Yaara Finkel

All Publications

• Author Correction: Viral entry shapes HCMV latency establishment. Nature communications Kitsberg, Y., Nachshon, A., Arazi, T., Broennimann, K., Fisher, T., Wainstein, A., Finkel, Y., Stern-Ginossar, N., Schwartz, M. 2026; 17 (1)

  View details for DOI 10.1038/s41467-026-73127-8

  View details for PubMedID 42151170

  View details for PubMedCentralID PMC13184286

• Viral entry shapes HCMV latency establishment. Nature communications Kitsberg, Y., Nachshon, A., Arazi, T., Broennimann, K., Fisher, T., Wainstein, A., Finkel, Y., Stern-Ginossar, N., Schwartz, M. 2025

  Abstract

  Human cytomegalovirus (HCMV) infection results in either productive or latent infection, the latter enabling life-long viral persistence. Monocytes support latent infection but become permissive to productive infection upon differentiation into macrophages. These differentiation-driven differences have been largely attributed to chromatin-mediated repression of the viral genome. Using metabolic labeling of newly synthesized RNA, we observe markedly lower viral transcription at early stages of infection in monocytes compared to macrophages. Unbiased comparison reveals that this difference is partly explained by inefficient viral entry in monocytes: fewer viruses enter, and correspondingly, fewer genomes reach the nucleus. Indeed, ectopic expression of known HCMV entry receptors in monocytes enhances viral entry and enables productive infection, demonstrating that these cells can support full lytic replication if entry is efficient. We further identify integrin β3 as a differentiation-induced surface protein playing an important role in HCMV entry into macrophages, partially accounting for the observed differences in entry efficiency. Finally, we show that cells receiving fewer viral genomes are the ones that establish latent infection and have the capacity to reactivate. Overall, our findings reveal that entry is a previously unrecognized factor contributing to latent infection in monocytes, adding a critical layer to the paradigm of HCMV latency.

  View details for DOI 10.1038/s41467-025-68063-y

  View details for PubMedID 41457095

• High-throughput mapping of modular regulatory domains in human RNA-binding proteins. Cell systems Thurm, A. R., Finkel, Y., Andrews, C., Cai, X. S., Benko, C., Bintu, L. 2025: 101450

  Abstract

  RNA regulation is central to tuning gene expression and is controlled by thousands of RNA-binding proteins (RBPs). While many RBPs require their full sequence to function, some act through modular domains that recruit larger regulatory complexes. Mapping these RNA-regulatory effector domains is important for understanding RBP function and designing compact RNA regulators. We developed a high-throughput recruitment assay (HT-RNA-Recruit) to identify RNA-downregulatory effector domains within human RBPs. By recruiting over 30,000 protein tiles from 367 RBPs to a reporter mRNA, we discovered over 100 RNA-downregulatory effector domains in 86 RBPs. Certain domains-for instance, KRABs-suppress gene expression upon recruitment to both DNA and RNA. We engineered inducible synthetic RNA regulators based on NANOS that can downregulate endogenous RNAs or maintain reporter expression at defined intermediate levels, as predicted by mathematical modeling. This work serves as a resource for understanding RNA regulators and expands the repertoire of RNA control tools. A record of this paper's transparent peer review process is included in the supplemental information.

  View details for DOI 10.1016/j.cels.2025.101450

  View details for PubMedID 41330376

• Multidimensional analysis of host-virus interactions using the virus-encoded CRISPR-based direct readout system (VECOS). Nature protocols Lilja, A., Finkel, Y., Aharon, E., Nachshon, A., Schwartz, M., Stern-Ginossar, N. 2025

  Abstract

  CRISPR-Cas9 technology has transformed the study of gene function, enabling the systematic investigation of host-virus interactions. However, most CRISPR-based screens in the context of viral infections rely on cell survival as a readout, which limits their sensitivity and biases results toward early infection stages. To address these challenges, we developed the virus-encoded CRISPR-based direct readout system (VECOS), a virus-centric approach in which human cytomegalovirus is engineered to express single-guide RNA (sgRNA) libraries directly from its genome. This system allows sgRNA abundance, embedded in the viral genome, to serve as a direct and quantitative readout of gene-perturbation effects on viral propagation. By tracking sgRNA levels at distinct stages of the viral infection cycle, VECOS enables a detailed, multidimensional analysis of virus-host interactions. Here we present a modular detailed Protocol for (1) constructing and reconstituting complex sgRNA libraries in double-stranded DNA viruses using bacterial artificial chromosomes, (2) performing multipassage screens to investigate perturbation effects on various stages of viral infection and (3) analyzing the multipassage and multistage sgRNA abundance measurements utilizing a comprehensive framework for data analysis. Successful implementation of this full Protocol takes 14-22 weeks and requires proficiency in molecular biology, as well as basic familiarity with Unix-based computing and programming in R for data processing. This Protocol offers researchers a robust tool for uncovering the molecular mechanisms that drive viral propagation and host-virus interactions.

