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

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.

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Figure 1: Motif Activity Response Analysis (MARA).
Figure 2: Statistical significance and consistency across replicates of the inferred motif activity profiles.
Figure 3: Inferred time-dependent activities of the key regulatory motifs.
Figure 4: Predicted core regulatory network of the 30 core motifs.
Figure 5: Validation of predicted target promoter sets using siRNA knockdowns.
Figure 6: Most significant motif activity changes (as measured by z value, red bars) for four TF gene knockdowns that induce motif activity changes that have a differentiative overlap with the PMA time course of more than 50%.

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Acknowledgements

We thank A. Ambesi, H. Atsui, M. Bansal, V. Belcastro, H. Daub, D. di Bernardo, M. Furuya, A. Hasegawa, K. Hayashida, A. Hirakiyama, F. Hori, K. Koseki, S. Kuhara, N. Miyamoto, S. Miyano, M. Nishikawa, C. Ohinata, M. Persson, S. Saihara, C. Sakaba, H. Sano, E. Shibazaki, T. Takagi, K. Toyoda, Y. Tsujimura and M. Yamamoto for discussion, encouragement and technical assistance. We thank M. Muramatsu, T. Ogawa, Y. Sakaki and A. Wada for support and encouragement. This work was mainly supported by grants for the Genome Network Project from the Ministry of Education, Culture, Sports, Science and Technology, Japan (Y.H.), Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government (Y.H.) and the RIKEN Frontier Research System, Functional RNA research program (Y.H.). A.R.R.F. is supported by a CJ Martin Fellowship from the Australian National Health and Medical Research Council (ID 428261). E.v.N. acknowledges support from SNF grant SNF #3100A0-118318.

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A.A., A.M.C., A.D., A. Kruger, A. Krogh, A.R., A.R.R.F., A.S., A.S.S., A.W., B.L., C.A.M., C.A.S., C.A.W., C.O.D., C.M., C. Simons, C. Schönbach, C.W., D.B., E.A., E.V., E.v.N., G.J.F., H. Kawaji, H. Kitano, H. Matsuda, J.L.F., J.G., J.M., J.Q., J.S., J.S.M., J.T., K. Ikeo, K.T., K.W., K.Y., L.H., M.d.H., M.E., M.G., M. Hörnquist, M. Kaur, M. Lizio, M. Maqungo, M.P., M. Sera, M.S.T., M.T., M.Z., N.B., N.C., O.H., O.W., P.J.B., P.G.E., R.I., R.J.T., R.S., R.D.T., S.F., S. Kondo, S. Katayama, S. Kimura, S. Meier, S.S., S. Teichmann, T.B., T.G., T.H., T.I., T. Konno, T.L., T.O., T.R., V.B.B., W.H., Y. Kimura, Y.N. and Y. Takenaka were involved in bioinformatic aspects of the project. A.G.B., A.J., A. Kaiho, A. Kubosaki, A. Kumar, A.L., A.R.R.F., C.A.W., C. Kai, C. Kawazu, C.O., C.P., C. Simon, C.W., D.A.H., E.B., E.M.-S., F.B., G.S.L., H. Koga, H. Miura, H.N., H.O.-Y., H.S., H.Y., J.B., J.C., J.K., J.O., J.S.M., J.Y., K.F., K. Imamura, K.M., K.M.I., K.N., K. Schroder, K. Shirahige, L.W., M.A., M.C.K., M.F., M. Hashimoto, M. Hatakeyama, M.J.S., M.K.-K., M. Kojima, M. Murata, M.N., M.R., M. Suzuki, M.T., N.A.M., N.I., N.N., N.P., R.K., R.D.T., S.M.G., S.H., S.I., S. Miyamoto, S. Noma, S. Nygaard, S. Takeda, T.A., T. Kawashima, T. Kojima, T. Sano, T. Suzuki, V.O., Y.A., Y. Hasegawa, Y.I., Y. Kitazume, Y.N., Y.O., Y. Takahashi and Y. Tomaru were involved in biological aspects of the project. A.M.C., A.R.R.F., A.S., B.L., C.O.D., D.F., E.A., E.v.N., G.J.F., H.A., H.S., J.D., J.M., J.Q., J.S.M., K.W., M. Lindow, M.Z., N.C., N.M., O.H., P.J.B., P.C., R.J.T., R.S., S.M.G., S. Kondo, T.L., T.R. and V.O. were involved in the genome-wide and RNA analyses. E.v.N. and P.J.B. designed and carried out the motif activity response analysis. A.R.R.F., E.v.N., Y. Tomaru and M.K.-K. carried out the siRNA analysis. A.R.R.F., C.O.D., D.A.H., E.v.N., H.S., J.K., P.C. and Y. Hayashizaki oversaw the project. H.S., A.R.R.F., E.v.N., and D.A.H. wrote the manuscript with assistance from T.R., T.L., M.J.S., Y. Hasegawa, M.d.H., K.M.I., K.Schloder, P.J.C., P.J.B., E.A., N.P., M.R., S.M.G., C.A.W., J.Q., W.H., A. Kubosaki, Y. Tomaru, V.B.B., M. Suzuki and Y. Hayashizaki.

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Correspondence to David A Hume or Yoshihide Hayashizaki.

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The FANTOM Consortium., Riken Omics Science Center. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41, 553–562 (2009). https://doi.org/10.1038/ng.375

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