@article{gawlitt_collins_yu_blackman_barquist_beisel_2024, title={Expanding the flexibility of base editing for high-throughput genetic screens in bacteria}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkae174}, abstractNote={Abstract}, journal={NUCLEIC ACIDS RESEARCH}, author={Gawlitt, Sandra and Collins, Scott P. and Yu, Yanying and Blackman, Samuel A. and Barquist, Lars and Beisel, Chase L.}, year={2024}, month={Mar} }
 @article{wimmer_englert_wandera_alkhnbashi_collins_backofen_beisel_2023, title={Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkad1097}, abstractNote={Abstract}, journal={NUCLEIC ACIDS RESEARCH}, author={Wimmer, Franziska and Englert, Frank and Wandera, Katharina G. and Alkhnbashi, Omer S. and Collins, Scott P. and Backofen, Rolf and Beisel, Chase L.}, year={2023}, month={Nov} }
 @article{collias_vialetto_yu_co_almasi_ruettiger_achmedov_strowig_beisel_2023, title={Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria}, volume={14}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-023-36283-9}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Collias, Daphne and Vialetto, Elena and Yu, Jiaqi and Co, Khoa and Almasi, Eva D. H. and Ruettiger, Ann-Sophie and Achmedov, Tatjana and Strowig, Till and Beisel, Chase L.}, year={2023}, month={Feb} }
 @article{vialetto_yu_collins_wandera_barquist_beisel_2022, title={A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13}, volume={30}, ISSN={["1934-6069"]}, DOI={10.1016/j.chom.2022.05.013}, abstractNote={CRISPR-Cas systems must enact robust immunity against foreign genetic material without inducing cytotoxic autoimmunity. For type VI systems that use Cas13 nucleases and recognize RNA targets, immune activation requires extensive CRISPR RNA (crRNA) guide-target complementarity and a target-flanking motif. Here, we report a third requirement shaping the immune response: the expression of the target transcript exceeding a threshold. We found that endogenous non-essential transcripts targeted by crRNAs rarely elicited autoimmunity. Instead, autoimmune induction required over-expressing the targeted transcripts above a threshold. A genome-wide screen confirmed target expression levels as a global determinant of cytotoxic autoimmunity and revealed that this threshold shifts with each guide-target pair. This threshold further ensured defense against a lytic bacteriophage yet allowed the tolerance of a targeted beneficial gene expressed from an invading plasmid. These findings establish target expression levels as an additional criterion for immune defense by RNA-targeting CRISPR-Cas systems, preventing autoimmunity and distinguishing pathogenic and benign invaders.}, number={8}, journal={CELL HOST & MICROBE}, author={Vialetto, Elena and Yu, Yanying and Collins, Scott P. and Wandera, Katharina G. and Barquist, Lars and Beisel, Chase L.}, year={2022}, month={Aug}, pages={1151-+} }
 @misc{collias_beisel_2021, title={CRISPR technologies and the search for the PAM-free nuclease}, volume={12}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-020-20633-y}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Collias, Daphne and Beisel, Chase L.}, year={2021}, month={Jan} }
 @article{yu_zhang_matei_marx_beisel_wei_2021, title={Coupling smartphone and CRISPR-Cas12a for digital and multiplexed nucleic acid detection}, volume={7}, ISSN={["1547-5905"]}, url={https://doi.org/10.1002/aic.17365}, DOI={10.1002/aic.17365}, abstractNote={Abstract}, number={12}, journal={AICHE JOURNAL}, publisher={Wiley}, author={Yu, Tao and Zhang, Shengwei and Matei, Razvan and Marx, William and Beisel, Chase L. and Wei, Qingshan}, year={2021}, month={Jul} }
 @article{durmusoglu_al'abri_collins_cheng_eroglu_beisel_crook_2021, title={In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii}, volume={10}, ISSN={["2161-5063"]}, url={https://doi.org/10.1021/acssynbio.0c00562}, DOI={10.1021/acssynbio.0c00562}, abstractNote={Saccharomyces boulardii is a probiotic yeast that exhibits rapid growth at 37 °C, is easy to transform, and can produce therapeutic proteins in the gut. To establish its ability to produce small molecules encoded by multigene pathways, we measured the amount and variance in protein expression enabled by promoters, terminators, selective markers, and copy number control elements. We next demonstrated efficient (>95%) CRISPR-mediated genome editing in this strain, allowing us to probe engineered gene expression across different genomic sites. We leveraged these strategies to assemble pathways enabling a wide range of vitamin precursor (β-carotene) and drug (violacein) titers. We found that S. boulardii colonizes germ-free mice stably for over 30 days and competes for niche space with commensal microbes, exhibiting short (1-2 day) gut residence times in conventional and antibiotic-treated mice. Using these tools, we enabled β-carotene synthesis (194 μg total) in the germ-free mouse gut over 14 days, estimating that the total mass of additional β-carotene recovered in feces was 56-fold higher than the β-carotene present in the initial probiotic dose. This work quantifies heterologous small molecule production titers by S. boulardii living in the mammalian gut and provides a set of tools for modulating these titers.}, number={5}, journal={ACS SYNTHETIC BIOLOGY}, publisher={American Chemical Society (ACS)}, author={Durmusoglu, Deniz and Al'Abri, Ibrahim S. and Collins, Scott P. and Cheng, Junrui and Eroglu, Abdulkerim and Beisel, Chase L. and Crook, Nathan}, year={2021}, month={May}, pages={1039–1052} }
 @article{collins_rostain_liao_beisel_2021, title={Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR-Cas12a gRNA switch}, volume={49}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkab100}, abstractNote={Abstract}, number={5}, journal={NUCLEIC ACIDS RESEARCH}, author={Collins, Scott P. and Rostain, William and Liao, Chunyu and Beisel, Chase L.}, year={2021}, month={Mar}, pages={2985–2999} }
 @article{collias_leenay_slotkowski_zuo_collins_mcgirr_liu_beisel_2020, title={A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9}, volume={6}, ISBN={2375-2548}, DOI={10.1126/sciadv.abb4054}, abstractNote={SpyCas9 and its engineered variants can recognize NYGG PAMs, affecting their use for genome editing and off-target predictions.}, number={29}, journal={SCIENCE ADVANCES}, author={Collias, D. and Leenay, R. T. and Slotkowski, R. A. and Zuo, Z. and Collins, S. P. and McGirr, B. A. and Liu, J. and Beisel, C. L.}, year={2020}, month={Jul} }
 @article{wandera_collins_wimmer_marshall_noireaux_beisel_2020, title={An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system}, volume={172}, ISSN={["1095-9130"]}, DOI={10.1016/j.ymeth.2019.05.014}, abstractNote={The characterization of CRISPR-Cas immune systems in bacteria was quickly followed by the discovery of anti-CRISPR proteins (Acrs) in bacteriophages. These proteins block different steps of CRISPR-based immunity and, as some inhibit Cas nucleases, can offer tight control over CRISPR technologies. While Acrs have been identified against a few CRISPR-Cas systems, likely many more await discovery and application. Here, we report a rapid and scalable method for characterizing putative Acrs against Cas nucleases using an E. coli-derived cell-free transcription-translation system. Using known Acrs against type II Cas9 nucleases as models, we demonstrate how the method can be used to measure the inhibitory activity of individual Acrs in under two days. We also show how the method can overcome non-specific inhibition of gene expression observed for some Acrs. In total, the method should accelerate the interrogation and application of Acrs as CRISPR-Cas inhibitors.}, journal={METHODS}, author={Wandera, Katharina G. and Collins, Scott P. and Wimmer, Franziska and Marshall, Ryan and Noireaux, Vincent and Beisel, Chase L.}, year={2020}, month={Feb}, pages={42–50} }
 @article{jacobsen_ttofali_liao_manchalu_gray_beisel_2020, title={Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs}, volume={48}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkaa272}, abstractNote={Abstract}, number={10}, journal={NUCLEIC ACIDS RESEARCH}, author={Jacobsen, Thomas and Ttofali, Fani and Liao, Chunyu and Manchalu, Srinivas and Gray, Benjamin N. and Beisel, Chase L.}, year={2020}, month={Jun}, pages={5624–5638} }
 @article{siedler_rau_bidstrup_vento_aunsbjerg_bosma_mcnair_beisel_neves_2020, title={Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products}, volume={86}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.02312-19}, abstractNote={
            In societies that have food choices, conscious consumers demand natural solutions to keep their food healthy and fresh during storage, simultaneously reducing food waste. The use of “good bacteria” to protect food against spoilage organisms has a long, successful history, even though the molecular mechanisms are not fully understood. In this study, we show that the depletion of free manganese is a major bioprotective mechanism of lactobacilli in dairy products. High manganese uptake and intracellular storage provide a link to the distinct, nonenzymatic, manganese-catalyzed oxidative stress defense mechanism, previously described for certain lactobacilli. The evaluation of representative
            Lactobacillus
            species in our study identifies multiple relevant species groups for fungal growth inhibition via manganese depletion. Hence, through the natural mechanism of nutrient depletion, the use of dedicated bioprotective lactobacilli constitutes an attractive alternative to artificial preservation.
