Lacra Bintu is an Assistant Professor in the Bioengineering Department at Stanford. Her lab performs single-cell and high-throughput measurements of chromatin and gene regulation dynamics, and uses these data to develop predictive models and improve mammalian cell engineering.

Lacra started working on the theory of gene regulation as an undergraduate with Jané Kondev from Brandeis University and Rob Phillips from Caltech. As a Physics PhD student in the lab of Carlos Bustamante at U.C. Berkeley, she used single-molecule methods to tease apart the molecular mechanisms of transcription through nucleosomes. She transitioned to studying the dynamics of epigenetic regulation in live cells during her postdoctoral fellowship with Michael Elowitz at Caltech.

Academic Appointments

Honors & Awards

  • Maximizing Investigators' Research Award, NIH-NIGMS (2018-2023)
  • Career Award at the Scientific Interface, Burroughs Wellcome Fund (2015-2020)
  • Postdoctoral Fellowship, Jane Coffin Childs Memorial Fund for Medical Research (2011-2014)
  • Beckman Fellowship, California Institute of Technology (2011-2014)
  • Harold M. Weintraub Graduate Student Award, Fred Hutchinson Center (2011)
  • Outstanding Graduate Student Instructor Award, University of California, Berkeley (2006)
  • Doris Brewer Cohen Endowment Award for best senior thesis, Brandeis University (2005)
  • Wien International Scholarship, Brandeis University (2001-2005)

Professional Education

  • Postdoctoral Fellow, California Institute of Technology, Biology and Biological Engineering (2016)
  • Ph.D., University of California, Berkeley, Physics (2010)
  • B.S., Brandeis University, Physics, Mathematics, Neuroscience (2005)

2023-24 Courses

Graduate and Fellowship Programs

All Publications

  • High-throughput discovery and characterization of viral transcriptional effectors in human cells. Cell systems Ludwig, C. H., Thurm, A. R., Morgens, D. W., Yang, K. J., Tycko, J., Bassik, M. C., Glaunsinger, B. A., Bintu, L. 2023; 14 (6): 482


    Viruses encode transcriptional regulatory proteins critical for controlling viral and host gene expression. Given their multifunctional nature and high sequence divergence, it is unclear which viral proteins can affect transcription and which specific sequences contribute to this function. Using a high-throughput assay, we measured the transcriptional regulatory potential of over 60,000 protein tiles across 1,500 proteins from 11 coronaviruses and all nine human herpesviruses. We discovered hundreds of transcriptional effector domains, including a conserved repression domain in all coronavirus Spike homologs, dual activation-repression domains in viral interferon regulatory factors (VIRFs), and an activation domain in six herpesvirus homologs of the single-stranded DNA-binding protein that we show is important for viral replication and late gene expression in Kaposi's sarcoma-associated herpesvirus (KSHV). For the effector domains we identified, we investigated their mechanisms via high-throughput sequence and chemical perturbations, pinpointing sequence motifs essential for function. This work massively expands viral protein annotations, serving as a springboard for studying their biological and health implications and providing new candidates for compact gene regulation tools.

    View details for DOI 10.1016/j.cels.2023.05.008

    View details for PubMedID 37348463

  • CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping. Genome biology Marinov, G. K., Kim, S. H., Bagdatli, S. T., Higashino, S. I., Trevino, A. E., Tycko, J., Wu, T., Bintu, L., Bassik, M. C., He, C., Kundaje, A., Greenleaf, W. J. 2023; 24 (1): 85


    Detecting and mitigating off-target activity is critical to the practical application of CRISPR-mediated genome and epigenome editing. While numerous methods have been developed to map Cas9 binding specificity genome-wide, they are generally time-consuming and/or expensive, and not applicable to catalytically dead CRISPR enzymes. We have developed CasKAS, a rapid, inexpensive, and facile assay for identifying off-target CRISPR enzyme binding and cleavage by chemically mapping the unwound single-stranded DNA structures formed upon binding of a sgRNA-loaded Cas9 protein. We demonstrate this method in both in vitro and in vivo contexts.

