View Item 

Show simple item record

A model of spatially restricted transcription in opposing gradients of activators and repressors
dc.contributor.authorWhite, Michael Aen_US
dc.contributor.authorParker, Davis Sen_US
dc.contributor.authorBarolo, Scotten_US
dc.contributor.authorCohen, Barak Aen_US
dc.date.accessioned2014-01-08T20:34:40Z
dc.date.available2014-01-08T20:34:40Z
dc.date.issued2012en_US
dc.identifier.citationWhite, Michael A; Parker, Davis S; Barolo, Scott; Cohen, Barak A (2012). "A model of spatially restricted transcription in opposing gradients of activators and repressors." Molecular Systems Biology 8(1): n/a-n/a. <http://hdl.handle.net/2027.42/102118>en_US
dc.identifier.issn1744-4292en_US
dc.identifier.issn1744-4292en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/102118
dc.publisherJohn Wiley & Sons, Ltden_US
dc.subject.otherThermodynamic Modelen_US
dc.subject.otherMorphogen Gradienten_US
dc.subject.otherCooperativityen_US
dc.subject.otherTranscriptionen_US
dc.titleA model of spatially restricted transcription in opposing gradients of activators and repressorsen_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelMolecular, Cellular and Developmental Biologyen_US
dc.subject.hlbtoplevelScienceen_US
dc.subject.hlbtoplevelHealth Sciencesen_US
dc.description.peerreviewedPeer Revieweden_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102118/1/msb201248-sup-0001.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102118/2/msb201248.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102118/3/msb201248.reviewer_comments.pdf
dc.identifier.doi10.1038/msb.2012.48en_US
dc.identifier.sourceMolecular Systems Biologyen_US
dc.identifier.citedreferenceSherman MS, Cohen BA ( 2012 ) Thermodynamic state ensemble models of cis‐regulation. PLoS Comp Biol 8: e1002407en_US
dc.identifier.citedreferenceKomada M, Saitsu H, Shiota K, Ishibashi M ( 2008 ) Expression of Fgf15 is regulated by both activator and repressor forms of Gli2 in vitro. Biochem Biophys Res Commun 369: 350 – 356en_US
dc.identifier.citedreferenceLee JJ, Kessler von DP, Parks S, Beachy PA ( 1992 ) Secretion and localized transcription suggest a role in positional signaling for products of the segmentation gene hedgehog. Cell 71: 33 – 50en_US
dc.identifier.citedreferenceLum L, Beachy P ( 2004 ) The Hedgehog response network: sensors, switches, and routers. Science 304: 1755en_US
dc.identifier.citedreferenceMéthot N, Basler K ( 1999 ) Hedgehog controls limb development by regulating the activities of distinct transcriptional activator and repressor forms of Cubitus interruptus. Cell 96: 819 – 831en_US
dc.identifier.citedreferenceOchoa‐Espinosa A, Yucel G, Kaplan L, Pare A, Pura N, Oberstein A, Papatsenko D, Small S ( 2005 ) The role of binding site cluster strength in Bicoid‐dependent patterning in Drosophila. Proc Natl Acad Sci USA 102: 4960en_US
dc.identifier.citedreferenceVon Ohlen T, Hooper JE ( 1997 ) Hedgehog signaling regulates transcription through Gli/Ci binding sites in the wingless enhancer. Mech Dev 68: 149 – 156en_US
dc.identifier.citedreferenceParker DS, White MA, Ramos AI, Cohen BA, Barolo S ( 2011 ) The cis‐regulatory logic of hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity. Sci Signal 4: ra38en_US
dc.identifier.citedreferenceRogers KW, Schier AF ( 2011 ) Morphogen gradients: from generation to interpretation. Annu Rev Cell Dev Biol 27: 377 – 407en_US
dc.identifier.citedreferenceRowan S, Siggers T, Lachke SA, Yue Y, Bulyk ML, Maas RL ( 2010 ) Precise temporal control of the eye regulatory gene Pax6 via enhancer‐binding site affinity. Genes Dev 24: 980 – 985en_US
dc.identifier.citedreferenceSegal E, Raveh‐Sadka T, Schroeder M, Unnerstall U, Gaul U ( 2008 ) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451: 535en_US
dc.identifier.citedreferenceShea MA, Ackers GK ( 1985 ) The OR control system of bacteriophage lambda. A physical‐chemical model for gene regulation. J Mol Biol 181: 211 – 230en_US
dc.identifier.citedreferenceEichberger T, Kaser A, Pixner C, Schmid C, Klingler S, Winklmayr M, Hauser‐Kronberger C, Aberger F, Frischauf AM ( 2008 ) GLI2‐specific transcriptional activation of the bone morphogenetic protein/activin antagonist follistatin in human epidermal cells. J Biol Chem 283: 12426 – 12437en_US
dc.identifier.citedreferenceVokes SA, Ji H, Wong WH, McMahon AP ( 2008 ) A genome‐scale analysis of the cis‐regulatory circuitry underlying sonic hedgehog‐mediated patterning of the mammalian limb. Genes Dev 22: 2651 – 2663en_US
dc.identifier.citedreferenceIkram MS, Neill GW, Regl G, Eichberger T, Frischauf AM, Aberger F, Quinn A, Philpott M ( 2004 ) GLI2 is expressed in normal human epidermis and BCC and induces GLI1 expression by binding to its promoter. J Invest Dermatol 122: 1503 – 1509en_US
