Periodic Reporting for period 1 - PREMETAZOAEPIGENOME (The role of genome regulation in the origin of animals)
Periodo di rendicontazione: 2017-09-01 al 2019-08-31
The origin of animals is perhaps one of the most dramatic events in the natural history. In order to illuminate how this transition from unicellular life to complex multicellularity occurred, my project aimed to study close relatives of animals that have branched from the lineage that led to animals recently, that is, close relatives of animals. By understanding the molecular biology of these organisms and using a comparative approach, we were hoping to infer what aspects of the complexity seen in animals already originated before the emergence of animals.
The particular focus of PREMETAZOAEPIGENOME was understanding the regulation of the genome in these unicellular relatives of animals. In animals, the expression of genes in time and space – the process that is regulated by complex mechanisms that involves networks of transcription factors as well as histone posttranslational modification. This regulatory complexity enables cell differentiation into multiple cell types. In contrast, the regulation of the genome in well-studied unicellular organisms was shown to be much less complex. Thus, the aim of the PREMETAZOAEPIGENOME was to investigate the genome regulation in a clade of close unicellular relatives of animals called ichthyosporeans.
In this project, we have successfully established one of the ichthyosporeans, Sphaeroforma arctica, as a tractable experimental organism. We have successfully characterized its life cycle in the laboratory, we have obtained a better version of its genome, and we have characterized the gene expression changes during its life cycle. These results will in the future enable us to understand how its genome is regulated, and whether it has some of the regulatory complexity seen in animals.
The particular focus of PREMETAZOAEPIGENOME was understanding the regulation of the genome in these unicellular relatives of animals. In animals, the expression of genes in time and space – the process that is regulated by complex mechanisms that involves networks of transcription factors as well as histone posttranslational modification. This regulatory complexity enables cell differentiation into multiple cell types. In contrast, the regulation of the genome in well-studied unicellular organisms was shown to be much less complex. Thus, the aim of the PREMETAZOAEPIGENOME was to investigate the genome regulation in a clade of close unicellular relatives of animals called ichthyosporeans.
In this project, we have successfully established one of the ichthyosporeans, Sphaeroforma arctica, as a tractable experimental organism. We have successfully characterized its life cycle in the laboratory, we have obtained a better version of its genome, and we have characterized the gene expression changes during its life cycle. These results will in the future enable us to understand how its genome is regulated, and whether it has some of the regulatory complexity seen in animals.
While the experimental work was initially intended to be performed in an organism called Creolimax fragrantissima, it soon became clear that due to technical challenges and irreproducibility of results, carrying out the project as was initially planned would not be possible. Instead, I switched focus to another ichthyosporean species called Sphaeroforma arctica. I serendipitously discovered that its unique cell division cycle can easily be synchronized, which allowed elegant experimental manipulation. Using my previous expertise in quantitative cell biology, I analyzed the relationship between the cell size and cell division using quantitative experiments and mathematical modeling. I found that in S. arctica, division of nuclei is under control of a timer, which is unique among unicellular organisms, and represents a significant discovery in the field of cell division cycle. The manuscript describing this work has been published in a prestigious journal Current Biology.
To begin to study the genome regulation in ichthyosporeans, I then analyzed gene expression throughout the entire cell cycle, making use of the protocols for synchronization. We found that there is a highly coordinated transacriptional regulation in the last stage of the cycle, where Sphaeroforma arctica cells undergo a coordinated transition into a transiently multicellular state. Furthermore, combining with a bioinformatics analysis, we found that this transiently multinucleated state involves upregulation of homologs of animal cell adhesion molecules. This discovery pointed out that multicellularity in animals and ichtyosporeans might have a common cell adhesion mechanism. The results of this study, which involved several collaborators and also included a comprehensive cell biological analysis of this transiently multicellular state using advanced microscopy, as well as re-sequencing of the entire genome of Sphaeroforma arctica, will soon be published.
Finally, to get insight into genome regulatory mechanisms, which was the initial main aim of PREMETAZOAEPIGENOME, we have, with Alfonso Mendaña Gomez, a MSc student in the lab, established and optimized protocols for the genomic assays, in both Sphaeroforma arctica and Creolimax fragrantissima. Establishment of these protocols is the first step towards the investigation of genome regulatory mechanisms.
To begin to study the genome regulation in ichthyosporeans, I then analyzed gene expression throughout the entire cell cycle, making use of the protocols for synchronization. We found that there is a highly coordinated transacriptional regulation in the last stage of the cycle, where Sphaeroforma arctica cells undergo a coordinated transition into a transiently multicellular state. Furthermore, combining with a bioinformatics analysis, we found that this transiently multinucleated state involves upregulation of homologs of animal cell adhesion molecules. This discovery pointed out that multicellularity in animals and ichtyosporeans might have a common cell adhesion mechanism. The results of this study, which involved several collaborators and also included a comprehensive cell biological analysis of this transiently multicellular state using advanced microscopy, as well as re-sequencing of the entire genome of Sphaeroforma arctica, will soon be published.
Finally, to get insight into genome regulatory mechanisms, which was the initial main aim of PREMETAZOAEPIGENOME, we have, with Alfonso Mendaña Gomez, a MSc student in the lab, established and optimized protocols for the genomic assays, in both Sphaeroforma arctica and Creolimax fragrantissima. Establishment of these protocols is the first step towards the investigation of genome regulatory mechanisms.
Overall, the research done in the scope of PREMETAZOAEPIGENOME has established Sphaeroforma arctica, an organism that was previously almost completely uncharacterized, as a promising novel model system for evolutionary cell biology, and has produced two high-level scientific publications in top journals. The work was also presented at several international conferences and invited seminars at several top-notch scientific institutions in Europe. Furthermore, carrying out this project has enabled me to hone my soft skills and leadership skills.