    View details for DOI 10.1186/s13059-023-02930-z

    View details for PubMedID 37085898

    View details for PubMedCentralID PMC10120127

  • Large-scale mapping and mutagenesis of human transcriptional effector domains. Nature DelRosso, N., Tycko, J., Suzuki, P., Andrews, C., Mukund, A., Liongson, I., Ludwig, C., Spees, K., Fordyce, P., Bassik, M. C., Bintu, L. 2023


    Human gene expression is regulated by more than 2,000 transcription factors and chromatin regulators1,2. Effector domains within these proteins can activate or repress transcription. However, for many of these regulators we do not know what type of effector domains they contain, their location in the protein, their activation and repression strengths, and the sequences that are necessary for their functions. Here, we systematically measure the effector activity of more than 100,000 protein fragments tiling across most chromatin regulators and transcription factors in human cells (2,047 proteins). By testing the effect they have when recruited at reporter genes, we annotate 374 activation domains and 715 repression domains, roughly 80% of which are new and have not been previously annotated3-5. Rational mutagenesis and deletion scans across all the effector domains reveal aromatic and/or leucine residues interspersed with acidic, proline, serine and/or glutamine residues are necessary for activation domain activity. Furthermore, most repression domain sequences contain sites for small ubiquitin-like modifier (SUMO)ylation, short interaction motifs for recruiting corepressors or are structured binding domains for recruiting other repressive proteins. We discover bifunctional domains that can both activate and repress, some of which dynamically split a cell population into high- and low-expression subpopulations. Our systematic annotation and characterization of effector domains provide a rich resource for understanding the function of human transcription factors and chromatin regulators, engineering compact tools for controlling gene expression and refining predictive models of effector domain function.

    View details for DOI 10.1038/s41586-023-05906-y

    View details for PubMedID 37020022

    View details for PubMedCentralID 4494013

  • Single-Molecule Mapping of Chromatin Accessibility Using NOMe-seq/dSMF. Methods in molecular biology (Clifton, N.J.) Hinks, M., Marinov, G. K., Kundaje, A., Bintu, L., Greenleaf, W. J. 2023; 2611: 101-119


    The bulk of gene expression regulation in most organisms is accomplished through the action of transcription factors (TFs) on cis-regulatory elements (CREs). In eukaryotes, these CREs are generally characterized by nucleosomal depletion and thus higher physical accessibility of DNA. Many methods exploit this property to map regions of high average accessibility, and thus putative active CREs, in bulk. However, these techniques do not provide information about coordinated patterns of accessibility along the same DNA molecule, nor do they map the absolute levels of occupancy/accessibility. SMF (Single-Molecule Footprinting) fills these gaps by leveraging recombinant DNA cytosine methyltransferases (MTase) to mark accessible locations on individual DNA molecules. In this chapter, we discuss current methods and important considerations for performing SMF experiments.

    View details for DOI 10.1007/978-1-0716-2899-7_8

    View details for PubMedID 36807067

  • The sound of silence: Transgene silencing in mammalian cell engineering. Cell systems Cabera, A., Edelstein, H. I., Glykofrydis, F., Love, K. S., Palacios, S., Tycko, J., Zhang, M., Lensch, S., Shields, C. E., Livingston, M., Weiss, R., Zhao, H., Haynes, K. A., Morsut, L., Chen, Y. Y., Khalil, A. S., Wong, W. W., Collins, J. J., Rosser, S. J., Polizzi, K., Elowitz, M. B., Fussenegger, M., Hilton, I. B., Leonard, J. N., Bintu, L., Galloway, K. E., Deans, T. L. 2022; 13 (12): 950-973


    To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.

