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The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. / Suzuki, Harukazu; Forrest, Alistair R R; van Nimwegen, Erik; Daub, Carsten O; Balwierz, Piotr J; Irvine, Katharine M; Lassmann, Timo; Ravasi, Timothy; Hasegawa, Yuki; de Hoon, Michiel J L; Katayama, Shintaro; Schroder, Kate; Carninci, Piero; Tomaru, Yasuhiro; Kanamori-Katayama, Mutsumi; Kubosaki, Atsutaka; Akalin, Altuna; Ando, Yoshinari; Arner, Erik; Asada, Maki; Asahara, Hiroshi; Bailey, Timothy; Bajic, Vladimir B; Bauer, Denis; Beckhouse, Anthony G; Bertin, Nicolas; Björkegren, Johan; Brombacher, Frank; Bulger, Erika; Chalk, Alistair M; Chiba, Joe; Cloonan, Nicole; Dawe, Adam; Dostie, Josee; Engström, Pär G; Essack, Magbubah; Faulkner, Geoffrey J; Fink, J Lynn; Fredman, David; Fujimori, Ko; Furuno, Masaaki; Gojobori, Takashi; Gough, Julian; Grimmond, Sean M; Jacobsen, Anders; Krogh, Anders; Nygaard, Sanne; Sandelin, Albin; Valen, Eivind; Winther, Ole; Riken Omics Science Center.
In:
Nature Genetics, Vol. 41, No. 5, 2009, p. 553-62.
Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
Suzuki, H, Forrest, ARR, van Nimwegen, E, Daub, CO, Balwierz, PJ, Irvine, KM, Lassmann, T, Ravasi, T, Hasegawa, Y, de Hoon, MJL, Katayama, S, Schroder, K, Carninci, P, Tomaru, Y, Kanamori-Katayama, M, Kubosaki, A, Akalin, A, Ando, Y, Arner, E, Asada, M, Asahara, H, Bailey, T, Bajic, VB, Bauer, D, Beckhouse, AG, Bertin, N, Björkegren, J, Brombacher, F, Bulger, E, Chalk, AM, Chiba, J, Cloonan, N, Dawe, A, Dostie, J, Engström, PG, Essack, M, Faulkner, GJ, Fink, JL, Fredman, D, Fujimori, K, Furuno, M, Gojobori, T, Gough, J, Grimmond, SM, Jacobsen, A
, Krogh, A, Nygaard, S
, Sandelin, A, Valen, E
, Winther, O & Riken Omics Science Center 2009, '
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line',
Nature Genetics, vol. 41, no. 5, pp. 553-62.
https://doi.org/10.1038/ng.375APA
Suzuki, H., Forrest, A. R. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J. L., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., ... Riken Omics Science Center (2009).
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Nature Genetics,
41(5), 553-62.
https://doi.org/10.1038/ng.375Vancouver
Suzuki H, Forrest ARR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM et al.
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Nature Genetics. 2009;41(5):553-62.
https://doi.org/10.1038/ng.375Author
Suzuki, Harukazu ; Forrest, Alistair R R ; van Nimwegen, Erik ; Daub, Carsten O ; Balwierz, Piotr J ; Irvine, Katharine M ; Lassmann, Timo ; Ravasi, Timothy ; Hasegawa, Yuki ; de Hoon, Michiel J L ; Katayama, Shintaro ; Schroder, Kate ; Carninci, Piero ; Tomaru, Yasuhiro ; Kanamori-Katayama, Mutsumi ; Kubosaki, Atsutaka ; Akalin, Altuna ; Ando, Yoshinari ; Arner, Erik ; Asada, Maki ; Asahara, Hiroshi ; Bailey, Timothy ; Bajic, Vladimir B ; Bauer, Denis ; Beckhouse, Anthony G ; Bertin, Nicolas ; Björkegren, Johan ; Brombacher, Frank ; Bulger, Erika ; Chalk, Alistair M ; Chiba, Joe ; Cloonan, Nicole ; Dawe, Adam ; Dostie, Josee ; Engström, Pär G ; Essack, Magbubah ; Faulkner, Geoffrey J ; Fink, J Lynn ; Fredman, David ; Fujimori, Ko ; Furuno, Masaaki ; Gojobori, Takashi ; Gough, Julian ; Grimmond, Sean M ; Jacobsen, Anders ; Krogh, Anders ; Nygaard, Sanne ; Sandelin, Albin ; Valen, Eivind ; Winther, Ole ; Riken Omics Science Center. / The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. In: Nature Genetics. 2009 ; Vol. 41, No. 5. pp. 553-62.