  View details for DOI 10.1038/s41596-025-01242-9

  View details for PubMedID 40983723

  View details for PubMedCentralID 8618713

• High-throughput discovery of regulatory effector domains in human RNA-binding proteins. bioRxiv : the preprint server for biology Thurm, A. R., Finkel, Y., Andrews, C., Cai, X. S., Benko, C., Bintu, L. 2024

  Abstract

  RNA regulation plays an integral role in tuning gene expression and is controlled by thousands of RNA-binding proteins (RBPs). We develop and use a high-throughput recruitment assay (HT-RNA-Recruit) to identify regulatory domains within human RBPs by recruiting over 30,000 protein tiles from 367 RBPs to a reporter mRNA. We discover over 100 unique RNA-regulatory effectors in 86 distinct RBPs, presenting evidence that RBPs contain functionally separable domains that dictate their post-transcriptional control of gene expression, and identify some with unique activity at 5' or 3'UTRs. We identify some domains that downregulate gene expression both when recruited to DNA and RNA, and dissect their mechanisms of regulation. Finally, we build a synthetic RNA regulator that can stably maintain gene expression at desired levels that are predictable by a mathematical model. This work serves as a resource for human RNA-regulatory effectors and expands the synthetic repertoire of RNA-based genetic control tools.Highlights: HT-RNA-Recruit identifies hundreds of RNA-regulatory effectors in human proteins.Recruitment to 5' and 3' UTRs identifies regulatory domains unique to each position.Some protein domains have both transcriptional and post-transcriptional regulatory activity.We develop a synthetic RNA regulator and a mathematical model to describe its behavior.

  View details for DOI 10.1101/2024.07.19.604317

  View details for PubMedID 39071298

• A virally encoded high-resolution screen of cytomegalovirus dependencies. Nature Finkel, Y., Nachshon, A., Aharon, E., Arazi, T., Simonovsky, E., Dobesova, M., Saud, Z., Gluck, A., Fisher, T., Stanton, R. J., Schwartz, M., Stern-Ginossar, N. 2024; 630 (8017): 712-719

  Abstract

  Genetic screens have transformed our ability to interrogate cellular factor requirements for viral infections1,2, but most current approaches are limited in their sensitivity, biased towards early stages of infection and provide only simplistic phenotypic information that is often based on survival of infected cells2-4. Here, by engineering human cytomegalovirus to express single guide RNA libraries directly from the viral genome, we developed virus-encoded CRISPR-based direct readout screening (VECOS), a sensitive, versatile, viral-centric approach that enables profiling of different stages of viral infection in a pooled format. Using this approach, we identified hundreds of host dependency and restriction factors and quantified their direct effects on viral genome replication, viral particle secretion and infectiousness of secreted particles, providing a multi-dimensional perspective on virus-host interactions. These high-resolution measurements reveal that perturbations altering late stages in the life cycle of human cytomegalovirus (HCMV) mostly regulate viral particle quality rather than quantity, establishing correct virion assembly as a critical stage that is heavily reliant on virus-host interactions. Overall, VECOS facilitates systematic high-resolution dissection of the role of human proteins during the infection cycle, providing a roadmap for in-depth study of host-herpesvirus interactions.

  View details for DOI 10.1038/s41586-024-07503-z

  View details for PubMedID 38839957

• Parsing the role of NSP1 in SARS-CoV-2 infection CELL REPORTS Fisher, T., Gluck, A., Narayanan, K., Kuroda, M., Nachshon, A., Hsu, J. C., Halfmann, P. J., Yahalom-Ronen, Y., Tamir, H., Finkel, Y., Schwartz, M., Weiss, S., Tseng, C. K., Israely, T., Paran, N., Kawaoka, Y., Makino, S., Stern-Ginossar, N. 2022; 39 (11): 110954

  Abstract

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leads to shutoff of protein synthesis, and nsp1, a central shutoff factor in coronaviruses, inhibits cellular mRNA translation. However, the diverse molecular mechanisms employed by nsp1 as well as its functional importance are unresolved. By overexpressing various nsp1 mutants and generating a SARS-CoV-2 mutant, we show that nsp1, through inhibition of translation and induction of mRNA degradation, targets translated cellular mRNA and is the main driver of host shutoff during infection. The propagation of nsp1 mutant virus is inhibited exclusively in cells with intact interferon (IFN) pathway as well as in vivo, in hamsters, and this attenuation is associated with stronger induction of type I IFN response. Therefore, although nsp1's shutoff activity is broad, it plays an essential role, specifically in counteracting the IFN response. Overall, our results reveal the multifaceted approach nsp1 uses to shut off cellular protein synthesis and uncover nsp1's explicit role in blocking the IFN response.