    View details for DOI 10.1016/j.cels.2022.11.005

    View details for PubMedID 36549273

  • Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nature biotechnology Durrant, M. G., Fanton, A., Tycko, J., Hinks, M., Chandrasekaran, S. S., Perry, N. T., Schaepe, J., Du, P. P., Lotfy, P., Bassik, M. C., Bintu, L., Bhatt, A. S., Hsu, P. D. 2022


    Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold and enabling the prediction of their insertion site specificities. We tested their recombination activity in human cells, classifying them as landing pad, genome-targeting or multi-targeting LSRs. Overall, we achieved up to seven-fold higher recombination than Bxb1 and genome integration efficiencies of 40-75% with cargo sizes over 7kb. We also demonstrate virus-free, direct integration of plasmid or amplicon libraries for improved functional genomics applications. This systematic discovery of recombinases directly from microbial sequencing data provides a resource of over 60 LSRs experimentally characterized in human cells for large-payload genome insertion without exposed DNA double-stranded breaks.

    View details for DOI 10.1038/s41587-022-01494-w

    View details for PubMedID 36217031

  • Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells. eLife Lensch, S., Herschl, M. H., Ludwig, C. H., Sinha, J., Hinks, M. M., Mukund, A., Fujimori, T., Bintu, L. 2022; 11


    In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation circuits. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by PRC2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.

    View details for DOI 10.7554/eLife.75115

    View details for PubMedID 35678392

  • Temporal signaling, population control, and information processing through chromatin-mediated gene regulation. Journal of theoretical biology Mukund, A., Bintu, L. 1800: 110977


    Chromatin regulation is a key pathway cells use to regulate gene expression in response to temporal stimuli, and is becoming widely used as a platform for synthetic biology applications. redHere, we build a mathematical framework for analyzing the response of genetic circuits containing chromatin regulators to temporal signals in mammalian cell populations. Chromatin regulators can silence genes in an all-or-none fashion at the single-cell level, with individual cells stochastically transitioning between active, reversibly silent, and irreversibly silent gene states at constant rates over time. redWe integrate this mode of regulation with classical gene regulatory motifs, such as autoregulatory and incoherent feedforward loops, to determine the types of responses achievable with duration-dependent signaling. We demonstrate that repressive regulators without long-term epigenetic memory can filter out high frequency noise, and as part of an autoregulatory loop can precisely tune the fraction of cells in a population that expresses a gene of interest. redAdditionally, we find that repressive regulators with epigenetic memory can sum up and encode the total duration of their recruitment in the fraction of cells irreversibly silenced and, when included in a feed forward loop, enable perfect adaptation. redLast, we use an information theoretic approach to show that all-or-none stochastic silencing can be used by populations to transmit information reliably and with high fidelity even in very simple genetic circuits. redAltogether, we show that chromatin-mediated gene control enables a repertoire of complex cell population responses to temporal signals and can transmit higher information levels than previously measured in gene regulation.

    View details for DOI 10.1016/j.jtbi.2021.110977

    View details for PubMedID 34919934

  • Nanobody-mediated control of gene expression and epigenetic memory. Nature communications Van, M. V., Fujimori, T. n., Bintu, L. n. 2021; 12 (1): 537


    Targeting chromatin regulators to specific genomic locations for gene control is emerging as a powerful method in basic research and synthetic biology. However, many chromatin regulators are large, making them difficult to deliver and combine in mammalian cells. Here, we develop a strategy for gene control using small nanobodies that bind and recruit endogenous chromatin regulators to a gene. We show that an antiGFP nanobody can be used to simultaneously visualize GFP-tagged chromatin regulators and control gene expression, and that nanobodies against HP1 and DNMT1 can silence a reporter gene. Moreover, combining nanobodies together or with other regulators, such as DNMT3A or KRAB, can enhance silencing speed and epigenetic memory. Finally, we use the slow silencing speed and high memory of antiDNMT1 to build a signal duration timer and recorder. These results set the basis for using nanobodies against chromatin regulators for controlling gene expression and epigenetic memory.

