Dynamic SPR monitoring of yeast nuclear protein binding to a cis-regulatory element

Biochemical and Biophysical Research Communications

Volumn 363, Issue 1, 2007, Pages 153-158

  Mao, Grace ^a   Brody, James P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

cis Regulatory elements; DNA protein binding; Kinetics; Surface plasmon resonance; Yeast cell cycle

Indexed keywords

DNA; GENE PRODUCT; NUCLEAR PROTEIN; RNR1 PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CELL CULTURE; CELL CYCLE; CELL CYCLE G1 PHASE; CELL LYSATE; CHROMOSOME 5; CONTROLLED STUDY; GENE EXPRESSION; MONITORING; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN IMMOBILIZATION; REGULATORY SEQUENCE; SACCHAROMYCES CEREVISIAE; SENSOR; SURFACE PLASMON RESONANCE; YEAST;

BINDING SITES; DNA-BINDING PROTEINS; NUCLEAR PROTEINS; PROTEIN BINDING; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SURFACE PLASMON RESONANCE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 34548731819     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2007.08.130     Document Type: Article

References (36)

1. Davidson E.H. Genomic Regulatory Systems (2001), Academic Press
2. Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.H., Minokawa T., Amore G., Hinman V., Arenas-Mena C., Otim O., Brown C.T., Livi C.B., Lee P.Y., Revilla R., Rust A.G., Pan Z., Schilstra M.J., Clarke P.J., Arnone M.I., Rowen L., Cameron R.A., McClay D.R., Hood L., and Bolouri Hq. A genomic regulatory network for development. Science 295 (2002) 1669-1678
3. de Leon S.B.-T., and Davidson E.H. Gene regulation: gene control network in development. Annu. Rev. Biophys Biomol. Struct. (2007). http://dx.doi.org/10.1146/annurev.biophys.35.040405.102002 10.1146/annurev.biophys.35.040405.102002
4. Prud'homme B., Gompel N., and Carroll S.B. Emerging principles of regulatory evolution. Proc. Natl. Acad. Sci. USA (2007). http://dx.doi.org/10.1073/pnas.0700488104 10.1073/pnas.0700488104
5. Niwa N., Hiromi Y., and Okabe M. A conserved developmental program for sensory organ formation in Drosophila melanogaster. Nat. Genet. 36 3 (2004) 293-297
6. Ruvinsky I., and Ruvkun G. Functional tests of enhancer conservation between distantly related species. Development 130 21 (2003) 5133-5142
7. Sharan R., Ovcharenko I., Ben-Hur A., and Karp R.M. CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics 19 Suppl 1 (2003) 283-291
8. Philippakis A.A., Busser B.W., Gisselbrecht S.S., He F.S., Estrada B., Michelson A.M., and Bulyk M.L. Expression-guided in silico evaluation of candidate cis regulatory codes for drosophila muscle founder cells. PLoS Comput. Biol. 2 5 (2006) e53. http://dx.doi.org/10.1371/journal.pcbi.0020053 10.1371/journal.pcbi.0020053
9. Hardison R.C. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16 9 (2000) 369-372
10. Dickmeis T., Plessy C., Rastegar S., Aanstad P., Herwig R., Chalmel F., Fischer N., and Strehle U. Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo. Genome Res. 14 2 (2004) 228-238. http://dx.doi.org/10.1101/gr.1819204 10.1101/gr.1819204
11. Hutton J.J., Jegga A.G., Kong S., Gupta A., Ebert C., Williams S., Katz J.D., and Aronow B.J. Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system. BMC Genomics 5 1 (2004) 82. http://dx.do.org/10.1186/1471-2164-5-82 10.1186/1471-2164-5-82
12. Jegga A.G., Sherwood S.P., Carman J.W., Pinski A.T., Phillips J.L., Pestian J.P., and Aronow B.J. Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res. 12 9 (2002) 1408-1417. http://dx.doi.org/10.1101/gr.255002 10.1101/gr.255002
13. Jegga A.G., Gupta A., Gowrisankar S., Deshmukh M.A., Connolly S., Finley K., and Aronow B.J. Cismols analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes. Nucleic Acids Res. 33 (2005). http://dx.doi.org/10.1093/nar/gki486 10.1093/nar/gki486 (Web Server issue): W408-W411
14. Mukherjee S., Berger M.F., Jona G., Wang X.S., Muzzey D., Snyder M., Young R.A., and Bulyk M.L. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet. 36 12 (2004) 1331-1339. http://dx.doi.org/10.1038/ng1473 10.1038/ng1473
