Figure 1: Using single-cell measurements of open chromatin (sciATAC-seq) we could order cells along developmental trajectories (left), predict single cell identities (middle), and tissue specific enhancers (right)(Cusanovich DA, Reddington JP, Garfield DA, et al., Nature 2018). Collaboration with Jay Shendure’s lab.
Figure 2: QTL analysis at three stages of embryogenesis identifies causal variants (left, Manhattan plot), revealing genetic epistasis within both promoters (Schor et al., Nature Genetics, 2017) and developmental enhancers (Cannavò E, Koelling N, et al., Nature, 2016). Collaboration with Ewan Birney and Oliver Stegle groups.
The Furlong group dissects general principles of genome regulation and enhancer function and how this drives cell fate decisions during development, focusing on organisational and functional properties of the genome.
Previous and current research
Precise regulation of gene expression is essential for almost all biological processes, and is a key driving force in development, evolution and disease. Expression states are initiated through diverse cues modulating transcription factor activity, which converge on cis regulatory elements such as enhancers. Enhancers thereby act as integration platforms to control specific patterns of expression, telling genes when and where to be expressed. Given their central role, mutations in enhancers often lead to devastating developmental defects and are becoming increasingly linked to human disease.
Our research focuses on dissecting general mechanisms of transcriptional regulation, including how the cis-regulatory genome is organised within the nucleus, and how chromatin state and transcription factor occupancy influence this process (Figure 1). We also investigate how natural sequence variation perturbs genome regulation, leading to specific phenotypes (Figure 2). Our work combines genomic, genetic, imaging and computational approaches to understand these processes, including the development of new genomic methods within the context of a multicellular embryo.
Future projects and goals
Chromatin topology – the 3D genome
How our huge genome is packaged within the confined space of the nucleus to facilitate transcription remains a longstanding question. For enhancers to function, they must come in proximity to their 'target genes’. We recently discovered that enhancers are often in proximity to their promoters hours before gene expression (Nature 2014). This raises many interesting questions, including how these pre-formed topologies are established, which we are investigating using high-resolution imaging, genomics and genetics.
Chromatin remodelling during cell fate decisions
To uncover general properties of enhancer function we developed methods to investigate tissue specific (Nature Genetics, 2012), and single-cell (Figure 1; Nature 2018) changes in chromatin state during cellular transitions within a multicellular embryo's development. Going forward, we will combine single cell methods with CRISPR/Cas9 technology to understand regulatory properties associated with developmental transitions.
Variation and plasticity in regulatory networks
Variation in the non-coding genome is widely associated with quantitative trait loci (QTL). Many disease-associated variants are in cis-regulatory elements, yet it is very difficult to pinpoint the causal SNP within the human genome and therefore dissect the underlying mechanism. We recently demonstrated that we can bridge this gap, thanks to the small blocks of LD and high sequence variation among wild Drosophila, we can identify functional variants essential for the precise genome regulation (Figure 2; Nature 2016; Nature Genetics 2017). We are using natural sequence variation as a perturbation tool to developmental programming.