          }, number={7}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Siedler, Solvej and Rau, Martin Holm and Bidstrup, Susanne and Vento, Justin M. and Aunsbjerg, Stina Dissing and Bosma, Elleke F. and McNair, Laura M. and Beisel, Chase L. and Neves, Ana Rute}, year={2020}, month={Apr} }
 @article{beisel_2020, title={Methods for characterizing, applying, and teaching CRISPR-Cas systems}, volume={172}, ISSN={["1095-9130"]}, DOI={10.1016/j.ymeth.2020.01.004}, journal={METHODS}, author={Beisel, Chase L.}, year={2020}, month={Feb}, pages={1–2} }
 @article{jacobsen_yi_al asafen_jermusyk_beisel_reeves_2020, title={Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems}, volume={15}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0232046}, abstractNote={Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in Drosophila embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5′ vs. 3′ untranslated region) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.}, number={4}, journal={PLOS ONE}, author={Jacobsen, Thomas and Yi, Gloria and Al Asafen, Hadel and Jermusyk, Ashley A. and Beisel, Chase L. and Reeves, Gregory T.}, year={2020}, month={Apr} }
 @article{collins_beisel_2020, title={Your Base Editor Might Be Flirting with Single (Stranded) DNA: Faithful On-Target CRISPR Base Editing without Promiscuous Deamination}, volume={79}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2020.07.030}, abstractNote={Jin et al., 2020Jin S. Fei H. Zhu Z. Luo Y. Liu J. Gao S. Zhang F. Chen Y.H. Wang Y. Gao C. Rationally Designed APOBEC3B Cytosine Base Editors with Improved Specificity.Mol. Cell. 2020; 79 (this issue): 728-740Abstract Full Text Full Text PDF PubMed Scopus (22) Google Scholar engineered new variants of CRISPR base editors that make precise genomic edits in rice protoplasts while minimizing untargeted mutagenesis.}, number={5}, journal={MOLECULAR CELL}, author={Collins, Scott P. and Beisel, Chase L.}, year={2020}, month={Sep}, pages={703–704} }
 @article{collias_marshall_collins_beisel_noireaux_2019, title={An educational module to explore CRISPR technologies with a cell-free transcription-translation system}, volume={4}, ISSN={["2397-7000"]}, DOI={10.1093/synbio/ysz005}, abstractNote={Abstract}, number={1}, journal={SYNTHETIC BIOLOGY}, author={Collias, Daphne and Marshall, Ryan and Collins, Scott P. and Beisel, Chase L. and Noireaux, Vincent}, year={2019} }
 @misc{vento_crook_beisel_2019, title={Barriers to genome editing with CRISPR in bacteria}, volume={46}, ISSN={["1476-5535"]}, url={https://doi.org/10.1007/s10295-019-02195-1}, DOI={10.1007/s10295-019-02195-1}, abstractNote={Abstract}, number={9-10}, journal={JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY}, publisher={Springer Science and Business Media LLC}, author={Vento, Justin M. and Crook, Nathan and Beisel, Chase L.}, year={2019}, month={Oct}, pages={1327–1341} }
 @article{liao_slotkowski_beisel_2019, title={CRATES: A one-step assembly method for Class 2 CRISPR arrays}, volume={629}, ISBN={["978-0-12-818671-8"]}, ISSN={["0076-6879"]}, DOI={10.1016/bs.mie.2019.04.011}, abstractNote={CRISPR-Cas systems naturally rely on CRISPR arrays to achieve immunity against multiple foreign invaders, where these arrays are also being utilized for multiplexed targeting as part of CRISPR technologies. However, CRISPR arrays have proven difficult to synthesize or assemble to-date due to the repetitive DNA repeats in each array. To overcome this barrier, we recently reported a cloning method we term CRATES (CRISPR Assembly through Trimmed Ends of Spacers) for the single-step, efficient generation of large Class 2 CRISPR arrays. CRATES generates CRISPR arrays through assembly of multiple repeat-spacer subunits using defined junction sequences within the trimmed portion of the CRISPR spacers. These arrays can be utilized by single-effector nucleases associated with Class 2 CRISPR-Cas systems, such as Cas9, Cas12a/Cpf1, or Cas13a/C2c2. Here, we describe in detail the steps for generating arrays utilized by Cas9 and Cas12a as well as composite arrays co-utilized by both nucleases. We also generate a representative three-spacer array and demonstrate multiplexed DNA cleavage through plasmid-clearance assays in Escherichia coli. This method is expected to simplify the study of natural CRISPR arrays and facilitate multiplexed targeting with programmable nucleases from Class 2 Cas nucleases across the myriad applications of CRISPR technologies.}, journal={TUMOR IMMUNOLOGY AND IMMUNOTHERAPY - MOLECULAR METHODS}, author={Liao, Chunyu and Slotkowski, Rebecca A. and Beisel, Chase L.}, year={2019}, pages={493–511} }
 @article{westbrook_tang_marshall_maxwell_chappell_agrawal_dunlop_noireaux_beisel_lucks_et al._2019, title={Distinct timescales of RNA regulators enable the construction of a genetic pulse generator}, volume={116}, ISSN={["1097-0290"]}, DOI={10.1002/bit.26918}, abstractNote={Abstract}, number={5}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Westbrook, Alexandra and Tang, Xun and Marshall, Ryan and Maxwell, Colin S. and Chappell, James and Agrawal, Deepak K. and Dunlop, Mary J. and Noireaux, Vincent and Beisel, Chase L. and Lucks, Julius and et al.}, year={2019}, month={May}, pages={1139–1151} }
 @article{leenay_vento_shah_martino_leulier_beisel_2019, title={Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods}, volume={14}, ISSN={["1860-7314"]}, DOI={10.1002/biot.201700583}, abstractNote={Lactic-acid bacteria such as Lactobacillus plantarum are commonly used for fermenting foods and as probiotics, where increasingly sophisticated genome-editing tools are employed to elucidate and enhance these microbes' beneficial properties. The most advanced tools to date utilize an oligonucleotide or double-stranded DNA donor for recombineering and Cas9 for targeted DNA cleavage. As the associated methods are often developed in isolation for one strain, it remains unclear how different Cas9-based editing methods compare across strains. Here, this work directly compares two methods in different strains of L. plantarum: one utilizing a plasmid-encoded recombineering template and another utilizing an oligonucleotide donor and an inducible DNA recombinase. This comparison reveals one instance in which only the recombineering-template method generates desired edits and another instance in which only the oligo method generates desired edits. It is further found that both methods exhibit highly variable success editing the same site across multiple L. plantarum strains. Finally, failure modes are identified for the recombineering-template method, including a consistent genomic deletion and reversion of a point mutation in the recombineering template. This study therefore highlights surprising differences for Cas9-mediated genome editing between methods and related strains, arguing for the need for multiple, distinct methods when performing CRISPR-based editing in bacteria.}, number={3}, journal={BIOTECHNOLOGY JOURNAL}, author={Leenay, Ryan T. and Vento, Justin M. and Shah, Malay and Martino, Maria Elena and Leulier, Francois and Beisel, Chase L.}, year={2019}, month={Mar} }
 @article{liao_ttofali_slotkowski_denny_cecil_leenay_keung_beisel_2019, title={Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis}, volume={10}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-019-10747-3}, abstractNote={Abstract}, journal={NATURE COMMUNICATIONS}, author={Liao, Chunyu and Ttofali, Fani and Slotkowski, Rebecca A. and Denny, Steven R. and Cecil, Taylor D. and Leenay, Ryan T. and Keung, Albert J. and Beisel, Chase L.}, year={2019}, month={Jul} }
