Tracking chromatin dynamics and bimodal foxd3 mechanism on neural crest gene regulation in vivo

Thesis

The neural crest (NC) is a transient embryonic stem cell-like population characterised by its multipotency and broad developmental potential. The core NC transcription factor foxd3, known to mediate late NC lineage decisions via transcriptional repression, is also pervasively expressed in the pre-migratory NC progenitors, where its putative role remains elusive.

To elucidate the mechanistic and temporal mode of foxd3 action, we analysed its genomewide binding profiles across multiple stages of zebrafish development. To this end, we have developed and used our novel biotin ChIP-seq approach allowing to specifically biotinylate factors of interest, such as foxd3 protein, in vivo. Foxd3 binding maps interpreted within the context of NC-specific transcriptional and epigenomic profiles of foxd3-mutant and control cells reveal that foxd3 acts bimodally throughout the NC ontogeny. We showed that first foxd3 functions globally as a pioneer factor to prime the onset of NC specification and migration genes by re-arranging their chromatin landscape. Strikingly, foxd3 then gradually switches from an activator to its well-described role as a transcriptional repressor and potentially uses different partners for each role.

By employing two enhancer reporter zebrafish lines, imaging and -omics tools, we have also shown that auto-regulation of foxd3 gene locus is involved during early cell-fate decisions and embryo patterning. In the cranial embryo regions, positive auto-regulatory foxd3 feedback is driving foxd3 expression that is needed for the NC and nervous system development. This auto-regulatory loop is ensured by a set of foxd3 cis-regulatory elements that exhibit NC-like regulatory signatures. Contrarily, foxd3 is auto-regulated by a different set of enhancers and, as a result, is expressed to lower levels during the apparent neuromesodermal progenitor specification in the caudal embryo regions.

Taken together, this thesis demonstrates that foxd3 needs to be tightly auto-regulated during early cell lineage decisions. Also, later in the NC development, foxd3 switches from a chromatin activator to a repressor in order to maintain NC multipotency and define its cell fates.

Authors: Lukoseviciute, M

• DOI: 10.5287/ora-qyxzrzv27
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: -omics; gene regulation; zebrafish; Neural crest; embryogenesis
• Subjects: Developmental Biology