Analysis of DNA-protein interactions: From nitrocellulose filter binding assays to microarray studies

Analytical and Bioanalytical Chemistry

Volumn 398, Issue 6, 2010, Pages 2551-2561

  Helwa, Reham ^a,b   Hoheisel, Jörg D ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b Ain Shams University   (Egypt)

Author keywords

DNA structure; DNA binding proteins; Regulation; Transcription factors

Indexed keywords

BINDING ASSAYS; BINDING SPECIFICITIES; CHARACTERISATION; DNA RESPONSE ELEMENT; DNA STRUCTURE; DNA-BINDING PROTEIN; DNA-BINDING PROTEINS; DNA-PROTEIN INTERACTION; GENETIC CODE; HIGH THROUGHPUT; HUMAN GENES; HUMAN GENOMES; MAMMALIAN PROTEINS; MOLECULAR MECHANISM; NEW TECHNOLOGIES; REGULATION; RESPONSE ELEMENTS;

ASSAYS; DNA; GENES; MAMMALS; NITROCELLULOSE; TRANSCRIPTION FACTORS;

TRANSCRIPTION;

DNA; DNA BINDING PROTEIN; PYROXYLIN;

BINDING SITE; CHEMISTRY; DNA METHYLATION; HUMAN; INSTRUMENTATION; METABOLISM; METHODOLOGY; MICROARRAY ANALYSIS; PROTEIN BINDING; REVIEW;

BINDING SITES; COLLODION; DNA; DNA METHYLATION; DNA-BINDING PROTEINS; HUMANS; MICROARRAY ANALYSIS; PROTEIN BINDING;

MAMMALIA;

EID: 78650222757     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-010-4096-7     Document Type: Review

References (74)