 @article{pickar-oliver_black_lewis_mutchnick_klann_gilcrest_sitton_nelson_barrera_bartelt_et al._2019, title={Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells}, volume={37}, ISSN={["1546-1696"]}, DOI={10.1038/s41587-019-0235-7}, abstractNote={Class 2 CRISPR–Cas systems, such as Cas9 and Cas12, have been widely used to target DNA sequences in eukaryotic genomes. However, class 1 CRISPR–Cas systems, which represent about 90% of all CRISPR systems in nature, remain largely unexplored for genome engineering applications. Here, we show that class 1 CRISPR–Cas systems can be expressed in mammalian cells and used for DNA targeting and transcriptional control. We repurpose type I variants of class 1 CRISPR–Cas systems from Escherichia coli and Listeria monocytogenes, which target DNA via a multi-component RNA-guided complex termed Cascade. We validate Cascade expression, complex formation and nuclear localization in human cells, and demonstrate programmable CRISPR RNA (crRNA)-mediated targeting of specific loci in the human genome. By tethering activation and repression domains to Cascade, we modulate the expression of targeted endogenous genes in human cells. This study demonstrates the use of Cascade as a CRISPR-based technology for targeted eukaryotic gene regulation, highlighting class 1 CRISPR–Cas systems for further exploration. Type I CRISPR–Cas systems, the largest group of CRISPR systems in nature, can be repurposed for DNA targeting and gene regulation in human cells}, number={12}, journal={NATURE BIOTECHNOLOGY}, publisher={Springer Science and Business Media LLC}, author={Pickar-Oliver, Adrian and Black, Joshua B. and Lewis, Mae M. and Mutchnick, Kevin J. and Klann, Tyler S. and Gilcrest, Kylie A. and Sitton, Madeleine J. and Nelson, Christopher E. and Barrera, Alejandro and Bartelt, Luke C. and et al.}, year={2019}, month={Dec}, pages={1493-+} }
 @article{jacobsen_liao_beisel_2019, title={The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs}, volume={366}, ISSN={["1574-6968"]}, DOI={10.1093/femsle/fnz085}, abstractNote={ABSTRACT}, number={8}, journal={FEMS MICROBIOLOGY LETTERS}, author={Jacobsen, Thomas and Liao, Chunyu and Beisel, Chase L.}, year={2019}, month={Apr} }
 @article{liao_slotkowski_achmedov_beisel_2019, title={The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays}, volume={16}, ISSN={["1555-8584"]}, DOI={10.1080/15476286.2018.1526537}, abstractNote={ABSTRACT The Class 2 Type V-A CRISPR effector protein Cas12a/Cpf1 has gained widespread attention in part because of the ease in achieving multiplexed genome editing, gene regulation, and DNA detection. Multiplexing derives from the ability of Cas12a alone to generate multiple guide RNAs from a transcribed CRISPR array encoding alternating conserved repeats and targeting spacers. While array design has focused on how to optimize guide-RNA sequences, little attention has been paid to sequences outside of the CRISPR array. Here, we show that a structured hairpin located immediately downstream of the 3ʹ repeat interferes with utilization of the adjacent encoded guide RNA by Francisella novicida (Fn)Cas12a. We first observed that a synthetic Rho-independent terminator immediately downstream of an array impaired DNA cleavage based on plasmid clearance in E. coli and DNA cleavage in a cell-free transcription-translation (TXTL) system. TXTL-based cleavage assays further revealed that inhibition was associated with incomplete processing of the transcribed CRISPR array and could be attributed to the stable hairpin formed by the terminator. We also found that the inhibitory effect partially extended to upstream spacers in a multi-spacer array. Finally, we found that removing the terminal repeat from the array increased the inhibitory effect, while replacing this repeat with an unprocessable terminal repeat from a native FnCas12a array restored cleavage activity directed by the adjacent encoded guide RNA. Our study thus revealed that sequences surrounding a CRISPR array can interfere with the function of a CRISPR nuclease, with implications for the design and evolution of CRISPR arrays.}, number={4}, journal={RNA BIOLOGY}, author={Liao, Chunyu and Slotkowski, Rebecca A. and Achmedov, Tatjana and Beisel, Chase L.}, year={2019}, month={Apr}, pages={404–412} }
 @article{maxwell_jacobsen_marshall_noireaux_beisel_2018, title={A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs}, volume={143}, ISSN={1046-2023}, url={http://dx.doi.org/10.1016/J.YMETH.2018.02.016}, DOI={10.1016/J.YMETH.2018.02.016}, abstractNote={The RNA-guided nucleases derived from the CRISPR-Cas systems in bacteria and archaea have found numerous applications in biotechnology, including genome editing, imaging, and gene regulation. However, the discovery of novel Cas nucleases has outpaced their characterization and subsequent exploitation. A key step in characterizing Cas nucleases is determining which protospacer-adjacent motif (PAM) sequences they recognize. Here, we report advances to an in vitro method based on an E. coli cell-free transcription-translation system (TXTL) to rapidly elucidate PAMs recognized by Cas nucleases. The method obviates the need for cloning Cas nucleases or gRNAs, does not require the purification of protein or RNA, and can be performed in less than a day. To advance our previously published method, we incorporated an internal GFP cleavage control to assess the extent of library cleavage as well as Sanger sequencing of the cleaved library to assess PAM depletion prior to next-generation sequencing. We also detail the methods needed to construct all relevant DNA constructs, and how to troubleshoot the assay. We finally demonstrate the technique by determining PAM sequences recognized by the Neisseria meningitidis Cas9, revealing subtle sequence requirements of this highly specific PAM. The overall method offers a rapid means to identify PAMs recognized by diverse CRISPR nucleases, with the potential to greatly accelerate our ability to characterize and harness novel CRISPR nucleases across their many uses.}, journal={Methods}, publisher={Elsevier BV}, author={Maxwell, Colin S. and Jacobsen, Thomas and Marshall, Ryan and Noireaux, Vincent and Beisel, Chase L.}, year={2018}, month={Jul}, pages={48–57} }
 @article{alper_beisel_2018, title={Advances in CRISPR Technologies for Microbial Strain Engineering}, volume={13}, ISSN={1860-6768}, url={http://dx.doi.org/10.1002/BIOT.201800460}, DOI={10.1002/BIOT.201800460}, abstractNote={CRISPR technologies are having a profound impact on our ability to manipulate the genomic content of different organisms. These technologies rely on prokaryotic immune systems called CRISPR-Cas systems and their RNA-directed nucleases that bind and cleave complementary sequences. Much of the fanfare around CRISPR technologies has been their application to higher eukaryotes such as mammals, plants, and insects. However, there have been similarly important advances in industrially-relevant microorganisms. These microorganisms have been mainstays of numerous industries devoted to the production of foods, fuels, pharmaceuticals, and commodity chemicals, where genetic manipulation has allowed the interrogation of their genetic features as well as the enhancement of their metabolic and physiological capabilities. While genome-editing tools were available prior to the advent of CRISPR, CRISPRmademanymanipulations simpler and faster. Given the ease in implementing CRISPR, it is has become a standard tool in virtually all industrial microbes. Despite these strides forward, CRISPR remains a fledgling technology that was established only a few years ago. Accordingly, new advances are continually being reported that improve upon CRISPR as a tool, extend CRISPR to new microorganisms, and establish novel applications relevant to strain development. We are pleased to present this special issue in Biotechnology Journal that addresses the forefront of CRISPR technologies and their application to microbial strain engineering. The issue entails a collection of five review articles and eleven original research articles highlighting what has been achieved with CRISPR to-date and what challenges await new discoveries and developments. We provide a brief overview of these articles that are organized based on generalized CRISPR technologies and their application to industrially-relevant strains of bacteria, yeast, and microalgae. Generalized CRISPR technologies. Four review articles offer insights into the state of CRISPR technologies applicable to all microorganisms. Tarasava and coworkers provide a comprehensive overview of how CRISPR has been applied for genome editing and gene regulation in bacteria and yeast. As part of their analyses, the authors compare the different available techniques, describe their application to metabolic engineering and synthetic circuit design, and highlight some of the limitations and workarounds for the original. In parallel, Naduthodi and coworkers review advances in genome editing with Cas9 in photosynthetic microorganisms, including cyanobacteria and microalgae. They summarize all instances of}, number={9}, journal={Biotechnology Journal}, publisher={Wiley}, author={Alper, Hal S. and Beisel, Chase L.}, year={2018}, month={Sep}, pages={1800460} }
