Abstract
The basic helix-loop-helix (bHLH) proteins play essential roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in over 20 organisms, including nematode, fruit fly, and human. Our study identified 114 rat and 14 additional mouse bHLH members in rat and mouse genomes, respectively. Phylogenetic analyses revealed that both rat and mouse had 49, 26, 15, 4, 12, and 4 bHLH members in groups A, B, C, D, E, and F, respectively. Only the rat Mxi1 gene has two copies in the genome. All other rat bHLH genes and all mouse bHLH genes are single-copy genes. The chromosomal distribution pattern of mouse, rat, and human bHLH genes suggests the emergence of some bHLH genes through gene duplication, which probably happened at least before the divergence of vertebrates from invertebrates. The present study provides useful information for future studies using rat as a model animal for mammalian development.
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References
Atchley WR, Terhalle W, Dress A (1999) Positional dependence, cliques, and predictive motifs in the bHLH protein domain. J Mol Evol 48(5):501–516
Buck MJ, Atchley WR (2003) Phylogenetic analysis of plant basic helix-loop-helix proteins. J Mol Evol 56(6):742–750
Ferre-D’Amare AR, Prendergast GC, Ziff EB, Burley SK (1993) Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363(6424):38–45
Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Sci 8:275–282
Ledent V, Vervoort M (2001) The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Res 11(5):754–770
Ledent V, Paquet O, Vervoort M (2002) Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biol 3(6):RESEARCH0030
Li X, Duan X, Jiang H, Sun Y, Tang Y et al (2006) Genome-wide analysis of basic helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol 141(4):1167–1184
Massari ME, Murre C (2000) Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol Cell Biol 20(2):429–440
Morrow EM, Furukawa T, Lee JE, Cepko CL (1999) NeuroD regulates multiple functions in the developing neural retina in rodent. Development 126(1):23–36
Nicholas KB, Nicholas HB Jr, Deerfield-II DW (1997) GeneDoc: analysis and visualization of genetic variation. Embnet News 4:14
Satou Y, Imai KS, Yamada L, Kohara Y, Rokhsar D et al (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Dev Genes Evol 213(5–6):213–221
Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502–504
Simionato E, Ledent V, Richards G, Thomas-Chollier M, Kerner P et al (2007) Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics. BMC Evol Biol 7:33
Stewart HJ, Zoidl G, Rossner M, Brennan A, Zoidl C et al (1997) Helix-loop-helix proteins in Schwann cells: a study of regulation and subcellular localization of Ids, REB, and E12/47 during embryonic and postnatal development. J Neurosci Res 50(5):684–701
Swofford DL (1998) PAUP* Phylogenetic analysis using parsimony, Version 4. Sinauer Associates, Sunderland, MA
Toledo-Ortiz G, Huq E, Quail PH (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15(8):1749–1770
Wang Y, Chen KP, Yao Q, Wang W, Zhu Z (2007) The basic helix-loop-helix transcription factor family in Bombyx mori. Dev Genes Evol 217(10):715–723
Wang Y, Chen KP, Yao Q, Wang WB, Zhu Z (2008) The basic helix-loop-helix transcription factor family in the honeybee, Apis mellifera. J Insect Sci 8(44)
Acknowledgments
We are grateful to Professor Bin Chen for comments on the manuscript. This work was supported by grants from Jiangsu Sci-Tech Support Project—Agriculture (No. BE2008379) and the China National “863” Project (No. 2008AA10Z145).
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X. Zheng and Y. Wang are jointly first authors.
An erratum to this article can be found at http://dx.doi.org/10.1007/s00335-009-9196-3
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Zheng, X., Wang, Y., Yao, Q. et al. A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse. Mamm Genome 20, 236–246 (2009). https://doi.org/10.1007/s00335-009-9176-7
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DOI: https://doi.org/10.1007/s00335-009-9176-7