Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells

Networks of transcription factors (TFs) are thought to determine and maintain the identity of cells. Here we systematically repressed each of 100 TFs with shRNA and carried out global gene expression profiling in mouse embryonic stem (ES) cells. Unexpectedly, only the repression of a handful of TFs...

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Vydané v:	Scientific reports Ročník 3; číslo 1; s. 1390
Hlavní autori:	Nishiyama, Akira, Sharov, Alexei A., Piao, Yulan, Amano, Misa, Amano, Tomokazu, Hoang, Hien G., Binder, Bernard Y., Tapnio, Richard, Bassey, Uwem, Malinou, Justin N., Correa-Cerro, Lina S., Yu, Hong, Xin, Li, Meyers, Emily, Zalzman, Michal, Nakatake, Yuhki, Stagg, Carole, Sharova, Lioudmila, Qian, Yong, Dudekula, Dawood, Sheer, Sarah, Cadet, Jean S., Hirata, Tetsuya, Yang, Hsih-Te, Goldberg, Ilya, Evans, Michele K., Longo, Dan L., Schlessinger, David, Ko, Minoru S. H.
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London Nature Publishing Group UK 06.03.2013 Nature Publishing Group
Predmet:	631/114/2114 631/136/142 631/208/199 631/532/2117 Animals Cell differentiation Cluster Analysis Embryonic Stem Cells - metabolism Gene expression Gene Expression Profiling Gene Expression Regulation, Developmental Gene Silencing Humanities and Social Sciences Mice Models, Biological multidisciplinary Oct-4 protein Pluripotency RNA Interference Science Transcription factors Transcription Factors - genetics Transcription Factors - metabolism Transcriptome
ISSN:	2045-2322, 2045-2322
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Abstract	Networks of transcription factors (TFs) are thought to determine and maintain the identity of cells. Here we systematically repressed each of 100 TFs with shRNA and carried out global gene expression profiling in mouse embryonic stem (ES) cells. Unexpectedly, only the repression of a handful of TFs significantly affected transcriptomes, which changed in two directions/trajectories: one trajectory by the repression of either Pou5f1 or Sox2 ; the other trajectory by the repression of either Esrrb , Sall4 , Nanog , or Tcfap4 . The data suggest that the trajectories of gene expression change are already preconfigured by the gene regulatory network and roughly correspond to extraembryonic and embryonic fates of cell differentiation, respectively. These data also indicate the robustness of the pluripotency gene network, as the transient repression of most TFs did not alter the transcriptomes.
AbstractList	Networks of transcription factors (TFs) are thought to determine and maintain the identity of cells. Here we systematically repressed each of 100 TFs with shRNA and carried out global gene expression profiling in mouse embryonic stem (ES) cells. Unexpectedly, only the repression of a handful of TFs significantly affected transcriptomes, which changed in two directions/trajectories: one trajectory by the repression of either Pou5f1 or Sox2; the other trajectory by the repression of either Esrrb, Sall4, Nanog, or Tcfap4. The data suggest that the trajectories of gene expression change are already preconfigured by the gene regulatory network and roughly correspond to extraembryonic and embryonic fates of cell differentiation, respectively. These data also indicate the robustness of the pluripotency gene network, as the transient repression of most TFs did not alter the transcriptomes. Networks of transcription factors (TFs) are thought to determine and maintain the identity of cells. Here we systematically repressed each of 100 TFs with shRNA and carried out global gene expression profiling in mouse embryonic stem (ES) cells. Unexpectedly, only the repression of a handful of TFs significantly affected transcriptomes, which changed in two directions/trajectories: one trajectory by the repression of either Pou5f1 or Sox2 ; the other trajectory by the repression of either Esrrb , Sall4 , Nanog , or Tcfap4 . The data suggest that the trajectories of gene expression change are already preconfigured by the gene regulatory network and roughly correspond to extraembryonic and embryonic fates of cell differentiation, respectively. These data also indicate the robustness of the pluripotency gene network, as the transient repression of most TFs did not alter the transcriptomes. Networks of transcription factors (TFs) are thought to determine and maintain the identity of cells. Here we systematically repressed each of 100 TFs with shRNA and carried out global gene expression profiling in mouse embryonic stem (ES) cells. Unexpectedly, only the repression of a handful of TFs significantly affected transcriptomes, which changed in two directions/trajectories: one trajectory by the repression of either Pou5f1 or Sox2; the other trajectory by the repression of either Esrrb, Sall4, Nanog, or Tcfap4. The data suggest that the trajectories of gene expression change are already preconfigured by the gene regulatory network and roughly correspond to extraembryonic and embryonic fates of cell differentiation, respectively. These data also indicate the robustness of the pluripotency gene network, as the transient repression of most TFs did not alter the transcriptomes.Networks of transcription factors (TFs) are thought to determine and maintain the identity of cells. Here we systematically repressed each of 100 TFs with shRNA and carried out global gene expression profiling in mouse embryonic stem (ES) cells. Unexpectedly, only the repression of a handful of TFs significantly affected transcriptomes, which changed in two directions/trajectories: one trajectory by the repression of either Pou5f1 or Sox2; the other trajectory by the repression of either Esrrb, Sall4, Nanog, or Tcfap4. The data suggest that the trajectories of gene expression change are already preconfigured by the gene regulatory network and roughly correspond to extraembryonic and embryonic fates of cell differentiation, respectively. These data also indicate the robustness of the pluripotency gene network, as the transient repression of most TFs did not alter the transcriptomes.