  View details for DOI 10.1016/j.celrep.2022.110954

  View details for Web of Science ID 000830949100005

  View details for PubMedID 35671758

  View details for PubMedCentralID PMC9133101

• Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2 NATURE COMMUNICATIONS Israeli, M., Finkel, Y., Yahalom-Ronen, Y., Paran, N., Chitlaru, T., Israeli, O., Cohen-Gihon, I., Aftalion, M., Falach, R., Rotem, S., Elia, U., Nemet, I., Kliker, L., Mandelboim, M., Beth-Din, A., Israely, T., Cohen, O., Stern-Ginossar, N., Bercovich-Kinori, A. 2022; 13 (1): 2237

  Abstract

  The global spread of SARS-CoV-2 led to major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SARS-CoV-2 can provide insights into the virus pathogenesis, and facilitate the development of novel therapeutics. Here, employing a genome-scale CRISPR screen, we provide a comprehensive data-set of cellular factors that are exploited by wild type SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. We identified several host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination, Heparan sulfate biogenesis and host phosphatidylglycerol biosynthesis. Comparative analysis of the different VOCs revealed the host factors KREMEN2 and SETDB1 as potential unique candidates required only to the Alpha variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential proviral gene for all variants inspected. We show that GATA6 directly regulates ACE2 transcription and accordingly, is critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals shows elevated levels of GATA6, suggesting a role in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 resulted in down-modulation of ACE2 and inhibition of viral infectivity. Overall, we show GATA6 may represent a target for the development of anti-SARS-CoV-2 therapeutic strategies and reaffirm the value of the CRISPR loss-of-function screens in providing a list of potential new targets for therapeutic interventions.

  View details for DOI 10.1038/s41467-022-29896-z

  View details for Web of Science ID 000787388900008

  View details for PubMedID 35469023

  View details for PubMedCentralID PMC9039069

• SARS-CoV-2 uses a multipronged strategy to impede host protein synthesis NATURE Finkel, Y., Gluck, A., Nachshon, A., Winkler, R., Fisher, T., Rozman, B., Mizrahi, O., Lubelsky, Y., Zuckerman, B., Slobodin, B., Yahalom-Ronen, Y., Tamir, H., Ulitsky, I., Israely, T., Paran, N., Schwartz, M., Stern-Ginossar, N. 2021; 594 (7862): 240-+

  Abstract

  The coronavirus SARS-CoV-2 is the cause of the ongoing pandemic of COVID-191. Coronaviruses have developed a variety of mechanisms to repress host mRNA translation to allow the translation of viral mRNA, and concomitantly block the cellular innate immune response2,3. Although several different proteins of SARS-CoV-2 have previously been implicated in shutting off host expression4-7, a comprehensive picture of the effects of SARS-CoV-2 infection on cellular gene expression is lacking. Here we combine RNA sequencing, ribosome profiling and metabolic labelling of newly synthesized RNA to comprehensively define the mechanisms that are used by SARS-CoV-2 to shut off cellular protein synthesis. We show that infection leads to a global reduction in translation, but that viral transcripts are not preferentially translated. Instead, we find that infection leads to the accelerated degradation of cytosolic cellular mRNAs, which facilitates viral takeover of the mRNA pool in infected cells. We reveal that the translation of transcripts that are induced in response to infection (including innate immune genes) is impaired. We demonstrate this impairment is probably mediated by inhibition of nuclear mRNA export, which prevents newly transcribed cellular mRNA from accessing ribosomes. Overall, our results uncover a multipronged strategy that is used by SARS-CoV-2 to take over the translation machinery and to suppress host defences.

