[RANdOM]
Systematic search of RegulAtory elements coNtrOlling Monoallelic expression
RANdOM
Random Monoallelic Expression, or RME, refers to the gene expression regulation activity that results in non-genetic and non-imprinted, mitotically stable biases of allelic expression in autosomes.
The EU-funded project, "RANdOM," was initially proposed to identify genetic patterns potentially responsible for the regulation of RME. RANdOM brought together MSCA Fellow Clara Alves-Pereira, molecular evolutionary biologist Aoife McLysaght, head of the Molecular Evolution Lab at Trinity College Dublin (Dublin, Ireland), and the team led by Alexander Gimelbrant, a pioneer in RME studies based at the Dana-Farber Cancer Institute and Harvard Medical School (Boston, US). Their collective aim is to enhance understanding of this form of gene expression.
Allelic imbalances of non-genetic nature are maintained mitotically in immortalized cell lines (A). Genes with this property are conserved between the Human and the Mouse, and yet, the biological implications of such features remain elusive. Accounting for these subtle epigenetic effects at the organismal level may unveil sources of phenotypic variation currently unanticipated (B), and potentially contribute to our understanding of genetic diseases of complex heritability.Â
Objective 1
To identify mechanisms of maintenance of epigenetic allelic biases in the mouse model.
As the team gathered at the beginning of the action in Boston, an impending breakthrough from the Gimelbrant Lab introduced a new exciting focus: identifying mechanisms that regulate mitotically stable allelic imbalances. Consequently, we contributed to describing for the first time the role of methylation in maintaining stable allelic imbalances in murine Abelson-immortalized cell lines (as discussed in Gupta et al). Our work demonstrates that 5-aza-2'-deoxycytidine can reverse the stable allelic biases in cell lines. This finding reveals potential implications of sporadic or continued exposure of cells to chemical compounds or drugs.
Objective 2
To explore the mitotic stability of random allelic imbalances
a) To study the dynamics of allelic imbalances along the cell cycle progression
We are further characterizing the dynamics of allele-specific expression along the cell cycle progression, by leveraging RNA-Seq in synchronous cell cycle stages in bulk and also in chromatin cell fractions.
b) To assess the extent of highly stable monoallelic expression states in hematopoietic stem cells in-vivo, in the mouse model
Finally, we are characterizing highly stable monoallelic expression states in hematopoietic stem cells in the mouse model, in vivo, for the first time: studying allelic imbalances of epigenetic nature requires overcoming the great technical challenge of isolating clonal populations of cells. This explains why the studies to date have been performed in immortalized cell lines. Leveraging the expertise of the researcher with the generation of in-vivo clonal assays of the mouse model, we have thus developed an assay to track clonal populations in-vivo. We have partnered with Vasco Barreto and Nadiya Kubasova, at CEDOC, Portugal, for the later study.
