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Natural Promoters

Synthetic Promoters

• Alberts, B. et al. Molecular Biology of the, Cell (5th edition). New York: Garland Science, p. 432-453

• Edelmann, G.M. et al. Synthetic promoter elements obtained by nucleotide sequence variation and selection for activity. PNAS 97, 3038-43 (2000).

• Ellis, T. et al. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology 27, 465-471 (2009).

• Venter, M. Synthetic promoters: genetic control through cis engineering. Trends in Plant Science 12, 118-124 (2007). (and the references cited therein)

• Rushton, P.J. et al. Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signalling. in Plant Cell 14, 749–762 (2002).

• Ogawa, R. Construction of strong mammalian promoters by random cis-acting element elongation. Biotechniques 42, 628-632 (2007).

• Stemmer, W.P.C. et al. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164, 49-53 (1995).

• Tornoe, J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 297, 21-32 (2002).

• Heintzman ND, Ren B. The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. Cellular and Molecular Life Science 64, 386-400 (2007).

• Fussenegger, M., Weber, W. Engineering of Synthetic Mammalian Gene Networks. Chemistry and Biology 16, 287-297 (2009).

• Gossen, M., Bujard, L. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. PNAS 89, 5547-5551 (1992).

• Dorer, D.E., Nettelbeck, D. Targeting cancer by transcriptional control in cancer gene therapy and viral oncolysis. Advanced Drug Delivery Reviews 61, 554-557 (2009).

• Rattner, A. NF-κ B activates the HIV promoter in neurons. EMBO 12, 4261–4267 (1993).

• Yokoyama KD et al. Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. Nuc Acids Res, 1-21 (2009).

• del Val C. et al. PromoterSweep: a tool for identification of transcription factor binding site. Theor Chem Acc (in press)

Stable cell line

Multi-color output

Modeling

HEARTBEAT Fuzzy Modeling

• Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).

• Hu, Z., Killion, P. J. & Iyer, V. R. Genetic reconstruction of a functional transcriptional regulatory network. Nature Genet. 39, 683-687 (2007).

• Gertz, J., Siggia E. D. & Cohen, B. A. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457. 215-218 (2009)

• Roider, H. G. et al. Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23, 134-141 (2006)

• ref to come

• Andianantoandro, E. et al. Synthetic biology: new engineering rules for an emerging discipline. Mol Sys Biol (2006)

• Alberts, B. et al. Molecular Biology of the Cell, 5th edition. Garland Science, 2008, Chapter 6

• Vardhanabhuti, S., Wang, J. & Hannenhalli, S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucl Acid Res 35, 3203-3213 (2007).

• Yokoyama, K. D., Ohler, U. & Wray, G. A. Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. Nucl Acid Res, 1-21 (2009)

• Nelles, O. Nonlinear System Identification. Springer, 2000.

• Bosl, W. J. BMC systems biology 1, 13 (2007).

• Mathematical modeling of the lambda switch:a fuzzy logic approach.

• B. B. Aldridge, J. Saez-Rodriguez, J. L. Muhlich et al., PLoS computational biology 5 (4), e1000340 (2009).

== Measurement

• Kelly J. R., Rubin A. J., Davis J. H., Ajo-Franklin C. M., Cumbers J., Czar M. J., de Mora K., Glieberman A. L., Monie D. D., Endy D. Measuring the activity of BioBrick promoters using an in vivo reference standard. Journal of Biological Engineering 3 (2009).
  

• Endy, D., Deese I. Adventures in synthetic biology (comic) Nature 438, 449-453 (2005). Available online at [http://www.nature.com/nature/comics/syntheticbiologycomic/index.html nature.com]
  

• Alberts, B., Johnson A., Walter P., Lewis J. Molecular Biology of the Cell, 5th edition, 2008. Garland Science) Chapter 6
  

• http://www.promega.com/tbs/tm058/tm058.html
  

• Zhou, H. Development of site-specific integration system to high-level expression recombinant proteins in CHO cells. Chinese journal of biotechnology 23: 756-62 (2007)

• Alberts, B., Johnson A., Walter P., Lewis J. Molecular Biology of the Cell, 5th edition, 2008. Garland Science) Chapter 7, p. 467-476
  

• Zhu, X. D. Sadowski P. D. Cleavage-dependent Ligation by the FLP Recombinase. J Biol Chem 270, 23044-23054 (1995).
  

