Methods for analysis of transcription factor DNA-binding specificity in vitro

Sub-Cellular Biochemistry

Volumn 52, Issue , 2011, Pages 155-173

  Jolma, Arttu ^a   Taipale, Jussi ^a  

^a Department of Biosciences and Nutrition ^*

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALIA;

DNA; PROTEIN BINDING; TRANSCRIPTION FACTOR;

ANIMAL; BINDING SITE; CHEMISTRY; GENETICS; GENOME; HUMAN; NUCLEOTIDE SEQUENCE;

ANIMALS; BASE SEQUENCE; BINDING SITES; DNA; GENOME; HUMANS; PROTEIN BINDING; TRANSCRIPTION FACTORS;

EID: 84872588984     PISSN: 03060225     EISSN: None     Source Type: Journal    
DOI: 10.1007/978-90-481-9069-0_7     Document Type: Article

References (69)

1. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10:252-263
2. Fulton DL, et al. (2009) TFCat: the curated catalog of mouse and human transcription factors. Genome Biol 10:R29
3. Bryne JC, et al. (2008) JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 36:D102-6
4. Newburger DE, Bulyk ML (2009) UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 37:D77-82
5. Tuupanen S, et al. (2009) The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet 41:885-890
6. Jiang J, Levine M (1993) Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen. Cell 72:741-752
7. Jen-Jacobson L (1997) Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state. Biopolymers 44:153-180
8. Berg OG, von Hippel PH (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol 193:723-750
9. von Hippel PH, Berg OG (1989) Facilitated target location in biological systems. J Biol Chem 264:675-678
10. Moss T, Leblanc B (2009) DNA-protein Interactions: Principles and Protocols (Humana Press, New York, NY)
11. Galas DJ, Schmitz A (1978) DNAse footprinting: a simple method for the detection of protein- DNA binding specificity. Nucleic Acids Res 5:3157-3170
12. Tullius TD, Dombroski BA, Churchill ME, Kam L (1987) Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts. Methods Enzymol 155:537-558
13. Connaghan-Jones KD, Moody AD, Bain DL (2008) Quantitative DNase footprint titration: a tool for analyzing the energetics of protein-DNA interactions. Nat Protoc 3:900-914
14. Jain SS, Tullius TD (2008) Footprinting protein-DNA complexes using the hydroxyl radical. Nat Protoc 3:1092-1100
15. Hughes TR, Weilbaecher RG, Walterscheid M, Lundblad V (2000) Identification of the singlestrand telomeric DNA binding domain of the Saccharomyces cerevisiae Cdc13 protein. Proc Natl Acad Sci U S A 97:6457-6462
16. Hellman LM, Fried MG (2007) Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc 2:1849-1861
17. Gille J, Swerlick RA, Caughman SW (1997) Transforming growth factor-alpha-induced transcriptional activation of the vascular permeability factor (VPF/VEGF) gene requires AP-2-dependent DNA binding and transactivation. EMBO J 16:750-759
18. Fried M, Crothers DM (1981) Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res 9:6505-6525
19. 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
20. Fried MG, Liu G (1994) Molecular sequestration stabilizes CAP-DNA complexes during polyacrylamide gel electrophoresis. Nucleic Acids Res 22:5054-5059
21. Hu S, et al. (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 139:610-622
22. Deplancke B, et al. (2006) A gene-centered C. elegans protein-DNA interaction network. Cell 125:1193-1205
23. Kadonaga JT, Tjian R (1986) Affinity purification of sequence-specific DNA binding proteins. Proc Natl Acad Sci U S A 83:5889-5893
24. 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: 284-293
25. 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 1:376-386
26. Markljung E, et al. (2009) ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol 7:e1000256
27. Dejardin J, Kingston RE (2009) Purification of proteins associated with specific genomic Loci. Cell 136:175-186
28. Wei GH, et al. (2010) Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J 29:2147-2160
29. 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
30. Ren B, et al. (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306-2309
31. Liu X, Noll DM, Lieb JD, Clarke ND (2005) DIP-chip: rapid and accurate determination of DNA-binding specificity. Genome Res 15:421-427
32. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502
33. Meng X, Brodsky MH, Wolfe SA (2005) A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol 23:988-994
34. Stormo GD, Zhao Y (2010) Determining the specificity of protein-DNA interactions. Nat Rev Genet 11:751-760
35. Jolma A, et al. (2010) Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res 20:861-873
36. Zykovich A, Korf I, Segal DJ (2009) Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res 37:e151
37. Zhao Y, Granas D, Stormo GD (2009) Inferring binding energies from selected binding sites. PLoS Comput Biol 5:e1000590
38. 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
39. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510
40. Roulet E, et al. (2002) High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol 20:831-835
41. Urrutia R (2003) KRAB-containing zinc-finger repressor proteins. Genome Biol 4:231
42. Gangwal K, et al. (2008) Microsatellites as EWS/FLI response elements in Ewing’s sarcoma. Proc Natl Acad Sci U S A 105:10149-10154
43. Hollenhorst PC, et al. (2009) DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet 5:e1000778
44. Noyes MB, et al. (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133:1277-1289
45. Berger MF, et al. (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133:1266-1276
46. Bulyk ML, Huang X, Choo Y, Church GM (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A 98: 7158-7163
47. Bulyk ML, Gentalen E, Lockhart DJ, Church GM (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol 17:573-577
48. Mukherjee S, et al. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet 36:1331-1339
49. Berger MF, et al. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 24:1429-1435
50. 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
51. Puckett JW, et al. (2007) Quantitative microarray profiling of DNA-binding molecules. J Am Chem Soc 129:12310-12319
52. Badis G, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324:1720-1723
53. Mintseris J, Eisen MB (2006) Design of a combinatorial DNA microarray for protein-DNA interaction studies. BMC Bioinformatics 7:429
54. Benos PV, Bulyk ML, Stormo GD (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 30:4442-4451
55. Agius P, Arvey A, Chang W, Noble WS, Leslie C (2010) High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. PLoS Comput Biol 6:e1000916
56. Sharon E, Lubliner S, Segal E (2008) A feature-based approach to modeling protein-DNA interactions. PLoS Comput Biol 4:e1000154
57. Scarano S, Mascini M, Turner AP, Minunni M (2010) Surface plasmon resonance imaging for affinity-based biosensors. Biosens Bioelectron 25:957-966
58. Shumaker-Parry JS, Aebersold R, Campbell CT (2004) Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy. Anal Chem 76:2071-2082
59. Maerkl SJ, Quake SR (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315:233-237
60. Hallikas O, et al. (2006) Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124:47-59
61. Hallikas O, Taipale J (2006) High-throughput assay for determining specificity and affinity of protein-DNA binding interactions. Nat Protoc 1:215-222
62. Negi S, Imanishi M, Matsumoto M, Sugiura Y (2008) New redesigned zinc-finger proteins: design strategy and its application. Chemistry 14:3236-3249
63. Li GW, Elf J (2009) Single molecule approaches to transcription factor kinetics in living cells. FEBS Lett 583:3979-3983
64. Elf J, Li GW, Xie XS (2007) Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316:1191-1194
65. Iwahara J, Clore GM (2006) Detecting transient intermediates in macromolecular binding by paramagnetic NMR. Nature 440:1227-1230
66. Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal AK (1999) Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex. Nature 397:714-719
67. Panne D, Maniatis T, Harrison SC (2004) Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer. EMBO J 23:4384-4393
68. Robertson G, et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651-657
69. Hampshire AJ, Rusling DA, Broughton-Head VJ, Fox KR (2007) Footprinting: a method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands. Methods 42:128-140