Academic Journal
Application of gene expression trajectories initiated from ErbB receptor activation highlights the dynamics of divergent promoter usage
| العنوان: | Application of gene expression trajectories initiated from ErbB receptor activation highlights the dynamics of divergent promoter usage |
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| المؤلفون: | Alistair R R Forrest, Hideya Kawaji, Michael Rehli, J Kenneth Baillie, Michiel J L de Hoon, Vanja Haberle, Timo Lassmann, Ivan V Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J Mungall, Terrence F Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A Semple, Yuri Ishizu, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M Altschuler, John A C Archer, Peter Arner, Magda Babina, Sarah Baker, Piotr J Balwierz, Anthony G Beckhouse, Swati Pradhan-Bhatt, Judith A Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A Maxwell Burroughs, Andrea Califano, Carlo V Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans C Clevers, Emiliano Dalla, Carrie A Davis, Bart Deplancke, Michael Detmar, Alexander D Diehl, Taeko Dohi, Finn Drabløs, Albert S B Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C Farach-Carson, Geoffrey J Faulkner, Alexander V Favorov, Malcolm E Fisher, Martin C Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B Geijtenbeek, Andrew Gibson, Thomas Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J Hitchens, Shannan J Ho Sui, Oliver M Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I Kawamura, Tsugumi Kawashima, Judith S Kempfle, Tony J Kenna, Juha Kere, Levon M Khachigian, Toshio Kitamura, S Peter Klinken, Alan J Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T Kwon, Jeroen F J Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-sim, Ri-ichiroh Manabe, Jessica C Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison Meynert, Yosuke Mizuno, David A de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine L Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G D Prendergast, Owen J L Rackham, Jordan A Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A Schultes, Gundula G Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Rolf K Swoboda, Peter A C 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E Vorontsov, Wyeth W Wasserman, Shoko Watanabe, Christine A Wells, Louise N Winteringham, Ernst Wolvetang, Emily J Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Suzan E Zabierowski, Peter G Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M Summers, Harukazu Suzuki, Carsten O Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C Freeman, Boris Lenhard, Vladimir B Bajic, Martin S Taylor, Vsevolod J Makeev, Albin Sandelin, David A Hume, Piero Carninci, Yoshihide Hayashizaki Carbajo D., Magi S., Itoh M., Kawaji H., Lassmann T., Arner E., Forrest A. R. R., Carninci P., Hayashizaki Y., Daub C. O., Okada-Hatakeyama M., Mar J. C. |
| المساهمون: | A.R. R Forrest, H. Kawaji, M. Rehli, J. Kenneth Baillie, M.J. L de Hoon, V. Haberle, T. Lassmann, I. V Kulakovskiy, M. Lizio, M. Itoh, R. Andersson, C. J Mungall, T. F Meehan, S. Schmeier, N. Bertin, M. Jørgensen, E. Dimont, E. Arner, C. Schmidl, U. Schaefer, Y. A Medvedeva, C. Plessy, M. Vitezic, J. Severin, C. A Semple, Y. Ishizu, M. Francescatto, I. Alam, D. Albanese, G. M Altschuler, J.A. C Archer, P. Arner, M. Babina, S. Baker, P. J Balwierz, A. G Beckhouse, S. Pradhan-Bhatt, J. A Blake, A. Blumenthal, B. Bodega, A. Bonetti, J. Brigg, F. Brombacher, A. Maxwell Burrough, A. Califano, C. V Cannistraci, D. Carbajo, Y. Chen, M. Chierici, Y. Ciani, H. C Clever, E. Dalla, C. A Davi, B. Deplancke, M. Detmar, A. D Diehl, T. Dohi, F. Drablø, A.S. B Edge, M. Edinger, K. Ekwall, M. Endoh, H. Enomoto, M. Fagiolini, L. Fairbairn, H. Fang, M. C Farach-Carson, G. J Faulkner, A. V Favorov, M. E Fisher, M. C Frith, R. Fujita, S. Fukuda, C. Furlanello, M. Furuno, J. Furusawa, T. B Geijtenbeek, A. Gibson, T. Gingera, D. Goldowitz, J. Gough, S. Guhl, R. Guler, S. Gustincich, T. J Ha, M. Hamaguchi, M. Hara, M. Harber, J. Harshbarger, A. Hasegawa, Y. Hasegawa, T. Hashimoto, M. Herlyn, K. J Hitchen, S. J Ho Sui, O. M Hofmann, I. Hoof, F. Hori, L. Huminiecki, K. Iida |
| بيانات النشر: | Public Library of Science |
| سنة النشر: | 2015 |
| المجموعة: | The University of Milan: Archivio Istituzionale della Ricerca (AIR) |
| مصطلحات موضوعية: | Apoptosi, Breast Neoplasm, Cell Cycle, Cell Differentiation, Cell Line, Tumor, Cell Proliferation, Enzyme Activation, Epidermal Growth Factor, ErbB Receptor, Extracellular Signal-Regulated MAP Kinase, Female, Focal Adhesion, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Human, MAP Kinase Signaling System, MCF-7 Cell, Neuregulin-1, Promoter Regions, Genetic, Tumor Suppressor Protein p53, Settore BIO/11 - Biologia Molecolare |
| الوصف: | Understanding how cells use complex transcriptional programs to alter their fate in response to specific stimuli is an important question in biology. For the MCF-7 human breast cancer cell line, we applied gene expression trajectory models to identify the genes involved in driving cell fate transitions. We modified trajectory models to account for the scenario where cells were exposed to different stimuli, in this case epidermal growth factor and heregulin, to arrive at different cell fates, i.e. proliferation and differentiation respectively. Using genome-wide CAGE time series data collected from the FANTOM5 consortium, we identified the sets of promoters that were involved in the transition of MCF-7 cells to their specific fates versus those with expression changes that were generic to both stimuli. Of the 1,552 promoters identified, 1,091 had stimulus-specific expression while 461 promoters had generic expression profiles over the time course surveyed. Many of these stimulus-specific promoters mapped to key regulators of the ERK (extracellular signal-regulated kinases) signaling pathway such as FHL2 (four and a half LIM domains 2). We observed that in general, generic promoters peaked in their expression early on in the time course, while stimulus- specific promoters tended to show activation of their expression at a later stage. The genes that mapped to stimulus-specific promoters were enriched for pathways that control focal adhesion, p53 signaling and MAPK signaling while generic promoters were enriched for cell death, transcription and the cell cycle. We identified 162 genes that were controlled by an alternative promoter during the time course where a subset of 37 genes had separate promoters that were classified as stimulus-specific and generic. The results of our study highlighted the degree of complexity involved in regulating a cell fate transition where multiple promoters mapping to the same gene can demonstrate quite divergent expression profiles. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | info:eu-repo/semantics/altIdentifier/pmid/26658111; info:eu-repo/semantics/altIdentifier/wos/WOS:000366715900029; volume:10; issue:12; firstpage:e0144176; journal:PLOS ONE; http://hdl.handle.net/2434/825362; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84957109643 |
| DOI: | 10.1371/journal.pone.0144176 |
| الاتاحة: | http://hdl.handle.net/2434/825362 https://doi.org/10.1371/journal.pone.0144176 |
| رقم الانضمام: | edsbas.EEDFCB0 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1371/journal.pone.0144176 |
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