The impact of 3D regulatory landscapes on the evolution of developmental programs

Introduction

Vertebrate genomes are organized in 3D regulatory landscapes that control pleiotropic gene expression. Within them, transcription emerges from a precise interplay between genes, regulatory elements, and 3D chromatin organization. We and others have shown how mutations in these regulatory layers can modulate phenotypes. However, how 3D regulatory landscapes shape the evolutionary history of developmental programs is still largely unexplored.

Limitations in Current Knowledge

Our limited capability to read, interpret, and modify genomes has constrained our knowledge on how gene regulation evolves. However, recent advances in long-range sequencing, single-cell, chromatin interaction, and genome editing methods offer novel tools to link genomic variation and phenotypes.

Research Objectives

Here, I will combine these methods to investigate how changes in 3D regulatory landscapes contribute to refine the function of developmental programs. As a testbed, I will study gonadal sex determination, an essential process for species perpetuation but characterized by remarkable evolutionary plasticity.

Methodology

1. Single-Cell Transcriptomics
   We will use single-cell transcriptomics across tetrapod clades to unravel the core and variable transcriptional network of sex determination.

2. Single-Cell Epigenomics
   Single-cell epigenomics and novel chromatin interaction methods will reconstruct 3D regulatory landscapes and infer sources of regulatory variation.

3. Phylogenomic Comparative Strategies
   With phylogenomic comparative strategies, we will estimate the contribution of different types of mutations to different sex determination programs, as well as the impact of whole genome duplications.

4. Transgenic Methods
   Finally, we will develop innovative transgenic methods for inter-species replacement of 3D regulatory landscapes, using this technology to activate early estrogen synthesis in mice.

Expected Outcomes

3D-REVOLUTION will provide ground-breaking insights on the evolution of gene regulation. This will improve our understanding of the genomic sources and underlying mechanisms of phenotypical variation, which are relevant for developmental and evolutionary genetics.