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The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Item Type:Article
Title:The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Creators Name:Suzuki, H and Forrest, ARR and van Nimwegen, E and Daub, CO and Balwierz, PJ and Irvine, KM and Lassmann, T and Ravasi, T and Hasegawa, Y and de Hoon, MJL and Katayama, S and Schroder, K and Carninci, P and Tomaru, Y and Kanamori-Katayama, M and Kubosaki, A and Akalin, A. and Ando, Y and Arner, E and Asada, M and Asahara, H and Bailey, T and Bajic, VB and Bauer, D and Beckhouse, AG and Bertin, N and Björkegren, J and Brombacher, F and Bulger, E and Chalk, AM and Chiba, J and Cloonan, N and Dawe, A and Dostie, J and Engstroem, PG and Essack, M and Faulkner, GJ and Fink, JL and Fredman, D and Fujimori, K and Furuno, M and Gojobori, T and Gough, J and Grimmond, SM and Gustafsson, M and Hashimoto, M and Hashimoto, T and Hatakeyama, M and Heinzel, S and Hide, W and Hofmann, O and Hörnquist, M and Huminiecki, L and Ikeo, K and Imamoto, N and Inoue, S and Inoue, Y and Ishihara, R and Iwayanagi, T and Jacobsen, A and Kaur, M and Kawaji, H and Kerr, MC and Kimura, R and Kimura, S and Kimura, Y and Kitano, H and Koga, H and Kojima, T and Kondo, S and Konno, T and Krogh, A and Kruger, A and Kumar, A and Lenhard, B and Lennartsson, A and Lindow, M and Lizio, M and Macpherson, C and Maeda, N and Maher, CA and Maqungo, M and Mar, J and Matigian, NA and Matsuda, H and Mattick, JS and Meier, S and Miyamoto, S and Miyamoto-Sato, E and Nakabayashi, K and Nakachi, Y and Nakano, M and Nygaard, S and Okayama, T and Okazaki, Y and Okuda-Yabukami, H and Orlando, V and Otomo, J and Pachkov, M and Petrovsky, N and Plessy, C and Quackenbush, J and Radovanovic, A and Rehli, M and Saito, R and Sandelin, A and Schmeier, S and Schönbach, C and Schwartz, AS and Semple, CA and Sera, M and Severin, J and Shirahige, K and Simons, C and St Laurent, G and Suzuki, M and Suzuki, T and Sweet, MJ and Taft, RJ and Takeda, S and Takenaka, Y and Tan, K and Taylor, MS and Teasdale, RD and Tegnér, J and Teichmann, S and Valen, E and Wahlestedt, C and Waki, K and Waterhouse, A and Wells, CA and Winther, O and Wu, L and Yamaguchi, K and Yanagawa, H and Yasuda, J and Zavolan, M and Hume, DA and Arakawa, T and Fukuda, S and Imamura, K and Kai, C and Kaiho, A and Kawashima, T and Kawazu, C and Kitazume, Y and Kojima, M and Miura, H and Murakami, K and Murata, M and Ninomiya, N and Nishiyori, H and Noma, S and Ogawa, C and Sano, T and Simon, C and Tagami, M and Takahashi, Y and Kawai, J and Hayashizaki, Y
Abstract:Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their time-dependent activities and target genes. Systematic siRNA knockdown of 52 transcription factors confirmed the roles of individual factors in the regulatory network. Our results indicate that cellular states are constrained by complex networks involving both positive and negative regulatory interactions among substantial numbers of transcription factors and that no single transcription factor is both necessary and sufficient to drive the differentiation process.
Keywords:Base Sequence, Cell Differentiation, Cell Line, Cell Proliferation, Gene Expression Profiling, Gene Regulatory Networks, Genetic Models, Genetic Promoter Regions, Genetic Transcription, Molecular Sequence Data, Myeloid Leukemia, Oligonucleotide Array Sequence Analysis, Small Interfering RNA
Source:Nature Genetics
Publisher:Nature Publishing Group
Page Range:553-562
Date:May 2009
Official Publication:https://doi.org/10.1038/ng.375
PubMed:View item in PubMed

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