Program > Browse abstracts by speaker > Marlow Sophie

Transposable elements (TEs) have been shown to play key roles in early mammalian development through acting as regulators of gene expression. However, little is understood about the role of TEs at post-implantation developmental stages, including development of the first organ, the heart. TEs remain notoriously difficult to study due to their repetitive nature hampering efforts to map individual TEs back to their unique loci. TEs are thus often studied in groups of loci, at the sub-family level. Here, we aim to characterise individual TE loci expressed at four stages of cardiomyocyte differentiation, mitigating for difficulties in mapping TEs by making use of the computational framework, TElocal. Secondly, we set out to determine whether TEs characteristic to cardiomyocyte differentiation stages could be acting as regulatory elements for genes governing cardiomyocyte differentiation. Using published bulk RNA-seq and ChIP-seq datasets over the course of cardiomyocyte differentiation, we detect and validate the transient expression of the RLTR4 and ETnERV3-int TE subfamilies, respectively. We also uncover the individual loci contributing to detection of these TE sub-families. Further to this, we find many of the transiently expressed TEs have expression profiles that mirrored peaks observed in H3K4me3 data. This indicates a role for these TE loci as promoters, which regulate the expression of genes involved in cardiomyocyte differentiation. Further insights will be provided with H3K4me1 data, to detect putative enhancers located at TEs which control cardiomyocyte differentiation. Additionally, single-cell long-read RNA-seq data will provide expression profiles of young TEs across cardiomyocyte differentiation which remain largely undetected in this study.