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Volumn 542, Issue 1, 2014, Pages 29-37

A genome-wide survey of bHLH transcription factors in the Placozoan Trichoplax adhaerens reveals the ancient repertoire of this gene family in metazoan

Author keywords

Basal metazoans; Basic helix loop helix proteins; Evolution; Genome wide survey

Indexed keywords

BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; PROTEIN; PROTEOME;

EID: 84897508478     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.03.024     Document Type: Article
Times cited : (18)

References (39)
  • 3
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology 1997, 268:78-94.
    • (1997) Journal of Molecular Biology , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 4
    • 80052100504 scopus 로고    scopus 로고
    • The basic helix-loop-helix transcription factor family in the pea aphid, Acyrthosiphon pisum
    • Dang C.W., Wang Y., Chen K.P., Yao Q., Zhang D.B., Guo M. The basic helix-loop-helix transcription factor family in the pea aphid, Acyrthosiphon pisum. Journal of Insect Science 2011, 11:84.
    • (2011) Journal of Insect Science , vol.11 , pp. 84
    • Dang, C.W.1    Wang, Y.2    Chen, K.P.3    Yao, Q.4    Zhang, D.B.5    Guo, M.6
  • 6
    • 0030464460 scopus 로고    scopus 로고
    • SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny
    • Galtier N., Gouy M., Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Computer Applications in the Biosciences 1996, 12:543-548.
    • (1996) Computer Applications in the Biosciences , vol.12 , pp. 543-548
    • Galtier, N.1    Gouy, M.2    Gautier, C.3
  • 7
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution 1997, 14:685-695.
    • (1997) Molecular Biology and Evolution , vol.14 , pp. 685-695
    • Gascuel, O.1
  • 8
    • 84886067979 scopus 로고    scopus 로고
    • Evolutionary aspects of variability in bHLH orthologous families: insights from the pearl oyster Pinctada fucata
    • Gyoja F., Satoh N. Evolutionary aspects of variability in bHLH orthologous families: insights from the pearl oyster Pinctada fucata. Zoological Science 2013, 30:868-876.
    • (2013) Zoological Science , vol.30 , pp. 868-876
    • Gyoja, F.1    Satoh, N.2
  • 9
    • 84862989404 scopus 로고    scopus 로고
    • A genomewide survey of bHLH transcription factors in the coral Acropora digitifera identifies three novel orthologous families, pearl, amber, and peridot
    • Gyoja F., Kawashima K., Satoh N. A genomewide survey of bHLH transcription factors in the coral Acropora digitifera identifies three novel orthologous families, pearl, amber, and peridot. Development Genes and Evolution 2012, 222:63-76.
    • (2012) Development Genes and Evolution , vol.222 , pp. 63-76
    • Gyoja, F.1    Kawashima, K.2    Satoh, N.3
  • 10
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 11
    • 4043141372 scopus 로고    scopus 로고
    • An overview of the basic helix-loop-helix proteins
    • Jones S. An overview of the basic helix-loop-helix proteins. Genome Biology 2004, 5:226.
    • (2004) Genome Biology , vol.5 , pp. 226
    • Jones, S.1
  • 14
    • 0025808242 scopus 로고
    • Functional activity of myogenic HLH proteins requires hetero-oligomerization with E12/E47-like protein in vivo
    • Lassar A., Davis R., Wright W.E., Kadesch T., Murre C., Voronova A., Baltimore D., Weintraub H. Functional activity of myogenic HLH proteins requires hetero-oligomerization with E12/E47-like protein in vivo. Cell 1991, 66:305-315.
    • (1991) Cell , vol.66 , pp. 305-315
    • Lassar, A.1    Davis, R.2    Wright, W.E.3    Kadesch, T.4    Murre, C.5    Voronova, A.6    Baltimore, D.7    Weintraub, H.8
  • 15
    • 0035001937 scopus 로고    scopus 로고
    • The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis
    • Ledent V., Vervoort M. The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Research 2001, 11:754-770.
    • (2001) Genome Research , vol.11 , pp. 754-770
    • Ledent, V.1    Vervoort, M.2
  • 16
    • 18744421788 scopus 로고    scopus 로고
    • Phylogenetic analysis of the human basic helix-loop-helix proteins
