Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 9, 2013, Pages 3645-3650

  Mirzaei, Hamid ^a,b   Knijnenburg, Theo A ^a,c   Kim, Bong ^a   Robinson, Max ^a   Picotti, Paola ^d,e   Carter, Gregory W ^a,f   Li, Song ^a   Dilworth, David J ^a   Eng, Jimmy K ^a,g   Aitchison, John D ^a   Shmulevich, Ilya ^a   Galitski, Timothy ^a,h   Aebersold, Ruedi ^d,e   Ranish, Jeffrey ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c NETHERLANDS CANCER INSTITUTE   (Netherlands)

^d ETH ZURICH   (Switzerland)

^e UNIVERSITY OF ZURICH   (Switzerland)

^f JACKSON LABORATORY   (United States)

^g UNIVERSITY OF WASHINGTON   (United States)

^h MILLIPORE CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL EXTRACT; DNA; PROTEOME; REGULATOR PROTEIN; RNA POLYMERASE II; TRANSCRIPTION FACTOR;

ARTICLE; AZF1 GENE; DNA BINDING; FLO11 GENE; FOLLOW UP; GENE; GENE EXPRESSION; MASS SPECTROMETRY; MOT3 GENE; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION;

CELL NUCLEUS; DNA, FUNGAL; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENETIC ASSOCIATION STUDIES; MASS SPECTROMETRY; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; PROTEOME; REPRESSOR PROTEINS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 84874478799     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1216918110     Document Type: Article

References (42)

