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Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

J. Boström, Z. Sramkova, A. Salašová, H. Johard, D. Mahdessian, R. Fedr, C. Marks, J. Medalová, K. Souček, E. Lundberg, S. Linnarsson, V. Bryja, P. Sekyrova, M. Altun, M. Andäng,

. 2017 ; 12 (12) : e0188772. [pub] 20171211

Language English Country United States

Document type Comparative Study, Journal Article, Validation Study

Persistent link   https://www.medvik.cz/link/bmc18010247

Grant support
NV15-33999A MZ0 CEP Register
NV15-28628A MZ0 CEP Register

The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development.

References provided by Crossref.org

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$a Boström, Johan $u Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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$a Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells / $c J. Boström, Z. Sramkova, A. Salašová, H. Johard, D. Mahdessian, R. Fedr, C. Marks, J. Medalová, K. Souček, E. Lundberg, S. Linnarsson, V. Bryja, P. Sekyrova, M. Altun, M. Andäng,
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$a The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development.
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$a Sramkova, Zuzana $u Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden. Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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$a Salašová, Alena $u Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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$a Johard, Helena $u Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden. Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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$a Mahdessian, Diana $u Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.
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$a Fedr, Radek $u Department of Cytokinetics, Institute of Biophysics CAS, v.v.i., Královopolská 135, Brno, Czech Republic. International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.
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$a Marks, Carolyn $u Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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$a Medalová, Jiřina $u Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
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$a Souček, Karel $u Department of Cytokinetics, Institute of Biophysics CAS, v.v.i., Královopolská 135, Brno, Czech Republic. International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic. Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
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$a Lundberg, Emma $u Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.
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$a Linnarsson, Sten $u Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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$a Bryja, Vítězslav $u Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
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$a Sekyrova, Petra $u Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden. Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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$a Altun, Mikael $u Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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$a Andäng, Michael $u Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden. Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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