Periodic Reporting for period 3 - GeneBodyMethylation (Resolving the Nuts and Bolts of Gene Body Methylation)
Período documentado: 2019-10-01 hasta 2021-03-31
DNA methylation, the binding of a methyl group (CH3) to cytosine base, regulates the genome activity and plays a fundamental developmental role in eukaryotes. Its epigenetic characteristics of regulating transcription without changing the genetic code together with the ability to be transmitted through DNA replication allow organisms to memorize cellular events for many generations. DNA methylation is mostly known for its role in transcriptional silencing; however, it can also be targeted inside actively transcribed genes, thus termed gene body methylation. Despite being an evolutionary conserved and a robust methylation pathway targeted to thousands of genes in animal and plant genomes, the function of gene body methylation is still poorly understood. To make major breakthroughs in the field, we integrate epigenomics data from diverse eukaryotes and generate gene-body-specific epi-mutants together with customized genetic and biochemical systems will allow us to discover regulators and to explore the particular biological roles of gene body methylation. Our data support the role of CMT in targeting de novo methylation in gene bodies. Additionally, our findings substantiate the role of CG methylation in transcriptional homeostasis. Moreover, we showed that genic non-CG methylation is a conserved feature in the animal nervous system. Furthermore, our results show that CG methylation is a moderate transcriptional inhibitor, explaining its role in actively transcribed genes. These findings enhance our understanding towards a full comprehension of the entire functional array of DNA methylation, and to its more precise exploitation in yielding better crops and in treating human diseases.
By investigating the role of DNA methylation enzymes in basal plants, we discovered the potential of a particular enzyme to trigger methylation in gene bodies (Yaari et al., 2019). Our data also propose a new paradigm for the establishment of gene body methylation in flowering plants (Yaari et al., 2019). Finally, by identifying the molecular mechanism of novel methylation enzymes, we can now artificially manipulate gene body methylation to our own needs.
By investigating the dynamics of gene body methylation in honey bees, an organism that mediates methylation specifically to gene bodies, we discovered that genic methylation globally fluctuates during honey bee development (Harris et al., 2019). However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Based on these results, we propose that gene body methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened genic methylation at CH sites (N=A, C or T) is a conserved regulator of animal nervous systems.
By collaborating with the Gideon Grafi’s group, we identified in the model plant, Arabidopsis thaliana, a transcriptional feedback loop between two methylation enzymes, which is based on a genic methylation of one of the methylases (Yadav et al., 2018).
By collaborating with Danny Chamovitz’s and Tamir Tuller’s groups, we identified a novel nuclear factor, COP9 signalosome, that its disruption alters DNA methylation particularly within genic regions (Tuller et al., 2018).
By manipulating the level of different methylation contexts in moss, we managed to create a plant that has comparable level of CG and non-CG methylation. We used this plants to investigate the transcriptional roles of the particular methylation contexts. This study which have been submitted for publication (Domb et al., 2020) shows that non-CG methylation is a stringer silencer than the canonical CG methylation. This result explain the development of non-CG methylation in plants and the ambient transcriptional role of CG methylation in genes.
We have developed a computational bioinformatic tool to analyze methylome NGS data in a single read resolution. We used this tool to reveal methylation processivity and stochasticity patterns of DNA methylases. Intriguingly, our data suggest that methylation in genes and TEs is processive and stochastic, respectively. This result implies on the biological regulation of these elements during development.
By investigating the dynamics of gene body methylation in honey bees, an organism that mediates methylation specifically to gene bodies, we discovered that genic methylation globally fluctuates during honey bee development (Harris et al., 2019). However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Based on these results, we propose that gene body methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened genic methylation at CH sites (N=A, C or T) is a conserved regulator of animal nervous systems.
By collaborating with the Gideon Grafi’s group, we identified in the model plant, Arabidopsis thaliana, a transcriptional feedback loop between two methylation enzymes, which is based on a genic methylation of one of the methylases (Yadav et al., 2018).
By collaborating with Danny Chamovitz’s and Tamir Tuller’s groups, we identified a novel nuclear factor, COP9 signalosome, that its disruption alters DNA methylation particularly within genic regions (Tuller et al., 2018).
By manipulating the level of different methylation contexts in moss, we managed to create a plant that has comparable level of CG and non-CG methylation. We used this plants to investigate the transcriptional roles of the particular methylation contexts. This study which have been submitted for publication (Domb et al., 2020) shows that non-CG methylation is a stringer silencer than the canonical CG methylation. This result explain the development of non-CG methylation in plants and the ambient transcriptional role of CG methylation in genes.
We have developed a computational bioinformatic tool to analyze methylome NGS data in a single read resolution. We used this tool to reveal methylation processivity and stochasticity patterns of DNA methylases. Intriguingly, our data suggest that methylation in genes and TEs is processive and stochastic, respectively. This result implies on the biological regulation of these elements during development.
Unraveling the role of DNMT3 orthologs, first time to be characterized in plants, in RdDM-independent de novo and heterochromatin CHH methylation.
Discovering the role of a chromomethylase in de novo methylation in planta.
Developing a computational tool to reveal methylation patterns of methylome NGS data at the level of single read.
Discovering that non-CG methylation is superior to CG methylation in genes and TE silencing in plants.
Discovering that gene body methylation can dramatically change only at the level of single cytosines but not at the level of exons and genes during honey bee development. These methylation dynamics associate with stable transcription and suggest that the functional unit of gene body methylation is at the level of complete exons or genes.
Discovering elevation of non-CG methylation in genes in honey bee head tissues, suggesting high conservation to non-CG methylation in mammalian brains.
Developing a synthetic tool to enhance non-CG methylation in mammalian gene bodies.
Discovering the role of a chromomethylase in de novo methylation in planta.
Developing a computational tool to reveal methylation patterns of methylome NGS data at the level of single read.
Discovering that non-CG methylation is superior to CG methylation in genes and TE silencing in plants.
Discovering that gene body methylation can dramatically change only at the level of single cytosines but not at the level of exons and genes during honey bee development. These methylation dynamics associate with stable transcription and suggest that the functional unit of gene body methylation is at the level of complete exons or genes.
Discovering elevation of non-CG methylation in genes in honey bee head tissues, suggesting high conservation to non-CG methylation in mammalian brains.
Developing a synthetic tool to enhance non-CG methylation in mammalian gene bodies.