All Publications

  • High-throughput biochemical profiling reveals functional adaptation of a bacterial Argonaute. Molecular cell Ober-Reynolds, B., Becker, W. R., Jouravleva, K., Jolly, S. M., Zamore, P. D., Greenleaf, W. J. 2022


    Argonautes are nucleic acid-guided proteins that perform numerous cellular functions across all domains of life. Little is known about how distinct evolutionary pressures have shaped each Argonaute's biophysical properties. We applied high-throughput biochemistry to characterize how Thermus thermophilus Argonaute (TtAgo), a DNA-guided DNA endonuclease, finds, binds, and cleaves its targets. We found that TtAgo uses biophysical adaptations similar to those of eukaryotic Argonautes for rapid association but requires more extensive complementarity to achieve high-affinity target binding. Using these data, we constructed models for TtAgo association rates and equilibrium binding affinities that estimate the nucleic acid- and protein-mediated components of the target interaction energies. Finally, we showed that TtAgo cleavage rates vary widely based on the DNA guide, suggesting that only a subset of guides cleaves targets on physiologically relevant timescales.

    View details for DOI 10.1016/j.molcel.2022.02.026

    View details for PubMedID 35298909

  • Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. The Journal of experimental medicine Wilk, A. J., Lee, M. J., Wei, B., Parks, B., Pi, R., Martinez-Colon, G. J., Ranganath, T., Zhao, N. Q., Taylor, S., Becker, W., Stanford COVID-19 Biobank, Jimenez-Morales, D., Blomkalns, A. L., O'Hara, R., Ashley, E. A., Nadeau, K. C., Yang, S., Holmes, S., Rabinovitch, M., Rogers, A. J., Greenleaf, W. J., Blish, C. A. 2021; 218 (8)


    Our understanding of protective versus pathological immune responses to SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses revealed widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, including prominent hyperactivation signatures in neutrophils and NK cells. We also identified chromatin accessibility changes at NF-kappaB binding sites within cytokine gene loci as a potential mechanism for the striking lack of pro-inflammatory cytokine production observed in monocytes in severe and fatal COVID-19. We further demonstrated that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity-associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.

    View details for DOI 10.1084/jem.20210582

    View details for PubMedID 34128959

  • Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement. Science advances Boyle, E. A., Becker, W. R., Bai, H. B., Chen, J. S., Doudna, J. A., Greenleaf, W. J. 2021; 7 (8)


    The RNA-guided nuclease Cas9 has unlocked powerful methods for perturbing both the genome through targeted DNA cleavage and the regulome through targeted DNA binding, but limited biochemical data have hampered efforts to quantitatively model sequence perturbation of target binding and cleavage across diverse guide sequences. We present scalable, sequencing-based platforms for high-throughput filter binding and cleavage and then perform 62,444 quantitative binding and cleavage assays on 35,047 on- and off-target DNA sequences across 90 Cas9 ribonucleoproteins (RNPs) loaded with distinct guide RNAs. We observe that binding and cleavage efficacy, as well as specificity, vary substantially across RNPs; canonically studied guides often have atypically high specificity; sequence context surrounding the target modulates Cas9 on-rate; and Cas9 RNPs may sequester targets in nonproductive states that contribute to "proofreading" capability. Lastly, we distill our findings into an interpretable biophysical model that predicts changes in binding and cleavage for diverse target sequence perturbations.

    View details for DOI 10.1126/sciadv.abe5496

    View details for PubMedID 33608277

  • A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins MOLECULAR CELL Jarmoskaite, I., Denny, S. K., Vaidyanathan, P. P., Becker, W. R., Andreasson, J. L., Layton, C. J., Kappel, K., Shivashankar, V., Sreenivasan, R., Das, R., Greenleaf, W. J., Herschlag, D. 2019; 74 (5): 966-+
  • Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2 RNA Becker, W. R., Jarmoskaite, I., Vaidyanathan, P. P., Greenleaf, W. J., Herschlag, D. 2019; 25 (6): 702–12
  • High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2. Molecular cell Becker, W. R., Ober-Reynolds, B. n., Jouravleva, K. n., Jolly, S. M., Zamore, P. D., Greenleaf, W. J. 2019


    Argonaute proteins loaded with microRNAs (miRNAs) or small interfering RNAs (siRNAs) form the RNA-induced silencing complex (RISC), which represses target RNA expression. Predicting the biological targets, specificity, and efficiency of both miRNAs and siRNAs has been hamstrung by an incomplete understanding of the sequence determinants of RISC binding and cleavage. We applied high-throughput methods to measure the association kinetics, equilibrium binding energies, and single-turnover cleavage rates of RISC. We find that RISC readily tolerates insertions of up to 7 nt in its target opposite the central region of the guide. Our data uncover specific guide:target mismatches that enhance the rate of target cleavage, suggesting novel siRNA design strategies. Using these data, we derive quantitative models for RISC binding and target cleavage and show that our in vitro measurements and models predict knockdown in an engineered cellular system.

    View details for DOI 10.1016/j.molcel.2019.06.012

    View details for PubMedID 31324449

  • Biaxial mechanical properties of swine uterosacral and cardinal ligaments BIOMECHANICS AND MODELING IN MECHANOBIOLOGY Becker, W. R., De Vita, R. 2015; 14 (3): 549–60


    Mechanical alterations to pelvic floor ligaments may contribute to the development and progression of pelvic floor disorders. In this study, the first biaxial elastic and viscoelastic properties were determined for uterosacral ligament (USL) and cardinal ligament (CL) complexes harvested from adult female swine. Biaxial stress-stretch data revealed that the ligaments undergo large strains. They are orthotropic, being typically stiffer along their main physiological loading direction (i.e., normal to the upper vaginal wall). Biaxial stress relaxation data showed that the ligaments relax equally in both loading directions and more when they are less stretched. In order to describe the experimental findings, a three-dimensional constitutive law based on the Pipkin-Rogers integral series was formulated. The model accounts for incompressibility, large deformations, nonlinear elasticity, orthotropy, and stretch-dependent stress relaxation. This combined theoretical and experimental study provides new knowledge about the mechanical properties of USLs and CLs that could lead to the development of new preventive and treatment methods for pelvic floor disorders.

    View details for DOI 10.1007/s10237-014-0621-5

    View details for Web of Science ID 000354408100008

    View details for PubMedID 25218641