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The Transposon Group is interested in the role of locus-specific transposable element expression in development.

Transposable elements – or TEs - are mobile genomic elements. TEs can insert additional copies of themselves in the genome. They are abundant and make up half of the genome. However, most biological studies have focused on protein coding genes, which make up only 2% of the genome. It is important to study TEs in development because, while in adults TEs are mostly silenced by epigenetic modifications in development, this silencing is lifted and TEs are expressed. When expressed TEs can jump into genes and disrupt genic function. TEs can also work as alternative promoters or enhancers to control gene expression. TEs are necessary for development. Silencing the expression of a family of TEs called LINE1s in development causes embryonic lethality. However, we still do not know how TEs control development. We will test whether locus-specific transposable element expression is essential for development.

So far TE function has been addressed in groups of cells and at the level of TE families. TE families are sequence identical TE loci in different genome locations. Knockdown of a family can therefore affect up to 10% of the genome. To solve these limitations, we developed CELLO-seq, a method to assess TE expression in single cells and at the level of individual TE loci. Using CELLO-seq, out of thousands of LINE1 loci we identified the 25 likely to be important in development. Therefore CELLO-seq gives us a handle to functionally study specific TE loci in development. Using our method and other experimental and computational tools, my aim is to uncover the role of locus-specific TE expression in development.

In the Berrens lab we combine a wide-range of state-of-the-art technologies like single-cell long read RNAseq (CELLO-seq), epigenetics and spatial chromosome organisation, computational biology, imaging and genome-editing approaches to dissect the heterogeneity of transposable element expression between and within cells and understand their function in development and as regulators of gene expression.

Our group seeks to

1) uncover transposable element expression at unique loci between cells in early mammalian development

2) discover locus-specific transposable element expression within cells in cellular differentiation; and

3) define rules of how transposable elements primarily control proximal and distal gene expression in lineage commitment.


Transposon Group

Selected publications