Bibtex
@article{7d1d1450625a11de8bc9000ea68e967b,
title = "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.",
author = "Harukazu Suzuki and Forrest, {Alistair R R} and {van Nimwegen}, Erik and Daub, {Carsten O} and Balwierz, {Piotr J} and Irvine, {Katharine M} and Timo Lassmann and Timothy Ravasi and Yuki Hasegawa and {de Hoon}, {Michiel J L} and Shintaro Katayama and Kate Schroder and Piero Carninci and Yasuhiro Tomaru and Mutsumi Kanamori-Katayama and Atsutaka Kubosaki and Altuna Akalin and Yoshinari Ando and Erik Arner and Maki Asada and Hiroshi Asahara and Timothy Bailey and Bajic, {Vladimir B} and Denis Bauer and Beckhouse, {Anthony G} and Nicolas Bertin and Johan Bj{\"o}rkegren and Frank Brombacher and Erika Bulger and Chalk, {Alistair M} and Joe Chiba and Nicole Cloonan and Adam Dawe and Josee Dostie and Engstr{\"o}m, {P{\"a}r G} and Magbubah Essack and Faulkner, {Geoffrey J} and Fink, {J Lynn} and David Fredman and Ko Fujimori and Masaaki Furuno and Takashi Gojobori and Julian Gough and Grimmond, {Sean M} and Anders Jacobsen and Anders Krogh and Sanne Nygaard and Albin Sandelin and Eivind Valen and Ole Winther and {Riken Omics Science Center}",
year = "2009",
doi = "10.1038/ng.375",
language = "English",
volume = "41",
pages = "553--62",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "nature publishing group",
number = "5",
}
RIS
TY - JOUR
T1 - The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
AU - Suzuki, Harukazu
AU - Forrest, Alistair R R
AU - van Nimwegen, Erik
AU - Daub, Carsten O
AU - Balwierz, Piotr J
AU - Irvine, Katharine M
AU - Lassmann, Timo
AU - Ravasi, Timothy
AU - Hasegawa, Yuki
AU - de Hoon, Michiel J L
AU - Katayama, Shintaro
AU - Schroder, Kate
AU - Carninci, Piero
AU - Tomaru, Yasuhiro
AU - Kanamori-Katayama, Mutsumi
AU - Kubosaki, Atsutaka
AU - Akalin, Altuna
AU - Ando, Yoshinari
AU - Arner, Erik
AU - Asada, Maki
AU - Asahara, Hiroshi
AU - Bailey, Timothy
AU - Bajic, Vladimir B
AU - Bauer, Denis
AU - Beckhouse, Anthony G
AU - Bertin, Nicolas
AU - Björkegren, Johan
AU - Brombacher, Frank
AU - Bulger, Erika
AU - Chalk, Alistair M
AU - Chiba, Joe
AU - Cloonan, Nicole
AU - Dawe, Adam
AU - Dostie, Josee
AU - Engström, Pär G
AU - Essack, Magbubah
AU - Faulkner, Geoffrey J
AU - Fink, J Lynn
AU - Fredman, David
AU - Fujimori, Ko
AU - Furuno, Masaaki
AU - Gojobori, Takashi
AU - Gough, Julian
AU - Grimmond, Sean M
AU - Jacobsen, Anders
AU - Krogh, Anders
AU - Nygaard, Sanne
AU - Sandelin, Albin
AU - Valen, Eivind
AU - Winther, Ole
AU - Riken Omics Science Center
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
U2 - 10.1038/ng.375
DO - 10.1038/ng.375
M3 - Journal article
C2 - 19377474
VL - 41
SP - 553
EP - 562
JO - Nature Genetics
JF - Nature Genetics
SN - 1061-4036
IS - 5
ER -
