메뉴 건너뛰기




Volumn 49, Issue 6, 2017, Pages 935-940

Conservation and innovation in the DUX4-family gene network

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DUX; TRANSCRIPTION FACTOR DUX4; UNCLASSIFIED DRUG; DUX4 PROTEIN, HUMAN; DUX4 PROTEIN, MOUSE; HOMEODOMAIN PROTEIN; RETROPOSON;

EID: 85018247895     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3846     Document Type: Article
Times cited : (231)

References (37)
  • 1
    • 84902517476 scopus 로고    scopus 로고
    • Facioscapulohumeral dystrophy: The path to consensus on pathophysiology
    • Tawil, R., van der Maarel, S.M. & Tapscott, S.J. Facioscapulohumeral dystrophy: the path to consensus on pathophysiology. Skelet. Muscle 4, 12 (2014).
    • (2014) Skelet. Muscle , vol.4 , pp. 12
    • Tawil, R.1    Van Der Maarel, S.M.2    Tapscott, S.J.3
  • 3
    • 79953292473 scopus 로고    scopus 로고
    • DUX4, a candidate gene for facioscapulohumeral muscular dystrophy, causes p53-dependent myopathy in vivo
    • Wallace, L.M. et al. DUX4, a candidate gene for facioscapulohumeral muscular dystrophy, causes p53-dependent myopathy in vivo. Ann. Neurol. 69, 540-552 (2011).
    • (2011) Ann. Neurol. , vol.69 , pp. 540-552
    • Wallace, L.M.1
  • 4
    • 84876821220 scopus 로고    scopus 로고
    • Intrinsic epigenetic regulation of the D4Z4 macrosatellite repeat in a transgenic mouse model for FSHD
    • Krom, Y.D. et al. Intrinsic epigenetic regulation of the D4Z4 macrosatellite repeat in a transgenic mouse model for FSHD. PLoS Genet. 9, e1003415 (2013).
    • (2013) PLoS Genet. , vol.9 , pp. e1003415
    • Krom, Y.D.1
  • 5
    • 84922547186 scopus 로고    scopus 로고
    • Dominant lethal pathologies in male mice engineered to contain an X-linked DUX4 transgene
    • Dandapat, A. et al. Dominant lethal pathologies in male mice engineered to contain an X-linked DUX4 transgene. Cell Rep. 8, 1484-1496 (2014).
    • (2014) Cell Rep. , vol.8 , pp. 1484-1496
    • Dandapat, A.1
  • 6
    • 84855956147 scopus 로고    scopus 로고
    • DUX4 activates germline genes, retroelements, and immune mediators: Implications for facioscapulohumeral dystrophy
    • Geng, L.N. et al. DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Dev. Cell 22, 38-51 (2012).
    • (2012) Dev. Cell , vol.22 , pp. 38-51
    • Geng, L.N.1
  • 7
    • 84888236297 scopus 로고    scopus 로고
    • DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis
    • Young, J.M. et al. DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. PLoS Genet. 9, e1003947 (2013).
    • (2013) PLoS Genet. , vol.9 , pp. e1003947
    • Young, J.M.1
  • 8
    • 70349621645 scopus 로고    scopus 로고
    • Biphasic myopathic phenotype of mouse DUX, an ORF within conserved FSHD-related repeats
    • Bosnakovski, D., Daughters, R.S., Xu, Z., Slack, J.M. & Kyba, M. Biphasic myopathic phenotype of mouse DUX, an ORF within conserved FSHD-related repeats. PLoS One 4, e7003 (2009).
    • (2009) PLoS One , vol.4 , pp. e7003
    • Bosnakovski, D.1    Daughters, R.S.2    Xu, Z.3    Slack, J.M.4    Kyba, M.5
  • 9
    • 84867632695 scopus 로고    scopus 로고
    • Evolution of DUX gene macrosatellites in placental mammals
    • Leidenroth, A. et al. Evolution of DUX gene macrosatellites in placental mammals. Chromosoma 121, 489-497 (2012).
    • (2012) Chromosoma , vol.121 , pp. 489-497
    • Leidenroth, A.1
  • 10
    • 78649330207 scopus 로고    scopus 로고
    • A family history of DUX4: Phylogenetic analysis of DUXA, B, C and Duxbl reveals the ancestral DUX gene
    • Leidenroth, A. & Hewitt, J.E. A family history of DUX4: phylogenetic analysis of DUXA, B, C and Duxbl reveals the ancestral DUX gene. BMC Evol. Biol. 10, 364 (2010).
