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International Worm Meeting,
2021]
Essential genes can be defined as the ones which are crucial for organism survival and reproduction. They are responsible for the functions which are most important for the organism fitness pointing out to the most fundamental biological processes. They play a significant role in evolution, as their loss leads to the organism death or inability to reproduce. But this simple definition is not sufficient as gene essentiality is context dependent and vary with genetic and environmental background. So, the same mutation might lead to cell/organism death or severe sickness in some but not all genetic and environmental contexts. Most studies on gene essentiality were done in one genetic background. That means, that many genes essential in other genetic contexts were probably unidentified. Although the number of studies analysing gene essentiality in different genetic and environmental contexts is increasing, they are mainly done with unicellular organisms or cell lines. There is noticeable underrepresentation of such studies in multicellular, whole organisms. In this study we aim to uncover context dependence of gene essentiality in model multicellular organism, Caenorhabditis elegans. We show how essentiality of genes is changing depending on genetic context by using three different wild type worm isolates: N2, LKC34, and MY16. Our set of targeted genes included 100 essential and 200 nonessential genes based on DEG database (www.essentialgene.org). Each query gene was inactivated by RNA interference (RNAi) and mutant fitness was measured quantitatively as the rate of bacterial food consumption. We identified new essential genes indispensable in i) all three (22), ii) two (10), and iii) only one (11) genetic background. From previously identified N2 essential genes, we confirmed their essentiality in two additional backgrounds (68 genes), or one of them (9 cases). As we see even in a study encompassing only three strains, and 300 genes, we can observe substantial context dependence of gene essentiality. This have very important practical consequences as well. When working on gene therapies researchers should consider that different strategies might be needed depending on genetic background in which they will be used.
[
International Worm Meeting,
2021]
A crucial process in life is the ability of cells to pass on information to their descendants. This transmission can occur at several levels from genetics to epigenetics. Epigenetic inheritance refers to the heritable phenotypes affected by gene expression without altering the DNA sequence and occurs through various factors including histone modifications. Interruption of this transmission process can lead to severe developmental defects and fertility diseases. Methylation of histone H3 at position 27 (H3K27me3) is an epigenetic mark that is associated with heterochromatin and repressed gene expression. Several studies have demonstrated that the genomic patterns of H3K27me3 can be inherited from one generation to the next by depositing H3K27me3 histones and PRC21. However, the limits of this inheritance are difficult to test because PRC2 mutants are maternal-effect sterile in C. elegans. We have recently shown that the expression of an H3.3K27M mutant acts in a dominant-negative manner and alters genomic H3K27me3 patterns and distribution of PRC2 and results in infertility phenotypes in C. elegans2. We used this strain to follow the trans-generational inheritance of the H3.3K27M-induced phenotypes. Strikingly, we observed that the altered patterning of H3K27me3 and the fertility defects are heritable for multiple generations after the H3.3K27M mutation is lost. These findings were also validated in a tetracycline-inducible system where we can abruptly switch on and off the H3.3K27M expression. We performed a targeted RNAi screen in our tetracycline-inducible system and detected several enhancer and suppressor modifiers of H3.3K27M defects such as chromatin remodeling complexes, the nuclear RNAi pathway, and histone writer and reader complexes. Overall, our results revealed that the transmission of H3K27me3 is an epigenetically programmed event that can last for generations and that several biological pathways seem to be involved in the regulation of transmission of H3K27me3 patterns across generations. 1. L. J. Gaydos, W. Wang, S. Strome. H3K27me and PRC2 transmit a memory of repression across generations and during development. Science 345, 1515-1518 American Association for the Advancement of Science (AAAS), 2014. 2. Kamila Delaney, Maude Strobino, Joanna M. Wenda, Andrzej Pankowski, Florian A. Steiner. H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans. Nature Communications 10 Springer Science and Business Media LLC, 2019.