An inference approach combines spatial and temporal gene expression data to predict gene regulatory networks in Arabidopsis stem cells
Abstract Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is key for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. For this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network (GRN) inference algorithm that combines clustering with Dynamic Bayesian Network (DBN) inference. We leveraged the topology of our networks to infer potential key regulators. The results presented in this work show that our combination of molecular biology approaches, computational biology and mathematical modeling was key to identify candidate factors that function in the stem cells. Specifically, through experimental validation and mathematical modeling, we identifiedPERIANTHIA (PAN)as an important molecular regulator of quiescent center (QC) function..
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Preprint| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
bioRxiv.org - (2023) vom: 23. Aug. Zur Gesamtaufnahme - year:2023 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
de Luis Balaguer, Maria Angels [VerfasserIn] |
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| Links: |
Volltext [kostenfrei] |
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| doi: |
10.1101/140269 |
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XBI000134767 |
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| 245 | 1 | 0 | |a An inference approach combines spatial and temporal gene expression data to predict gene regulatory networks in Arabidopsis stem cells |
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| 520 | |a Abstract Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is key for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. For this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network (GRN) inference algorithm that combines clustering with Dynamic Bayesian Network (DBN) inference. We leveraged the topology of our networks to infer potential key regulators. The results presented in this work show that our combination of molecular biology approaches, computational biology and mathematical modeling was key to identify candidate factors that function in the stem cells. Specifically, through experimental validation and mathematical modeling, we identifiedPERIANTHIA (PAN)as an important molecular regulator of quiescent center (QC) function. | ||
| 650 | 4 | |a Biology |7 (dpeaa)DE-84 | |
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| 700 | 1 | |a Fisher, Adam P. |4 aut | |
| 700 | 1 | |a Clark, Natalie M. |4 aut | |
| 700 | 1 | |a Fernandez-Espinosa, Maria Guadalupe |4 aut | |
| 700 | 1 | |a Möller, Barbara K. |4 aut | |
| 700 | 1 | |a Weijers, Dolf |4 aut | |
| 700 | 1 | |a Lohmann, Jan U. |4 aut | |
| 700 | 1 | |a Williams, Cranos |4 aut | |
| 700 | 1 | |a Lorenzo, Oscar |4 aut | |
| 700 | 1 | |a Sozzani, Rosangela |4 aut | |
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