Team:Heidelberg/Project References

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-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, JR et al. Measuring the activity of BioBrick promoters using an in vivo reference standard. Journal of Biological Engineering 3 (2009).
  

• Endy, D. et al. Adventures in synthetic biology (comic) Nature 438, 449-453 (2005). Available online at nature.com
  

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

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

• Alberts, B. et al.: „Molecular Biology of the Cell“ (Book. 5th edition, 2008. Garland Science) Chapter 7, p. 467-476
  

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

• York JD et al. A phospholipase C-dependent inositol polyphosphate kinase pathway required for efficient messenger RNA export. Science 285, 96-100 (1999).
  

• Alberts, B. et al.: „Molecular Biology of the Cell“ (Book. 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. et al.: „Molecular Biology of the Cell“ (Book. 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. et al. Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signalling. Plant Cell 14, 749-762 (2002)
  

• Degenhardt, T. et al. 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.

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).[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).