All Publications


  • 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

    Abstract

    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

  • 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

    Abstract

    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

  • Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens NATURE GENETICS Haney, M. S., Bohlen, C. J., Morgens, D. W., Ousey, J. A., Barkal, A. A., Tsui, C., Ego, B. K., Levin, R., Kamber, R. A., Collins, H., Tucker, A., Li, A., Vorselen, D., Labitigan, L., Crane, E., Boyle, E., Jiang, L., Chan, J., Rincon, E., Greenleaf, W. J., Li, B., Snyder, M. P., Weissman, I. L., Theriot, J. A., Collins, S. R., Barres, B. A., Bassik, M. C. 2018; 50 (12): 1716-+
  • Phagolysosome resolution requires contacts with the endoplasmic reticulum and phosphatidylinositol-4-phosphate signalling. Nature cell biology Levin-Konigsberg, R., Montano-Rendon, F., Keren-Kaplan, T., Li, R., Ego, B., Mylvaganam, S., DiCiccio, J. E., Trimble, W. S., Bassik, M. C., Bonifacino, J. S., Fairn, G. D., Grinstein, S. 2019

    Abstract

    Phosphoinositides have a pivotal role in the maturation of nascent phagosomes into microbicidal phagolysosomes. Following degradation of their contents, mature phagolysosomes undergo resolution, a process that remains largely uninvestigated. Here we studied the role of phosphoinositides in phagolysosome resolution. Phosphatidylinositol-4-phosphate (PtdIns(4)P), which is abundant in maturing phagolysosomes, was depleted as they tubulated and resorbed. Depletion was caused, in part, by transfer of phagolysosomal PtdIns(4)P to the endoplasmic reticulum, a process mediated by oxysterol-binding protein-related protein 1L (ORP1L), a RAB7 effector. ORP1L formed discrete tethers between the phagolysosome and the endoplasmic reticulum, resulting in distinct regions with alternating PtdIns(4)P depletion and enrichment. Tubules emerged from PtdIns(4)P-rich regions, where ADP-ribosylation factor-like protein 8B (ARL8B) and SifA- and kinesin-interacting protein/pleckstrin homology domain-containing family M member 2 (SKIP/PLEKHM2) accumulated. SKIP binds preferentially to monophosphorylated phosphoinositides, of which PtdIns(4)P is most abundant in phagolysosomes, contributing to their tubulation. Accordingly, premature hydrolysis of PtdIns(4)P impaired SKIP recruitment and phagosome resolution. Thus, resolution involves phosphoinositides and tethering of phagolysosomes to the endoplasmic reticulum.

    View details for DOI 10.1038/s41556-019-0394-2

    View details for PubMedID 31570833