title: A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL.
abstract: Regulation of transcription is fundamental to development and physiology, and occurs through binding of transcription factors to specific DNA sequences in the genome. CSL (CBF1/Suppressor of Hairless/LAG-1), a core component of the Notch signaling pathway, is one such transcription factor that acts in concert with co-activators or co-repressors to control the activity of associated target genes. One fundamental question is how CSL can recognize and select among different DNA sequences available in vivo and whether variations between selected sequences can influence its function. We have therefore investigated CSL-DNA recognition using computational approaches to analyze the energetics of CSL bound to different DNAs and tested the in silico predictions with in vitro and in vivo assays. Our results reveal novel aspects of CSL binding that may help explain the range of binding observed in vivo. In addition, using molecular dynamics simulations, we show that domain-domain correlations within CSL differ significantly depending on the DNA sequence bound, suggesting that different DNA sequences may directly influence CSL function. Taken together, our results, based on computational chemistry approaches, provide valuable insights into transcription factor-DNA binding, in this particular case increasing our understanding of CSL-DNA interactions and how these may impact on its transcriptional control.
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge, UK.
authors.forename: Rubben
authors.initials: R
authors.lastname: Torella
authors.affiliation: Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
authors.forename: Jinghua
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, UK Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Eddie
authors.initials: E
authors.lastname: Kinrade
authors.affiliation: Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Cerda-Moya
authors.affiliation: University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way CARE4836, Cincinnati, OH 45267-0524, USA.
authors.forename: Ashley N
authors.initials: AN
authors.lastname: Contreras
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, UK Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Robert
authors.initials: R
authors.lastname: Foy
authors.affiliation: Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Robert
authors.initials: R
authors.lastname: Stojnic
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge, UK sjb32@cam.ac.uk.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Glen
authors.affiliation: University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way CARE4836, Cincinnati, OH 45267-0524, USA.
authors.forename: Rhett A
authors.initials: RA
authors.lastname: Kovall
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, UK Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK sjb32@cam.ac.uk.
authors.forename: Boris
authors.initials: B
authors.lastname: Adryan
authors.affiliation: Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK sjb32@cam.ac.uk.
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Bray
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D016384:Consensus Sequence; D003596:Cytosine / Q000032:analysis; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D051819:Immunoglobulin J Recombination Signal Sequence-Binding Protein / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D059372:Nucleotide Motifs; D011485:Protein Binding; D050436:Regulatory Elements, Transcriptional; D012984:Software
chemical_list: D051819:Immunoglobulin J Recombination Signal Sequence-Binding Protein; C497571:Rbpj protein, mouse; D003596:Cytosine; D004247:DNA
references.citation: Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):7877-81
references.pmid: 10884418
references.citation: Nat Rev Genet. 2010 Nov;11(11):751-60
references.pmid: 20877328
references.citation: Development. 2000 Aug;127(16):3441-55
references.pmid: 10903170
references.citation: Genes Dev. 2007 Jun 1;21(11):1322-7
references.pmid: 17545467
references.citation: Protein Sci. 2010 Jan;19(1):34-46
references.pmid: 19866488
references.citation: J Chem Theory Comput. 2012 May 8;8(5):1542-1555
references.pmid: 22582031
references.citation: J Biol Chem. 2008 May 23;283(21):14781-91
references.pmid: 18381292
