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

  • Myeloid lncRNA LOUP mediates opposing regulatory effects of RUNX1 and RUNX1-ETO in t(8;21) AML (vol 138 pg 1331, 2021) BLOOD Trinh, B. Q., Ummarino, S., Zhang, Y., Ebralidze, A. K., Bassal, M. A., Nguyen, T. M., Heller, G., Coffey, R., Tenen, D. E., van der Kouwe, E., Fabiani, E., Gurnari, C., Wu, C., Angarica, V., Yang, H., Chen, S., Zhang, H., Thurm, A. R., Marchi, F., Levantini, E., Staber, P. B., Zhang, P., Voso, M., Pandol, P., Kobayashi, S. S., Chai, L., Di Ruscio, A., Tenen, D. G. 2023; 141 (20): 2542
  • Myeloid lncRNA LOUP Mediates Opposing Regulatory Effects of RUNX1 and RUNX1-ETO in t(8;21) AML. Blood Trinh, B. Q., Ummarino, S. n., Zhang, Y. n., Ebralidze, A. K., Bassal, M. A., Nguyen, T. M., Heller, G. n., Coffey, R. n., Tenen, D. E., van der Kouwe, E. n., Fabiani, E. n., Gurnari, C. n., Wu, C. S., Espinosa Angarica, V. n., Yang, H. n., Chen, S. n., Zhang, H. n., Thurm, A. R., Marchi, F. n., Levantini, E. n., Staber, P. B., Zhang, P. n., Voso, M. T., Pandolfi, P. P., Kobayashi, S. S., Chai, L. n., Di Ruscio, A. n., Tenen, D. G. 2021


    The mechanism underlying cell type-specific gene induction conferred by ubiquitous transcription factors as well as disruptions caused by their chimeric derivatives in leukemia is not well understood. Here we investigate whether RNAs coordinate with transcription factors to drive myeloid gene transcription. In an integrated genome-wide approach surveying for gene loci exhibiting concurrent RNA- and DNA-interactions with the broadly expressed transcription factor RUNX1, we identified the long noncoding RNA LOUP. This myeloid-specific and polyadenylated lncRNA induces myeloid differentiation and inhibits cell growth, acting as a transcriptional inducer of the myeloid master regulator PU.1. Mechanistically, LOUP recruits RUNX1 to both the PU.1 enhancer and the promoter, leading to the formation of an active chromatin loop. In t(8;21) acute myeloid leukemia, wherein RUNX1 is fused to ETO, the resulting oncogenic fusion protein RUNX1-ETO limits chromatin accessibility at the LOUP locus, causing inhibition of LOUP and PU.1 expression. These findings highlight the important role of the interplay between cell type-specific RNAs and transcription factors as well as their oncogenic derivatives in modulating lineage-gene activation and raise the possibility that RNA regulators of transcription factors represent alternative targets for therapeutic development.

    View details for DOI 10.1182/blood.2020007920

    View details for PubMedID 33971010