    View details for DOI 10.1038/s41467-020-20757-1

    View details for PubMedID 33483487

  • High-Throughput Discovery and Characterization of Human Transcriptional Effectors. Cell Tycko, J. n., DelRosso, N. n., Hess, G. T., Aradhana, n. n., Banerjee, A. n., Mukund, A. n., Van, M. V., Ego, B. K., Yao, D. n., Spees, K. n., Suzuki, P. n., Marinov, G. K., Kundaje, A. n., Bassik, M. C., Bintu, L. n. 2020


    Thousands of proteins localize to the nucleus; however, it remains unclear which contain transcriptional effectors. Here, we develop HT-recruit, a pooled assay where protein libraries are recruited to a reporter, and their transcriptional effects are measured by sequencing. Using this approach, we measure gene silencing and activation for thousands of domains. We find a relationship between repressor function and evolutionary age for the KRAB domains, discover that Homeodomain repressor strength is collinear with Hox genetic organization, and identify activities for several domains of unknown function. Deep mutational scanning of the CRISPRi KRAB maps the co-repressor binding surface and identifies substitutions that improve stability/silencing. By tiling 238 proteins, we find repressors as short as ten amino acids. Finally, we report new activator domains, including a divergent KRAB. These results provide a resource of 600 human proteins containing effectors and demonstrate a scalable strategy for assigning functions to protein domains.

    View details for DOI 10.1016/j.cell.2020.11.024

    View details for PubMedID 33326746

  • Mapping chromatin modifications at the single cell level. Development (Cambridge, England) Ludwig, C. H., Bintu, L. n. 2019; 146 (12)


    Understanding chromatin regulation holds enormous promise for controlling gene regulation, predicting cellular identity, and developing diagnostics and cellular therapies. However, the dynamic nature of chromatin, together with cell-to-cell heterogeneity in its structure, limits our ability to extract its governing principles. Single cell mapping of chromatin modifications, in conjunction with expression measurements, could help overcome these limitations. Here, we review recent advances in single cell-based measurements of chromatin modifications, including optimization to reduce DNA loss, improved DNA sequencing, barcoding, and antibody engineering. We also highlight several applications of these techniques that have provided insights into cell-type classification, mapping modification co-occurrence and heterogeneity, and monitoring chromatin dynamics.

    View details for DOI 10.1242/dev.170217

    View details for PubMedID 31249006

  • Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nature communications Tycko, J. n., Wainberg, M. n., Marinov, G. K., Ursu, O. n., Hess, G. T., Ego, B. K., Aradhana, n. n., Li, A. n., Truong, A. n., Trevino, A. E., Spees, K. n., Yao, D. n., Kaplow, I. M., Greenside, P. G., Morgens, D. W., Phanstiel, D. H., Snyder, M. P., Bintu, L. n., Greenleaf, W. J., Kundaje, A. n., Bassik, M. C. 2019; 10 (1): 4063


    Pooled CRISPR-Cas9 screens are a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we investigate Cas9, dCas9, and CRISPRi/a off-target activity in screens for essential regulatory elements. The sgRNAs with the largest effects in genome-scale screens for essential CTCF loop anchors in K562 cells were not single guide RNAs (sgRNAs) that disrupted gene expression near the on-target CTCF anchor. Rather, these sgRNAs had high off-target activity that, while only weakly correlated with absolute off-target site number, could be predicted by the recently developed GuideScan specificity score. Screens conducted in parallel with CRISPRi/a, which do not induce double-stranded DNA breaks, revealed that a distinct set of off-targets also cause strong confounding fitness effects with these epigenome-editing tools. Promisingly, filtering of CRISPRi libraries using GuideScan specificity scores removed these confounded sgRNAs and enabled identification of essential regulatory elements.

    View details for DOI 10.1038/s41467-019-11955-7

    View details for PubMedID 31492858

  • Advancing towards a global mammalian gene regulation model through single-cell analysis and synthetic biology Current Opinion in Biomedical Engineering Tycko, J., Van, M. V., Elowitz, M. B., Bintu, L. 2017; 4: 174-193