• York J. D., Odom A. R., Murphy R., Ives E. B., Wente S. R. A phospholipase C-dependent inositol polyphosphate kinase pathway required for efficient messenger RNA export. Science 285, 96-100 (1999).
  

• Alberts, B., Johnson A., Walter P., Lewis J. Molecular Biology of the Cell, 5th edition, 2008. Garland Science) Chapter 7, p. 905-908
  

• Tornoe, J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 297, 21-32 (2002),
  

• Alberts, B., Johnson A., Walter P., Lewis J. Molecular Biology of the Cell, 5th edition, 2008. Garland Science) Chapter 7, p. 492
  

• Ducrest, A-L et al. Detection of promoter activity by flow cytometric analysis of GFP reporter expression. Nucleic Acids Res. 30, e65 (2002).
  

• Rushton P. J., Reinstädler A., Lipka V., Lippok B., Somssich I. E. Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signalling. Plant Cell 14, 749-762 (2002)
  

• Degenhardt T., Rybakova K. N., Tomaszewska A., Moné M. J., Westerhoff H. V., Bruggeman F. J., Carlberg C. Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription. Cell 138, 489-501 (2009).
  

• Lottspeich, F. and Engels, J. W.: "Bioanalytik" (Book. 2nd edition, 2006. Spektrum Akademischer Verlag) Chapter 5, p. 95-96.

• http://www1.qiagen.com/Products/RnaStabilizationPurification/RNeasySystem/RNeasyPlantMini.aspx

• http://www1.qiagen.com/products/automation/qiacube.aspx

• http://www1.qiagen.com/literature/render.aspx?id=398

• https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=604109&tab=DetailInfo

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Material and Methods

Eukaryopedia

Cell lines

• Clark, R. The process of malignant progression in human breast cancer. Annals of oncology: official journal of the European Society for Medical Oncology/ESMO 1, 401-407 (1990).

• Osborne, C. K., Hobbs, K. & Trent, J. M. Biological differences among, MCF-7 human breast cancer cell lines from different laboratories. Breast Cancer Research and Treatment 9, 111-121 (1987).

• Dickson, R. B., Bates, S. E., McManaway, M. E. & Lippman, M. E. Characterization of Estrogen Responsive Transforming Activity in Human Breast Cancer Cell Lines. Cancer Research 46, 1707-1713 (1986).

• Booth, B. W. & Smith, G. H. Roles of transforming growth factor-α in mammary development and disease. Growth Factors 25, 227-235 (2007).

• Gey, G. O., Coffman, W. D. & Kubicek, M. T. Tissue culture studies of the proliferative capacity of cervical carcinoma and norml epithelium. Cancer Research 12, 264-265 (1952).

• Macville, M., Schroeck, E., Padilla-Nash, H., Keck, C., Ghadimi, M. B.,Zimonjic, D., Pospecu, N. & Ried, T. Comprehensive and definitive moleculare cytogenic characterization of HeLa cells by spectral karyotyping. Cancer Research 59, 141-150 (1999).

• Masters, J. R. HeLa cells 50 years on: the good, the bad and the ugly. Nature Reviews 2, 315-319 (2002).

• Ek, E. T. H., Dass, C. R. & Choong, P. F. M. Commonly used mouse models of osteosarcoma. Critical Reviews in Oncology/Hematology 60, 1-8 (2006).

• Ponten, J. & Saksela, E. Two established in vitro cell lines from human mesenchymal tumours. International Journal of Cancer 2, 434-447 (1967).

