, P., Aulakh, K., Brown, K.R., Haider, S., Marcon, E., Braunschweig, U., Pu, S., Habsid, A., Christie, N., Budylowski, P., Astori, A., Ghalami, A., Mubareka, S., Greenblatt, J., Gray-Owen, S., Raught, B., Blencowe, B.J., Taipale, M. and *Moffat, J. (2022) “Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors” Helyon (in press)
259. Song, J., Nabeel-Shah, S., Pu, S., Lee, H., Braunschweig, U., Ni, Z., Ahmed, N., Marcon, E., Zhong, G., Ray, R., Ha, K.C.H., Guo, X., Zhang, Z., Hughes, T.R., Blencowe B.J. and *Greenblatt, J.F. (2022) “Regulation of alternative polyadenylation by the C2H2-zinc finger protein Sp1” Molecular Cell 82: 3135-3150.e9.
260. Han, H., Best, A.J., Braunschweig, U., Mikolajewicz, N., Li, J., Roth, J., Chowdhury, F., Mantica, F., Nabeel-Shah, S., Parada, G., Brown, K., O'Hanlon, D., Wei, J., Yao, Y., Zid, A.A., Comsa, E., Jen, M., Wang, J., Datti, A., Gonatopoulos-Pournatzis, T., Weatheritt, R., Greenblatt, J.F., Wrana, J.L., Irimia, M., Gingras, A.-C., *Moffat, J. and *Blencowe, B.J. (2022) “Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis” Molecular Cell 82: 2982-2999.e14.
261. Farooq, Z., Kusuma, F., Burke, P., Dufour, C.R., Lee, D., Tabatabaei, N., Toboz, P., Radovani, E., Greenblatt, J., Rehman, J., Class, J., Khoutorsky, A., Fonseca, B.D., Richner, J.M., Mercier, E., Bourque, G., Giguère, V., Subramaniam, A.R., Han, J. and *Tahmasebi, S. (2022) “The amino acid sensor GCN2 suppresses TOP mRNA translation via LARP1” (2022) J. Biol. Chem. (submitted)
262. Liu, Y., Iqbal, A., Li, W., Ni, Z., Wang,Y., Ramprasad, J., Abraham, K.J., Zhang, M., Zhao, D.Y., Qin, S., Loppnau, P., Jiang, H., Guo, X., Brown, P.J., Zhen, X., Xu, G., Mekhail, K., Ji, X., Bedford, M.T., Greenblatt J.F. and *Min J. (2022) ”A small molecule antagonist for the Tudor domain of SMN disrupts the interaction between SMN and RNAP II” Nature Commun. 13: 5453.
263. Segal, S., Maier, S.K., Qian, W., Mastromarco, G., Nabeel-Shah, S., Lee,H., Lacoste, J., Larsen, B., Lin, Z.-Y., Selvabaskaran, A., Liu, K., Smibert, C., Zhang, Z., Greenblatt, J., Lee, H., Peng, J., Gingras, A.-C., and *Taipale, M. (2022) “A central chaperone-like role for 14-3-3 proteins in human cells” (Molecular Cell, submitted)
264. Nabeel-Shah, S., Garg, J., Ashraf, K., Jeyapala, R., Lee, H., Petrova, A., Burns, J., Pu, S., Zhang, Z., Greenblatt, J.F., Pearlman, R.E., Lambert, J.-P. and *Fillingham, J. (2022) “Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena” Nucleic Acids Res. (submitted)
265. Ray, D., U. Laverty, K.U., Jolma, A., Nie, K., Samson, R., Pour, S.E., Tam, C.L, Nabeel-Shah, S., Albu, M., Zheng,H., Perron, G., Braunschweig, U., Najafabadi, H., Blencowe, B., Greenblatt, J., Morris, Q. and *HughesT.R. (2022) “RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific” Scientific Reports (submitted)
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