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Biography

Kedar Natarajan is a D-IAS Assistant Professor at Functional Genomics and Metabolism Unit and Department of Biochemistry and Molecular Biology Department at University of Southern Denmark. Kedar’s research group investigates the fundamental process of cell cycle and gene expression regulation during embryonic development using integrative state-of-art high-throughput approaches including single-cell RNA-sequencing, imaging, CRISPR and functional genomics tools.

Prior to starting his group, Kedar worked as a Postdoctoral fellow with joint appointments at Wellcome Sanger Institute and European Bioinformatics Institute, Cambridge, UK. He holds a PhD from Imperial College London, UK, working jointly between Faculty of Medicine and Department of Mathematics. He has Master’s and Bachelor’s degree in Biotechnology and a dual Bachelor’s in Computer Sciences from India.


Abstract

Cell cycle dynamics in embryonic stem cells at the single-cell level

Kedar Natarajan 1,2

1 Danish Institute of Advanced Study, Functional Genomics and Metabolism Unit, University of Southern Denmark, Odense 5200, Denmark

2Wellcome Sanger Institute and European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB101SA, United Kingdom

During development, pluripotent embryonic stem cells (ESCs) differentiate to give rise to all different cell types in the organism. ESCs have a unique cell cycle structure and gene expression profile that facilitates differentiation into lineages alongside a scaling up of cell numbers. We have generated transgenic mouse FUCCI-ESCs that capture spatio-temporal cell cycle progression at the single-cell level. Here I present our on-going work investigating cell cycle dynamics in FUCCI-ESCs.

Combining single-cell flow cytometry (FACS) and single-cell RNA sequencing (scRNA-seq), we profile gene expression of ~700 single ESCs throughout the entire cell cycle and across two ESC culture conditions. Integrating quantitative FACS measurements with scRNA-seq, we assess how changes over cell cycle and cellular features (cell volume, DNA, cell cycle marker fluorescence etc.) affect individual gene behaviour and dynamics at single-cell level. We reconstruct gene expression profiles over cell cycle and predict gene contribution to cell cycle, cell fate (ESC differentiation) and in maintaining cellular homeostasis.

We provide a resource of single-cell data across entire cell cycle and describe methods to integrate complementary cellular measurements. Our work uncovers critical genes involved in cell cycle phase transition and gene expression regulation and shed light complex repertoire of crosstalk during embryonic development.

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