A systematic approach to identify functional motifs within vertebrate developmental enhancers

Developmental Biology

Volumn 337, Issue 2, 2010, Pages 484-495

  Li, Qiang ^a   Ritter, Deborah ^b   Yang, Nan ^a   Dong, Zhiqiang ^a   Li, Hao ^c   Chuang, Jeffrey H ^b   Guo, Su ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BOSTON COLLEGE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Brain development; Conserved non coding elements; Enhancers; Motifs; Zebrafish

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BINDING SITE; BRAIN DEVELOPMENT; BRAIN REGION; CONTROLLED STUDY; EMBRYO; ENHANCER REGION; FOREBRAIN; GENE EXPRESSION; GENETIC CONSERVATION; GENETIC DATABASE; NONHUMAN; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MOTIF; TISSUE SPECIFICITY; TRANSGENICS; VERTEBRATE; ZEBRA FISH;

DANIO RERIO; VERTEBRATA;

EID: 72649101692     PISSN: 00121606     EISSN: 1095564X     Source Type: Journal    
DOI: 10.1016/j.ydbio.2009.10.019     Document Type: Article

References (68)

1. Ao W., Gaudet J., Kent W.J., Muttumu S., and Mango S.E. Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR. Science 305 (2004) 1743-1746
2. Appel B., Korzh V., Glasgow E., Thor S., Edlund T., Dawid I.B., and Eisen J.S. Motoneuron fate specification revealed by patterned LIM homeobox gene expression in embryonic zebrafish. Development 121 (1995) 4117-4125
3. Bailey T.L., and Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (1994), AAAI Press, Menlo Park, California 28-36
4. Bally-Cuif L., and Boncinelli E. Transcription factors and head formation in vertebrates. Bioessays 19 (1997) 127-135
5. Bieker J.J. Kruppel-like factors: three fingers in many pies. J. Biol. Chem. 276 (2001) 34355
6. Birney E., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (2007) 799-816
7. Blackwood E.M., and Kadonaga J.T. Going the distance: a current view of enhancer action. Science 281 (1998) 60-63
8. Bussemaker H.J., Li H., and Siggia E.D. Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc. Natl. Acad. Sci. 97 (2000) 10096
9. Chen B., Schaevitz L.R., and McConnell S.K. Fezl regulates the differentiation and axon targeting of layer 5 subcortical projection neurons in cerebral cortex. Proc. Natl. Acad. Sci. 102 (2005) 17184-17189
10. Curiel T.J. Regulatory T-cell development: is Foxp3 the decider?. Nat. Med. 13 (2007) 250
11. Davidson E.H. Genomic regulatory systems: development and evolution (2001), Academic Press, San Diego
12. Gray P.A., et al. Mouse brain organization revealed through direct genome-scale TF expression analysis. Science 306 (2004) 2255-2257
13. Guo S., Wilson S.W., Cooke S., Chitnis A.B., Driever W., and Rosenthal A. Mutations in the zebrafish unmask shared regulatory pathways controlling the development of catecholaminergic neurons. Dev. Biol. 208 (1999) 473-487
14. Hare E.E., Peterson B.K., Iyer V.N., Meier R., and Eisen M.B. Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet. 4 (2008) e1000106
15. Hashimoto H., et al. Expression of the zinc finger gene fez-like in zebrafish forebrain. Mech. Dev. 97 (2000) 191-195
16. Higashijima S., Hotta Y., and Okamoto H. Visualization of cranial motor neurons in live transgenic zebrafish expressing green fluorescent protein under the control of the islet-1 promoter/enhancer. J. Neurosci. 20 (2000) 206-218
17. Hirata T., Nakazawa M., Yoshihara S., Miyachi H., Kitamura K., Yoshihara Y., and Hibi M. Zinc-finger gene Fez in the olfactory sensory neurons regulates development of the olfactory bulb non-cell-autonomously. Development 133 (2006) 1433-1443
18. Hirata T., Suda Y., Nakao K., Narimatsu M., Hirano T., and Hibi M. Zinc finger gene fez-like functions in the formation of subplate neurons and thalamocortical axons. Dev. Dyn. 230 (2004) 546-556
