Periodic Reporting for period 3 - ZygoticFate (Zygotic Cell Fate and Parent-Biased Gene Expression in Fission Yeast)
Okres sprawozdawczy: 2023-12-01 do 2025-05-31
Fertilization marks the beginning of new life in sexually reproducing organisms. Importantly, this moment when two haploid gametes (e.g. egg and sperm cells) fuse is also the time when the newly formed diploid cell switches fate and becomes a zygote. Gamete-to-zygote fate switch is, on one hand, important to stop further mating and refertilization, and thus prevent abnormal ploidy. On the other hand, zygotic fate acquisition is crucial to initiate development, which is best evident in animal species where terminally differentiated egg and sperm cells fuse to gives rise to a totipotent zygote capable of developing into a new individual. What are the molecular mechanisms that drive the gamete-to-zygote transition has been difficult to study in animal species, where gametes and zygotes are often poorly accessible and with limited genetic tools. We previously showed striking similarities between zygotes of fission yeast and higher eukaryotes and in this ERC-funded project use this powerful model to explore molecular mechanisms that regulate zygotic fate establishment and subsequent development.
Specifically, our work has the following two aims:
1. Defining the regulation of zygotic gene expression, signalling and mechanisms that prevent refertilization. In this study, we aim to fill the knowledge gap concerning how both transcriptional and post-transcriptional regulation contribute to the development of zygotes. On one hand, we will aim to identify key molecular player and the pathways they regulate in zygotes. On the other hand, by looking and multiple pathways we aim to uncover how these regulatory modules come together and thus understand how a single decision to switch fate leads to coordinated changes in different aspects of cellular physiology, helping us grasp the principles of cell fate switching. Additionally, we will explore how fungi prevent re-fertilization, a critical aspect that is currently very poorly understood. By dissecting the molecular mechanisms behind fungal re-fertilization blocks, we may identify conserved mechanisms that are relevant to sexual reproduction in other phyla. Furthermore, studying re-fertilization blocks in a microbial context may unveil unexpected adaptive roles, as polyploidy resulting from re-fertilization can enhance fitness under specific conditions in both non-pathogenic and pathogenic species.
2. Characterizing the prevalence, roles and regulation of parent-biased allele expression. This work pushes beyond our discovery that fission yeast asymmetrically rely on parental alleles, which underlies several phenomena of non-Mendelian inheritance in higher eukaryotes. Multiple theoretical frameworks propose mechanisms for their selective evolution and yet, little experimental evidence is available since means to manipulate current model systems are limited. By identifying novel examples and roles for parent-biased allelic expression, we may introduce fission yeast as a model system, where experimental evolution is feasible, to study parent-biased gene expression. Thus, our work holds potential for major impact on understanding the evolutionary pressures that shape asymmetry in contributions of parental genomes in other phyla.
Specifically, our work has the following two aims:
1. Defining the regulation of zygotic gene expression, signalling and mechanisms that prevent refertilization. In this study, we aim to fill the knowledge gap concerning how both transcriptional and post-transcriptional regulation contribute to the development of zygotes. On one hand, we will aim to identify key molecular player and the pathways they regulate in zygotes. On the other hand, by looking and multiple pathways we aim to uncover how these regulatory modules come together and thus understand how a single decision to switch fate leads to coordinated changes in different aspects of cellular physiology, helping us grasp the principles of cell fate switching. Additionally, we will explore how fungi prevent re-fertilization, a critical aspect that is currently very poorly understood. By dissecting the molecular mechanisms behind fungal re-fertilization blocks, we may identify conserved mechanisms that are relevant to sexual reproduction in other phyla. Furthermore, studying re-fertilization blocks in a microbial context may unveil unexpected adaptive roles, as polyploidy resulting from re-fertilization can enhance fitness under specific conditions in both non-pathogenic and pathogenic species.
2. Characterizing the prevalence, roles and regulation of parent-biased allele expression. This work pushes beyond our discovery that fission yeast asymmetrically rely on parental alleles, which underlies several phenomena of non-Mendelian inheritance in higher eukaryotes. Multiple theoretical frameworks propose mechanisms for their selective evolution and yet, little experimental evidence is available since means to manipulate current model systems are limited. By identifying novel examples and roles for parent-biased allelic expression, we may introduce fission yeast as a model system, where experimental evolution is feasible, to study parent-biased gene expression. Thus, our work holds potential for major impact on understanding the evolutionary pressures that shape asymmetry in contributions of parental genomes in other phyla.
In the following paragraphs I summarize the progress we have made in the first half of the project.
Gene expression is a critical aspect of development, and we sought to investigate how RNA profiles change during zygote formation in fission yeast. Our RNA analyses showed surprising results: unlike budding yeast but similar to animals, fission yeast zygotic fate does not require immediate and widespread changes in RNA abundance. Instead, robust up- and down-regulation of RNAs occurs only after zygotes enter the cell cycle. These findings challenge the conventional understanding of how fungal zygotes regulate gene expression and have significant implications for subsequent research.
