Comparative analysis of conservation and regulatory network on core transcription factors in mouse inner ear development
Received date: 2013-04-22
Revised date: 2013-07-21
Online published: 2013-10-25
During vertebrate inner ear development, several core genes, such as Six1, Six4, Pax2, Pax8, Foxi1, Dlx5, Gbx2, Irx2/3, and Msx1, are crucial to the regulation of the otic placode induction. In order to get the gene regulatory network during inner ear development, bioinformatics methods were adopted to analyze conservation and regulation of the core transcription factors in mice. Pax2, Pax8, Foxi1, and Dlx5 remained to be the main regulators during inner ear development, which was consistent with the gene regulatory network from literature. Six1 was regulated by many transcription factors, and Gbx2, Irx2/3, and Msx1 played important roles in the regulatory network. The differences in the constructed regulatory network were reasonably analyzed. It was predicted that Msx1 regulated the expression of Six1 and Gbx2. In addition, several transcription factors, such as Sox5, Lhx2, Rax, Otx1, Otx2, Pitx1, Pitx2, Nkx2-5, Irx4, Irx6, Dlx2, Hmx1/2/3, Pou4f3, Pax4 and Tlx2, were found to be involved in the regulatory network. Our results provide an improved understanding of the regu-latory mechanism during inner ear development.
Key words： inner ear development; transcription factors; regulation network
CHEN Zhi-Qiang HAN Xin-Huan WEI Qin-Jun XING Guang-Qian CAO Xin . Comparative analysis of conservation and regulatory network on core transcription factors in mouse inner ear development[J]. Hereditas(Beijing), 2013 , 35(10) : 1198 -1208 . DOI: 10.3724/SP.J.1005.2013.01198
[1] Chatterjee S, Kraus P, Lufkin T. A symphony of inner ear developmental control genes. BMC Genet, 2010, 11: 68.<\p>
[2] Brown AS, Epstein DJ. Otic ablation of smoothened re-veals direct and indirect requirements for Hedgehog sig-naling in inner ear development. Development, 2011, 138(18): 3967–3976.<\p>
[3] Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li WZ, Lopez R, McWilliam R, Soding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality pro-tein multiple sequence alignments using Clustal Omega. Mol Syst Biol, 2011, 7(1): 539.<\p>
[4] Prestridge DS. Predicting Pol II promoter sequences using transcription factor binding sites. J Mol Biol, 1995, 249(5): 923–932.<\p>
[5] Knudsen S. Promoter2.0: for the recognition of PolII promoter sequences. Bioinformatics, 1999, 15(5): 356– 361.<\p>
[6] Sandelin A, Wasserman WW, Lenhard B. ConSite: web- based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res, 2004, 32(Suppl. 2): W249– W252.<\p>
[7] Messeguer X, Escudero R, Farre D, Núñez O, Martinez J, Alba MM. PROMO: detection of known transcription regulatory elements using species-tailored searches. Bio-informatics, 2002, 18(2): 333–334.<\p>
[8] Farré D, Roset R, Huerta M, Adsuara JE, Rosello L, Albà MM, Messeguer X. Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. Nucleic Acids Res, 2003, 31(13): 3651–3653.<\p>
[9] Frith MC, Hansen U, Weng ZP. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics, 2001, 17(10): 878–889.<\p>
[10] Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res, 2010, 38(Database issue): D105–D110.<\p>
[11] Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A. JASPAR, the open access database of transcription factor-binding pro-files: new content and tools in the 2008 update. Nucleic Acids Res, 2008, 36(Database issue): D102–D106.<\p>
[12] 陈鸿飞, 王进科. 转录因子相关数据库. 遗传, 2010, 32(10): 1009–1017.<\p>
[13] Longabaugh WJR, Davidson EH, Bolouri H. Computa-tional representation of developmental genetic regulatory networks. Dev Biol, 2005, 283(1): 1–16.<\p>
[14] Longabaugh WJ, Davidson EH, Bolouri H. Visualization, documentation, analysis, and communication of large- scale gene regulatory networks. Biochim Biophys Acta, 2009, 1789(4): 363–374.<\p>
[15] Grocott T, Tambalo M, Streit A. The peripheral sensory nervous system in the vertebrate head: a gene regulatory perspective. Dev Biol, 2012, 370(1): 3–23.<\p>
[16] Sato S, Ikeda K, Shioi G, Ochi H, Ogino H, Yajima H, Kawakami K. Conserved expression of mouse Six1 in the pre-placodal region (PPR) and identification of an enhan-cer for the rostral PPR. Dev Biol, 2010, 344(1): 158–171. <\p>
[17] Christophorou NAD, Bailey AP, Hanson S, Streit A. Acti-vation of Six1 target genes is required for sensory placode formation. Dev Biol, 2009, 336(2): 327–336.<\p>
[18] Burton Q, Cole LK, Mulheisen M, Chang W, Wu DK. The role of Pax2 in mouse inner ear development. Dev Biol, 2004, 272(1): 161–175.<\p>
[19] Bouchard M, de Caprona D, Busslinger M, Xu PX, Fritzsch B. Pax2 and Pax8 cooperate in mouse inner ear morphogenesis and innervation. BMC Dev Biol, 2010, 10(1): 89.<\p>
[20] Kwon HJ, Bhat N, Sweet EM, Cornell RA, Riley BB. Identification of early requirements for preplacodal ecto-derm and sensory organ development. PLoS Genet, 2010, 6(9): e1001133.<\p>
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