The Bose lab is interested in how the epigenetic-machinery that controls gene expression can be regulated by RNA. We use diverse techniques to study how RNA interacts with these machines over a range of scales, from functional genomics at a cellular level, to biochemistry and cryo-electron microscopy to understand molecular-mechanisms and structural architectures.
We use a variety of modern functional genomics approaches in the lab, underpinned by next-generation sequencing (seq) and analysis. These include PAR-CLIPseq to identify RNAs interacting with epigenetic-enzymes, ChIPseq to study sites of chromatin binding across the genome and nascent RNA sequencing to identify sites of non-coding and eRNA transcription. Together with CRISPR/Cas mediated genome editing, these approaches provide a powerful way to to characterise and test the interactions made by our protein and RNA targets across the genome.
The last few years have seen a 'revolution' in cryo-EM, driven by technological and software developments that make high-resolution structural analyses possible. Cryo-EM (together with single-particle processing) has always enabled structural analysis of large, often unstable multi-subunit complexes that are otherwise inaccessible to techniques such as x-ray crystallography. In the Bose Lab, we use cryo-EM to analyse the structural organisation of epigenetic enzyme complexes, shedding light on their interactions with non-coding RNAs and engagement with chromatin.
All of the work in the lab is underpinned by modern biochemistry, molecular biology and cell biology. We carry out extensive biochemical characterisations of the interactions between eRNAs and epigenetic enzymes, both in vitro and in cells. We also characterise the effect of eRNA binding on the activities of these enzymes using enzymatic assays. Our work often requires the expression, purification and analysis of the large multi-component complexes that we study.