    • 0030.1-0030.18
    • Ledent V., Paquet O., Vervoort M. Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biology 2002, 3:0030.1-0030.18.
    • (2002) Genome Biology , vol.3
    • Ledent, V.1    Paquet, O.2    Vervoort, M.3
  • 17
    • 84865568203 scopus 로고    scopus 로고
    • A genome-wide identification and analysis of the basic helix-loop-helix transcription factors in the ponerine ant, Harpegnathos saltator
    • Liu A., Wang Y., Dang C., Zhang D., Song H., Yao Q., et al. A genome-wide identification and analysis of the basic helix-loop-helix transcription factors in the ponerine ant, Harpegnathos saltator. BMC Evolutionary Biology 2012, 12:165.
    • (2012) BMC Evolutionary Biology , vol.12 , pp. 165
    • Liu, A.1    Wang, Y.2    Dang, C.3    Zhang, D.4    Song, H.5    Yao, Q.6
  • 18
    • 84881137881 scopus 로고    scopus 로고
    • Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis
    • Liu A., Wang Y., Zhang D., Wang X., Song H., Dang C., Yao Q., Chen K. Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis. Molecular Genetics and Genomics 2013, 288:365-380.
    • (2013) Molecular Genetics and Genomics , vol.288 , pp. 365-380
    • Liu, A.1    Wang, Y.2    Zhang, D.3    Wang, X.4    Song, H.5    Dang, C.6    Yao, Q.7    Chen, K.8
  • 19
    • 0033980393 scopus 로고    scopus 로고
    • Helix-loop-helix proteins: regulators of transcription in eukaryotic organisms
    • Massari M.E., Murre C. Helix-loop-helix proteins: regulators of transcription in eukaryotic organisms. Molecular and Cellular Biology 2000, 20:429-440.
    • (2000) Molecular and Cellular Biology , vol.20 , pp. 429-440
    • Massari, M.E.1    Murre, C.2
  • 21
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: a novel method for fast and accurate multiple sequence alignment
    • Notredame C., Higgins D.G., Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 2000, 302:205-217.
    • (2000) Journal of Molecular Biology , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 22
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 23
    • 84860109324 scopus 로고    scopus 로고
    • MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
    • Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Höhna S., et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 2011, 61:539-542.
    • (2011) Systematic Biology , vol.61 , pp. 539-542
    • Ronquist, F.1    Teslenko, M.2    van der Mark, P.3    Ayres, D.L.4    Darling, A.5    Höhna, S.6
  • 24
    • 0038150206 scopus 로고    scopus 로고
    • A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors
    • Satou Y., Imai K.S., Levine M., Kohara Y., Rokhsar D., Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Development Genes and Evolution 2003, 213:213-221.
    • (2003) Development Genes and Evolution , vol.213 , pp. 213-221
    • Satou, Y.1    Imai, K.S.2    Levine, M.3    Kohara, Y.4    Rokhsar, D.5    Satoh, N.6
  • 25
    • 79952143437 scopus 로고    scopus 로고
    • Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki
    • Sebe-Pedros A., Mendoza A., Lang B.F., Degnan B.M., Ruiz-Trillo I. Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Molecular Biology and Evolution 2011, 28:1241-1254.
    • (2011) Molecular Biology and Evolution , vol.28 , pp. 1241-1254
    • Sebe-Pedros, A.1    Mendoza, A.2    Lang, B.F.3    Degnan, B.M.4    Ruiz-Trillo, I.5
  • 26
    • 1942489682 scopus 로고    scopus 로고
    • Developmental and evolutionary aspects of the basic helix-loop-helix transcription factors Atonal-like 1 and Achaete-scute homolog 2 in the jellyfish
    • Seipel K., Yanze N., Schmid V. Developmental and evolutionary aspects of the basic helix-loop-helix transcription factors Atonal-like 1 and Achaete-scute homolog 2 in the jellyfish. Developmental Biology 2004, 269:331-345.
    • (2004) Developmental Biology , vol.269 , pp. 331-345
    • Seipel, K.1    Yanze, N.2    Schmid, V.3
  • 27
    • 33947252158 scopus 로고    scopus 로고
    • Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics
    • Simionato E., Ledent V., Richards G., Thomas-Chollier M., Kerner P., Coornaert D., et al. Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics. BMC Evolutionary Biology 2007, 7:33.
    • (2007) BMC Evolutionary Biology , vol.7 , pp. 33
    • Simionato, E.1    Ledent, V.2    Richards, G.3    Thomas-Chollier, M.4    Kerner, P.5    Coornaert, D.6
  • 28
    • 47349105277 scopus 로고    scopus 로고
    • Atonal- and achaete-scute-related genes in the annelid Platynereis dumerilii: insights into the evolution of neural basic-helix-loop-helix genes
    • Simionato E., Kerner P., Dray N., Le Gouar M., Ledent V., Arendt D., et al. Atonal- and achaete-scute-related genes in the annelid Platynereis dumerilii: insights into the evolution of neural basic-helix-loop-helix genes. BMC Evolutionary Biology 2008, 8:170.
    • (2008) BMC Evolutionary Biology , vol.8 , pp. 170
    • Simionato, E.1    Kerner, P.2    Dray, N.3    Le Gouar, M.4    Ledent, V.5    Arendt, D.6
  • 29
    • 55449128042 scopus 로고    scopus 로고
    • The HLH-6 transcription factor regulates C. elegans pharyngeal gland development and function
    • Smit R.B., Schnabel R., Gaudet J. The HLH-6 transcription factor regulates C. elegans pharyngeal gland development and function. PLoS Genetics 2008, 4(10):e1000222.
    • (2008) PLoS Genetics , vol.4 , Issue.10
    • Smit, R.B.1    Schnabel, R.2    Gaudet, J.3
  • 31
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 2007, 56:564-577.
    • (2007) Systematic Biology , vol.56 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 32
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 2011, 28:2731-2739.
    • (2011) Molecular Biology and Evolution , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 33
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994, 22:4673-4680.
    • (1994) Nucleic Acids Research , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 34
    • 35148836132 scopus 로고    scopus 로고
    • The basic helix-loop-helix transcription factor family in Bombyx mori
    • Wang Y., Chen K., Yao Q., Wang W., Zhi Z. The basic helix-loop-helix transcription factor family in Bombyx mori. Development Genes and Evolution 2007, 217:715-723.
    • (2007) Development Genes and Evolution , vol.217 , pp. 715-723
    • Wang, Y.1    Chen, K.2    Yao, Q.3    Wang, W.4    Zhi, Z.5
  • 35
    • 45349099945 scopus 로고    scopus 로고
    • The basic helix-loop-helix transcription factor family in the honey bee, Apis mellifera
    • Wang Y., Chen K., Yao Q., Wang W., Zhu Z. The basic helix-loop-helix transcription factor family in the honey bee, Apis mellifera. Journal of Insect Science 2008, 8:1-12.
    • (2008) Journal of Insect Science , vol.8 , pp. 1-12
    • Wang, Y.1    Chen, K.2    Yao, Q.3    Wang, W.4    Zhu, Z.5
  • 36
    • 67349144743 scopus 로고    scopus 로고
    • Phylogenetic analysis of zebrafish basic helix-loop-helix transcription factors
    • Wang Y., Chen K., Yao Q., Zheng X., Yang Z. Phylogenetic analysis of zebrafish basic helix-loop-helix transcription factors. Journal of Molecular Evolution 2009, 68:629-640.
    • (2009) Journal of Molecular Evolution , vol.68 , pp. 629-640
    • Wang, Y.1    Chen, K.2    Yao, Q.3    Zheng, X.4    Yang, Z.5
  • 37
    • 0035894449 scopus 로고    scopus 로고
    • Sgn1, a basic helix-loop-helix transcription factor delineates the salivary gland duct cell lineage in mice
    • Yoshida S., Ohbo K., Takakura A., Takebayashi H., Okada T., Abe K., Nabeshima Y. Sgn1, a basic helix-loop-helix transcription factor delineates the salivary gland duct cell lineage in mice. Developmental Biology 2001, 240:517-530.
    • (2001) Developmental Biology , vol.240 , pp. 517-530
    • Yoshida, S.1    Ohbo, K.2    Takakura, A.3    Takebayashi, H.4    Okada, T.5    Abe, K.6    Nabeshima, Y.7
  • 39
    • 64949151123 scopus 로고    scopus 로고
    • A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse
    • 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. Mammalian Genome 2009, 20:236-246.
    • (2009) Mammalian Genome , vol.20 , pp. 236-246
    • Zheng, X.1    Wang, Y.2    Yao, Q.3    Yang, Z.4    Chen, K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.