 @article{martino_joncour_leenay_gervais_shah_hughes_gillet_beisel_leulier_2018, title={Bacterial Adaptation to the Host's Diet Is a Key Evolutionary Force Shaping Drosophila-Lactobacillus LESymbiosis}, volume={24}, ISSN={["1934-6069"]}, DOI={10.1016/j.chom.2018.06.001}, abstractNote={Animal-microbe facultative symbioses play a fundamental role in ecosystem and organismal health. Yet, due to the flexible nature of their association, the selection pressures that act on animals and their facultative symbionts remain elusive. Here we apply experimental evolution to Drosophila melanogaster associated with its growth-promoting symbiont Lactobacillus plantarum, representing a well-established model of facultative symbiosis. We find that the diet of the host, rather than the host itself, is a predominant driving force in the evolution of this symbiosis. Furthermore, we identify a mechanism resulting from the bacterium's adaptation to the diet, which confers growth benefits to the colonized host. Our study reveals that bacterial adaptation to the host's diet may be the foremost step in determining the evolutionary course of a facultative animal-microbe symbiosis.}, number={1}, journal={CELL HOST & MICROBE}, author={Martino, Maria Elena and Joncour, Pauline and Leenay, Ryan and Gervais, Hugo and Shah, Malay and Hughes, Sandrine and Gillet, Benjamin and Beisel, Chase and Leulier, Francois}, year={2018}, month={Jul}, pages={109-+} }
 @article{dugar_leenay_eisenbart_bischler_aul_beisel_sharma_2018, title={CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9}, volume={69}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2018.01.032}, abstractNote={Cas9 nucleases naturally utilize CRISPR RNAs (crRNAs) to silence foreign double-stranded DNA. While recent work has shown that some Cas9 nucleases can also target RNA, RNA recognition has required nuclease modifications or accessory factors. Here, we show that the Campylobacter jejuni Cas9 (CjCas9) can bind and cleave complementary endogenous mRNAs in a crRNA-dependent manner. Approximately 100 transcripts co-immunoprecipitated with CjCas9 and generally can be subdivided through their base-pairing potential to the four crRNAs. A subset of these RNAs was cleaved around or within the predicted binding site. Mutational analyses revealed that RNA binding was crRNA and tracrRNA dependent and that target RNA cleavage required the CjCas9 HNH domain. We further observed that RNA cleavage was PAM independent, improved with greater complementarity between the crRNA and the RNA target, and was programmable in vitro. These findings suggest that C. jejuni Cas9 is a promiscuous nuclease that can coordinately target both DNA and RNA.}, number={5}, journal={MOLECULAR CELL}, author={Dugar, Gaurav and Leenay, Ryan T. and Eisenbart, Sara K. and Bischler, Thorsten and Aul, Belinda U. and Beisel, Chase L. and Sharma, Cynthia M.}, year={2018}, month={Mar}, pages={893-+} }
 @article{beisel_2018, title={CRISPR tool puts RNA on the record}, volume={562}, ISSN={0028-0836 1476-4687}, url={http://dx.doi.org/10.1038/D41586-018-06869-1}, DOI={10.1038/D41586-018-06869-1}, abstractNote={The bacterial-defence system CRISPR–Cas can store DNA snippets that correspond to encountered viral RNA sequences. One such system has now been harnessed to record gene expression over time in bacteria. RNA expression can be recorded in bacterial cells.}, number={7727}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Beisel, Chase L.}, year={2018}, month={Oct}, pages={347–349} }
 @article{agrawal_tang_westbrook_marshall_maxwell_lucks_noireaux_beisel_dunlop_franco_2018, title={Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression}, volume={7}, ISSN={["2161-5063"]}, DOI={10.1021/acssynbio.8b00040}, abstractNote={Feedback allows biological systems to control gene expression precisely and reliably, even in the presence of uncertainty, by sensing and processing environmental changes. Taking inspiration from natural architectures, synthetic biologists have engineered feedback loops to tune the dynamics and improve the robustness and predictability of gene expression. However, experimental implementations of biomolecular control systems are still far from satisfying performance specifications typically achieved by electrical or mechanical control systems. To address this gap, we present mathematical models of biomolecular controllers that enable reference tracking, disturbance rejection, and tuning of the temporal response of gene expression. These controllers employ RNA transcriptional regulators to achieve closed loop control where feedback is introduced via molecular sequestration. Sensitivity analysis of the models allows us to identify which parameters influence the transient and steady state response of a target gene expression process, as well as which biologically plausible parameter values enable perfect reference tracking. We quantify performance using typical control theory metrics to characterize response properties and provide clear selection guidelines for practical applications. Our results indicate that RNA regulators are well-suited for building robust and precise feedback controllers for gene expression. Additionally, our approach illustrates several quantitative methods useful for assessing the performance of biomolecular feedback control systems.}, number={5}, journal={ACS SYNTHETIC BIOLOGY}, author={Agrawal, Deepak K. and Tang, Xun and Westbrook, Alexandra and Marshall, Ryan and Maxwell, Colin S. and Lucks, Julius and Noireaux, Vincent and Beisel, Chase L. and Dunlop, Mary J. and Franco, Elisa}, year={2018}, month={May}, pages={1219–1228} }
 @article{marshall_maxwell_collins_jacobsen_luo_begemann_gray_january_singer_he_et al._2018, title={Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System}, volume={69}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2017.12.007}, abstractNote={CRISPR-Cas systems offer versatile technologies for genome engineering, yet their implementation has been outpaced by ongoing discoveries of new Cas nucleases and anti-CRISPR proteins. Here, we present the use of E. coli cell-free transcription-translation (TXTL) systems to vastly improve the speed and scalability of CRISPR characterization and validation. TXTL can express active CRISPR machinery from added plasmids and linear DNA, and TXTL can output quantitative dynamics of DNA cleavage and gene repression—all without protein purification or live cells. We used TXTL to measure the dynamics of DNA cleavage and gene repression for single- and multi-effector CRISPR nucleases, predict gene repression strength in E. coli, determine the specificities of 24 diverse anti-CRISPR proteins, and develop a fast and scalable screen for protospacer-adjacent motifs that was successfully applied to five uncharacterized Cpf1 nucleases. These examples underscore how TXTL can facilitate the characterization and application of CRISPR technologies across their many uses.}, number={1}, journal={MOLECULAR CELL}, author={Marshall, Ryan and Maxwell, Colin S. and Collins, Scott P. and Jacobsen, Thomas and Luo, Michelle L. and Begemann, Matthew B. and Gray, Benjamin N. and January, Emma and Singer, Anna and He, Yonghua and et al.}, year={2018}, month={Jan}, pages={146-+} }
