Contribution of transposable elements in cell fate decision (360G-Wellcome-213612_Z_18_Z)

Transposable elements (TEs) are long known to be expressed in different cells during early mammalian development. However, the role of TEs in cellular differentiation has remained elusive. This proposal aims to develop new experimental and computational methods to understand the role of TEs in cellular differentiation. Single cell (sc) RNA sequencing (RNA-seq) has been developed extensively in recent years to study cell-to-cell variability of gene expression. These methods, however, have exclusively used short read sequencing technologies, which do not allow for TE mapping. I will develop a novel plate-based long read scRNA-seq protocol, which will overcome this limitation. Transcripts will be tagged with unique molecular identifiers (UMIs) prior to amplification, permitting accurate transcript counting. I will devise a computational method to error correct reads using UMIs, by calculating a consensus from multiple sequence alignments of all reads flagged as PCR duplicates. This protocol thus allows for accurate sequencing of complete transcripts in single cells, which I will apply to cells during mouse embryonic development to investigate the role of TEs in cellular differentiation. In particular, I will investigate whether TEs exhibit heterogeneous expression across cells. Together, these methods and experiments will improve our understandings of TEs in mammalian development.