Retrotransposon functions in preimplantation embryos
Lin He, Professor
Molecular and Cell Biology
Applications for Fall 2025 are closed for this project.
The earliest step of mammalian development from a fertilized egg to a complex organism is the preimplantation development. During this stage, a fertilized zygote develops into a 100-cell blastocyst in 3.5 days in mice (or 5–6 days in humans). In this short window, the embryo undergoes remarkable changes, including cell fate determination, zygotic genome activation, epigenetic reprogramming, and transient, robust retrotransposon induction. Transposons make up 40% of mammalian genomes because they propagate efficiently within the ancestral host genomes. They were historically seen as parasitic invaders that become inactivated through degenerative mutations and transcriptional or post-transcriptional silencing. Although retrotransposons are silenced in most somatic tissues, about 20% of the total transcriptome in mouse preimplantation embryos originates from transposons. Rather than being harmful “genome parasites,” retrotransposons provide promoters, enhancers, and regulatory RNAs that influence embryonic gene networks.
Previous studies from our lab comprehensively analyzed retrotransposon expression and retrotransposon-mediated gene regulation in preimplantation embryos from eight mammalian species. We identified numerous alternative gene promoters derived from LTR retrotransposons and characterized the gene structures of the retrotransposon-dependent gene isoforms. This year, we generated our own long-read RNA-seq (PacBio) dataset covering mouse development from the oocyte to the blastocyst stage, allowing us to capture retrotransposon expression with unprecedented resolution. Using this resource, we identified a previously unrecognized mode of retrotransposon-gene regulation: retrotransposons antisense-inserted within introns of protein-coding genes can act as negative regulators of host gene expression.
Taken together, our project is both conceptually and technically innovative to investigate the cellular and molecular mechanisms of how retrotransposons regulate gene expression in mouse preimplantation embryos. A key goal is to apply computational approaches to systematically profile novel regulatory interactions between transposons and host genes.
Role: We are particularly interested in recruiting undergrads with bioinformatics training to contribute to data analysis. Students who join the project will need to have strong learning skills in bioinformatics. We ask for a commitment of approximately 15 hours per week.
Qualifications: We are seeking curious, highly motivated students with strong communication skills who enjoy learning and working in a collaborative research environment.
Day-to-day supervisor for this project: Yang Han, Post-Doc
Hours: 12 or more hours
Related website: https://www.helabucb.org/
Biological & Health Sciences