 @article{bober_beisel_nair_2018, title={Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications}, volume={20}, ISSN={["1545-4274"]}, DOI={10.1146/annurev-bioeng-062117-121019}, abstractNote={ An increasing number of studies have strongly correlated the composition of the human microbiota with many human health conditions and, in several cases, have shown that manipulating the microbiota directly affects health. These insights have generated significant interest in engineering indigenous microbiota community members and nonresident probiotic bacteria as biotic diagnostics and therapeutics that can probe and improve human health. In this review, we discuss recent advances in synthetic biology to engineer commensal and probiotic lactic acid bacteria, bifidobacteria, and Bacteroides for these purposes, and we provide our perspective on the future potential of these technologies. }, journal={ANNUAL REVIEW OF BIOMEDICAL ENGINEERING, VOL 20}, author={Bober, Josef R. and Beisel, Chase L. and Nair, Nikhil U.}, year={2018}, pages={277–300} }
 @article{fagen_collias_singh_beisel_2017, title={Advancing the design and delivery of CRISPR antimicrobials}, volume={4}, ISSN={2468-4511}, url={http://dx.doi.org/10.1016/J.COBME.2017.10.001}, DOI={10.1016/J.COBME.2017.10.001}, abstractNote={CRISPR-Cas systems are prokaryotic immune systems whose RNA-guided nucleases have been co-opted for applications ranging from genome editing and gene regulation to in vitro diagnostics and DNA imaging. Here, we review the current efforts toward repurposing CRISPR nucleases as programmable antimicrobials. Antimicrobial activity is achieved by targeted cleavage of multidrug-resistance plasmids or the bacterial chromosome, resulting in antibiotic sensitivity or cell death. As part of the review, we discuss the different types of nucleases available for CRISPR antimicrobials, the use of bacteriophages as delivery vehicles, and opportunities to enhance antimicrobial activity, delivery, and specificity. Through further advances, these programmable DNA-targeting antimicrobials may help quell the spread of antimicrobial resistance and provide a tool for the manipulation of complex microbial communities.}, journal={Current Opinion in Biomedical Engineering}, publisher={Elsevier BV}, author={Fagen, Jennie R. and Collias, Daphne and Singh, Atul K. and Beisel, Chase L.}, year={2017}, month={Dec}, pages={57–64} }
 @misc{leenay_beisel_2017, title={Deciphering, Communicating, and Engineering the CRISPR PAM}, volume={429}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2016.11.024}, abstractNote={Clustered regularly interspaced short palindromic repeat (CRISPR) loci and their flanking CRISPR-associated (cas) genes make up RNA-guided, adaptive immune systems in prokaryotes whose effector proteins have become powerful tools for basic research and biotechnology. While the Cas effector proteins are remarkably diverse, they commonly rely on protospacer-adjacent motifs (PAMs) as the first step in target recognition. PAM sequences are known to vary considerably between systems and have proven to be difficult to predict, spurring the need for new tools to rapidly identify and communicate these sequences. Recent advances have also shown that Cas proteins can be engineered to alter PAM recognition, opening new opportunities to develop CRISPR-based tools with enhanced targeting capabilities. In this review, we discuss the properties of the CRISPR PAM and the emerging tools for determining, visualizing, and engineering PAM recognition. We also propose a standard means of orienting the PAM to simplify how its location and sequence are communicated.}, number={2}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Leenay, Ryan T. and Beisel, Chase L.}, year={2017}, month={Jan}, pages={177–191} }
 @article{marshall_maxwell_collins_beisel_noireaux_2017, title={Short DNA Containing chi Sites Enhances DNA Stability and Gene Expression in E-coli Cell-Free Transcription-Translation Systems}, volume={114}, ISSN={["1097-0290"]}, DOI={10.1002/bit.26333}, abstractNote={ABSTRACT}, number={9}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Marshall, Ryan and Maxwell, Colin S. and Collins, Scott P. and Beisel, Chase L. and Noireaux, Vincent}, year={2017}, month={Sep}, pages={2137–2141} }
 @article{waller_bober_nair_beisel_2017, title={Toward a genetic tool development pipeline for host-associated bacteria}, volume={38}, ISSN={1369-5274}, url={http://dx.doi.org/10.1016/J.MIB.2017.05.006}, DOI={10.1016/J.MIB.2017.05.006}, abstractNote={Bacteria reside in externally accessible niches on and in multicellular organisms, often forming mutualistic relationships with their host. Recent studies have linked the composition of these microbial communities with alterations in the host’s health, behavior, and development, yet the causative mediators of host–microbiota interactions remain poorly understood. Advances in understanding and engineering these interactions require the development of genetic tools to probe the molecular interactions driving the structure and function of microbial communities as well as their interactions with their host. This review discusses the current challenges to rendering culturable, non-model members of microbial communities genetically tractable – including overcoming barriers to DNA delivery, achieving predictable gene expression, and applying CRISPR-based tools – and details recent efforts to create generalized pipelines that simplify and expedite the tool-development process. We use the bacteria present in the human gastrointestinal tract as representative microbiota to illustrate some of the recent achievements and future opportunities for genetic tool development.}, journal={Current Opinion in Microbiology}, publisher={Elsevier BV}, author={Waller, Matthew C and Bober, Josef R and Nair, Nikhil U and Beisel, Chase L}, year={2017}, month={Aug}, pages={156–164} }
 @article{chen_shapiro_ruder_ye_kiani_moon_raman_beisel_barnes_2017, title={What is the role of circuit design in the advancement of synthetic biology? Part 1 enabling real-world applications and therapeutics}, volume={4}, number={4}, journal={Cell Systems}, author={Chen, Y. Y. and Shapiro, M. G. and Ruder, W. and Ye, H. F. and Kiani, S. and Moon, T. S. and Raman, S. and Beisel, C. and Barnes, C.}, year={2017}, pages={370–372} }
 @misc{luo_leenay_beisel_2016, title={Current and future prospects for CRISPR-based tools in bacteria}, volume={113}, ISSN={["1097-0290"]}, DOI={10.1002/bit.25851}, abstractNote={ABSTRACT}, number={5}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Luo, Michelle L. and Leenay, Ryan T. and Beisel, Chase L.}, year={2016}, month={May}, pages={930–943} }
 @article{luo_beisel_2016, title={Engineering genes with CRISPR-Cas9}, volume={112}, number={9}, journal={Chemical Engineering Progress }, author={Luo, M. L. and Beisel, C. L.}, year={2016}, pages={36–41} }
 @article{leenay_maksimchuk_slotkowski_agrawal_gomaa_briner_barrangou_beisel_2016, title={Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems}, volume={62}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2016.02.031}, abstractNote={<h2>Summary</h2> CRISPR-Cas adaptive immune systems in prokaryotes boast a diversity of protein families and mechanisms of action, where most systems rely on protospacer-adjacent motifs (PAMs) for DNA target recognition. Here, we developed an in vivo, positive, and tunable screen termed PAM-SCANR (PAM screen achieved by NOT-gate repression) to elucidate functional PAMs as well as an interactive visualization scheme termed the PAM wheel to convey individual PAM sequences and their activities. PAM-SCANR and the PAM wheel identified known functional PAMs while revealing complex sequence-activity landscapes for the <i>Bacillus halodurans</i> I-C (Cascade), <i>Escherichia coli</i> I-E (Cascade), <i>Streptococcus thermophilus</i> II-A CRISPR1 (Cas9), and <i>Francisella novicida</i> V-A (Cpf1) systems. The PAM wheel was also readily applicable to existing high-throughput screens and garnered insights into SpyCas9 and SauCas9 PAM diversity. These tools offer powerful means of elucidating and visualizing functional PAMs toward accelerating our ability to understand and exploit the multitude of CRISPR-Cas systems in nature.}, number={1}, journal={MOLECULAR CELL}, publisher={Elsevier BV}, author={Leenay, Ryan T. and Maksimchuk, Kenneth R. and Slotkowski, Rebecca A. and Agrawal, Roma N. and Gomaa, Ahmed A. and Briner, Alexandra E. and Barrangou, Rodolphe and Beisel, Chase L.}, year={2016}, month={Apr}, pages={137–147} }
