title: Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.
abstract: BACKGROUND
  Sox10, a member of the Sry-related HMG-Box gene family, is a critical transcription factor for several important cell lineages, most notably the neural crest stem cells and the derivative peripheral glial cells and melanocytes. Thus far, only a handful of direct target genes are known for this transcription factor limiting our understanding of the biological network it governs.
  
  
  RESULTS
  We describe identification of multiple direct regulatory target genes of Sox10 through a procedure based on function and conservation. By combining RNA interference technique and DNA microarray technology, we have identified a set of genes that show significant down-regulation upon introduction of Sox10 specific siRNA into Schwannoma cells. Subsequent comparative genomics analyses led to potential binding sites for Sox10 protein conserved across several mammalian species within the genomic region proximal to these genes. Multiple sites belonging to 4 different genes (proteolipid protein, Sox10, extracellular superoxide dismutase, and pleiotrophin) were shown to directly interact with Sox10 by chromatin immunoprecipitation assay. We further confirmed the direct regulation through the identified cis-element for one of the genes, extracellular superoxide dismutase, using electrophoretic mobility shift assay and reporter assay.
  
  
  CONCLUSIONS
  In sum, the process of combining differential expression profiling and comparative genomics successfully led to further defining the role of Sox10, a critical transcription factor for the development of peripheral glia. Our strategy utilizing relatively accessible techniques and tools should be applicable to studying the function of other transcription factors.
authors.affiliation: Division of Life and Pharmaceutical Sciences and the Center for Cell Signaling & Drug Discovery Research, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul, 120-750, Korea. kamsi97@hanmail.net
authors.forename: Kyung Eun
authors.initials: KE
authors.lastname: Lee
authors.forename: Seungyoon
authors.initials: S
authors.lastname: Nam
authors.forename: Eun-ah
authors.initials: EA
authors.lastname: Cho
authors.forename: Ikjoo
authors.initials: I
authors.lastname: Seong
authors.forename: Jin-Kyung
authors.initials: JK
authors.lastname: Limb
authors.forename: Sanghyuk
authors.initials: S
authors.lastname: Lee
authors.forename: Jaesang
authors.initials: J
authors.lastname: Kim
mesh_terms: D000818:Animals; D001665:Binding Sites; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods*; D006609:High Mobility Group Proteins / Q000378:metabolism*; D006801:Humans; D009457:Neuroglia / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D034622:RNA Interference; D055757:SOXE Transcription Factors; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D006609:High Mobility Group Proteins; C527923:SOX10 protein, human; D055757:SOXE Transcription Factors; D014157:Transcription Factors
references.citation: Genome Res. 2005 Aug;15(8):1034-50
references.pmid: 16024819
references.citation: Ann Neurol. 2003 Mar;53(3):354-65
references.pmid: 12601703
references.citation: Nat Immunol. 2004 Aug;5(8):768-74
references.pmid: 15282556
references.citation: Arch Biochem Biophys. 2002 Jan 15;397(2):162-71
references.pmid: 11795867
references.citation: J Neurosci. 1998 Jan 1;18(1):237-50
references.pmid: 9412504
references.citation: EMBO J. 1992 Oct;11(10):3705-12
references.pmid: 1396566
references.citation: Nucleic Acids Res. 1994 Apr 25;22(8):1500-1
references.pmid: 8190643
references.citation: Hum Mol Genet. 2002 Nov 15;11(24):3075-85
references.pmid: 12417529
references.citation: Proc Natl Acad Sci U S A. 2006 May 16;103(20):7871-6
references.pmid: 16684879
references.citation: Brain Res Dev Brain Res. 1993 Mar 19;72(1):133-44
references.pmid: 8453763
references.citation: Mol Vis. 2007 Jan 05;13:1-11
references.pmid: 17242675
references.citation: Hum Mol Genet. 2001 Nov 15;10(24):2783-95
references.pmid: 11734543
references.citation: Nat Genet. 1998 Jan;18(1):60-4
references.pmid: 9425902
references.citation: J Biol Chem. 2000 Dec 1;275(48):37978-83
references.pmid: 10973953
references.citation: Cancer Res. 2006 May 1;66(9):4574-83
references.pmid: 16651407
references.citation: Cancer Res. 2006 Nov 15;66(22):11039-46
references.pmid: 17108143
references.citation: Pigment Cell Res. 2004 Aug;17(4):352-62
references.pmid: 15250937
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D108-10
references.pmid: 16381825
references.citation: J Cell Biol. 1996 May;133(3):667-81
references.pmid: 8636240
references.citation: Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2229-34
references.pmid: 10688915
references.citation: Genes Dev. 2002 Jan 15;16(2):165-70
references.pmid: 11799060
references.citation: J Neurosci. 2006 Apr 12;26(15):3933-41
references.pmid: 16611809
references.citation: Neurochem Res. 2007 Feb;32(2):343-51
references.pmid: 17191136
references.citation: Development. 2003 Apr;130(7):1243-54
references.pmid: 12588842
references.citation: Bioessays. 2006 Aug;28(8):788-98
references.pmid: 16927299
references.citation: Mol Cell Biol. 2000 May;20(9):3198-209
references.pmid: 10757804
references.citation: Genes Dev. 2001 Jan 1;15(1):66-78
references.pmid: 11156606
references.citation: Exp Biol Med (Maywood). 2004 Sep;229(8):705-21
references.pmid: 15337825
references.citation: Differentiation. 2006 Dec;74(9-10):542-51
references.pmid: 17177851
references.citation: Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6264-8
references.pmid: 7603981
references.citation: Hum Genet. 2000 Jul;107(1):1-6
references.pmid: 10982026
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8
references.pmid: 16381938
references.citation: Nucleic Acids Res. 1999 Mar 1;27(5):1359-64
references.pmid: 9973626
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4664-9
references.pmid: 17360581
references.citation: Neuron. 2003 Apr 10;38(1):17-31
references.pmid: 12691661
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3576-9
references.pmid: 12824369
references.citation: Nat Genet. 1998 Feb;18(2):171-3
references.pmid: 9462749
references.citation: J Neurosci Res. 2004 Dec 15;78(6):796-802
references.pmid: 15523643