title: Comparative analysis of MTF-1 binding sites between human and mouse.
abstract: MTF-1 is a crucial transcription factor involved in the cellular response to heavy-metal load and other stresses by specifically binding to metal response elements (MREs). Thus far only a handful of direct target genes are known for this transcription factor, limiting our understanding of the biological network it governs. In this article we try to employ a computational strategy based on the generation of literature-based positional weight matrices (PWM) and log-likelihood scoring of the candidate binding sites (BSs) for identification of direct targets of the transcription factor MTF-1 in human and mouse. Through comparisons, we explore the conservation and unique characteristics between two species. Our results show that the numbers of MREs differ dramatically between species and their positions relative to their cognate promoter is also flexible. Importantly, we identify a set of target genes generally well conserved between human and mouse. Finally, by combining expression analysis we provide two putative targets (HMGCR and CYP51A), which regulate lipid metabolism conserved in human and mouse. Overall, interspecies comparison from our study may provide some valuable information for further studying human Wilson disease (WD) using mouse model systems.
authors.affiliation: Department of Animal Sciences, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Minghui
authors.initials: M
authors.lastname: Wang
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.forename: Xiangzhe
authors.initials: X
authors.lastname: Zhang
authors.forename: Hongbo
authors.initials: H
authors.lastname: Zhao
authors.forename: Qishan
authors.initials: Q
authors.lastname: Wang
authors.forename: Yuchun
authors.initials: Y
authors.lastname: Pan
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000378:metabolism*; D016678:Genome; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D013045:Species Specificity; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic; D000097809:Transcription Factor MTF-1
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D000097809:Transcription Factor MTF-1
references.citation: Eur J Biochem. 1999 Feb;259(3):635-42
references.pmid: 10092847
references.citation: Genome Res. 2006 May;16(5):595-605
references.pmid: 16606705
references.citation: Biometals. 2001 Sep-Dec;14(3-4):223-37
references.pmid: 11831458
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):137-40
references.pmid: 11125071
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W369-73
references.pmid: 16845028
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):43-50
references.pmid: 12519944
references.citation: Cancer Res. 1999 Mar 15;59(6):1315-22
references.pmid: 10096565
references.citation: Physiol Genomics. 2009 Aug 7;38(3):386-401
references.pmid: 19549813
references.citation: Atherosclerosis. 2003 Jul;169(1):71-6
references.pmid: 12860252
references.citation: Proc Natl Acad Sci U S A. 1984 Dec;81(23):7318-22
references.pmid: 6095286
references.citation: BMC Bioinformatics. 2008 Nov 26;9:495
references.pmid: 19036135
references.citation: EMBO J. 1994 Jun 15;13(12):2870-5
references.pmid: 8026472
references.citation: Nucleic Acids Res. 2006;34(14):3862-77
references.pmid: 16899447
references.citation: Front Biosci. 2008 Jan 01;13:929-43
references.pmid: 17981601
references.citation: Mol Cell Biol. 1989 Mar;9(3):1376-80
references.pmid: 2725504
references.citation: Nucleic Acids Res. 2005 Oct 12;33(18):5715-27
references.pmid: 16221973
references.citation: Nat Rev Genet. 2007 Mar;8(3):206-16
references.pmid: 17304246
references.citation: J Biol Inorg Chem. 2007 May;12(4):495-507
references.pmid: 17211630
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5117-22
references.pmid: 19282476
references.citation: Nature. 2005 Feb 3;433(7025):481-7
references.pmid: 15690032
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12114-9
references.pmid: 15297614
references.citation: Genome Res. 2005 Jun;15(6):848-55
references.pmid: 15930495
references.citation: Cancer Res. 2001 Mar 15;61(6):2696-703
references.pmid: 11289150
references.citation: Endocrinology. 2009 Apr;150(4):1801-8
references.pmid: 19022893
references.citation: J Biol Chem. 1996 Oct 18;271(42):26233-41
references.pmid: 8824273
references.citation: Biochem Biophys Res Commun. 2005 Nov 25;337(3):860-7
references.pmid: 16216223
references.citation: Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4459-64
references.pmid: 15753290
references.citation: Genomics. 2009 Apr;93(4):383-91
references.pmid: 19103278
references.citation: Nucleic Acids Res. 2001 Apr 1;29(7):1514-23
references.pmid: 11266553
references.citation: J Biol Chem. 2000 Nov 3;275(44):34803-9
references.pmid: 10952993
references.citation: EMBO J. 1998 May 15;17(10):2846-54
references.pmid: 9582278
references.citation: Proc Natl Acad Sci U S A. 2005 May 17;102(20):7079-84
references.pmid: 15883375
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6275-80
references.pmid: 16606849
references.citation: Biochem Soc Trans. 2008 Dec;36(Pt 6):1252-7
references.pmid: 19021535
references.citation: Genome Biol. 2006;7(10):R97
references.pmid: 17064417
references.citation: Clin Chem. 1993 Apr;39(4):561-77
references.pmid: 8472349
references.citation: Nature. 1985 Oct 31-Nov 6;317(6040):828-31
references.pmid: 4058587
references.citation: J Biol Chem. 2007 Mar 16;282(11):8343-55
references.pmid: 17205981
references.citation: Cell. 2005 Jul 15;122(1):33-43
references.pmid: 16009131
references.citation: Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8605-12
references.pmid: 17494759
references.citation: Biochem Pharmacol. 2000 Jan 1;59(1):95-104
references.pmid: 10605938
references.citation: Am J Respir Cell Mol Biol. 2009 Jul;41(1):69-75
references.pmid: 19097988
references.citation: Cell. 2004 Feb 20;116(4):499-509
references.pmid: 14980218
references.citation: Nucleic Acids Res. 2004 Feb 26;32(4):1372-81
references.pmid: 14988425
references.citation: Biochemistry. 1999 Sep 28;38(39):12915-25
references.pmid: 10504263
references.citation: Hum Genomics. 2009 Apr;3(3):221-35
references.pmid: 19403457
references.citation: BMC Genomics. 2008 Sep 11;9:408
references.pmid: 18786246