Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family

Biochemical and Biophysical Research Communications

Volumn 350, Issue 3, 2006, Pages 648-656

  Li, Jing ^a   Liu, Qi ^a   Qiu, Mengsheng ^b   Pan, Yuchun ^a   Li, Yixue ^c   Shi, Tieliu ^c,d  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b University of Louisville School of Medicine   (United States)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^d SHANGHAI UNIVERSITY   (China)

Author keywords

Basic Helix Loop Helix; Dynamic programming; Mouse; Predictive motif; Transcription factor

Indexed keywords

HELIX LOOP HELIX PROTEIN;

ARTICLE; CELL DIFFERENTIATION; CELL MATURATION; GENE FUNCTION; MOUSE; NOMENCLATURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FUNCTION; STATISTICAL ANALYSIS; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; ANIMALS; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; BINDING SITES; CHROMOSOME MAPPING; DNA; MICE; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; SEQUENCE ANALYSIS, PROTEIN;

EID: 33749628461     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.09.114     Document Type: Article

References (30)

1. Wasserman W.W., and Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5 (2004) 276-287
2. Atchley W.R., and Fitch W.M. A natural classification of the basic helix-loop-helix class of transcription factors. Proc. Natl. Acad. Sci. USA 94 (1997) 5172-5176
3. Ferre-D'Amare A.R., Pognonec P., Roeder R.G., and Burley S.K. Structure and function of the b/HLH/Z domain of USF. EMBO J. 13 (1994) 180-189
4. Shimizu T., Toumoto A., Ihara K., Shimizu M., Kyogoku Y., Ogawa N., Oshima Y., and Hakoshima T. Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition. EMBO J. 16 (1997) 4689-4697
5. Murre C., McCaw P.S., Vaessin H., Caudy M., Jan L.Y., Jan Y.N., Cabrera C.V., Buskin J.N., Hauschka S.D., Lassar A.B., et al. Interactions between heterologous helix-loop-helix proteins generate complexes that bind specifically to a common DNA sequence. Cell 58 (1989) 537-544
6. Ledent V., and Vervoort M. The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Res. 11 (2001) 754-770
7. Fisher A., and Caudy M. The function of hairy-related bHLH repressor proteins in cell fate decisions. Bioessays 20 (1998) 298-306
8. Ledent V., Paquet O., and Vervoort M. Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biol. 3 (2002) RESEARCH0030
9. Toledo-Ortiz G., Huq E., and Quail P.H. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15 (2003) 1749-1770
10. Atchley W.R., Terhalle W., and Dress A. Positional dependence, cliques, and predictive motifs in the bHLH protein domain. J. Mol. Evol. 48 (1999) 501-516
11. Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., Antonarakis S.E., Attwood J., Baertsch R., Bailey J., Barlow K., Beck S., Berry E., Birren B., Bloom T., Bork P., Botcherby M., Bray N., Brent M.R., Brown D.G., Brown S.D., Bult C., Burton J., Butler J., Campbell R.D., Carninci P., Cawley S., Chiaromonte F., Chinwalla A.T., Church D.M., Clamp M., Clee C., Collins F.S., Cook L.L., Copley R.R., Coulson A., Couronne O., Cuff J., Curwen V., Cutts T., Daly M., David R., Davies J., Delehaunty K.D., Deri J., Dermitzakis E.T., Dewey C., Dickens N.J., Diekhans M., Dodge S., Dubchak I., Dunn D.M., Eddy S.R., Elnitski L., Emes R.D., Eswara P., Eyras E., Felsenfeld A., Fewell G.A., Flicek P., Foley K., Frankel W.N., Fulton L.A., Fulton R.S., Furey T.S., Gage D., Gibbs R.A., Glusman G., Gnerre S., Goldman N., Goodstadt L., Grafham D., Graves T.A., Green E.D., Gregory S., Guigo R., Guyer M., Hardison R.C., Haussler D., Hayashizaki Y., Hillier L.W., Hinrichs A., Hlavina W., Holzer T., Hsu F., Hua A., Hubbard T., Hunt A., Jackson I., Jaffe D.B., Johnson L.S., Jones M., Jones T.A., Joy A., Kamal M., Karlsson E.K., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562
