Periodic Reporting for period 4 - TransposonsReprogram (How retrotransposons remodel the genome during early development and reprogramming)
Okres sprawozdawczy: 2021-07-01 do 2022-12-31
The overall goal, objectives and why this research is important for society
Around half of the DNA within the human genome is derived from ancient viruses or “transposons,” most of which use a copy-and-paste mechanism to make new copies of their own DNA to insert into our genome, allowing for their stable inheritance. This part of our genome of viral origin is often referred to as “dark matter” because little is known about its function. The overall goal of our ERC starting grant is to understand how DNA-sequences of viral origin have been beneficially repurposed in mammals to allow normal progression through development. Understanding these novel mechanisms is important for society because it will help us to direct which type of cell a pluripotent cell will ultimately become and how to reprogram committed cells back into pluripotent cells, which can then be used to form new cell types. Such research is relevant to making more effective stem cell therapies. More broadly, though, this research will help us to understand how genetic mutations within non-coding regions can lead to developmental diseases in which transposons are implicated, such as Repeat Expansion Disorders or Aicardi Goutières Syndrome. We hypothesize that ancient transposon-derived DNA sequences play essential roles in cell fate transitions in early development and during reprogramming. We think this because viruses are ideal tools that the cell can repurpose as regulatory hubs because they contain compact promoters, enhancers and silencers within a short long terminal repeat (LTR) sequence, for example, and mounting evidence shows these ancient viruses to be switched on in early development. In contrast, the bulk of most viral coding sequences of transposons may have been lost through genetic drift and recombination. The key objectives of this ERC starting grant are to identify the functions of several types of transposons during early development and reprogramming and assess the mechanisms of how they remodel the genome to control cell fate. Our approach is to employ two novel zinc finger proteins that bind to transposon DNA as tools to explore the function of these transposons.
Summary image caption (see the summary image)
We are exploring how retrotransposons remodel the genome during early development and reprogramming. We are using the term “remodel the genome” to refer to changes in enhancer and promoter activity and changes to chromatin structure that ultimately lead to cell fate transitions. (1) This diagram shows how chromatin can be remodelled from an inactive state (left) to an active state where a network of genes becomes switched on (right). (2) Little is known to date on how transposon-derived DNA sequences can direct cell fate and we are addressing this question by focusing on zinc finger proteins (ZFPs) specific for transposon-derived DNA. ZFPs recruit the epigenetic complexes stated here to mediate gene silencing. We have performed targeted CRISPR/Cas9-mediated knockout of these ZFPs in a developmental model as a tool to address the roles of their cognate transposons in regulating cell fate. (3) The model that we are using is naïve mouse embryonic stem cells, which are representative of early embryos that we differentiate in vitro into neural progenitor cells (NPCs) and neurons. We hypothesize that although these ZFPs may have evolved to block the spread of transposons, they now may function to regulate cell fate transitions and our results to date support this notion. (4) The concepts we discover in our mouse model of development with also be relevant for understanding human gene regulation and the importance of non-coding DNA in developmental and neurodevelopmental diseases.