 @article{beisel_afroz_2016, title={Rethinking the Hierarchy of Sugar Utilization in Bacteria}, volume={198}, ISSN={["1098-5530"]}, DOI={10.1128/jb.00890-15}, abstractNote={ABSTRACT}, number={3}, journal={JOURNAL OF BACTERIOLOGY}, author={Beisel, Chase L. and Afroz, Taliman}, year={2016}, month={Feb}, pages={374–376} }
 @article{luo_jackson_denny_tokmina-lukaszewska_maksimchuk_lin_bothner_wiedenheft_beisel_2016, title={The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers}, volume={44}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkw421}, abstractNote={Bacteria and archaea acquire resistance to foreign genetic elements by integrating fragments of foreign DNA into CRISPR (clustered regularly interspaced short palindromic repeats) loci. In Escherichia coli, CRISPR-derived RNAs (crRNAs) assemble with Cas proteins into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade recognizes DNA targets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairing between the crRNA spacer and the DNA target. Previously determined structures of Cascade showed that the crRNA is stretched along an oligomeric protein assembly, leading us to ask how crRNA length impacts the assembly and function of this complex. We found that extending the spacer portion of the crRNA resulted in larger Cascade complexes with altered stoichiometry and preserved in vitro binding affinity for target DNA. Longer spacers also preserved the in vivo ability of Cascade to repress target gene expression and to recruit the Cas3 endonuclease for target degradation. Finally, longer spacers exhibited enhanced silencing at particular target locations and were sensitive to mismatches within the extended region. These findings demonstrate the flexibility of the Type I-E CRISPR machinery and suggest that spacer length can be modified to fine-tune Cascade activity.}, number={15}, journal={NUCLEIC ACIDS RESEARCH}, author={Luo, Michelle L. and Jackson, Ryan N. and Denny, Steven R. and Tokmina-Lukaszewska, Monika and Maksimchuk, Kenneth R. and Lin, Wayne and Bothner, Brian and Wiedenheft, Blake and Beisel, Chase L.}, year={2016}, month={Sep}, pages={7385–7394} }
 @article{sun_ji_hall_hu_wang_beisel_gu_2015, title={Cover Picture: Self-Assembled DNA Nanoclews for the Efficient Delivery of CRISPR-Cas9 for Genome Editing (Angew. Chem. Int. Ed. 41/2015)}, volume={54}, ISSN={1433-7851}, url={http://dx.doi.org/10.1002/ANIE.201508399}, DOI={10.1002/ANIE.201508399}, abstractNote={A biologically inspired carrier for the delivery of CRISPR–Cas9 that is based on yarn-like DNA nanoparticles, so-called DNA nanoclews, is described by Z. Gu, C. L. Beisel, and co-workers in their Communication on page 12029 ff. DNA nanoclews (the flying saucers), partially complementary to the single guide RNA (sgRNA), were efficiently loaded with Cas9/sgRNA complexes (the missiles) and delivered the complexes into human cells for genome editing. A biologically inspired carrier for the delivery of CRISPR–Cas9 that is based on yarn-like DNA nanoparticles, so-called DNA nanoclews, is described by Z. Gu, C. L. Beisel, and co-workers in their Communication on page 12029 ff. DNA nanoclews (the flying saucers), partially complementary to the single guide RNA (sgRNA), were efficiently loaded with Cas9/sgRNA complexes (the missiles) and delivered the complexes into human cells for genome editing. Propylene Epoxidation Catalysts Main Group Chemistry}, number={41}, journal={Angewandte Chemie International Edition}, publisher={Wiley}, author={Sun, Wujin and Ji, Wenyan and Hall, Jordan M. and Hu, Quanyin and Wang, Chao and Beisel, Chase L. and Gu, Zhen}, year={2015}, month={Sep}, pages={11877–11877} }
 @article{afroz_luo_beisel_2015, title={Impact of Residual Inducer on Titratable Expression Systems}, volume={10}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0137421}, abstractNote={Inducible expression systems are widely employed for the titratable control of gene expression, yet molecules inadvertently present in the growth medium or synthesized by the host cells can alter the response profile of some of these systems. Here, we explored the quantitative impact of these residual inducers on the apparent response properties of inducible systems. Using a simple mathematical model, we found that the presence of residual inducer shrinks the apparent dynamic range and causes the apparent Hill coefficient to converge to one. We also found that activating systems were more sensitive than repressing systems to the presence of residual inducer and the response parameters were most heavily dependent on the original Hill coefficient. Experimental interrogation of common titratable systems based on an L-arabinose inducible promoter or a thiamine pyrophosphate-repressing riboswitch in Escherichia coli confirmed the predicted trends. We finally found that residual inducer had a distinct effect on “all-or-none” systems, which exhibited increased sensitivity to the added inducer until becoming fully induced. Our findings indicate that residual inducer or repressor alters the quantitative response properties of titratable systems, impacting their utility for scientific discovery and pathway engineering.}, number={9}, journal={PLOS ONE}, author={Afroz, Taliman and Luo, Michelle L. and Beisel, Chase L.}, year={2015}, month={Sep} }
 @article{luo_mullis_leenay_beisel_2015, title={Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression}, volume={43}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gku971}, abstractNote={CRISPR-Cas systems have shown tremendous promise as heterologous tools for genome editing and transcriptional regulation. Because these RNA-directed immune systems are found in most prokaryotes, an opportunity exists to harness the endogenous systems as convenient tools in these organisms. Here, we report that the Type I-E CRISPR-Cas system in Escherichia coli can be co-opted for programmable transcriptional repression. We found that deletion of the signature cas3 gene converted this immune system into a programmable gene regulator capable of reversible gene silencing of heterologous and endogenous genes. Targeting promoter regions yielded the strongest repression, whereas targeting coding regions showed consistent strand bias. Furthermore, multi-targeting CRISPR arrays could generate complex phenotypes. This strategy offers a simple approach to convert many endogenous Type I systems into transcriptional regulators, thereby expanding the available toolkit for CRISPR-mediated genetic control while creating new opportunities for genome-wide screens and pathway engineering.}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Luo, Michelle L. and Mullis, Adam S. and Leenay, Ryan T. and Beisel, Chase L.}, year={2015}, month={Jan}, pages={674–681} }
 @article{sun_ji_hall_hu_wang_beisel_gu_2015, title={Self-Assembled DNA Nanoclews for the Efficient Delivery of CRISPR-Cas9 for Genome Editing}, volume={54}, ISSN={1433-7851}, url={http://dx.doi.org/10.1002/ANIE.201506030}, DOI={10.1002/ANIE.201506030}, abstractNote={Abstract}, number={41}, journal={Angewandte Chemie International Edition}, publisher={Wiley}, author={Sun, Wujin and Ji, Wenyan and Hall, Jordan M. and Hu, Quanyin and Wang, Chao and Beisel, Chase L. and Gu, Zhen}, year={2015}, month={Aug}, pages={12029–12033} }
