Epigenetic regulator function through mouse gastrulation

Abstract

Summary paragraph: During ontogeny, proliferating cells become restricted in their fate through the combined action of cell-type specific transcription factors and ubiquitous epigenetic machinery, which recognize universally available histone residues or nucleotides but are nonetheless deployed in a highly context-dependent manner 1 , 2 . The molecular functions of these regulators are generally well understood, but assigning direct developmental roles is hampered by complex mutant phenotypes that often emerge following gastrulation 3 , 4 . Recently, single-cell RNA sequencing (scRNA-seq) and analytical approaches have explored this highly conserved process across numerous model organisms 5 – 8 , including mouse 9 – 18 . To elaborate on these strategies, we investigated a panel of ten essential regulators using a combined zygotic perturbation, scRNA-seq platform where many mutant embryos can be assayed simultaneously to recover robust transcriptional and morphological information. Deeper analysis of central Polycomb Repressive Complex (PRC) 1 and 2 members indicate substantial cooperativity, but distinguishes a PRC2-dominant role in restricting the germline that emerges from gross molecular changes within the initial conceptus. We believe our experimental framework will eventually allow for a fully quantitative view of how cellular diversity emerges using an identical genetic template and from a single totipotent cell.

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

“…Lineage priming, cell fate specification and tissue patterning during early mammalian development are complex processes involving signals from surrounding tissues, mechanical constraints, and transcriptional and epigenetic changes, which together prompt the adoption of unique cell fates 1–7 . All of these factors play key roles in gastrulation, the process by which the three germ layers emerge, and the body axis is established.…”

Establishment and function of chromatin modification at enhancers

“…Novel imaging techniques will reveal the spatio-temporal dynamics of enhancer–promoter interactions in living cells, allowing greater understanding of how and when proximity is required developmentally [ 211 , 212 ]. Improved genomic approaches allowing resolution at the single-cell level coupled with elegant genetic and pharmacological perturbation techniques will increase our understanding of how and when chromatin states are established and decommissioned developmentally [ 213 , 214 ]. New protocols to perform multiple ‘omics’ experiments at the single cell level will result in greater understanding of the relationship between chromatin states and transcriptional output [ 215 , 216 ].…”

New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency

“…A landmark study in the field showed that in Dnmt1 knockout embryos, maintenance of XCI is unaffected in the extraembryonic endoderm while XCR takes place in the embryonic lineage [ 103 ]. A more recent study that combined genetic perturbations with single-cell RNA sequencing (scRNA-seq) in mouse embryos confirmed the role of Eed in maintenance of imprinted XCI in the TE [ 128 ]. However, Eed knockout had little impact on maintenance of XCI in the PE, indicating that distinct mechanisms maintain imprinted XCI in TE and PE lineages [ 128 ].…”

“…A more recent study that combined genetic perturbations with single-cell RNA sequencing (scRNA-seq) in mouse embryos confirmed the role of Eed in maintenance of imprinted XCI in the TE [ 128 ]. However, Eed knockout had little impact on maintenance of XCI in the PE, indicating that distinct mechanisms maintain imprinted XCI in TE and PE lineages [ 128 ]. Given that humans have no imprinted XCI, and also have a much longer development and gestational period compared with mice, it will be interesting to define the factors and mechanisms involved in induction, maintenance and reversal of XCI in human extraembryonic lineages, which is discussed in Section 10 .…”