  View details for DOI 10.1038/s41586-021-03610-3

  View details for Web of Science ID 000657238000001

  View details for PubMedID 33979833

• Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution VIROLOGY Jungreis, I., Nelson, C. W., Ardern, Z., Finkel, Y., Krogan, N. J., Sato, K., Ziebuhr, J., Stern-Ginossar, N., Pavesi, A., Firth, A. E., Gorbalenya, A. E., Kellis, M. 2021; 558: 145-151

  Abstract

  At least six small alternative-frame open reading frames (ORFs) overlapping well-characterized SARS-CoV-2 genes have been hypothesized to encode accessory proteins. Researchers have used different names for the same ORF or the same name for different ORFs, resulting in erroneous homological and functional inferences. We propose standard names for these ORFs and their shorter isoforms, developed in consultation with the Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. We recommend calling the 39 codon Spike-overlapping ORF ORF2b; the 41, 57, and 22 codon ORF3a-overlapping ORFs ORF3c, ORF3d, and ORF3b; the 33 codon ORF3d isoform ORF3d-2; and the 97 and 73 codon Nucleocapsid-overlapping ORFs ORF9b and ORF9c. Finally, we document conflicting usage of the name ORF3b in 32 studies, and consequent erroneous inferences, stressing the importance of reserving identical names for homologs. We recommend that authors referring to these ORFs provide lengths and coordinates to minimize ambiguity caused by prior usage of alternative names.

  View details for DOI 10.1016/j.virol.2021.02.013

  View details for Web of Science ID 000637394600006

  View details for PubMedID 33774510

  View details for PubMedCentralID PMC7967279

• The coding capacity of SARS-CoV-2 NATURE Finkel, Y., Mizrahi, O., Nachshon, A., Weingarten-Gabbay, S., Morgenstern, D., Yahalom-Ronen, Y., Tamir, H., Achdout, H., Stein, D., Israeli, O., Beth-Din, A., Melamed, S., Weiss, S., Israely, T., Paran, N., Schwartz, M., Stern-Ginossar, N. 2021; 589 (7840): 125-U254

  Abstract

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic1. To understand the pathogenicity and antigenic potential of SARS-CoV-2 and to develop therapeutic tools, it is essential to profile the full repertoire of its expressed proteins. The current map of SARS-CoV-2 coding capacity is based on computational predictions and relies on homology with other coronaviruses. As the protein complement varies among coronaviruses, especially in regard to the variety of accessory proteins, it is crucial to characterize the specific range of SARS-CoV-2 proteins in an unbiased and open-ended manner. Here, using a suite of ribosome-profiling techniques2-4, we present a high-resolution map of coding regions in the SARS-CoV-2 genome, which enables us to accurately quantify the expression of canonical viral open reading frames (ORFs) and to identify 23 unannotated viral ORFs. These ORFs include upstream ORFs that are likely to have a regulatory role, several in-frame internal ORFs within existing ORFs, resulting in N-terminally truncated products, as well as internal out-of-frame ORFs, which generate novel polypeptides. We further show that viral mRNAs are not translated more efficiently than host mRNAs; instead, virus translation dominates host translation because of the high levels of viral transcripts. Our work provides a resource that will form the basis of future functional studies.

  View details for DOI 10.1038/s41586-020-2739-1

  View details for Web of Science ID 000585787500001

  View details for PubMedID 32906143

• Comprehensive annotations of human herpesvirus 6A and 6B genomes reveal novel and conserved genomic features ELIFE Finkel, Y., Schmiedel, D., Tai-Schmiedel, J., Nachshon, A., Winkler, R., Dobesova, M., Schwartz, M., Mandelboim, O., Stern-Ginossar, N. 2020; 9

  Abstract

  Human herpesvirus-6 (HHV-6) A and B are ubiquitous betaherpesviruses, infecting the majority of the human population. They encompass large genomes and our understanding of their protein coding potential is far from complete. Here, we employ ribosome-profiling and systematic transcript-analysis to experimentally define HHV-6 translation products. We identify hundreds of new open reading frames (ORFs), including upstream ORFs (uORFs) and internal ORFs (iORFs), generating a complete unbiased atlas of HHV-6 proteome. By integrating systematic data from the prototypic betaherpesvirus, human cytomegalovirus, we uncover numerous uORFs and iORFs conserved across betaherpesviruses and we show uORFs are enriched in late viral genes. We identified three highly abundant HHV-6 encoded long non-coding RNAs, one of which generates a non-polyadenylated stable intron appearing to be a conserved feature of betaherpesviruses. Overall, our work reveals the complexity of HHV-6 genomes and highlights novel features conserved between betaherpesviruses, providing a rich resource for future functional studies.

  View details for DOI 10.7554/eLife.50960

  View details for Web of Science ID 000508130800001

  View details for PubMedID 31944176

  View details for PubMedCentralID PMC6964970