• Nelissen, J. M. D. T., Torensma, R., Pluyter, M., Adema, G. J., Raymakers, R. A. P., van Kooyk, Y. & Figdor, C. G. Molecular analysis of the hematopoiesis supporting osteoblastic cell line U2-OS. Experimental Hematology 28, 422-432 (2000).

Transcription factors

• May and Ghosh. Rel/NF-κB and IKB proteins: an overview. Seminars in Cancer Biology, 8, 63-73 (1997).

• Courtois G. The NF-kB signaling pathway in human genetic diseases. Cell. Mol. Life Sci. 62 1682-1691 (2005).

• Vazquez A., Bond EE, Levine AJ, Bond GL. The genetics of the p53 pathway, apoptosis and cancer therapy. Nat Rev Drug Discov, 7(12), 979-87 (2008).

• Mangelsdorf, D. J., Evans, R. M. The RXR heterodimers and orphan receptors. Cell 83, 841–850, (1995).

• H. Phillip Koeffler. Peroxisome Proliferator-activated Receptor and Cancers. Clinical Cancer Research 9, 1-9 (2003).

• Suh, N. et al. A novel synthetic oleanane triterpenoid, 2-cyano-3,12-dioxoolean-1,9- dien-28-oic acid, with potent differentiating, antiproliferative, and antiinflammatory activity. Cancer Res. 59, 336–341 (1999).

• Brown MS, Goldstein JL . The SREBP pathway: regulation of cholesterol metabolism by proteolysis of a membrane-bound transcription factor. Cell 89 (3), 331–40 (1997).

• Briggs, M. R., J. T. Kadonaga, S. P. Bell, and R. Tjian. Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science 234, 47-52. (1986).

• Stielow, B., A. Sapetschnig, C. Wink, I. Kruger, and G. Suske. SUMO-modified Sp3 represses transcription by provoking local heterochromatic gene silencing. EMBO Rep. 9, 899-906 (2008).

• Zhang, Y., M. Liao, and M. L. Dufau. Unlocking repression of the human luteinizing hormone receptor gene by trichostatin A-induced cell-specific phosphatase release. J. Biol. Chem. 283, 24039-24046 (2008).

• Nicole Y. Tan and Levon M. Khachigian. Sp1 Phosphorylation and Its Regulation of Gene Transcription. Molecular and Cellular Biology 29, 2483-2488 (2009).

• Cai-Yun Zhong, Ya-Mei Zhou, Gordon C.Douglas, Hanspeter Witschi and Kent E.Pinkerton. MAPK/AP-1 signal pathway in tobacco smoke-induced cell proliferation and quamous metaplasia in the lungs of rats. Carcinogenesis, 26 (no.12), 2187–2195 (2005).

• Hess J, Angel P, Schorpp-Kistner M. AP-1 subunits: quarrel and harmony among siblings. J. Cell. Sci. 117, 5965–73 (2004).

• C. S. Sheela Rani, Mei Qiang, and Maharaj K. Ticku. Potential Role of cAMP Response Element-Binding Protein in Ethanol-Induced N-Methyl-D-aspartate Receptor 2B Subunit Gene Transcription in Fetal Mouse Cortical Cells . Molecular Pharmacology Fast Forward (2005).

• Yin JC, Tully T. CREB and the formation of long-term memory. Curr Opin Neurobiol. 6(2), 264-8 (1996) .

• PANDEY Subhash C., CHARTOFF Elena H., CARLEZON William A., JIAN ZOU, HUAIBO ZHANG, KREIBICH Arati S., BLENDY Julie A., CREWS Fulton T. CREB gene transcription factors : Role in molecular mechanisms of alcohol and drug addiction. Alcohol Clin Exp Res. 29(2), 176-184 (2005).

