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.
Highlights
Plant cells differentiate from stem cells into specialized tissue cells and back to cope with varying environmental cues
Previous analyses of detached leaflets that transdifferentiate into apical stem cells showed the importance of the P. patens ortholog of the polycomb group protein FERTILIZATION INDEPENDENT ENDOSPERM (FIE) as a marker for newly reprogrammed stem cells [2]
Our microarray data confirmed the activation and time course of two previously reported markers for transdifferentiation: the expression of CYCD;1 (Phypa_226408) [3] and the FIE transcript, Phypa_61985 [2], being continuously up-regulated over the whole time course, respectively transiently up-regulated between 6–36 h a.d. (Fig. S2A). This demonstrates that a minority of leaflet cells is strongly expressing CYCD;1 and FIE, the RNA derived from the mixed cell population can be employed to detect expression profiles of such a subset
Summary
Plant cells differentiate from stem cells into specialized tissue cells and back to cope with varying environmental cues. Processes in animal cells that evolve on time scales of hours to days, like differentiation, have been shown to exhibit a strong correlation between transcriptome kinetics, de novo protein synthesis and long-term cell behavior [4,5,6]. This finding is possibly rooted in the fact that complex regulatory networks are controlled by their slowest evolving subsystems [4,7]. We assumed the same to be true for plant cell dynamics
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