Team:Heidelberg/Project References

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References

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-kappa 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

Measurement

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-kB 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).


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).