Elucidating the role of chromatin organization during cell fate specification and vertebrate organogenesis

Abstract

The basic body plan is determined within hours to a few days of embryonic development. This window is characterized by zygotic genome activation, lineage specification and morphogenetic events during organogenesis. Early embryonic patterning and morphogenesis are regulated by the interplay between various maternally deposited as well as zygotically transcribed RNA and protein determinants. However, understanding of precise transcriptional mechanisms sculpting embryonic structures remains inadequate. In the quest to identify novel mechanisms, here, we generated the lineagespecific transcriptional and chromatin accessibility profiles of gastrulating embryos. Our study highlighted Nodal signalling mediated dynamic chromatin remodelling activities necessary for segregation of axial mesoderm and endoderm progenitors. Moreover, our analysis offered an opportunity to identify and characterize understudied chromatin organizers during germ layer segregation. We characterized the function of one such lineage-restricted protein Satb2. Studies using transient knockdown allowed us to identify a novel Wnt-dependent role of Satb2 during early cell fate specification events. Generation of tractable loss of function and gain of function models in zebrafish enabled us to dissect molecular mechanisms underlying pathological conditions associated with satb2 mutation. Moreover, integrative analysis of the transcriptome, genome-wide occupancy and chromatin accessibility revealed molecular interplays by which Satb2 performs contrasting functions during major gene regulatory transitions throughout early embryogenesis. We found maternal Satb2 negatively regulate zygotic genes by influencing the interplay between the pluripotency factors whereas, zygotic Satb2 activates the same group of genes during neural crest development. The comparative analysis underscores how these antithetical activities are temporally coordinated and functionally implemented. Taken together, our study highlights the evolutionary implications of chromatin organization in the regulation of landmark developmental transitions.