Hereditas (Beijing) (遗传) 2012/34:1 PP.59-71
Xenopus is an important model animal for biomedicine researches. In order to probe into the classification and function of the basic helix-loop-helix (bHLH) transcription factor family, we conducted a genome-wide survey and identified 70 bHLH transcription factors using the Xenopus tropicalis genome project data in the study. Among these transcription factors, 69 bHLH transcription factors were classified into 6 large groups composed of 34 sub-families and the remaining one was classified as ‘orphan’. Results of Gene Ontology (GO) enrichment statistics showed 51 frequent GO annotation categories. Statistical analysis of the GO annotations showed that these 70 bHLH proteins tended to be frequently related to transcription regulator activity, regulation of transcription, DNA binding, regulation of RNA metabolic process, DNA-dependent regulation of transcription, transcription, and transcription factor activity, indicating that they were expected to be the most common GO categories of transcriptional factors. Moreover, a number of bHLH genes were revealed to play important regulation roles in special development and physiological processes, such as muscle tissue and organ (striated muscle, skeletal muscle, eye muscle, and pharyngeal muscle) differentiation and development, e.g., digestive system development, pharynx development and sensory organ development, regulation of nucleobase, nucleoside and nucleotide and nucleic acid metabolic process, regulation of biosynthetic process, DNA binding, and protein heterodimerization activity, etc. There were also some important signaling pathways in the significant GO categories. We made the evolutionary analysis of Hes transcription factor family as well. This preliminary result lays a solid foundation for further researches on X. tropicalis.
 Boggon TJ, Shan WS, Santagata S, Myers SC, Shapiro L. Implication of tubby proteins as transcription factors by structure-based functional analysis. Science, 1999, 286(5447): 2119-2125.
 Luscombe NM, Austin SE, Berman HM, Thornton JM. An overview of the structures of protein-DNA complexes. Genome Biol, 2000, 1(1): 1-37.
 Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu GL. Arabidopsis transcription factors: genome-wide comparative analysis among eu-karyotes. Science, 2000, 290(5499): 2105-2110.
 Atchley WR, Fitch WM. A natural classification of the basic helix-loop-helix class of transcription factors. Proc Natl Acad Sci USA, 1997, 94(10): 5172-5176.
 Massari ME, Murre C. Helix-loop-helix proteins: Regulators of transcription in eucaryotic organisms. Mol Cell Biol, 2000, 20(2): 429-440.
 Ledent V, Vervoort M. The basic helix-loop-helix protein family: Comparative genomics and phylogenetic analysis. Genome Res, 2001, 11(5): 754-770.
 Stevens JD, Roalson EH, Skinner MK. Phylogenetic and expression analysis of the basic helix-loop-helix tran-scription factor gene family: genomic approach to cellular differentiation. Differentiation, 2008, 76(9): 1006-1022.
 Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martínez-García JF, Bilbao-Castro JR, Robertson DL. Genome-Wide Classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiol, 2010, 153(3): 1398-1412.
 Murre C, McCaw PS, Baltimore D. A new DNA binding and dimerization motif in immunoglobulin enhancer binding, Daughterless, MyoD and Myc proteins. Cell, 1989, 56(5): 777-783.
 Atchley WR, Terhalle W, Dress A. Positional dependence, cliques, and predictive motifs in the bHLH protein domain. J Mol Evol, 1999, 48(5): 501-516.
 Ledent V, Paquet O, Vervoort M. Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biol, 2002, 3(6): 301-3018.
 Toledo-Ortiz G, Huq E, Quail PH. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 2003, 15(8): 1749-1770.
 Li J, Liu Q, Qiu MS, Pan YC, Li YX, Shi TL. Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family. Biochem Biophys Res Commun, 2006, 350(3): 648-656.
 Simionato E, Ledent V, Richards G, Thomas-Chollier M, Kerner P, Coornaert D, Degnan BM, Vervoort M. Origin and diversification of the basic helix-loop-helix gene family in metazoans: Insights from comparative genomics. BMC Evol Biol, 2007, 7: 33.
 Wang Y, Chen KP, Yao Q, Wang WB, Zhu Z. The basic helix-loop-helix transcription factor family in Bombyx mori. Dev Genes Evol, 2007, 217(10): 715-723.
 Wang Y, Chen KP, Yao Q, Zheng XD, Yang Z. Phylogenetic analysis of zebrafish basic helix-loop-helix transcription factors. J Mol Evol, 2009, 68(6): 629-640.
 Liu WY, Zhao CJ. Genome-wide identification and analysis of the chicken basic helix-loop-helix factors. Comp Funct Genomics, 2010: 682095.
 Zheng X, Wang Y, Yao Q, Yang Z, Chen K. A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse. Mamm Genome, 2009, 20(4): 236-246.
 Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu SQ, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS. The genome of the Western clawed frog Xenopus tropicalis. Science, 2010, 328(5978): 633-636.
 Bowes JB, Snyder KA, Segerdell E, Gibb R, Jarabek C, Noumen E, Pollet N, Vize PD. Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res, 2008, 36: D761-D767.
 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by qual-ity analysis tools. Nucleic Acids Res, 1997, 25(24): 4876-4882.
 Nicholas KB, Nicholas HB, Deerfield DW. GeneDoc: analysis and visualization of genetic variation. EMBNET News, 1997, 4: 14.
 Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 2003, 19(12): 1572-1574.
 Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likeli-hood. Syst Biol, 2003, 52(5): 696-704.
 Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol, 2003, 4(5): P3-last page.
 Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bio-informatics resources. Nat Protocol, 2009, 4(1): 44-57.
 Nei M, Gu X, Sitnikova T. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc Natl Acad Sci USA, 1997, 94(15): 7799-7806.