Single-cell and single-molecule imaging approaches in stem cell biology
Laboratory: Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre
Departmental Affiliation: Biochemistry
Biography
Srinjan trained in physics, chemistry and biology at the University of Cambridge. During his PhD at Harvard University, he developed Raman-based label-free imaging of nuclear architecture to track chromatin live in dividing cells within mouse skin but also to rapidly identify tumours in human tissue. He also co-authored one of the first papers imaging single transcription factors as they interact with chromatin in live mammalian cells.
He then returned to Cambridge as a postdoc, where he continued to pioneer approaches that allow the field to probe chromatin at single-molecule and single-cell resolution. He used single-cell Hi-C to determine the architecture of the entire mouse genome at the level of a single pluripotent cell. This revealed considerable cell heterogeneity in the relative positions of enhancers and promoters. Furthermore, it uncovered nuclear hubs enriched for enhancers and promoters but also transcription factors. These studies lay the foundation for and emphasise the importance of probing genome structures at the single-cell level in heterogeneous cell populations during lineage specification.
To further reveal how single proteins and even protein complexes assemble on chromatin, he developed 3D single-molecule tracking and live-cell single-molecule FRET. He has alsoestablished machine-learningalgorithms that classify different types of motion toreveal the chromatin binding kinetics of these key protein complexes but alsoto determine how they control chromatin movement at specific genomic loci.
As a Group Leader at CSCI, he is now using these methodologies to address how chromatin regulators influence mammalian embryo development. He has revealed the chromatin binding kinetics of key chromatin regulators such asheterochromatin protein HP1gamma and a chromatin remodeller called the NuRD complex. He has also recently shown how the NuRD complex modulates enhancer movement to control transcription.
His work increases collaboration between mathematicians, physicists, chemists and biologists and trains a new generation of interdisciplinary researchers. His work increases technology development in bioimaging and next-generation sequencing, training students in interdisciplinary and data-driven biology involving analysis of complex imaging and ‘omics datasets.
Furthermore, as chair of equality, diversity and inclusion, he is pushing his own lab and the wider research community towards better and more inclusive research practices.
Research
The Basu Lab focuses on developing single-cell and single-molecule imaging approaches to improve our understanding of stem cell renewal and differentiation.
In particular, they are interested in how chromatin binding proteins regulate genome architecture and gene expression during stem cell fate transitions and why they are often misregulated during early cancer progression. Single-cell approaches are key to understanding how these proteins work due to the considerable cell heterogeneity that occurs during stem cell fate transitions.
In recent years, the Basu Lab has developed several biophysical and computational approaches to answer these questions. For example, they have established a method combining imaging and single-cell Hi-C to study genome architecture inside individual embryonic stem cells. To understand how proteins interact with each other and with chromatin, they set up several in vitro and live-cell single-molecule imaging approaches capable of localising single proteins at <15 nm resolution.
The Lab is continuing to develop novel single-cell and single-molecule imaging approaches but also using the techniques described above to gain insight into the role of key protein complexes involved in stem cell differentiation.
(left to right) Srinjan Basu, Oliver Davis, Deep Adhya, Maike Steindel, Stanley Strawbridge, Annabelle Wurmser, Maciej Zurowski, Laura Říhová, Sebastian Berger
