Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Halfon, Marc S ^a,b,c   Zhu, Qianqian ^a,d   Brennan, Elizabeth R ^a   Zhou, Yiyun ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

^c ROSWELL PARK CANCER INSTITUTE   (United States)

^d DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ACCURACY; ARTICLE; BINDING SITE; CIS REGULATORY MODULE; CONTROLLED STUDY; DROSOPHILA; DROSOPHILA PSEUDOOBSCURA; GENE EXPRESSION; GENETIC CONSERVATION; LOSS OF FUNCTION MUTATION; NONHUMAN; PREDICTION; REGULATORY SEQUENCE; REPORTER GENE; SITE DIRECTED MUTAGENESIS; TRANSCRIPTION BINDING SITE; ANIMAL; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT;

ANIMALS; BINDING SITES; CONSERVED SEQUENCE; DROSOPHILA; GENE EXPRESSION REGULATION; MUTAGENESIS, SITE-DIRECTED; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

EID: 82055175738     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-578     Document Type: Article

References (34)

1. Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 2006, 7:29-59. 10.1146/annurev.genom.7.080505.115623, 16719718.
2. Noonan JP, McCallion AS. Genomics of long-range regulatory elements. Annu Rev Genomics Hum Genet 2010, 11:1-23. 10.1146/annurev-genom-082509-141651, 20438361.
3. Haeussler M, Joly JS. When needles look like hay: how to find tissue-specific enhancers in model organism genomes. Dev Biol 2011, 350(2):239-254. 10.1016/j.ydbio.2010.11.026, 21130761.
4. Van Loo P, Marynen P. Computational methods for the detection of cis-regulatory modules. Brief Bioinform 2009, 10(5):509-524. 10.1093/bib/bbp025, 19498042.
5. Vavouri T, Elgar G. Prediction of cis-regulatory elements using binding site matrices -- the successes, the failures and the reasons for both. Current Opinion in Genetics & Development 2005, 15(4):395-402. 10.1016/j.gde.2005.05.002, 22030243.
6. Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5(4):276-287. 10.1038/nrg1315, 15131651.
7. Markstein M, Markstein P, Markstein V, Levine MS. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci USA 2002, 99(2):763-768. 10.1073/pnas.012591199, 117379, 11752406.
8. Ochoa-Espinosa A, Yucel G, Kaplan L, Pare A, Pura N, Oberstein A, Papatsenko D, Small S. The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. PNAS 2005, 0500373102.
9. Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol 2004, 5(9):R61. 10.1186/gb-2004-5-9-r61, 522868, 15345045.
10. Grad YH, Roth FP, Halfon MS, Church GM. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics 2004, 20(16):2738-2750. 10.1093/bioinformatics/bth320, 15145800.
11. Halfon MS, Grad Y, Church GM, Michelson AM. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res 2002, 12(7):1019-1028. 186630, 12097338.
12. Krivan W, Wasserman WW. A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 2001, 11(9):1559-1566. 10.1101/gr.180601, 311083, 11544200.
13. Philippakis AA, Busser BW, Gisselbrecht SS, He FS, Estrada B, Michelson AM, Bulyk ML. Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells. PLoS Computational Biology 2006, 2(5):e53. 10.1371/journal.pcbi.0020053, 1464814, 16733548.
14. Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, Rajewsky N, Siggia ED, Gaul U. Transcriptional Control in the Segmentation Gene Network of Drosophila. PLoS Biology 2004, 2(9):e271. 10.1371/journal.pbio.0020271, 514885, 15340490.
15. Halfon MS, Carmena A, Gisselbrecht S, Sackerson CM, Jimenez F, Baylies MK, Michelson AM. Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors. Cell 2000, 103(1):63-74. 10.1016/S0092-8674(00)00105-7, 11051548.
16. Negre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, Henikoff JG, Feng X, Ahmad K, Russell S, White RA, Stein L, Henikoff S, Kellis M, White KP. A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet 2010, 6(1):e1000814. 10.1371/journal.pgen.1000814, 2797089, 20084099.
17. Niwa R, Niimi T, Honda N, Yoshiyama M, Itoyama K, Kataoka H, Shinoda T. Juvenile hormone acid O-methyltransferase in Drosophila melanogaster. Insect biochemistry and molecular biology 2008, 38(7):714-720. 10.1016/j.ibmb.2008.04.003, 18549957.
18. Morgenstern B. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15(3):211-218. 10.1093/bioinformatics/15.3.211, 10222408.
19. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15(8):1034-1050. 10.1101/gr.3715005, 1182216, 16024819.
20. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12(6):996-1006. 186604, 12045153.
21. Su J, Teichmann SA, Down TA. Assessing computational methods of cis-regulatory module prediction. PLoS Comput Biol 2010, 6(12):e1001020. 10.1371/journal.pcbi.1001020, 2996316, 21152003.
22. Li L, Zhu Q, He X, Sinha S, Halfon M. Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biology 2007, 8(6):R101. 10.1186/gb-2007-8-6-r101, 2394749, 17550599.
23. Estrada B, Choe SE, Gisselbrecht SS, Michaud S, Raj L, Busser BW, Halfon MS, Church GM, Michelson AM. An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes. PLoS Genetics 2006, 2(2):e16. 10.1371/journal.pgen.0020016, 1366495, 16482229.
24. Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Gottgens B, Halfon MS, Sinha S. Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Dev Cell 2009, 17(4):568-579. 10.1016/j.devcel.2009.09.002, 2768654, 19853570.
25. Liu YH, Jakobsen JS, Valentin G, Amarantos I, Gilmour DT, Furlong EE. A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development. Dev Cell 2009, 16(2):280-291. 10.1016/j.devcel.2009.01.006, 19217429.
26. Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EEM. A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev 2007, 21(4):436-449. 10.1101/gad.1509007, 1804332, 17322403.
27. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009, 457(7231):854-858. 10.1038/nature07730, 2745234, 19212405.
28. Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev 2007, 21(4):385-390. 10.1101/gad.1509607, 1804326, 17322397.
29. Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 2008, 6(2):e27. 10.1371/journal.pbio.0060027, 2235902, 18271625.
30. Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol 2010, 8(8).
31. Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE. A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Dev Cell 2006, 10(6):797-807. 10.1016/j.devcel.2006.04.009, 16740481.
32. Kahana S, Pnueli L, Kainth P, Sassi HE, Andrews B, Kassir Y. Functional dissection of IME1 transcription using quantitative promoter-reporter screening. Genetics 2010, 186(3):829-841. 10.1534/genetics.110.122200, 2975282, 20739709.
33. Bray N, Dubchak I, Pachter L. AVID: A global alignment program. Genome Res 2003, 13(1):97-102. 10.1101/gr.789803, 430967, 12529311.
34. Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS. REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res 2011, (39 Database):D118-123.