X chromosome inactivation (XCI) occurs early during development in female embryos, ensuring the transcriptional silencing of one of two X chromosomes in somatic cells. Once established, silencing is maintained through subsequent cell divisions, and the inactive X (Xi) is heterochromatinized and replicates late during S-phase. Chromosome homologs replicate highly synchronously with few exceptions, thus late replication of the Xi in somatic cells represents an extreme instance of replication asynchrony.
The germline however is different – germ cells undergo genome-wide reprogramming – which including re-expressing pluripotency genes, DNA demethylation, imprint erasure and dynamic alterations in histone modifications. Specifically, female germ cells undergo X chromosome reactivation (XCR). Importantly XCR and perturbations in replication timing have both been implicated in genomic stability and cancer.
This PhD explores the relationship between DNA replication, chromatin structure and transcription during germline development and XCR. Specifically the candidate will test if replication asynchrony exists between homologs in early germ cells, and conversely if synchrony is a requirement for germ cell progression in females. Because germ cell XCR is developmentally regulated, we will explore if replication timing and gene expression are temporally co-regulated. A combination of mouse genetics (e.g. F1-mice; skewed X inactivation), incorporation of selective germ cell reporters and high-throughput sequencing technology will enable the candidate to evidence these basic questions.
1. Yr1/rotation – developmental genetics; learn critical multi-modal techniques (e.g. bulk Repli-seq and Hi-C). Data integration
2. Yr2 – single cell Repli-seq of germ and somatic cells (controls)
3. Yr3 – explore specific histone marks associated with expression
4. Yr4 – complete analysis; write-up