15. Bulyk M.L., Gentalen E., Lockhart D.J., and Church G.M. Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat. Biotechnol. 17 6 (1999) 573-577. http://dx.doi.org/10.1038/9878 10.1038/9878
16. Bulyk M.L. DNA microarray technologies for measuring protein-DNA interactions. Curr. Opin. Biotechnol. 17 4 (2006) 422-430. http://dx.doi.org/10.1016/j.copbio.2006.06.015 10.1016/j.copbio.2006.06.015
17. Limin Lin, An SPR-Based Sensor to Measure DNA-Protein Interactions, PhD thesis, University of California, Irvine, 2005.
18. Bondeson K., Frostell-Karlsson A., Fugerstam L., and Magnusson G. Lactose repressor-operator DNA interactions: kinetic analysis by a surface plasmon resonance biosensor. Anal. Biochem. 214 1 (1993) 245-251
19. Majka J., and Speck C. Analysis of protein-DNA interactions using surface plasmon resonance. Adv. Biochem. Eng. Biotechnol. 104 (2007) 13-36
20. Teh H.F., Peh W.Y.X., Su X., and Thomsen J.S. Characterization of protein-DNA interactions using surface plasmon resonance spectroscopy with various assay schemes. Biochemistry 46 8 (2007) 2127-2135. http://dx.doi.org/10.1021/bi061903t 10.1021/bi061903t
21. Elledge S.J., and Davis R.W. Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase. Genes Dev. 4 5 (1990) 740-751
22. Elledge S.J., Zhou Z., and Allen J.B. Ribonucleotide reductase: regulation, regulation, regulation. Trends Biochem. Sci. 17 3 (1992) 119-123
23. Elledge S.J., Zhou Z., Allen J.B., and Navas T.A. DNA damage and cell cycle regulation of ribonucleotide reductase. Bioessays 15 5 (1993) 333-339. http://dx.doi.org/10.1002/bies.950150507 10.1002/bies.950150507
24. Yao R., Zhang Z., An X., Bucci B., Perlstein D.L., Stubbe J., and Huang M. Subcellular localization of yeast ribonucleotide reductase regulated by the DNA replication and damage checkpoint pathways. Proc. Natl. Acad. Sci. USA 100 11 (2003) 6628-6633. http://dx.doi.org/10.1073/pnas.1131932100 10.1073/pnas.1131932100
25. Zhou Z., and Elledge S.J. Dun1 encodes a protein kinase that controls the DNA damage response in yeast. Cell 75 6 (1993) 1119-1127
26. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Botstein D., and Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9 12 (1998) 3273-3297
27. Harbison C.T., Benjamin Gordon D., Lee T.I., Rinaldi N.J., Macisaac K.D., Danford T.W., Hannett N.M., Tagne J.-B., Reynolds D.B., Yoo J., Jennings E.G., Zeitlinger J., Pokholok D.K., Kellis M., Alex Rolfe P., Takusagawa K.T., Lander E.S., Gifford D.K., Fraenkel E., and Young R.A. Transcriptional regulatory code of a eukaryotic genome. Nature 431 7004 (2004) 99-104. http://dx.doi.org/10.1038/nature02800 10.1038/nature02800
28. Kaiser P., Sia R.A., Bardes E.G., Lew D.J., and Reed S.I. Cdc34 and the f-box protein met30 are required for degradation of the cdk-inhibitory kinase swe1. Genes Dev. 12 16 (1998) 2587-2597
29. Reed S.I., Hadwiger J.A., and Lerincz A.T. Protein kinase activity associated with the product of the yeast cell division cycle gene cdc28. Proc. Natl. Acad. Sci. USA 82 12 (1985) 4055-4059
30. Watson J.V., Chambers S.H., and Smith P.J. A pragmatic approach to the analysis of DNA histograms with a definable g1 peak. Cytometry 8 1 (1987) 1-8. http://dx.doi.org/10.1002/cyto.990080101 10.1002/cyto.990080101
31. Ormerod M.G., Payne A.W., and Watson J.V. Improved program for the analysis of DNA histograms. Cytometry 8 6 (1987) 637-641. http://dx.doi.org/10.1002/cyto.990080617 10.1002/cyto.990080617
32. Dove J.E., Brockenbrough J.S., and Aris J.P. Isolation of nuclei and nucleoli from the yeast Saccharomyces cerevisiae. Methods Cell Biol. 53 (1998) 33-46
33. Rieder S.E., and Emr S.D. Subcellular fractionation and isolation of organelles. Current Protocols in Molecular Biology (2004), Wiley
34. Sazer S., and Sherwood S.W. Mitochondrial growth and DNA synthesis occur in the absence of nuclear DNA replication in fission yeast. J. Cell. Sci. 97 Pt 3 (1990) 509-516
35. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
36. Lin L., Harris J.W., Garrett H., Thompson R., and Brody J.P. Surface plasmon resonance-based sensors to identify cis-regulatory elements. Anal. Chem. 76 22 (2004) 6555-6559. http://dx.doi.org/10.1021/ac049371e 10.1021/ac049371e