ArticleNumber	1390
Author	Longo, Dan L. Nakatake, Yuhki Amano, Misa Malinou, Justin N. Bassey, Uwem Meyers, Emily Schlessinger, David Sharov, Alexei A. Dudekula, Dawood Ko, Minoru S. H. Correa-Cerro, Lina S. Qian, Yong Cadet, Jean S. Nishiyama, Akira Stagg, Carole Hoang, Hien G. Tapnio, Richard Evans, Michele K. Amano, Tomokazu Sharova, Lioudmila Zalzman, Michal Yu, Hong Hirata, Tetsuya Goldberg, Ilya Piao, Yulan Yang, Hsih-Te Sheer, Sarah Xin, Li Binder, Bernard Y.
Author_xml	– sequence: 1 givenname: Akira surname: Nishiyama fullname: Nishiyama, Akira organization: National Institute on Aging, National Institutes of Health – sequence: 2 givenname: Alexei A. surname: Sharov fullname: Sharov, Alexei A. organization: National Institute on Aging, National Institutes of Health – sequence: 3 givenname: Yulan surname: Piao fullname: Piao, Yulan organization: National Institute on Aging, National Institutes of Health – sequence: 4 givenname: Misa surname: Amano fullname: Amano, Misa organization: National Institute on Aging, National Institutes of Health – sequence: 5 givenname: Tomokazu surname: Amano fullname: Amano, Tomokazu organization: National Institute on Aging, National Institutes of Health – sequence: 6 givenname: Hien G. surname: Hoang fullname: Hoang, Hien G. organization: National Institute on Aging, National Institutes of Health – sequence: 7 givenname: Bernard Y. surname: Binder fullname: Binder, Bernard Y. organization: National Institute on Aging, National Institutes of Health – sequence: 8 givenname: Richard surname: Tapnio fullname: Tapnio, Richard organization: National Institute on Aging, National Institutes of Health – sequence: 9 givenname: Uwem surname: Bassey fullname: Bassey, Uwem organization: National Institute on Aging, National Institutes of Health – sequence: 10 givenname: Justin N. surname: Malinou fullname: Malinou, Justin N. organization: National Institute on Aging, National Institutes of Health – sequence: 11 givenname: Lina S. surname: Correa-Cerro fullname: Correa-Cerro, Lina S. organization: National Institute on Aging, National Institutes of Health – sequence: 12 givenname: Hong surname: Yu fullname: Yu, Hong organization: National Institute on Aging, National Institutes of Health – sequence: 13 givenname: Li surname: Xin fullname: Xin, Li organization: National Institute on Aging, National Institutes of Health – sequence: 14 givenname: Emily surname: Meyers fullname: Meyers, Emily organization: National Institute on Aging, National Institutes of Health – sequence: 15 givenname: Michal surname: Zalzman fullname: Zalzman, Michal organization: National Institute on Aging, National Institutes of Health – sequence: 16 givenname: Yuhki surname: Nakatake fullname: Nakatake, Yuhki organization: National Institute on Aging, National Institutes of Health, Department of Systems Medicine, Sakaguchi Laboratory, Keio University School of Medicine – sequence: 17 givenname: Carole surname: Stagg fullname: Stagg, Carole organization: National Institute on Aging, National Institutes of Health – sequence: 18 givenname: Lioudmila surname: Sharova fullname: Sharova, Lioudmila organization: National Institute on Aging, National Institutes of Health – sequence: 19 givenname: Yong surname: Qian fullname: Qian, Yong organization: National Institute on Aging, National Institutes of Health – sequence: 20 givenname: Dawood surname: Dudekula fullname: Dudekula, Dawood organization: National Institute on Aging, National Institutes of Health – sequence: 21 givenname: Sarah surname: Sheer fullname: Sheer, Sarah organization: National Institute on Aging, National Institutes of Health – sequence: 22 givenname: Jean S. surname: Cadet fullname: Cadet, Jean S. organization: National Institute on Aging, National Institutes of Health – sequence: 23 givenname: Tetsuya surname: Hirata fullname: Hirata, Tetsuya organization: National Institute on Aging, National Institutes of Health – sequence: 24 givenname: Hsih-Te surname: Yang fullname: Yang, Hsih-Te organization: National Institute on Aging, National Institutes of Health – sequence: 25 givenname: Ilya surname: Goldberg fullname: Goldberg, Ilya organization: National Institute on Aging, National Institutes of Health – sequence: 26 givenname: Michele K. surname: Evans fullname: Evans, Michele K. organization: National Institute on Aging, National Institutes of Health – sequence: 27 givenname: Dan L. surname: Longo fullname: Longo, Dan L. organization: National Institute on Aging, National Institutes of Health – sequence: 28 givenname: David surname: Schlessinger fullname: Schlessinger, David organization: National Institute on Aging, National Institutes of Health – sequence: 29 givenname: Minoru S. H. surname: Ko fullname: Ko, Minoru S. H. organization: National Institute on Aging, National Institutes of Health, Department of Systems Medicine, Sakaguchi Laboratory, Keio University School of Medicine
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Snippet	Networks of transcription factors (TFs) are thought to determine and maintain the identity of cells. Here we systematically repressed each of 100 TFs with...
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SubjectTerms	631/114/2114 631/136/142 631/208/199 631/532/2117 Animals Cell differentiation Cluster Analysis Embryonic Stem Cells - metabolism Gene expression Gene Expression Profiling Gene Expression Regulation, Developmental Gene Silencing Humanities and Social Sciences Mice Models, Biological multidisciplinary Oct-4 protein Pluripotency RNA Interference Science Transcription factors Transcription Factors - genetics Transcription Factors - metabolism Transcriptome
Title	Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells
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