1. Garner MM, Revzin A (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res 9(13): 3047-3060.
2. Fried M, Crothers DM (1981) Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res 9(23): 6505-6525.
3. Zhu C, et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4): 556-566.
4. Li JJ, Herskowitz I (1993) Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science 262(5141): 1870-1874.
5. Ren B, et al. (2000) Genome-wide location and function of DNA binding proteins. Science 290(5500): 2306-2309.
6. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316(5830): 1497-1502.
7. Harbison CT, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431(7004): 99-104.
8. Ranish JA, et al. (2003) The study of macromolecular complexes by quantitative proteomics. Nat Genet 33(3): 349-355.
9. Mittler G, Butter F, Mann M (2009) A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res 19(2): 284-293.
10. Himeda CL, Ranish JA, Hauschka SD (2008) Quantitative proteomic identification of MAZ as a transcriptional regulator of muscle-specific genes in skeletal and cardiac myocytes. Mol Cell Biol 28(20): 6521-6535.
11. Domon B, Aebersold R (2010) Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol 28(7): 710-721.
12. Picotti P, et al. (2010) High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods 7(1): 43-46.
13. Lange V, et al. (2008) Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics 7(8): 1489-1500.
14. Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM (2007) Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci USA 104(14): 5860-5865.
15. Addona TA, et al. (2009) Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 27(7): 633-641.
16. Lo WS, Dranginis AM (1998) The cell surface flocculin Flo11 is required for pseudohyphae formation and invasion by Saccharomyces cerevisiae. Mol Biol Cell 9(1): 161-171.
17. Rupp S, Summers E, Lo HJ, Madhani H, Fink G (1999) MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene. EMBO J 18(5): 1257-1269.
18. Pan X, Heitman J (2002) Protein kinase A operates a molecular switch that governs yeast pseudohyphal differentiation. Mol Cell Biol 22(12): 3981-3993.
19. Braus GH, Grundmann O, Brückner S, Mösch HU (2003) Amino acid starvation and Gcn4p regulate adhesive growth and FLO11 gene expression in Saccharomyces cerevisiae. Mol Biol Cell 14(10): 4272-4284.
20. Carter GW, et al. (2007) Prediction of phenotype and gene expression for combinations of mutations. Mol Syst Biol 3(96): 96.
21. Barrales RR, Jimenez J, Ibeas JI (2008) Identification of novel activation mechanisms for FLO11 regulation in Saccharomyces cerevisiae. Genetics 178(1): 145-156.
22. Lambrechts MG, Bauer FF, Marmur J, Pretorius IS (1996) Muc1, a mucin-like protein that is regulated by Mss10, is critical for pseudohyphal differentiation in yeast. Proc Natl Acad Sci USA 93(16): 8419-8424.
23. Gagiano M, Van Dyk D, Bauer FF, Lambrechts MG, Pretorius IS (1999) Divergent regulation of the evolutionarily closely related promoters of the Saccharomyces cerevisiae STA2 and MUC1 genes. J Bacteriol 181(20): 6497-6508.
24. Deutsch EW, Lam H, Aebersold R (2008) PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows. EMBO Rep 9(5): 429-434.
25. Picotti P, et al. (2008) A database of mass spectrometric assays for the yeast proteome. Nat Methods 5(11): 913-914.
26. Mallick P, et al. (2007) Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol 25(1): 125-131.
27. Stahl-Zeng J, et al. (2007) High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 6(10): 1809-1817.
28. Mirzaei H, et al. (2009) Halogenated peptides as internal standards (H-PINS): Introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry. Mol Cell Proteomics 8(8): 1934-1946.
29. Ghaemmaghami S, et al. (2003) Global analysis of protein expression in yeast. Nature 425(6959): 737-741.
30. Ong SE, et al. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5): 376-386.
31. MacIsaac KD, et al. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7(113): 113.
32. Grishin AV, Rothenberg M, Downs MA, Blumer KJ (1998) Mot3, a Zn finger transcription factor that modulates gene expression and attenuates mating pheromone signaling in Saccharomyces cerevisiae. Genetics 149(2): 879-892.
33. Jin R, Dobry CJ, McCown PJ, Kumar A (2008) Large-scale analysis of yeast filamentous growth by systematic gene disruption and overexpression. Mol Biol Cell 19(1): 284-296.
34. Newcomb LL, Hall DD, Heideman W (2002) AZF1 is a glucose-dependent positive regulator of CLN3 transcription in Saccharomyces cerevisiae. Mol Cell Biol 22(5): 1607-1614.
35. Slattery MG, Liko D, Heideman W (2006) The function and properties of the Azf1 transcriptional regulator change with growth conditions in Saccharomyces cerevisiae. Eukaryot Cell 5(2): 313-320.
36. Gagiano M, Bauer FF, Pretorius IS (2002) The sensing of nutritional status and the relationship to filamentous growth in Saccharomyces cerevisiae. FEMS Yeast Res 2(4): 433-470.
37. Hongay C, Jia N, Bard M, Winston F (2002) Mot3 is a transcriptional repressor of ergosterol biosynthetic genes and is required for normal vacuolar function in Saccharomyces cerevisiae. EMBO J 21(15): 4114-4124.
38. Mennella TA, Klinkenberg LG, Zitomer RS (2003) Recruitment of Tup1-Ssn6 by yeast hypoxic genes and chromatin-independent exclusion of TATA binding protein. Eukaryot Cell 2(6): 1288-1303.
39. Sertil O, Vemula A, Salmon SL, Morse RH, Lowry CV (2007) Direct role for the Rpd3 complex in transcriptional induction of the anaerobic DAN/TIR genes in yeast. Mol Cell Biol 27(6): 2037-2047.
40. Conlan RS, Tzamarias D (2001) Sfl1 functions via the co-repressor Ssn6-Tup1 and the cAMP-dependent protein kinase Tpk2. J Mol Biol 309(5): 1007-1015.
41. Kadosh D, Johnson AD (2001) Rfg1, a protein related to the Saccharomyces cerevisiae hypoxic regulator Rox1, controls filamentous growth and virulence in Candida albicans. Mol Cell Biol 21(7): 2496-2505.
42. Reiter L, et al. (2011) mProphet: Automated data processing and statistical validation for large-scale SRM experiments. Nat Methods 8(5): 430-435.