    • (2010) BMC Evol. Biol. , vol.10 , pp. 364
    • Leidenroth, A.1    Hewitt, J.E.2
  • 11
    • 34547754037 scopus 로고    scopus 로고
    • Evolutionary conservation of a coding function for D4Z4, the tandem DNA repeat mutated in facioscapulohumeral muscular dystrophy
    • Clapp, J. et al. Evolutionary conservation of a coding function for D4Z4, the tandem DNA repeat mutated in facioscapulohumeral muscular dystrophy. Am. J. Hum. Genet. 81, 264-279 (2007).
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 264-279
    • Clapp, J.1
  • 12
    • 85014379519 scopus 로고    scopus 로고
    • Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4
    • Eidahl, J.O. et al. Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4. Hum. Mol. Genet. 25, 4577-4589 (2016).
    • (2016) Hum. Mol. Genet. , vol.25 , pp. 4577-4589
    • Eidahl, J.O.1
  • 13
    • 84995387826 scopus 로고    scopus 로고
    • DUX4 induces a transcriptome more characteristic of a less-differentiated cell state and inhibits myogenesis
    • Knopp, P. et al. DUX4 induces a transcriptome more characteristic of a less-differentiated cell state and inhibits myogenesis. J. Cell Sci. 129, 3816-3831 (2016).
    • (2016) J. Cell Sci. , vol.129 , pp. 3816-3831
    • Knopp, P.1
  • 14
    • 34347263069 scopus 로고    scopus 로고
    • Zscan4: A novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells
    • Falco, G. et al. Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells. Dev. Biol. 307, 539-550 (2007).
    • (2007) Dev. Biol. , vol.307 , pp. 539-550
    • Falco, G.1
  • 15
    • 33750215791 scopus 로고    scopus 로고
    • Zfp206 regulates ES cell gene expression and differentiation
    • Zhang, W. et al. Zfp206 regulates ES cell gene expression and differentiation. Nucleic Acids Res. 34, 4780-4790 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. 4780-4790
    • Zhang, W.1
  • 16
    • 84863458292 scopus 로고    scopus 로고
    • Embryonic stem cell potency fluctuates with endogenous retrovirus activity
    • Macfarlan, T.S. et al. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487, 57-63 (2012).
    • (2012) Nature , vol.487 , pp. 57-63
    • Macfarlan, T.S.1
  • 17
    • 84947790475 scopus 로고    scopus 로고
    • Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells
    • Akiyama, T. et al. Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells. DNA Res. 22, 307-318 (2015).
    • (2015) DNA Res. , vol.22 , pp. 307-318
    • Akiyama, T.1
  • 18
    • 85002032285 scopus 로고    scopus 로고
    • Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells
    • Jagannathan, S. et al. Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells. Hum. Mol. Genet. 25, 4419-4431 (2016).
    • (2016) Hum. Mol. Genet. , vol.25 , pp. 4419-4431
    • Jagannathan, S.1
  • 19
    • 84976897928 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • NCBI Resource Coordinators
    • NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 44, D7-D19 (2016).
    • (2016) Nucleic Acids Res. , vol.44 , pp. D7-D19
  • 20
    • 67849122320 scopus 로고    scopus 로고
    • MEME SUITE: Tools for motif discovery and searching
    • Bailey, T.L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202-W208 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. W202-W208
    • Bailey, T.L.1
  • 21
    • 45449111373 scopus 로고    scopus 로고
    • Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
    • Noyes, M.B. et al. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133, 1277-1289 (2008).
    • (2008) Cell , vol.133 , pp. 1277-1289
    • Noyes, M.B.1
  • 22
    • 5044251591 scopus 로고    scopus 로고
    • Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos
    • Peaston, A.E. et al. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7, 597-606 (2004).
    • (2004) Dev. Cell , vol.7 , pp. 597-606
    • Peaston, A.E.1
  • 23
    • 85018449904 scopus 로고    scopus 로고
    • Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons
    • Hendrickson, P.G. et al. Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nat. Genet. http://dx.doi.org/10.1038/ng.3844 (2017).
    • (2017) Nat. Genet.
    • Hendrickson, P.G.1
  • 24
    • 54349088194 scopus 로고    scopus 로고
    • An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies
    • Bosnakovski, D. et al. An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies. EMBO J. 27, 2766-2779 (2008).
    • (2008) EMBO J. , vol.27 , pp. 2766-2779
    • Bosnakovski, D.1
  • 25
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 26
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 27
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 28
    • 33646361583 scopus 로고    scopus 로고
    • GenePattern 2.0
    • Reich, M. et al. GenePattern 2.0. Nat. Genet. 38, 500-501 (2006).
    • (2006) Nat. Genet. , vol.38 , pp. 500-501
    • Reich, M.1
  • 29
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550 (2005).
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1
  • 30
    • 84976875034 scopus 로고    scopus 로고
    • PANTHER version 10: Expanded protein families and functions, and analysis tools
    • Mi, H., Poudel, S., Muruganujan, A., Casagrande, J.T. & Thomas, P.D. PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res. 44 D1, D336-D342 (2016).
    • (2016) Nucleic Acids Res. , vol.44 D1 , pp. D336-D342
    • Mi, H.1    Poudel, S.2    Muruganujan, A.3    Casagrande, J.T.4    Thomas, P.D.5
  • 31
    • 84958692273 scopus 로고    scopus 로고
    • Distinct activities of Myf5 and MyoD indicate separate roles in skeletal muscle lineage specification and differentiation
    • Conerly, M.L., Yao, Z., Zhong, J.W., Groudine, M. & Tapscott, S.J. Distinct activities of Myf5 and MyoD indicate separate roles in skeletal muscle lineage specification and differentiation. Dev. Cell 36, 375-385 (2016).
    • (2016) Dev. Cell , vol.36 , pp. 375-385
    • Conerly, M.L.1    Yao, Z.2    Zhong, J.W.3    Groudine, M.4    Tapscott, S.J.5
  • 32
    • 77951935861 scopus 로고    scopus 로고
    • Genome-wide MyoD binding in skeletal muscle cells: A potential for broad cellular reprogramming
    • Cao, Y. et al. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev. Cell 18, 662-674 (2010).
    • (2010) Dev. Cell , vol.18 , pp. 662-674
    • Cao, Y.1
  • 33
    • 84878580738 scopus 로고    scopus 로고
    • The Subread aligner: Fast, accurate and scalable read mapping by seed-and-vote
    • Liao, Y., Smyth, G.K. & Shi, W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 41, e108 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. e108
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 34
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
    • (2008) Genome Biol. , vol.9 , pp. R137
    • Zhang, Y.1
  • 35
    • 84901830680 scopus 로고    scopus 로고
    • Motif-based analysis of large nucleotide data sets using MEME-ChIP
    • Ma, W., Noble, W.S. & Bailey, T.L. Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nat. Protoc. 9, 1428-1450 (2014).
    • (2014) Nat. Protoc. , vol.9 , pp. 1428-1450
    • Ma, W.1    Noble, W.S.2    Bailey, T.L.3
  • 36
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 37
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar, R., Domrachev, M. & Lash, A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.