12. Wang S.S., Betz A.G., and Reed R.R. Cloning of a novel Olf-1/EBF-like gene, O/E-4, by degenerate oligo-based direct selection. Mol. Cell. Neurosci. 20 (2002) 404-414
13. Bramblett D.E., Copeland N.G., Jenkins N.A., and Tsai M.J. BHLHB4 is a bHLH transcriptional regulator in pancreas and brain that marks the dimesencephalic boundary. Genomics 79 (2002) 402-412
14. Bramblett D.E., Pennesi M.E., Wu S.M., and Tsai M.J. The transcription factor Bhlhb4 is required for rod bipolar cell maturation. Neuron 43 (2004) 779-793
15. Gray P.A., Fu H., Luo P., Zhao Q., Yu J., Ferrari A., Tenzen T., Yuk D.I., Tsung E.F., Cai Z., Alberta J.A., Cheng L.P., Liu Y., Stenman J.M., Valerius M.T., Billings N., Kim H.A., Greenberg M.E., McMahon A.P., Rowitch D.H., Stiles C.D., and Ma Q. Mouse brain organization revealed through direct genome-scale TF expression analysis. Science 306 (2004) 2255-2257
16. Fisher F., and Goding C.R. Single amino acid substitutions alter helix-loop-helix protein specificity for bases flanking the core CANNTG motif. EMBO J. 11 (1992) 4103-4109
17. Fujii Y., Shimizu T., Toda T., Yanagida M., and Hakoshima T. Structural basis for the diversity of DNA recognition by bZIP transcription factors. Nat. Struct. Biol. 7 (2000) 889-893
18. Ma P.C., Rould M.A., Weintraub H., and Pabo C.O. Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation. Cell 77 (1994) 451-459
19. Crews S.T. Control of cell lineage-specific development and transcription by bHLH-PAS proteins. Genes Dev. 12 (1998) 607-620
20. Ohsako S., Hyer J., Panganiban G., Oliver I., and Caudy M. Hairy function as a DNA-binding helix-loop-helix repressor of Drosophila sensory organ formation. Genes Dev. 8 (1994) 2743-2755
21. Van Doren M., Bailey A.M., Esnayra J., Ede K., and Posakony J.W. Negative regulation of proneural gene activity: hairy is a direct transcriptional repressor of achaete. Genes Dev. 8 (1994) 2729-2742
22. Massari M.E., and Murre C. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol. Cell Biol. 20 (2000) 429-440
23. Ellenberger T., Fass D., Arnaud M., and Harrison S.C. Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer. Genes Dev. 8 (1994) 970-980
24. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16 (1988) 10881-10890
25. Brownlie P., Ceska T., Lamers M., Romier C., Stier G., Teo H., and Suck D. The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control. Structure 5 (1997) 509-520
26. Harris M.A., Clark J., Ireland A., Lomax J., Ashburner M., Foulger R., Eilbeck K., Lewis S., Marshall B., Mungall C., Richter J., Rubin G.M., Blake J.A., Bult C., Dolan M., Drabkin H., Eppig J.T., Hill D.P., Ni L., Ringwald M., Balakrishnan R., Cherry J.M., Christie K.R., Costanzo M.C., Dwight S.S., Engel S., Fisk D.G., Hirschman J.E., Hong E.L., Nash R.S., Sethuraman A., Theesfeld C.L., Botstein D., Dolinski K., Feierbach B., Berardini T., Mundodi S., Rhee S.Y., Apweiler R., Barrell D., Camon E., Dimmer E., Lee V., Chisholm R., Gaudet P., Kibbe W., Kishore R., Schwarz E.M., Sternberg P., Gwinn M., Hannick L., Wortman J., Berriman M., Wood V., de la Cruz N., Tonellato P., Jaiswal P., Seigfried T., and White R. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32 (2004) D258-D261
27. Mount D.W. Bioinformatics: Sequence and Genome Analysis (2001), Cold Spring Harbor Laboratory Press, New York 64-65 pp
28. Higgins D.G., Thompson J.D., and Gibson T.J. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266 (1996) 383-402
29. Kumar S., Tamura K., and Nei M. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 5 (2004) 150-163
30. Zhang B., Schmoyer D., Kirov S., and Snoddy J. GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics 5 (2004) 16