All Publications

  • Evolution at the Cutting Edge: CRISPR-Mediated Directed Evolution. Molecular cell Abbott, T. R., Qi, L. S. 2018; 72 (3): 402–3


    In a recent issue of Nature, Halperin etal. (2018) develop a new technology to continuously diversify specific genomic loci by combining CRISPR-Cas9 with error-prone DNA polymerases.

    View details for PubMedID 30388408

  • Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system. Nature communications Kipniss, N. H., Dingal, P. C., Abbott, T. R., Gao, Y. n., Wang, H. n., Dominguez, A. A., Labanieh, L. n., Qi, L. S. 2017; 8 (1): 2212


    G-protein-coupled receptors (GPCRs) are the largest and most diverse group of membrane receptors in eukaryotes and detect a wide array of cues in the human body. Here we describe a molecular device that couples CRISPR-dCas9 genome regulation to diverse natural and synthetic extracellular signals via GPCRs. We generate alternative architectures for fusing CRISPR to GPCRs utilizing the previously reported design, Tango, and our design, ChaCha. Mathematical modeling suggests that for the CRISPR ChaCha design, multiple dCas9 molecules can be released across the lifetime of a GPCR. The CRISPR ChaCha is dose-dependent, reversible, and can activate multiple endogenous genes simultaneously in response to extracellular ligands. We adopt the design to diverse GPCRs that sense a broad spectrum of ligands, including synthetic compounds, chemokines, mitogens, fatty acids, and hormones. This toolkit of CRISPR-coupled GPCRs provides a modular platform for rewiring diverse ligand sensing to targeted genome regulation for engineering cellular functions.

    View details for PubMedID 29263378

  • Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators RNA Takahashi, M. K., Watters, K. E., Gasper, P. M., Abbott, T. R., Carlson, P. D., Chen, A. A., Lucks, J. B. 2016; 22 (6): 920–33


    Antisense RNA-mediated transcriptional regulators are powerful tools for controlling gene expression and creating synthetic gene networks. RNA transcriptional repressors derived from natural mechanisms called attenuators are particularly versatile, though their mechanistic complexity has made them difficult to engineer. Here we identify a new structure-function design principle for attenuators that enables the forward engineering of new RNA transcriptional repressors. Using in-cell SHAPE-Seq to characterize the structures of attenuator variants within Escherichia coli, we show that attenuator hairpins that facilitate interaction with antisense RNAs require interior loops for proper function. Molecular dynamics simulations of these attenuator variants suggest these interior loops impart structural flexibility. We further observe hairpin flexibility in the cellular structures of natural RNA mechanisms that use antisense RNA interactions to repress translation, confirming earlier results from in vitro studies. Finally, we design new transcriptional attenuators in silico using an interior loop as a structural requirement and show that they function as desired in vivo. This work establishes interior loops as an important structural element for designing synthetic RNA gene regulators. We anticipate that the coupling of experimental measurement of cellular RNA structure and function with computational modeling will enable rapid discovery of structure-function design principles for a diverse array of natural and synthetic RNA regulators.

    View details for DOI 10.1261/rna.054916.115

    View details for Web of Science ID 000376205600010

    View details for PubMedID 27103533

    View details for PubMedCentralID PMC4878617

  • Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq. Nucleic acids research Watters, K. E., Abbott, T. R., Lucks, J. B. 2016; 44 (2): e12


    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell.

    View details for DOI 10.1093/nar/gkv879

    View details for PubMedID 26350218

    View details for PubMedCentralID PMC4737173