Reverse engineering gene regulatory circuitries in neural crest development and evolution

Thesis

The neural crest (NC) is an emblematic population of embryonic, stem-like cells characterised by their unique multipotency, migratory behaviour and broad developmental potential. Acquisition of these cells represents one major evolutionary transition in the tree of life, endowing vertebrates with their unique body plan.

A gene regulatory network (GRN) has been proposed to orchestrate NC development. To interrogate the NC-GRN at unprecedented resolution in a genome-wide fashion, we employed single cell transcriptomics and epigenomics at multiple stages of avian NC development. Development of a new pipeline allowed us to reverse engineer the NC-GRN in an unbiased manner. This approach enabled us to identify the cis-regulatory architecture embedding the logic of NC ontogeny. We identified regulatory circuitries involved in the pre-patterning of the early NC. Interrogation of the combinatorial cis-regulatory codes encoded in these enhancers revealed opposing circuitries controlling NC fate decisions.

We next compared the transcriptional heterogeneity of NC cells at single cell resolution across three-species: mouse, chicken and zebrafish. Our results indicate conservation of transcriptional states despite extensive divergence of genomic sequences across these species. Moreover, we also pioneered single-cell transcriptomics in the marine lamprey, enabling us to identify novel genes likely involved in lamprey NC development.

Finally, we interrogated the cis-regulatory landscape of zebrafish and lamprey NC cells, revealing conserved properties between chicken, zebrafish and lampreys, such as motif content, enhancer-promoter communications and dynamics of chromatin accessibility during development. We identified a group of pleiotropic enhancers involved in NC-dependent neurogenesis. We propose these elements have played a pivotal role in the early elaboration of multipotent NC in the stem vertebrate lineage via pleiotropic changes in ancestral enhancer elements. Taken together, this thesis provides important insights into the cis-regulatory basis of NC development and evolution.

Authors: Candido-Ferreira, IL

• DOI: 10.5287/ora-0z5ykvka0
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: gene regulatory networks; enhancers; transcription; genomics; evolution; neural crest
• Subjects: developmental biology; regulatory genomics