Mapping the dark genome in early embryonic development: Mechanisims establishing and maintaining epigenetic stability

University of Leicester • GB • 1w ago

How does a single pluripotent cell reorganise its genome as it becomes a specialised cell? While we know much about the genes that define cell identity, far less is understood about the “dark genome”, repressed and structurally complex regions whose organisation within the nucleus helps determine which genes can be used. This project will explore how this hidden layer of genome regulation is established and remodelled during early mammalian development and how stable epigenetic states emerge as cells choose their developmental fate.

The student will use complementary mouse and human pluripotent stem-cell models, combining controlled 2D models of early developmental transitions with 3D gastruloids that recreate key features of self-organisation, patterning and differentiation towards ectoderm, mesoderm and endoderm. A mechanistic focus will be SET8/KMT5A and H4K20me1, providing an entry point to discover how chromatin structure and heterochromatin organisation are established and maintained during development.

Using CRISPR genome engineering, SET8 will be perturbed at defined developmental stages to reveal when epigenetic organisation is required. Cutting-edge 3D, high- and super-resolution imaging, including lattice light-sheet microscopy, will allow the student to visualise nuclear and chromatin organisation across scales. These approaches will be integrated with epigenetic and transcriptomic profiling to connect genome architecture with gene regulation and cell fate.

By combining developmental biology, epigenetics, genome engineering, functional genomics and advanced microscopy, this project will uncover fundamental principles governing how the genome is organised as cells acquire identity—and how epigenetic states remain robust while development unfolds.

Techniques that will be undertaken during the project

• Embryonic stem-cell cultures and differentiation models including gastruloid generation

• 3D quantitative fluorescence imaging

• High- and super-resolution microscopy

• Lattice light-sheet microscopy

• Immunofluorescence staining for heterochromatin, epigenetic and cell-lineage markers

• Quantitative image analysis of heterochromatin organisation and nuclear architecture

• CRISPR-Cas9 genome editing and perturbation of epigenetic regulators

• Molecular and cellular analysis of pluripotency and ectodermal, mesodermal and endodermal differentiation

• Transcriptomic profiling and gene-expression analysis

• Integration of imaging and transcriptomic datasets to relate chromatin organisation to cell fate

Enquiries