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

Johan Boström; Zuzana Sramkova; Alena Salašová; Helena Johard; Diana Mahdessian; Radek Fedr; Carolyn Marks; Jiřina Medalová; Karel Souček; Emma Lundberg; Sten Linnarsson; Vítězslav Bryja; Petra Sekyrova; Mikael Altun; Michael Andäng

doi:10.1371/journal.pone.0188772

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

Johan Boström, Zuzana Sramkova, Alena Salašová, Helena Johard, Diana Mahdessian, Radek Fedr, Carolyn Marks, Jiřina Medalová, Karel Souček, Emma Lundberg, Sten Linnarsson, Vítězslav Bryja, Petra Sekyrova, Mikael Altun, Michael Andäng

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17 Citations (Scopus)

Abstract

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 unsynchro-nized 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.

Original language	English
Article number	e0188772
Journal	PLOS ONE
Volume	12
Issue	12
ISSN	1932-6203
DOIs	https://doi.org/10.1371/journal.pone.0188772
Publication status	Published - Dec 2017
Externally published	Yes

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Boström, J., Sramkova, Z., Salašová, A., Johard, H., Mahdessian, D., Fedr, R., Marks, C., Medalová, J., Souček, K., Lundberg, E., Linnarsson, S., Bryja, V., Sekyrova, P., Altun, M., & Andäng, M. (2017). Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells. PLOS ONE, 12(12), Article e0188772. https://doi.org/10.1371/journal.pone.0188772

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title = "Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells",

abstract = "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 unsynchro-nized 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.",

author = "Johan Bostr{\"o}m and Zuzana Sramkova and Alena Sala{\v s}ov{\'a} and Helena Johard and Diana Mahdessian and Radek Fedr and Carolyn Marks and Ji{\v r}ina Medalov{\'a} and Karel Sou{\v c}ek and Emma Lundberg and Sten Linnarsson and V{\'i}t{\v e}zslav Bryja and Petra Sekyrova and Mikael Altun and Michael And{\"a}ng",

note = "Publisher Copyright: {\textcopyright} 2017 Bostr{\"o}m et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

year = "2017",

month = dec,

doi = "10.1371/journal.pone.0188772",

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Boström, J, Sramkova, Z, Salašová, A, Johard, H, Mahdessian, D, Fedr, R, Marks, C, Medalová, J, Souček, K, Lundberg, E, Linnarsson, S, Bryja, V, Sekyrova, P, Altun, M & Andäng, M 2017, 'Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells', PLOS ONE, vol. 12, no. 12, e0188772. https://doi.org/10.1371/journal.pone.0188772

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells. / Boström, Johan; Sramkova, Zuzana; Salašová, Alena et al.
In: PLOS ONE, Vol. 12, No. 12, e0188772, 12.2017.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

AU - Boström, Johan

AU - Sramkova, Zuzana

AU - Salašová, Alena

AU - Johard, Helena

AU - Mahdessian, Diana

AU - Fedr, Radek

AU - Marks, Carolyn

AU - Medalová, Jiřina

AU - Souček, Karel

AU - Lundberg, Emma

AU - Linnarsson, Sten

AU - Bryja, Vítězslav

AU - Sekyrova, Petra

AU - Altun, Mikael

AU - Andäng, Michael

N1 - Publisher Copyright: © 2017 Boström et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2017/12

Y1 - 2017/12

N2 - 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 unsynchro-nized 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.

AB - 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 unsynchro-nized 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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SN - 1932-6203

VL - 12

JO - PLOS ONE

JF - PLOS ONE

IS - 12

M1 - e0188772

ER -

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

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