We discovered that genes necessary for early zygotic development, such as meiotic recombination genes, are induced ahead of fertilization. Interestingly, their induction occurs asymmetrically, with expression observed in only in one type of gametes. We demonstrated that early expression of these genes imposes fitness costs on the gamete that expresses them, influencing their competitive advantage during evolution. This novel finding promotes our understanding of the driving forces behind the emergence of anisogametes and genders.
Given that zygote formation does not trigger widespread changes in RNA abundance, we focused on understanding how post-transcriptional regulation promotes the gamete-to-zygote transition. Our investigations revealed the critical role of the zygote-specific signalling in regulating the lifecycle of RNAs that is likely working though regulating stability, processing, and translation of numerous RNAs.
After fertilization, zygotes must quickly prevent further mating and refertilization, a process that remains poorly understood. Our investigations revealed distinct mechanisms operating in early and late zygotes. Late zygotes downregulate mating genes through the cell-cycle regulated transcription, while early zygotes maintain high RNA and protein levels of mating regulators, relying on post-translational regulation to block mating. These results validated our experimental approach and set the foundation for further studies in this area.
In the course of our research, we also developed two innovative methodologies. First, we designed oxygen-permeable chambers to enhance live-cell fluorescence imaging, reducing signal variability and increasing imaging resolution. Second, we collaborated to create a user-friendly computer application that automates image processing, making state-of-the-art machine learning tools more accessible to cell biologists.
Gene expression is a critical aspect of development, and we sought to investigate how RNA profiles change during zygote formation in fission yeast. Our RNA analyses showed surprising results: unlike budding yeast but similar to animals, fission yeast zygotic fate does not require immediate and widespread changes in RNA abundance. Instead, robust up- and down-regulation of RNAs occurs only after zygotes enter the cell cycle. These findings challenge the conventional understanding of how fungal zygotes regulate gene expression and have significant implications for subsequent research.
We discovered that genes necessary for early zygotic development, such as meiotic recombination genes, are induced ahead of fertilization. Interestingly, their induction occurs asymmetrically, with expression observed in only in one type of gametes. We demonstrated that early expression of these genes imposes fitness costs on the gamete that expresses them, influencing their competitive advantage during evolution. This novel finding promotes our understanding of the driving forces behind the emergence of anisogametes and genders.
Given that zygote formation does not trigger widespread changes in RNA abundance, we focused on understanding how post-transcriptional regulation promotes the gamete-to-zygote transition. Our investigations revealed the critical role of the zygote-specific signalling in regulating the lifecycle of RNAs that is likely working though regulating stability, processing, and translation of numerous RNAs.
After fertilization, zygotes must quickly prevent further mating and refertilization, a process that remains poorly understood. Our investigations revealed distinct mechanisms operating in early and late zygotes. Late zygotes downregulate mating genes through the cell-cycle regulated transcription, while early zygotes maintain high RNA and protein levels of mating regulators, relying on post-translational regulation to block mating. These results validated our experimental approach and set the foundation for further studies in this area.
In the course of our research, we also developed two innovative methodologies. First, we designed oxygen-permeable chambers to enhance live-cell fluorescence imaging, reducing signal variability and increasing imaging resolution. Second, we collaborated to create a user-friendly computer application that automates image processing, making state-of-the-art machine learning tools more accessible to cell biologists.
Our findings thus far have changed the ideas on how zygotic cell fate is established and how parents can make distinct contributions to zygotic development. Several of the above described results are being prepared for publication in open access scientific peer-reviewed journals. I highlight two of our findings that are making strong contributions to the progress of the field.
1. Our research revealed intriguing insights into how parental genomes contribute differently to offspring development. We discovered novel examples of zygotic factors that are asymmetrically contributed by parents and found that this asymmetry plays a significant functional role. These factors lead to parent-offspring conflicts, where early production is necessary for offspring development but potentially harmful to the parent. We propose that evolution minimized this conflict by restricting the expression of such genes to only one parent. These findings have broader implications for understanding how parent-offspring conflicts may influence evolutionary differences between parents.
2. Our investigation into zygotic fate establishment uncovered surprising aspects of post-transcriptional regulation. We define novel pathways for zygote-specific regulation of localization and processing of RNAs. This work opens up exciting opportunities to further explore the roles and pathways for post-transcriptional regulation in zygotes and its impact on development.
1. Our research revealed intriguing insights into how parental genomes contribute differently to offspring development. We discovered novel examples of zygotic factors that are asymmetrically contributed by parents and found that this asymmetry plays a significant functional role. These factors lead to parent-offspring conflicts, where early production is necessary for offspring development but potentially harmful to the parent. We propose that evolution minimized this conflict by restricting the expression of such genes to only one parent. These findings have broader implications for understanding how parent-offspring conflicts may influence evolutionary differences between parents.
2. Our investigation into zygotic fate establishment uncovered surprising aspects of post-transcriptional regulation. We define novel pathways for zygote-specific regulation of localization and processing of RNAs. This work opens up exciting opportunities to further explore the roles and pathways for post-transcriptional regulation in zygotes and its impact on development.