Abstract
Transcription factors (TFs) often trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. Here we present a method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Basic Helix-Loop-Helix Transcription Factors / physiology
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Bryopsida / genetics*
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Bryopsida / growth & development
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Cell Transdifferentiation / genetics
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Gene Expression Profiling / methods
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Gene Expression Regulation, Plant / physiology
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Gene Ontology
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Plant Leaves / cytology
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Stem Cells / physiology*
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Stress, Physiological / genetics
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Systems Theory
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Tissue Array Analysis
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Transcription Factors / genetics
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Transcription Factors / metabolism*
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Transcriptome / physiology
Substances
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Basic Helix-Loop-Helix Transcription Factors
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Transcription Factors
Grants and funding
This study was supported by the Excellence Initiative of the German Federal and State Governments (FRIAS LifeNet to H.B. and M.B.; EXC 294 to S.A.R.) and by the German Federal Ministry of Education and Research (Freiburg Initiative for Systems Biology, 0313921, to S.A.R.; Medical Systems Biology, LungSys, to J.B.). The article processing charge was funded by the German Research Foundation (DFG) and the Albert Ludwigs University Freiburg in the funding programme Open Access Publishing. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.