references.citation: Proteins. 2006 Nov 15;65(3):712-25
references.pmid: 16981200
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3312-7
references.pmid: 17360644
references.citation: G3 (Bethesda). 2012 Jan;2(1):79-82
references.pmid: 22384384
references.citation: Dev Biol. 2000 Nov 15;227(2):520-32
references.pmid: 11071771
references.citation: Nucleic Acids Res. 2010 Nov;38(21):7422-31
references.pmid: 20685816
references.citation: Bioinformatics. 2000 Jan;16(1):16-23
references.pmid: 10812473
references.citation: Elife. 2013 Apr 02;2:e00482
references.pmid: 23599895
references.citation: Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10147-52
references.pmid: 16006526
references.citation: Nat Struct Mol Biol. 2010 Nov;17(11):1312-7
references.pmid: 20972443
references.citation: Nat Biotechnol. 2005 Aug;23(8):988-94
references.pmid: 16041365
references.citation: Cell. 2006 Mar 10;124(5):985-96
references.pmid: 16530045
references.citation: Methods Enzymol. 2011;498:3-18
references.pmid: 21601671
references.citation: Nature. 2000 May 18;405(6784):364-8
references.pmid: 10830967
references.citation: J Comput Chem. 2005 Dec;26(16):1668-88
references.pmid: 16200636
references.citation: Bioinformatics. 1999 Jul-Aug;15(7-8):563-77
references.pmid: 10487864
references.citation: Nucleic Acids Res. 2014 Feb;42(4):2099-111
references.pmid: 24243859
references.citation: Dev Cell. 2011 Oct 18;21(4):611-26
references.pmid: 22014521
references.citation: Proteins. 2005 Nov 1;61(2):366-76
references.pmid: 16121395
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D142-7
references.pmid: 24194598
references.citation: Curr Top Dev Biol. 2010;92:31-71
references.pmid: 20816392
references.citation: Nucleic Acids Res. 1994 Mar 25;22(6):965-71
references.pmid: 8152928
references.citation: J Mol Biol. 1993 Dec 5;234(3):779-815
references.pmid: 8254673
references.citation: BMC Struct Biol. 2010 Nov 24;10:42
references.pmid: 21106075
references.citation: EMBO J. 2004 Sep 1;23(17):3441-51
references.pmid: 15297877
references.citation: ACS Chem Biol. 2010 Mar 19;5(3):265-72
references.pmid: 20151694
references.citation: Proc Natl Acad Sci U S A. 1976 Mar;73(3):804-8
references.pmid: 1062791
references.citation: Curr Opin Struct Biol. 2009 Apr;19(2):171-7
references.pmid: 19362815
references.citation: PLoS One. 2010 Nov 24;5(11):e15034
references.pmid: 21124806
references.citation: Genes Dev. 2002 Jun 1;16(11):1397-411
references.pmid: 12050117
references.citation: Cell. 1992 Jun 26;69(7):1199-212
references.pmid: 1617730
references.citation: Nature. 2009 Oct 29;461(7268):1248-53
references.pmid: 19865164
references.citation: J Biol Chem. 2003 Jun 6;278(23):21232-9
references.pmid: 12644465
references.citation: Dev Biol. 1999 Sep 1;213(1):33-53
references.pmid: 10452845
references.citation: Cell. 2006 Mar 10;124(5):973-83
references.pmid: 16530044
references.citation: Genes Dev. 1994 Oct 15;8(20):2491-503
references.pmid: 7958912
references.citation: PLoS One. 2011;6(11):e27986
references.pmid: 22125648
references.citation: Annu Rev Biochem. 2010;79:233-69
references.pmid: 20334529
references.citation: EMBO J. 2006 Jul 12;25(13):3191-202
references.pmid: 16763555
references.citation: J Mol Biol. 2002 Jul 5;320(2):369-87
references.pmid: 12079393
references.citation: Mol Cell Biol. 2002 Nov;22(22):7812-9
references.pmid: 12391150
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6
references.pmid: 18006571
references.citation: Bioinformatics. 2009 Jan 15;25(2):167-74
references.pmid: 19017655
references.citation: Genome Res. 2004 Jun;14(6):1188-90
references.pmid: 15173120
references.citation: Protein Sci. 2000 Sep;9(9):1753-73
references.pmid: 11045621
references.citation: PLoS Comput Biol. 2009 Mar;5(3):e1000323
references.pmid: 19300478
references.citation: Nature. 1988 Sep 22;335(6188):321-9
references.pmid: 3419502
references.citation: Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4875-80
references.pmid: 22403063
references.citation: PLoS Comput Biol. 2012;8(3):e1002433
references.pmid: 22457611
references.citation: BMC Bioinformatics. 2011 Dec 30;12:495
references.pmid: 22208852
references.citation: PLoS One. 2012;7(5):e36990
references.pmid: 22606323
references.citation: Proteins. 2005 Dec 1;61(4):704-21
references.pmid: 16231289