dc.identifier.citedreferenceWang QT, Holmgren RA ( 1999 ) The subcellular localization and activity of Drosophila cubitus interruptus are regulated at multiple levels. Development 126: 5097 – 5106en_US
dc.identifier.citedreferenceWharton SJ, Basu SP, Ashe HL ( 2004 ) Smad affinity can direct distinct readouts of the embryonic extracellular Dpp gradient in Drosophila. Curr Biol 14: 1550 – 1558en_US
dc.identifier.citedreferenceWinklmayr M, Schmid C, Laner‐Plamberger S, Kaser A, Aberger F, Eichberger T, Frischauf A‐M ( 2010 ) Non‐consensus GLI binding sites in Hedgehog target gene regulation. BMC Mol Biol 11: 2en_US
dc.identifier.citedreferenceKasper M, Schnidar H, Neill GW, Hanneder M, Klingler S, Blaas L, Schmid C, Hauser‐Kronberger C, Regl G, Philpott MP, Aberger F ( 2006 ) Selective modulation of Hedgehog/GLI target gene expression by epidermal growth factor signaling in human keratinocytes. Mol Cell Biol 26: 6283 – 6298en_US
dc.identifier.citedreferenceEichberger T, Regl G, Ikram MS, Neill GW, Philpott MP, Aberger F, Frischauf AM ( 2004 ) FOXE1, a new transcriptional target of GLI2 is expressed in human epidermis and basal cell carcinoma. J Invest Dermatol 122: 1180 – 1187en_US
dc.identifier.citedreferenceRegl G, Kasper M, Schnidar H, Eichberger T, Neill GW, Philpott MP, Esterbauer H, Hauser‐Kronberger C, Frischauf AM, Aberger F ( 2004 ) Activation of the BCL2 promoter in response to Hedgehog/GLI signal transduction is predominantly mediated by GLI2. Cancer Res 64: 7724 – 7731en_US
dc.identifier.citedreferenceArnosti DN, Barolo S, Levine M, Small S ( 1996 ) The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. Development 122: 205 – 214en_US
dc.identifier.citedreferenceAshe HL, Briscoe J ( 2006 ) The interpretation of morphogen gradients. Development 133: 385 – 394en_US
dc.identifier.citedreferenceBalaskas N, Ribeiro A, Panovska J, Dessaud E, Sasai N, Page KM, Briscoe J, Ribes V ( 2012 ) Gene regulatory logic for reading the sonic Hedgehog signaling gradient in the vertebrate neural tube. Cell 148: 273 – 284en_US
dc.identifier.citedreferenceBuchler NE, Gerland U, Hwa T ( 2003 ) On schemes of combinatorial transcription logic. Proc Natl Acad Sci USA 100: 5136 – 5141en_US
dc.identifier.citedreferenceBurz DS, Rivera‐Pomar R, Jäckle H, Hanes SD ( 1998 ) Cooperative DNA‐binding by Bicoid provides a mechanism for threshold‐dependent gene activation in the Drosophila embryo. EMBO J 17: 5998 – 6009en_US
dc.identifier.citedreferenceCantor C, Schimmel P ( 1980 ) Biophysical Chemistry: The Behavior of Biological Macromolecules Part III New York: W.H. Freeman and Company,en_US
dc.identifier.citedreferenceClark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW et al ( 2007 ) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203 – 218en_US
dc.identifier.citedreferenceDessaud E, Ribes V, Balaskas N, Yang LL, Pierani A, Kicheva A, Novitch BG, Briscoe J, Sasai N ( 2010 ) Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen sonic Hedgehog. PLoS Biol 8: e1000382en_US
dc.identifier.citedreferenceDriever W, Thoma G, Nüsslein‐Volhard C ( 1989 ) Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen. Nature 340: 363 – 367en_US
dc.identifier.citedreferenceFakhouri WD, Ay A, Sayal R, Dresch J, Dayringer E, Arnosti DN ( 2010 ) Deciphering a transcriptional regulatory code: modeling short‐range repression in the Drosophila embryo. Mol Syst Biol 6: 341en_US
dc.identifier.citedreferenceGertz J, Cohen BA ( 2009 ) Environment‐specific combinatorial cis‐regulation in synthetic promoters. Mol Syst Biol 5: 244en_US
dc.identifier.citedreferenceGertz J, Siggia ED, Cohen BA ( 2008 ) Analysis of combinatorial cis‐regulation in synthetic and genomic promoters. Nature 457: 215en_US
dc.identifier.citedreferenceHe X, Samee MAH, Blatti C, Sinha S ( 2010 ) Thermodynamics‐based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short‐range repression. PLoS Comp Biol 6: pii: e1000935en_US
dc.identifier.citedreferenceJanssens H, Hou S, Jaeger J, Kim A‐R, Myasnikova E, Sharp D, Reinitz J ( 2006 ) Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat Genet 38: 1159en_US
dc.identifier.citedreferenceJiang J, Levine M ( 1993 ) Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen. Cell 72: 741 – 752en_US
dc.identifier.citedreferenceKent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler AD ( 2002 ) The Human Genome Browser at UCSC. Genome Res 12: 996 – 1006en_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Name:
msb201248-sup-0001.pdf
Size:
356.0KB
Format:
PDF
View/Open
Name:
msb201248.pdf
Size:
337.6KB
Format:
PDF
View/Open
Name:
msb201248.reviewer_comments.pdf
Size:
295.6KB
Format:
PDF
View/Open

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.