Genome regulation and topology during embryonic development

The Furlong lab dissects fundamental principles of transcriptional regulation, and how it drives cell fate decisions during development, focusing on the organisational and functional properties of the genome.

Complex patterns of spatial and temporal gene expression are a hallmark of development, and a central driving force for the progressive restriction of cell fates during embryogenesis. How a single genome can generate such a diversity of cells, and how transcriptional networks control and buffer the process of differentiation, are the two overarching questions in the lab. To tackle these, the group optimises and pushes genomic methods for use within complex multicellular embryos. We make use of the systematic unbiased nature of genomics, the power of Drosophila genetics, high-resolution imaging and approaches from developmental and evolutionary biology, to understand how the genome is regulated and organised during development.

Understanding how enhancers function

Despite the crucial role of enhancers in development, evolution, and disease, we still have a poor understanding of how they function. After almost 30 years, for example, it is still not possible to predict enhancer activity, or the affect of a genetic variant within an enhancer, based on sequence information alone.

We are studying enhancer function during key transitions in embryonic development, dissecting the interplay between transcription factor (TF) occupancy, chromatin state and enhancer output, understanding the functional role, if any, of enhancer RNA, and building new tools to dissect the underlying mechanisms involved. We are using methods we developed to study tissue-specific enhancer (chromatin, TF) activity, combined with single cell methods and CRISPR/Cas9 technology to understand regulatory properties of enhancers

Chromatin topology: three-dimensional enhancer promoter interactions

Although fundamental to understanding gene expression, how enhancers find their appropriate promoters, the dynamics of these interactions and the regulatory factors that control them are largely unknown.

We recently showed that enhancer-promoter interactions are present hours before a gene is expressed. For genes whose expression initiates at mid-embryogenesis (stage 11), for example, their enhancers are already in proximity to the promoter two hours before the gene is expressed, and are generally associated with paused RNA polymerase, suggesting that the system is primed ready for activation. This raises a number of interesting questions that we are now addressing, by integrating information from high-resolution chromatin conformation capture, high-resolution imaging and genome engineering to dissect the relationship topology and transcription

How is robustness imparted on developmental programs?


By treating genetic variants as genome-wide perturbations to developmental programming, we are using eQTL mapping as 1) a method to gain new mechanistic insights into the genetic control of gene expression itself and 2) as a tool to understand how gene regulatory networks instantiate robust developmental programs from noisy transcriptional inputs. Our current QTL studies demonstrate that Drosophila wild-isolates have exceptional power for association studies, given the resolution to directly detect causal variants.