Novel computational analysis of protein binding array data identifies direct targets of Nkx2.2 in the pancreas

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Hill, Jonathon T ^a   Anderson, Keith R ^b   Mastracci, Teresa L ^a   Kaestner, Klaus H ^c   Sussel, Lori ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL ANALYSIS; GENE REGULATORY NETWORKS; NUCLEAR RECEPTORS; PANCREATIC ISLET; PREDICTION METHODS; RELATIVE BINDING AFFINITY; TRANSCRIPTION FACTOR BINDING; TRANSCRIPTION FACTOR BINDING SITES;

ALGORITHMS; BINDING ENERGY; BIOCHEMISTRY; FORECASTING; TRANSCRIPTION FACTORS;

GENES;

PHYTOLACCACEAE;

HOMEODOMAIN PROTEIN; NKX 2.2 HOMEDOMAIN PROTEIN; NKX-2.2 HOMEDOMAIN PROTEIN; TRANSCRIPTION FACTOR;

ALGORITHM; ANIMAL; ARTICLE; BINDING SITE; BIOLOGY; GENETICS; GENOME; METHODOLOGY; MOUSE; PANCREAS; PROMOTER REGION; PROTEIN BINDING; PROTEIN MICROARRAY; REGRESSION ANALYSIS;

ALGORITHMS; ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; GENOME; HOMEODOMAIN PROTEINS; MICE; PANCREAS; PROMOTER REGIONS, GENETIC; PROTEIN ARRAY ANALYSIS; PROTEIN BINDING; REGRESSION ANALYSIS; TRANSCRIPTION FACTORS;

EID: 79951943956     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-62     Document Type: Article

References (38)

1. Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 2008, 451(7178):535-540.
2. Tanay A. Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res 2006, 16(8):962-972.
3. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, et al. Diversity and complexity in DNA recognition by transcription factors. Science 2009, 324(5935):1720-1723.
4. Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Pena-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 2008, 133(7):1266-1276.
5. Elnitski L, Jin VX, Farnham PJ, Jones SJ. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res 2006, 16(12):1455-1464.
6. Frech K, Quandt K, Werner T. Finding protein-binding sites in DNA sequences: the next generation. Trends Biochem Sci 1997, 22(3):103-104.
7. Robison K, McGuire AM, Church GM. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol 1998, 284(2):241-254.
8. Stormo GD. DNA binding sites: representation and discovery. Bioinformatics 2000, 16(1):16-23.
9. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23(1):137-144.
10. O'Flanagan RA, Paillard G, Lavery R, Sengupta AM. Non-additivity in protein-DNA binding. Bioinformatics 2005, 21(10):2254-2263.
11. Djordjevic M, Sengupta AM, Shraiman BI. A biophysical approach to transcription factor binding site discovery. Genome Res 2003, 13(11):2381-2390.
12. Bulyk ML, Johnson PL, Church GM. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res 2002, 30(5):1255-1261.
13. Man TK, Stormo GD. Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res 2001, 29(12):2471-2478.
14. Liu J, Stormo GD. Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions. Nucleic Acids Res 2005, 33(17):e141.
15. Sussel L, Kalamaras J, Hartigan-O'Connor DJ, Meneses JJ, Pedersen RA, Rubenstein JL, German MS. Mice lacking the homeodomain transcription factor Nkx2.2 have diabetes due to arrested differentiation of pancreatic beta cells. Development 1998, 125(12):2213-2221.
16. Watada H, Mirmira RG, Kalamaras J, German MS. Intramolecular control of transcriptional activity by the NK2-specific domain in NK-2 homeodomain proteins. Proc Natl Acad Sci USA 2000, 97(17):9443-9448.
17. Cissell MA, Zhao L, Sussel L, Henderson E, Stein R. Transcription factor occupancy of the insulin gene in vivo. Evidence for direct regulation by Nkx2.2. J Biol Chem 2003, 278(2):751-756.
18. Raum JC, Gerrish K, Artner I, Henderson E, Guo M, Sussel L, Schisler JC, Newgard CB, Stein R. FoxA2, Nkx2.2, and PDX-1 regulate islet beta-cell-specific mafA expression through conserved sequences located between base pairs -8118 and -7750 upstream from the transcription start site. Mol Cell Biol 2006, 26(15):5735-5743.
19. Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 2006, 24(11):1429-1435.
20. Anderson KR, Torres CA, Solomon K, Becker TC, Newgard CB, Wright CV, Hagman J, Sussel L. Cooperative transcriptional regulation of the essential pancreatic islet gene NeuroD1 (beta2) by Nkx2.2 and neurogenin 3. J Biol Chem 2009, 284(45):31236-31248.
21. Chen X, Hughes TR, Morris Q. RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics 2007, 23(13):i72-79.
22. Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, Walhout AJ. A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell 2009, 138(2):314-327.
23. Doyle MJ, Loomis ZL, Sussel L. Nkx2.2-repressor activity is sufficient to specify alpha-cells and a small number of beta-cells in the pancreatic islet. Development 2007, 134(3):515-523.
24. Prado CL, Pugh-Bernard AE, Elghazi L, Sosa-Pineda B, Sussel L. Ghrelin cells replace insulin-producing beta cells in two mouse models of pancreas development. Proc Natl Acad Sci USA 2004, 101(9):2924-2929.
25. Anderson KR, White P, Kaestner KH, Sussel L. Identification of known and novel pancreas genes expressed downstream of Nkx2.2 during development. BMC Dev Biol 2009, 9:65.
26. Gerrish K, Van Velkinburgh JC, Stein R. Conserved transcriptional regulatory domains of the pdx-1 gene. Mol Endocrinol 2004, 18(3):533-548.
27. Brodbelt JS. Evaluation of DNA/Ligand interactions by electrospray ionization mass spectrometry. Annu Rev Anal Chem (Palo Alto Calif) 2010, 3:67-87.
28. Wang LH, Chmelik R, Nirenberg M. Sequence-specific DNA binding by the vnd/NK-2 homeodomain of Drosophila. Proc Natl Acad Sci USA 2002, 99(20):12721-12726.
29. Jiang G, Sladek FM. The DNA binding domain of hepatocyte nuclear factor 4 mediates cooperative, specific binding to DNA and heterodimerization with the retinoid X receptor alpha. J Biol Chem 1997, 272(2):1218-1225.
30. Kel AE, Niehof M, Matys V, Zemlin R, Borlak J. Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context. Genome Biol 2008, 9(2):R36.
31. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316(5830):1497-1502.
32. Djordjevic M. SELEX experiments: new prospects, applications and data analysis in inferring regulatory pathways. Biomol Eng 2007, 24(2):179-189.
33. Das MK, Dai HK. A survey of DNA motif finding algorithms. BMC Bioinformatics 2007, 8(Suppl 7):S21.
34. Hill JT, Chao CS, Anderson KR, Kaufman F, Johnson CW, Sussel L. Nkx2.2 activates the ghrelin promoter in pancreatic islet cells. Mol Endocrinol 2010, 24(2):381-390.
35. Doyle MJ, Sussel L. Nkx2.2 regulates beta-cell function in the mature islet. Diabetes 2007, 56(8):1999-2007.
36. Steadman DJ, Giuffrida D, Gelmann EP. DNA-binding sequence of the human prostate-specific homeodomain protein NKX3.1. Nucleic Acids Res 2000, 28(12):2389-2395.
37. Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 2008, 133(7):1277-1289.
38. Newburger DE, Bulyk ML. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 2009, (37 Database):D77-82.