• RANY Istvan, MEGYESI Judit K., REUSCH Jane E. B., SAFIRSTEIN Robert L. CREB mediates ERK-induced survival of mouse renal tubular cells after oxidant stress. Kidney Int. 68(4), 1573-82 (2005).

• Matuoka K, Chen KY. Transcriptional regulation of cellular ageing by the CCAAT box-binding factor CBF/NF-Y. Ageing Res Rev. 1(4), 639-51 (2002).[32] Carlberg C, Seuter S. A genomic perspective on vitamin D signaling. Anticancer Res. 9, 3485-93 (2009).

• Bertone-Johnson ER. Vitamin D and breast cancer. Ann Epidemiol. 7, 462-7 (2009).

• Obata T, Yanagidani A, Yokoro K, Numoto M, Yamamoto S. Analysis of the consensus binding sequence and the DNA-binding domain of ZF5. Biochem Biophys Res Commun. 255(2), 528-34, (1999).

• Numoto M, Yokoro K, Koshi J. ZF5, which is a Kruppel-type transcriptional repressor, requires the zinc finger domain for self-association. Biochem Biophys Res Commun. 256(3), 573-8 (1999).

• Johanna M. Pellikainen, Veli-Matti Kosma1,2. Activator protein-2 in carcinogenesis with a special reference to breast cancer—A mini review. Int. J. Cancer 120, 2061–2067 (2007).

• Hilger-Eversheim K, Moser M, Schorle H, Buettner R. Regulatory roles of AP-2 transcription factors in vertebrate development, apoptosis and cell-cycle control. Gene, 260(1-2), 1-12. (2000).

• Scholz H, Wagner KD, Wagner N. Role of the Wilms' tumour transcription factor, Wt1, in blood vessel formation. Pflugers Arch. 458(2), 315-23, (2009).

• Sakamoto Y, Mariya Y, Sasaki S, Teshiromori R, Oshikiri T, Segawa M, Ogura K, Akagi T, Kubo K, Kaimori M, Funato T. WT1 mRNA level in peripheral blood is a sensitive biomarker for monitoring minimal residual disease in acute myeloid leukemia. Tohoku J Exp Med. 219(2), 169-76, (2009).

• Dollé P. Developmental expression of retinoic acid receptors (RARs). Nucl Recept Signal. 7 (2009).

• Oh-hora M, Rao A. The calcium/NFAT pathway: role in development and function of regulatory T cells. Microbes Infect. 11(5), 612-9. (2009)

Proteins

• Hegardt FG. Transcriptional regulation of mitochondrial HMG-CoA synthase in the control of ketogenesis. Biochimie, 80(10), 803-6, (1998).

• Yu, J., Zhang, L. PUMA, a potent killer with or without p53. Oncogene 27, S71-S83 (2008).

• Li Z, Srivastava P. Heat-shock proteins. Curr Protoc Immunol. Appendix 1:Appendix 1T, (2004).

• Patrick Tso, Min Liu, Theodore John Kalogeris, Alan BR Thomson.THE ROLE OF APOLIPOPROTEIN A-IV IN THE REGULATION OF FOOD INTAKE Annu. Rev. Nutr. 21, 231–54 (2001).

• Androutsopoulos VP, Tsatsakis AM, Spandidos DA.Cytochrome P450 CYP1A1: wider roles in cancer progression and prevention. BMC Cancer, 16;9, 187, (2009).

RNA-processing and transcriptional regulation

• Moore MJ, Proudfoot NJ.Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136(4), 688-700 (2009).

• Berg, Jeremy M., John L. Tymoczko & Lubert Stryer. Biochemistry (6 ed.) New York: WH Freeman & Co, 2007.

• D. A. Day, M. F. Tuite, Post-transcriptional gene regulatory mechanisms in eukaryotes: an overview, J. Endocrinol. 157, 361-371 (1998).

• Litt M, Qiu Y, Huang S. Histone arginine methylations: their roles in chromatin dynamics and transcriptional regulation. 29(2), 131-41 (2009).

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