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

Akira Nishiyama, Alexei A. Sharov, Yulan Piao, Misa Amano, Tomokazu Amano, Hien G. Hoang, Bernard Y. Binder, Richard Tapnio, Uwem Bassey, Justin N. Malinou, Lina S. Correa-Cerro, Hong Yu, Li Xin, Emily Meyers, Michal Zalzman, Yuki Nakatake, Carole Stagg, Lioudmila Sharova, Yong Qian, Dawood Dudekula & 9 others Sarah Sheer, Jean S. Cadet, Tetsuya Hirata, Hsih Te Yang, Ilya Goldberg, Michele K. Evans, Dan L. Longo, David Schlessinger, Minoru Ko

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Article number1390
JournalScientific Reports
Volume3
DOIs
Publication statusPublished - 2013

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Embryonic Stem Cells
Transcription Factors
Gene Expression
Gene Regulatory Networks
Transcriptome
Gene Expression Profiling
Small Interfering RNA
Cell Differentiation

ASJC Scopus subject areas

  • General

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Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. / 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, Yuki; 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.

In: Scientific Reports, Vol. 3, 1390, 2013.

Research output: Contribution to journalArticle

Nishiyama, A, Sharov, AA, Piao, Y, Amano, M, Amano, T, Hoang, HG, Binder, BY, Tapnio, R, Bassey, U, Malinou, JN, Correa-Cerro, LS, Yu, H, Xin, L, Meyers, E, Zalzman, M, Nakatake, Y, Stagg, C, Sharova, L, Qian, Y, Dudekula, D, Sheer, S, Cadet, JS, Hirata, T, Yang, HT, Goldberg, I, Evans, MK, Longo, DL, Schlessinger, D & Ko, M 2013, 'Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells', Scientific Reports, vol. 3, 1390. https://doi.org/10.1038/srep01390
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, Yuki ; 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. / Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. In: Scientific Reports. 2013 ; Vol. 3.
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AU - Hoang, Hien G.

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AU - Sharova, Lioudmila

AU - Qian, Yong

AU - Dudekula, Dawood

AU - Sheer, Sarah

AU - Cadet, Jean S.

AU - Hirata, Tetsuya

AU - Yang, Hsih Te

AU - Goldberg, Ilya

AU - Evans, Michele K.

AU - Longo, Dan L.

AU - Schlessinger, David

AU - Ko, Minoru

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