Select Publications
Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing.
Blattman, S.B.*, Jiang, W.*, Oikonomou, P. and Tavazoie, S. Nature microbiology (2020) [pdf]
First demonstration of high-throughput bacterial single-cell RNA sequencing.
Despite great advances of single-cell RNA sequencing technology in eukaryotes, similar technology in bacteria did not exist due to many challenges specific to prokaryotes such as lack of mRNA polyadenylation and presence of thick cell walls. We developed the first bacterial high-throughput single-cell RNA sequencing technology named PETRI-seq. Using a split-pool combinatorial indexing strategy, PETRI-seq can barcode and sequence 10^7 single cells in a single experiment. PETRI-seq has high single-cell purity, high correlation to bulk RNA-seq, and mRNA capture rate (2.5-10%) similar to contemporary eukaryotic methods. A principally similar method, microSPLiT, was also developed by Georg Seelig’s group at University of Washington. We anticipate that scRNA-seq will have broad utility in studying complex heterogenous microbial community in the future.
Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity.
Jiang, W., Oikonomou, P. and Tavazoie, S. Cell (2020) [pdf]
Current way of generating large-scale CRISPR libraries relies on array based oligo synthesis, which is resource- and time-consuming, and is not compatible with great majority of bacteria harboring restriction-modification systems. To overcome these challenges, we developed CRISPR Adaptation-mediated Library Manufacturing (CALM). Acting as a microbial biofactory, CALM takes genomic DNA as input, and produces CRISPR libraries as output. With the cost of ~$100 and in a single day, CALM generates CRISPR libraries more comprehensive than any existing genome-scale libraries created by oligo synthesis. We showed that the highly comprehensive libraries vastly enhance the screening sensitivity and enable discovery of novel genetic pathways of antibiotic sensitivity in bacteria.
Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity.
Jiang, W., Samai, P. and Marraffini, L.A. Cell (2016) [pdf]
Unlike CRISPR-Cas9, the type III CRISPR-Cas10 system encodes an elaborate molecular machinery that cleaves both DNA and RNA targets. By performing genetic, biochemical and functional studies (together with previous work Goldberg et al, Nature, 2014 and Samai et al, Cell, 2015), we found that DNA and RNA cleavages by CRISPR-Cas10 are differentially required for immunity during distinct stages of phage infections. RNA cleavage is especially required for CRISPR immunity in late stage of phage infection as host bacterial cells are loaded with phage transcripts encoding lytic enzymes. Our studies established a new paradigm describing a rather elaborate CRISPR-Cas system that cleaves both DNA and RNA targets. These findings expanded our current knowledge on the evolutionary arms race between bacteria and their viral predators.
RNA-guided editing of bacterial genomes using CRISPR-Cas systems.
Jiang, W.*, Bikard, D.*, Cox, D., Zhang, F. and Marraffini, L.A. Nature biotechnology (2013) [pdf]
First demonstration of CRISPR-mediated genome editing in bacteria; >2,000 citations
We developed the first CRISPR-Cas9 genome editing technology (US Patent: 9822372) and subsequently, a gene expression modulation technology utilizing nuclease-dead Cas9 (dCas9) (Bikard*, Jiang* et al, Nucleic Acids Research, 2013) in bacteria. CRISPR-Cas9 is an adaptive immune system that protects prokaryotes from viral infection. It confers immunity by using small CRISPR RNAs (crRNAs) to base-pair and destroy target viral genomes. Exploiting CRISPR’s ability to bind and cut DNA in a sequence-specific manner, we re-programmed the 20-nt crRNA sequence such that it can guide the Cas9 nuclease or its nuclease-dead variant (dCas9) to target virtually any sequence in the bacterial genome. As such, our engineered CRISPR-Cas9 system enables sequence-specific genome editing, transcriptional repression and activation, in a manner that is substantially easier, faster, more precise and scalable than existing bacterial technologies such as allelic replacement and antisense RNAs.
All Publications
Genetic Architecture of Antibiotic Sensitivity in Staphylococcus aureus.
Jiang, W., Liu, M. and Tavazoie, S. (In preparation)
Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing.
Blattman, S.B.*, Jiang, W.*, Oikonomou, P. and Tavazoie, S. Nature microbiology (2020)
First demonstration of high-throughput bacterial single-cell RNA sequencing.
Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity.
Jiang, W., Oikonomou, P. and Tavazoie, S. Cell (2020)
Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts.
Goldberg, G.W., McMillan, E.A., Varble, A., Modell, J.W., Samai, P., Jiang, W. and Marraffini, L.A. Nature communications (2018)
CRISPR-Cas systems exploit viral DNA injection to establish and maintain adaptive immunity.
Modell, J.W., Jiang, W. and Marraffini, L.A. Nature (2017)
Impact of Different Target Sequences on Type III CRISPR-Cas Immunity.
Maniv, I., Jiang, W., Bikard, D. and Marraffini, L.A. Journal of bacteriology (2016)
Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity.
Jiang, W., Samai, P. and Marraffini, L.A. Cell (2016)
CRISPR-Cas: New Tools for Genetic Manipulations from Bacterial Immunity Systems.
Jiang, W. and Marraffini, L.A. Annual review of microbiology (2015)
Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity.
Samai, P., Pyenson, N.*, Jiang, W.*, Goldberg, G.W., Hatoum-Aslan, A. and Marraffini, L.A. Cell (2015)
Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials.
Bikard, D., Euler, C.W.*, Jiang, W.*, Nussenzweig, P.M., Goldberg, G.W., Duportet, X., Fischetti, V.A. and Marraffini, L.A. Nature biotechnology (2014)
Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting.
Goldberg, G.W., Jiang, W., Bikard, D. and Marraffini, L.A. Nature (2014)
Dealing with the Evolutionary Downside of CRISPR Immunity: Bacteria and Beneficial Plasmids.
Jiang, W., Maniv, I., Arain, F., Wang, Y., Levin, B.R. and Marraffini, L.A. PLoS genetics (2013)
Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system.
Bikard, D.*, Jiang, W.*, Samai, P., Hochschild, A., Zhang, F. and Marraffini, L.A. Nucleic acids research (2013)
RNA-guided editing of bacterial genomes using CRISPR-Cas systems.
Jiang, W.*, Bikard, D.*, Cox, D., Zhang, F. and Marraffini, L.A. Nature biotechnology (2013)
First demonstration of CRISPR-mediated genome editing in bacteria; >2,000 citations
Multiplex genome engineering using CRISPR/Cas systems.
Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A. and Zhang, F. Science (2013)
First demonstration of CRISPR-mediated genome editing in eukaryotes; >10,000 citations
A Ruler Protein in a Complex for Antiviral Defense Determines the Length of Small Interfering CRISPR RNAs.
Hatoum-Aslan, A., Samai, P., Maniv, I., Jiang, W. and Marraffini, L.A. The Journal of biological chemistry (2013)
* Equal contribution