Faithful modeling of transient expression and its application to elucidating negative feedback regulation

Abstract

Modeling and analysis of genetic regulatory networks is essential both for better understanding their dynamic behavior and for elucidating and refining open issues. We hereby present a discrete computational model that effectively describes the transient and sequential expression of a network of genes in a representative developmental pathway. Our model system is a transcriptional cascade that includes positive and negative feedback loops directing the initiation and progression through meiosis in budding yeast. The computational model allows qualitative analysis of the transcription of early meiosis-specific genes, specifically, Ime2 and their master activator, Ime1. The simulations demonstrate a robust transcriptional behavior with respect to the initial levels of Ime1 and Ime2. The computational results were verified experimentally by deleting various genes and by changing initial conditions. The model has a strong predictive aspect, and it provides insights into how to distinguish among and reason about alternative hypotheses concerning the mode by which negative regulation through Ime1 and Ime2 is accomplished. Some predictions were validated experimentally, for instance, showing that the decline in the transcription of IME1 depends on Rpd3, which is recruited by Ime1 to its promoter. Finally, this general model promotes the analysis of systems that are devoid of consistent quantitative data, as is often the case, and it can be easily adapted to other developmental pathways.budding yeast ͉ computational modeling ͉ meiosis ͉ systems biology ͉ transcriptional networks

Cell Differentiation and Spatial Organization in Yeast Colonies: Role of Cell-Wall Integrity Pathway

“…IME1 and IME2 are regulated through both positive-and negative-feedback loops (Rubinstein et al 2007;Ray et al 2013). To determine whether Rlm1 acts entirely upstream of IME1 vs. via feedback controls, we measured ime1D-lacZ expression in strains lacking functional Ime1 (i.e., ime1D-lacZ/ime1D), and we also measured ime2D-GFP expression in strains lacking functional Ime2 (i.e., ime2D-GFP/ime2D).…”

“…Consistent with the ime1D-lacZ results, we found that ime2D-GFP/IME2 + strain expressed the fusion gene to higher levels in wild-type (RLM1 + ) colonies than in rlm1D colonies (Figure 2A, right). Thus, Rlm1 promotes transcription of both IME1 and IME2 in colonies.IME1 and IME2 are regulated through both positive-and negative-feedback loops (Rubinstein et al 2007;Ray et al 2013). To determine whether Rlm1 acts entirely upstream of IME1 vs. via feedback controls, we measured ime1D-lacZ expression in strains lacking functional Ime1 (i.e., ime1D-lacZ/ime1D), and we also measured ime2D-GFP expression in strains lacking functional Ime2 (i.e., ime2D-GFP/ime2D).…”

A nutrient dependant switch explains mutually exclusive existence of meiosis and mitosis initiation in budding yeast

“…Comparably, there are fewer mathematical studies of meiosis (Ray et al, 2013;Rubinstein et al, 2007;Shen et al, 2010) than mitosis in the literature; and among them, two mathematical models (Ray et al, 2013;Rubinstein et al, 2007) have been proposed to describe meiosis initiation. The most common feature of these two modelling studies is that both of them investigate the feedback loops involved in meiotic initiation.…”

“…However, the model restricts the protein/RNA expression level to a maximum value of nine which limits the protein and mRNA expression only to that threshold cutting off further expression ( Fig. 2A and Fig.3A in (Rubinstein et al, 2007)). Further, the weights for each edge are decided without considering the actual mechanisms and do not provide a detailed representation hindering the model's predictive capability.…”

“…The most common feature of these two modelling studies is that both of them investigate the feedback loops involved in meiotic initiation. The model developed by Rubinstein et al, (2007) is a Boolean network of meiosis initiation of budding yeast, which includes main initiator proteins, Ime1 and Ime2, their regulators, Ume6 and Rpd3, and two putative nodes representing the negative regulation of Ime1 and Ime2. (The model is a discrete transition system representing the initiation process by a graph whose nodes represent RNA or proteins, and the edges denote regulation.)…”