All Publications

  • Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcription. bioRxiv : the preprint server for biology Mahat, D. B., Tippens, N. D., Martin-Rufino, J. D., Waterton, S. K., Fu, J., Blatt, S. E., Sharp, P. A. 2023


    Transcription is the primary regulatory step in gene expression. Divergent transcription initiation from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers1-5. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations6-9. However, fundamental questions in the temporal regulation of transcription and enhancer-gene synchrony remain unanswered primarily due to the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq - a novel single-cell nascent RNA sequencing assay using click-chemistry - and unveil the coordinated transcription throughout the genome. scGRO-seq demonstrates the episodic nature of transcription, and estimates burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells. It reveals the co-transcription of functionally related genes and leverages the replication-dependent non-polyadenylated histone genes transcription to elucidate cell-cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq identifies networks of enhancers and genes and indicates that the bursting of transcription at super-enhancers precedes the burst from associated genes. By imparting insights into the dynamic nature of transcription and the origin and propagation of transcription signals, scGRO-seq demonstrates its unique ability to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression.

    View details for DOI 10.1101/2023.09.15.558015

    View details for PubMedID 37745427

    View details for PubMedCentralID PMC10516050

  • Engineering tRNA abundances for synthetic cellular systems. Nature communications Maheshwari, A. J., Calles, J., Waterton, S. K., Endy, D. 2023; 14 (1): 4594


    Routinizing the engineering of synthetic cells requires specifying beforehand how many of each molecule are needed. Physics-based tools for estimating desired molecular abundances in whole-cell synthetic biology are missing. Here, we use a colloidal dynamics simulator to make predictions for how tRNA abundances impact protein synthesis rates. We use rational design and direct RNA synthesis to make 21 synthetic tRNA surrogates from scratch. We use evolutionary algorithms within a computer aided design framework to engineer translation systems predicted to work faster or slower depending on tRNA abundance differences. We build and test the so-specified synthetic systems and find qualitative agreement between expected and observed systems. First principles modeling combined with bottom-up experiments can help molecular-to-cellular scale synthetic biology realize design-build-work frameworks that transcend tinker-and-test.

    View details for DOI 10.1038/s41467-023-40199-9

    View details for PubMedID 37524714

    View details for PubMedCentralID 307586