1. Bain G, Maandag EC, Izon DJ, Amsen D, Kruisbeek AM, Weintraub BC, Krop I, Schlissel MS, Feeney AJ, van Roon M, Vandervalk M, Teriele HPJ, Berns A, Murre C (1994) E2A proteins are required for proper B cell development and initiation of immunoglobulin gene rearrangements. Cell 79:885-892
2. Dynlacht BD (1997) Regulation of transcription by proteins that control the cell cycle. Nature 389:149-152
3. Accili D, Arden KC (2004) FoxOs at the crossroads of cellular metabolism differentiation and transformation. Cell 117:421-426
4. Lemon B, Tjian R (2000) Orchestrated response: A symphony of transcription factors for gene control. Genes Dev 14:2551-2569
5. Furney SJ, Higgins DG, Ouzounis CA, Lopez-Bigas N (2006) Structural and functional properties of genes involved in human cancer. BMC Genomics 7:3
6. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LSB, Gong FC, Guan P, Harris NL, Hay BA, Hoskins RA, Li JY, Li ZY, Hynes RO, Jones SJM, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XQH, Zhong F, Zhong WY, Gibbs R, Venter JC, Adams MD, Lewis S (2000) Comparative genomics of the eukaryotes. Science 287:2204-2215
7. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254
8. Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76
9. Hughes JR, Cheng JF, Ventress N, Prabhakar S, Clark K, Anguita E, De Gobbi M, de Jong P, Rubin E, Higgs DR (2005) Annotation of cis-regulatory elements by identification subclassification and functional assessment of multispecies conserved sequences. Proc Natl Acad Sci U S A 102:9830-9835
10. Venkatesh B, Yap WH (2005) Comparative genomics using fugu: A tool for the identification of conserved vertebrate cis-regulatory elements. Bioessays 27:100-107
11. Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 11:1175-1186
12. Messina DN, Glasscock J, Gish W, Lovett M (2004) An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. Genome Res 14:2041-2047
13. Hu S, Xie Z, Onishi A, Yu X, Jiang L, Lin J, Rho HS, Woodard C, Wang H, Jeong JS, Long SY, He XF, Wade H, Blackshaw S, Qian J, Zhu H (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 139:610-622
14. Riggs AD, Bourgeois S, Newby RF, Cohn M (1968) DNA binding of the lac repressor. J Mol Biol 34:365-368
15. Riggs AD, Bourgeois S, Cohn M (1970) The lac repressoroperator interaction. 3. Kinetic studies. J Mol Biol 53:401-417
16. Towbin H, Staehelin T, Gordon J (1979) Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: Procedure and some applications. Proc Natl Acad Sci U S A 76:4350-4354
17. Woodbury CP Jr, von Hippel PH (1983) On the determination of deoxyribonucleic acid-protein interaction parameters using the nitrocellulose filter-binding assay. Biochemistry 22:4730-4737
18. Beattie KL, Wiegand RC, Radding CM (1977) Uptake of homologous single-stranded fragments by superhelical DNA. II. Characterization of the reaction. J Mol Biol 116:783-803
19. Tullius TD (1989) Physical studies of protein-DNA complexes by footprinting. Annu Rev Biophys Biophys Chem 18:213-237
20. Galas DJ, Schmitz A (1978) DNAse footprinting: A simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5:3157-3170
21. Brenowitz M, Senear DF, Shea MA, Ackers GK (1986) Quantitative DNase footprint titration: A method for studying protein-DNA interactions. Methods Enzymol 130:132-181
22. Maxam AM, Gilbert W (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol 65:499-560
23. Siebenlist U, Gilbert W (1980) Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. Proc Natl Acad Sci U S A 77:122-126
24. Yang VW (1998) Eukaryotic transcription factors: identification characterization and functions. J Nutr 128:2045-2051
25. Fried M, Crothers DM (1981) Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res 9:6505-6525
26. 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 9:3047-3060
27. Carey J (1991) Gel retardation. Methods Enzymol 208:103-117
28. Hellman LM, Fried MG (2007) Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc 2:1849-1861
29. Fried MG, Bromberg JL (1997) Factors that affect the stability of protein-DNA complexes during gel electrophoresis. Electrophoresis 18:6-11
30. Massie CE, Mills IG (2008) ChIPping away at gene regulation. EMBO Rep 9:337-343
31. Hoffman BG, Jones SJ (2009) Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. J Endocrinol 201:1-13
32. Wu J, Smith LT, Plass C, Huang TH (2006) ChIP-chip comes of age for genome-wide functional analysis. Cancer Res 66:6899-6902
33. Mardis ER (2007) ChIP-seq: Welcome to the new frontier. Nat Methods 4:613-614
34. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431:99-104
35. Vogel MJ, Peric-Hupkes D, van Steensel B (2007) Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2:1467-1478
36. Lee TI, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1:729-748
37. Johne B, Gadnell M, Hansen K (1993) Epitope mapping and binding kinetics of monoclonal antibodies studied by real time biospecific interaction analysis using surface plasmon resonance. J Immunol Methods 160:191-198
38. Buckle M, Williams RM, Negroni M, Buc H (1996) Real time measurements of elongation by a reverse transcriptase using surface plasmon resonance. Proc Natl Acad Sci U S A 93:889-894
39. Rich RL, Myszka DG (2006) Survey of the year 2005 commercial optical biosensor literature. J Mol Recognit 19:478-534
40. Oliphant AR, Brandl CJ, 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