19. Inoue A., Takahashi M., Hatta K., Hotta Y., and Okamoto H. Developmental regulation of islet-1 mRNA expression during neuronal differentiation in embryonic zebrafish. Dev. Dyn. 199 (1994) 1-11
20. Jeong J., et al. Neurogenin1 is a determinant of zebrafish basal forebrain dopaminergic neurons and is regulated by the conserved zinc finger protein Tof/Fezl. Proc. Natl. Acad. Sci. 103 (2006) 5143-5148
21. Jeong J., Einhorn Z., Mathur P., Chen L., Lee S., Kawakami K., and Guo S. Patterning the zebrafish diencephalon by the conserved zinc finger protein Fezl. Development 134 (2007) 127-136
22. Kafri R., Levy M., and Pilpel Y. The regulatory utilization of genetic redundancy through responsive backup circuits. Proc. Natl. Acad. Sci. 103 (2006) 11653-11658
23. Kawakami K., and Shima A. Identification of the Tol2 transposase of the medaka fish Oryzias latipes that catalyzes excision of a nonautonomous Tol2 element in zebrafish Danio rerio. Gene 240 (1999) 239-244
24. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., and Haussler D. The human genome browser at UCSC. Genome Res. 12 (2002) 996-1006
25. Khoury G., and Gruss P. Enhancer Elements. Cell 33 (1983) 313-314
26. Kiecker C., and Lumsden A. Compartments and their boundaries in vertebrate brain development. Nat. Rev. Neurosci. 6 (2005) 553-564
27. Kimmel C.B., Ballard W.W., Kimmel S.R., Ullmann B., and Schilling T.F. Stages of embryonic development of the zebrafish. Dev. Dyn. 203 (1995) 253-310
28. Korzh V., Edlund T., and Thor S. Zebrafish primary neurons initiate expression of the LIM homeodomain protein Isl-1 at the end of gastrulation. Development 118 (1993) 417-425
29. Levine M., and Tijan R. Transcription regulation and animal diversity. Nature 424 (2003) 147-151
30. Levkowitz G., et al. Zinc finger protein too few controls the development of monoaminergic neurons. Nat. Neurosci. 6 (2003) 28-33
31. Levraud J.P., Boudinot P., Colin I., Benmansour A., Peyrieras N., Herbomel P., and Lutfalla G. Identification of the zebrafish IFN receptor: implications for the origin of the vertebrate IFN system. J. Immunol. 178 (2007) 4385-4394
32. Lumsden A., and Krumlauf R. Patterning the vertebrate neuraxis. Science 274 (1996) 1109-1114
33. Mahony S., and Benos P.V. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 35 (2007) W253
34. Markstein M., Zinzen R., Markstein P., Yee K.P., Erives A., Stathopoulos A., and Levine M. A regulatory code for neurogenic gene expression in the Drosophila embryo. Development 131 (2004) 2387-2394
35. Molyneaux B.J., Arlotta P., Hirata T., Hibi M., and Macklis J.D. Fezl is required for the birth and specification of corticospinal motor neurons. Neuron 47 (2005) 817-831
36. Navratilova P., Fredman D., Hawkins T.A., Turner K., Lenhard B., and Becker T.S. Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev. Biol. 327 (2009) 526-540
37. Nobrega M.A., Ovcharenko I., Afzal V., and Rubin E.M. Scanning human gene deserts for long-range enhancers. Science 302 (2003) 413
38. Ovcharenko I., Nobrega M.A., Loots G.G., and Stubbs L. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res. 32 (2004) W280-286
39. Pennacchio L.A., and Rubin E.M. Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet. 2 (2001) 100-109
40. Pennacchio L.A., et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444 (2006) 499-502
41. Persampieri J., Ritter D.I., Lees D., Lehoczky J., Li Q., Guo S., and Chuang J.H. cneViewer: a database of conserved noncoding elements for studies of tissue-specific gene regulation. Bioinformatics 24 (2008) 2418-2419