 @article{afroz_biliouris_boykin_kaznessis_beisel_2015, title={Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control}, volume={4}, ISSN={["2161-5063"]}, DOI={10.1021/sb400162z}, abstractNote={Titratable systems are common tools in metabolic engineering to tune the levels of enzymes and cellular components as part of pathway optimization. For nonmodel microorganisms with limited genetic tools, inducible sugar utilization pathways offer built-in titratable systems. However, these pathways can exhibit undesirable single-cell behaviors that hamper the uniform and tunable control of gene expression. Here, we applied mathematical modeling and single-cell measurements of l-arabinose utilization in Escherichia coli to systematically explore how sugar utilization pathways can be altered to achieve desirable inducible properties. We found that different pathway alterations, such as the removal of catabolism, constitutive expression of high-affinity or low-affinity transporters, or further deletion of the other transporters, came with trade-offs specific to each alteration. For instance, sugar catabolism improved the uniformity and linearity of the response at the cost of requiring higher sugar concentrations to induce the pathway. Within these alterations, we also found that a uniform and linear response could be achieved with a single alteration: constitutively expressing the high-affinity transporter. Equivalent modifications to the d-xylose utilization pathway yielded similar responses, demonstrating the applicability of our observations. Overall, our findings indicate that there is no ideal set of typical alterations when co-opting natural utilization pathways for titratable control and suggest design rules for manipulating these pathways to advance basic genetic studies and the metabolic engineering of microorganisms for optimized chemical production.}, number={2}, journal={ACS SYNTHETIC BIOLOGY}, author={Afroz, Taliman and Biliouris, Konstantinos and Boykin, Kelsey E. and Kaznessis, Yiannis and Beisel, Chase L.}, year={2015}, month={Feb}, pages={141–149} }
 @article{beisel_gomaa_barrangou_2014, title={A CRISPR design for next-generation antimicrobials}, volume={15}, ISSN={["1474-760X"]}, DOI={10.1186/s13059-014-0516-x}, abstractNote={Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance.}, number={11}, journal={GENOME BIOLOGY}, publisher={Springer Nature}, author={Beisel, Chase L. and Gomaa, Ahmed A. and Barrangou, Rodolphe}, year={2014} }
 @article{afroz_biliouris_kaznessis_beisel_2014, title={Bacterial sugar utilization gives rise to distinct single-cell behaviours}, volume={93}, ISSN={["1365-2958"]}, DOI={10.1111/mmi.12695}, abstractNote={Summary}, number={6}, journal={MOLECULAR MICROBIOLOGY}, author={Afroz, Taliman and Biliouris, Konstantinos and Kaznessis, Yiannis and Beisel, Chase L.}, year={2014}, month={Sep}, pages={1093–1103} }
 @article{beisel_bloom_smolke_2014, title={Construction of ligand-responsive microRNAs that operate through inhibition of Drosha processing}, volume={1111}, journal={Artificial riboswitches: methods and protocols}, author={Beisel, C. L. and Bloom, R. J. and Smolke, C. D.}, year={2014}, pages={259–267} }
 @article{briner_donohoue_gomaa_selle_slorach_nye_haurwitz_beisel_may_barrangou_2014, title={Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality}, volume={56}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2014.09.019}, abstractNote={The RNA-guided Cas9 endonuclease specifically targets and cleaves DNA in a sequence-dependent manner and has been widely used for programmable genome editing. Cas9 activity is dependent on interactions with guide RNAs, and evolutionarily divergent Cas9 nucleases have been shown to work orthogonally. However, the molecular basis of selective Cas9:guide-RNA interactions is poorly understood. Here, we identify and characterize six conserved modules within native crRNA:tracrRNA duplexes and single guide RNAs (sgRNAs) that direct Cas9 endonuclease activity. We show the bulge and nexus are necessary for DNA cleavage and demonstrate that the nexus and hairpins are instrumental in defining orthogonality between systems. In contrast, the crRNA:tracrRNA complementary region can be modified or partially removed. Collectively, our results establish guide RNA features that drive DNA targeting by Cas9 and open new design and engineering avenues for CRISPR technologies.}, number={2}, journal={MOLECULAR CELL}, publisher={Elsevier BV}, author={Briner, Alexandra E. and Donohoue, Paul D. and Gomaa, Ahmed A. and Selle, Kurt and Slorach, Euan M. and Nye, Christopher H. and Haurwitz, Rachel E. and Beisel, Chase L. and May, Andrew P. and Barrangou, Rodolphe}, year={2014}, month={Oct}, pages={333–339} }
 @article{gomaa_klumpe_luo_selle_barrangou_beisel_2014, title={Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems}, volume={5}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.00928-13}, abstractNote={ABSTRACT}, number={1}, journal={MBIO}, publisher={American Society for Microbiology}, author={Gomaa, Ahmed A. and Klumpe, Heidi E. and Luo, Michelle L. and Selle, Kurt and Barrangou, Rodolphe and Beisel, Chase L.}, year={2014} }
 @article{afroz_beisel_2013, title={Understanding and exploiting feedback in synthetic biology}, volume={103}, ISSN={["1873-4405"]}, DOI={10.1016/j.ces.2013.02.017}, abstractNote={Synthetic biology employs traditional engineering concepts in the construction of cells and organisms. One of the most fundamental concepts is feedback, where the activity of a system is influenced by its output. Feedback can imbue the system with a range of desirable properties such as reducing the rise time or exhibiting an ultrasensitive response. Feedback is also commonly found in nature, further supporting the incorporation of feedback into synthetic biological systems. In this review, we discuss the common attributes of negative and positive feedback loops in gene regulatory networks, whether alone or in combination, and describe recent applications of feedback in metabolic engineering, population control, and the development of advanced biosensors. The examples principally come from synthetic systems in the bacterium Escherichia coli and in the budding yeast Saccharomyces cerevisiae, the two major workhorses of synthetic biology. Through this review, we argue that biological feedback represents a powerful yet underutilized tool that can advance the construction of biological systems.}, journal={CHEMICAL ENGINEERING SCIENCE}, author={Afroz, Taliman and Beisel, Chase L.}, year={2013}, month={Nov}, pages={79–90} }
 @article{beisel_updegrove_janson_storz_2012, title={Multiple factors dictate target selection by Hfq-binding small RNAs}, volume={31}, ISSN={0261-4189}, url={http://dx.doi.org/10.1038/emboj.2012.52}, DOI={10.1038/emboj.2012.52}, abstractNote={Hfq-binding small RNAs (sRNAs) in bacteria modulate the stability and translational efficiency of target mRNAs through limited base-pairing interactions. While these sRNAs are known to regulate numerous mRNAs as part of stress responses, what distinguishes targets and non-targets among the mRNAs predicted to base pair with Hfq-binding sRNAs is poorly understood. Using the Hfq-binding sRNA Spot 42 of Escherichia coli as a model, we found that predictions using only the three unstructured regions of Spot 42 substantially improved the identification of previously known and novel Spot 42 targets. Furthermore, increasing the extent of base-pairing in single or multiple base-pairing regions improved the strength of regulation, but only for the unstructured regions of Spot 42. We also found that non-targets predicted to base pair with Spot 42 lacked an Hfq-binding site, folded into a secondary structure that occluded the Spot 42 targeting site, or had overlapping Hfq-binding and targeting sites. By modifying these features, we could impart Spot 42 regulation on non-target mRNAs. Our results thus provide valuable insights into the requirements for target selection by sRNAs.}, number={8}, journal={The EMBO Journal}, publisher={Wiley}, author={Beisel, Chase L and Updegrove, Taylor B and Janson, Ben J and Storz, Gisela}, year={2012}, month={Mar}, pages={1961–1974} }
 @article{beisel cl_yy_hoff kg_cd_2011, title={Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing}, volume={39}, number={7}, journal={Nucleic Acids Research}, author={Beisel CL, Chen and YY, Culler SJ and Hoff KG and CD, Smolke}, year={2011}, pages={2981–2994} }
 @article{beisel_storz_2011, title={Discriminating tastes: physiological contributions of the Hfq-binding small RNA Spot 42 to catabolite repression}, volume={8}, journal={RNA Biology}, author={Beisel, C. L. and Storz, G.}, year={2011}, pages={1–5} }