41. Roulet E, Busso S, Camargo AA, Simpson AJ, Mermod N, Bucher P (2002) High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol 20:831-835
42. Deplancke B, Dupuy D, Vidal M, Walhout AJ (2004) A gatewaycompatible yeast one-hybrid system. Genome Res 14:2093-2101
43. Deplancke B, Mukhopadhyay A, Ao W, Elewa AM, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Reece-Hoyes JS, Hope IA, Tissenbaum HA, Mango SE, Walhout AJM (2006) A gene-centered C elegans protein-DNA interaction network. Cell 125:1193-1205
44. Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133:1277-1289
45. Bulyk ML (2006) DNA microarray technologies for measuring protein-DNA interactions. Curr Opin Biotechnol 17:422-430
46. Bulyk ML, Gentalen E, Lockhart DJ, Church GM (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol 17:573-577
47. Beier M, Stephan A, Hoheisel JD (2001) Synthesis of photolabile 5'-O-phosphoramidites for the production of microarrays of inversely oriented oligonucleotides. Helv Chim Acta 84:2089-2095
48. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306-2309
49. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28:327-334
50. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804
51. Berger MF, Bulyk ML (2006) Protein binding microarrays (PBMs) for rapid high-throughput characterization of the sequence specificities of DNA binding proteins. Methods Mol Biol 338:245-260
52. Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML (2004) Rapid analysis of the DNAbinding specificities of transcription factors with DNA microarrays. Nat Genet 36:1331-1339
53. Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Pena-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133:1266-1276
54. Warren CL, Kratochvil NC, Hauschild KE, Foister S, Brezinski ML, Dervan PB, Phillips GN Jr, Ansari AZ (2006) Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci U S A 103:867-872
55. Berger MF, Bulyk ML (2009) Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc 4:393-411
56. Ho SW, Jona G, Chen CT, Johnston M, Snyder M (2006) Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc Natl Acad Sci U S A 103:9940-9945
57. Gong W, He K, Covington M, Dinesh-Kumar SP, Snyder M, Harmer SL, Zhu YX, Deng XW (2008) The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Mol Plant 1:27-41
58. He M, Taussig MJ (2001) Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res 29:E73
59. Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau AY, Walter JC, LaBaer J (2004) Self-assembling protein microarrays. Science 305:86-90
60. Angenendt P, Kreutzberger J, Glokler J, Hoheisel JD (2006) Generation of high density protein microarrays by cell-free in situ expression of unpurified PCR products. Mol Cell Proteomics 5:1658-1666
61. Gustafsdottir SM, Schlingemann J, Rada-Iglesias A, Schallmeiner E, Kamali-Moghaddam M, Wadelius C, Landegren U (2007) In vitro analysis of DNA-protein interactions by proximity ligation. Proc Natl Acad Sci U S A 104:3067-3072
62. Conze T, Shetye A, Tanaka Y, Gu JJ, Larsson C, Goeransson J, Tavoosidana G, Soederberg O, Nilsson M, Landegren U (2009) Analysis of genes, transcripts, and proteins via DNA ligation. Ann Rev Anal Chem 2:215-239
63. Bustamante C, Rivetti C (1996) Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope. Annu Rev Biophys Biomol Struct 25:395-429
64. Hansma HG (2001) Surface biology of DNA by atomic force microscopy. Annu Rev Phys Chem 52:71-92
65. Conlin RM, Brown RS (2001) Reconstitution of protein-DNA complexes for crystallization. Methods Mol Biol 148:547-556
66. Moss T (2001) DNA-protein interaction: Principles and protocols, 2nd edn. Humana, Totowa, NJ
67. Masotti C, Armelin-Correa LM, Splendore A, Lin CJ, Barbosa A, Sogayar MC, Passos-Bueno MR (2005) A functional SNP in the promoter region of TCOF1 is associated with reduced gene expression and YY1 DNA-protein interaction. Gene 359:44-52
68. Taulan M, Lopez E, Guittard C, Rene C, Baux D, Altieri JP, DesGeorges M, Claustres M, Romey MC (2007) First functional polymorphism in CFTR promoter that results in decreased transcriptional activity and Sp1/USF binding. Biochem Biophys Res Commun 361:775-781
69. Champigny MJ, Mitchell M, Fox-Robichaud A, Trigatti BL, Igdoura SA (2009) A point mutation in the neu1 promoter recruits an ectopic repressor Nkx32 and results in a mouse model of sialidase deficiency. Mol Genet Metab 97:43-52
70. Hoff JH, te Morsche RH, Roelofs HM, van der Logt EM, Nagengast FM, Peters WH (2009) COX-2 polymorphisms - 765G→C and -1195A→G and colorectal cancer risk. World J Gastroenterol 15:4561-4565
71. The International Cancer Genome Consortium (2010) International network of cancer genome projects. Nature 464:993-998
72. Marcy Y, Cousin PY, Rattier M, Cerovic G, Escalier G, Bena G, Gueron M, McDonagh L, le Boulaire F, Benisty H, Qeisbuch C, Avarre JC (2008) Innovative integrated system for real-time measurement of hybridization and melting on standard format microarrays. Biotechniques 44:913-920
73. Ericsson O, Jarvius J, Schallmeiner E, Howell M, Nong RY, Reuter H, Hahn M, Stenberg J, Nilsson M, Landegren U (2008) A dual-tag microarray platform for high-performance nucleic acid and protein analyses. Nucleic Acids Res 36:e45
74. Hesse J, Jacak J, Kasper M, Regl G, Eichberger T, Winklmayr M, Aberger F, Sonnleitner M, Schlapak R, Howorka S, Muresan L, Frischauf AM, Schütz GJ (2006) RNA expression profiling at the single molecule level. Genome Res 16:1041-1045