42. Petruk S., et al. Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference. Cell 127 (2006) 1209-1221
43. Pheasant M., and Mattick J.S. Raising the estimate of functional human sequences. Genome Res. 17 (2007) 1245-1253
44. Place R.F., Li L.C., Pookot D., Noonan E.J., and Dahiya R. MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc. Natl. Acad. Sci. 105 (2008) 1608-1613
45. Rastegar S., et al. The words of the regulatory code are arranged in a variable manner in highly conserved enhancers. Dev. Biol. 318 (2008) 366-377
46. Redies C., and Puelles L. Modularity in vertebrate brain development and evolution. Bioessays 23 (2001) 1100-1111
47. Reuter I., and Schacherer F. TRANSFAC: an integrated system for gene expression regulation. 28, 316-319. Nucleic Acids Res. 28 (2000) 316-319
48. Rubenstein J.L., Shimamura K., Martinez S., and Puelles L. Regionalization of the prosencephalic neural plate. Annu. Rev. Neurosci. 21 (1998) 445-477
49. Sanchez-Elsner T., Gou D., Kremmer E., and Sauer F. Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 311 (2006) 1118-1123
50. Shin J.T., Priest J.R., Ovcharenko I., Ronco A., Moore R.K., Burns C.G., and MacRae C.A. Human-zebrafish non-coding conserved elements act in vivo to regulate transcription. Nucleic Acids Res. 33 (2005) 5437-5445
51. Simeone A., Acampora D., Gulisano M., Stornaiuolo A., and Boncinelli E. Nested expression domains of four homeobox genes in developing brain. Nature 358 (1992) 687-690
52. Small S., Blair A., and Levine M. Regulation of even-skipped strip 2 in the Drosophila embryo. EMBO J. 11 (1992) 4047-4057
53. Sprague J., et al. The zebrafish information network: the zebrafish model organism database. Nucleic Acids Res. 34 (2006) D581-586
54. Stathopoulos A., Van Drenth M., Erives A., Markstein M., and Levine M. Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell 111 (2002) 687-701
55. Stern C.D. Initial patterning of the central nervous system: how many organizers. Nat. Rev. Neurosci. 2 (2001) 92-98
56. Su A.I., et al. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. 99 (2002) 4465-4470
57. Takasaki N., Kurokawa D., Nakayama R., Nakayama J., and Aizawa S. Acetylated YY1 regulates Otx2 expression in anterior neuroectoderm at two cis-sites 90 kb apart. EMBO J. 26 (2007) 1649-1659
58. Thisse, C., Thisse, B., High Throughput Expression Analysis of ZF-Models Consortium Clones. ZFIN Direct Data Submission (http://zfin.org). 2005.
59. Tokumoto M., Gong Z., Tsubokawa T., Hew C.L., Uyemura K., Hotta Y., and Okamoto H. Molecular heterogeneity among primary motoneurons and within myotomes revealed by the differential mRNA expression of novel islet-1 homologs in embryonic zebrafish. Dev. Biol. 171 (1995) 578-589
60. Tompa M., et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 23 (2005) 137-144
61. Visel A., et al. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat. Genet. 40 (2008) 158-160
62. Visel A., et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457 (2009) 854-858
63. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562
64. Westerfield M. The zebrafish book: a guide for the laboratory use of zebrafish, Brachydanio rerio (1995), The University of Oregon Press, Eugene, OR
65. Wilson S.W., and Houart C. Early steps in the development of the forebrain. Dev. Cell 6 (2004) 167-181
66. Wingender E., et al. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res. 28 (2000) 316-319
67. Woolfe A., et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3 (2005) 1-15
68. Woolfe A., et al. CONDOR: a database resource of developmentally associated conserved non-coding elements. BMC Dev. Biol. 7 (2007) 100