 @article{beisel_storz_2011, title={The Base-Pairing RNA Spot 42 Participates in a Multioutput Feedforward Loop to Help Enact Catabolite Repression in Escherichia coli}, volume={41}, ISSN={1097-2765}, url={http://dx.doi.org/10.1016/j.molcel.2010.12.027}, DOI={10.1016/j.molcel.2010.12.027}, abstractNote={Bacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base-pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse nonpreferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multioutput feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base-pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression.}, number={3}, journal={Molecular Cell}, publisher={Elsevier BV}, author={Beisel, Chase L. and Storz, Gisela}, year={2011}, month={Feb}, pages={286–297} }
 @article{cl_g_2011, title={The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli}, volume={41}, journal={Molecular Cell}, author={CL, Beisel and G, Storz}, year={2011}, pages={1–12} }
 @misc{beisel_storz_2010, title={Base pairing small RNAs and their roles in global regulatory networks}, volume={34}, ISSN={["0168-6445"]}, DOI={10.1111/j.1574-6976.2010.00241.x}, abstractNote={Bacteria use a range of RNA regulators collectively termed small RNAs (sRNAs) to help respond to changes in the environment. Many sRNAs regulate their target mRNAs through limited base-pairing interactions. Ongoing characterization of base-pairing sRNAs in bacteria has started to reveal how these sRNAs participate in global regulatory networks. These networks can be broken down into smaller regulatory circuits that have characteristic behaviors and functions. In this review, we describe the specific regulatory circuits that incorporate base-pairing sRNAs and the importance of each circuit in global regulation. Because most of these circuits were originally identified as network motifs in transcriptional networks, we also discuss why sRNAs may be used over protein transcription factors to help transduce environmental signals.}, number={5}, journal={FEMS MICROBIOLOGY REVIEWS}, author={Beisel, Chase L. and Storz, Gisela}, year={2010}, month={Sep}, pages={866–882} }
 @article{bayer ts_beisel cl_cd_2009, title={Conformational analysis of gossypol and its derivatives by molecular mechanics}, volume={3}, number={1}, journal={Journal of Molecular Structure [including Theochem]}, author={Bayer TS, Hoff KG and Beisel CL, Lee JJ and CD, Smolke}, year={2009} }
 @article{beisel_smolke_2009, title={Design Principles for Riboswitch Function}, volume={5}, ISSN={["1553-7358"]}, DOI={10.1371/journal.pcbi.1000363}, abstractNote={Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems. RNA provides a promising building block for the construction of tunable regulatory components based on its rich regulatory capacity and our current understanding of the sequence–function relationship. One prominent example of RNA-based regulatory components is riboswitches, genetic elements that mediate ligand control of gene expression through diverse regulatory mechanisms. While characterization of natural and synthetic riboswitches has revealed that riboswitch function can be modulated through sequence alteration, no quantitative frameworks exist to investigate or guide riboswitch tuning. Here, we combined mathematical modeling and experimental approaches to investigate the relationship between riboswitch function and performance. Model results demonstrated that the competition between reversible and irreversible rate constants dictates performance for different regulatory mechanisms. We also found that practical system restrictions, such as an upper limit on ligand concentration, can significantly alter the requirements for riboswitch performance, necessitating alternative tuning strategies. Previous experimental data for natural and synthetic riboswitches as well as experiments conducted in this work support model predictions. From our results, we developed a set of general design principles for synthetic riboswitches. Our results also provide a foundation from which to investigate how natural riboswitches are tuned to meet systems-level regulatory demands.}, number={4}, journal={PLOS COMPUTATIONAL BIOLOGY}, author={Beisel, Chase L. and Smolke, Christina D.}, year={2009}, month={Apr} }
 @article{beisel cl_hoff kg_cd_2008, title={Model-guided design of ligand-regulated RNAi for programmable control of gene expression}, volume={4}, journal={Molecular Systems Biology}, author={Beisel CL, Bayer TS and Hoff KG and CD, Smolke}, year={2008}, pages={224} }
 @article{beisel_bayer_hoff_smolke_2008, title={Model‐guided design of ligand‐regulated RNAi for programmable control of gene expression}, volume={4}, ISSN={1744-4292 1744-4292}, url={http://dx.doi.org/10.1038/msb.2008.62}, DOI={10.1038/msb.2008.62}, abstractNote={Progress in constructing biological networks will rely on the development of more advanced components that can be predictably modified to yield optimal system performance. We have engineered an RNA-based platform, which we call an shRNA switch, that provides for integrated ligand control of RNA interference (RNAi) by modular coupling of an aptamer, competing strand, and small hairpin (sh)RNA stem into a single component that links ligand concentration and target gene expression levels. A combined experimental and mathematical modelling approach identified multiple tuning strategies and moves towards a predictable framework for the forward design of shRNA switches. The utility of our platform is highlighted by the demonstration of fine-tuning, multi-input control, and model-guided design of shRNA switches with an optimized dynamic range. Thus, shRNA switches can serve as an advanced component for the construction of complex biological systems and offer a controlled means of activating RNAi in disease therapeutics.}, number={1}, journal={Molecular Systems Biology}, publisher={EMBO}, author={Beisel, Chase L and Bayer, Travis S and Hoff, Kevin G and Smolke, Christina D}, year={2008}, month={Jan}, pages={224} }
 @article{beisel_dowd_reilly_2005, title={Conformational analysis of gossypol and its derivatives by molecular mechanics}, volume={730}, ISSN={0166-1280}, url={http://dx.doi.org/10.1016/j.theochem.2005.05.010}, DOI={10.1016/j.theochem.2005.05.010}, abstractNote={Conformations and inversion pathways leading to racemization of all the tautomers of gossypol, gossypolone, anhydrogossypol, and a diethylamine Schiff's base of gossypol were investigated with MM3(2000). All forms have hindered rotation because of clashes between the methyl carbon atom and oxygen-containing moieties ortho to the bond linking the two naphthalene rings. Inversion energies generally agree with available experimental data. Gossypol preferentially inverts in its dihemiacetal tautomeric form through the cis pathway (where similar groups clash). Gossypolone inverts more easily than gossypol, and preferentially through the trans pathway (where dissimilar groups clash) when one of its outer rings has an enol-keto group and the other has an aldehyde group. Anhydrogossypol racemizes through the cis pathway. The bridge bond and the ortho exo-cyclic bonds in all the structures bend from planarity, and the inner naphthalene rings pucker to accommodate the inversion. For gossypol, the transition is achieved through greater bending of the exo-cyclic bonds (up to 12°) and less distortion of the inner benzyl rings (q≤0.34 Å), (up to 12.7°) . For gossypolone the transition occurs with greater distortion of the inner benzyl rings (q≤0.63 Å) and less out-of-plane bending (up to 8.4°). By isolating individual clashes, their contribution to the overall barrier can be analyzed, as shown for the dialdehyde tautomer of gossypol.}, number={1-3}, journal={Journal of Molecular Structure: THEOCHEM}, publisher={Elsevier BV}, author={Beisel, Chase L. and Dowd, Michael K. and Reilly, Peter J.}, year={2005}, month={Oct}, pages={51–58} }
 @article{beisel cl_pj_2005, title={Conformational analysis of gossypol and its derivatives by molecular mechanics}, volume={730}, journal={Journal of Molecular Structure}, author={Beisel CL, Dowd MK and PJ, Reilly}, year={2005}, pages={51–58} }