The general transcription factor TFIIB is a target for transcriptome control during cellular stress and viral infection.

Many stressors, including viral infection, induce a widespread suppression of cellular RNA polymerase II (RNAPII) transcription, yet the mechanisms underlying transcriptional repression are not well understood. Here we find that a crucial component of the RNA polymerase II holoenzyme, general transcription factor IIB (TFIIB), is targeted for post-translational turnover by two pathways, each of which contribute to its depletion during stress. Upon DNA damage, translational stress, apoptosis, or replication of the oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV), TFIIB is cleaved by activated caspase-3, leading to preferential downregulation of pro-survival genes. TFIIB is further targeted for rapid proteasome-mediated turnover by the E3 ubiquitin ligase TRIM28. KSHV counteracts proteasome-mediated turnover of TFIIB, thereby preserving a sufficient pool of TFIIB for transcription of viral genes. Thus, TFIIB may be a lynchpin for transcriptional outcomes during stress and a key target for nuclear replicating DNA viruses that rely on host transcriptional machinery. Significance Statement: Transcription by RNA polymerase II (RNAPII) synthesizes all cellular protein-coding mRNA. Many cellular stressors and viral infections dampen RNAPII activity, though the processes underlying this are not fully understood. Here we describe a two-pronged degradation strategy by which cells respond to stress by depleting the abundance of the key RNAPII general transcription factor, TFIIB. We further demonstrate that an oncogenic human gammaherpesvirus antagonizes this process, retaining enough TFIIB to support its own robust viral transcription. Thus, modulation of RNAPII machinery plays a crucial role in dictating the outcome of cellular perturbation.

Coding and non-coding elements comprise a regulatory network controlling transcription in Kaposi's sarcoma-associated herpesvirus.

Gene regulation in eukaryotes relies on many mechanisms for optimal expression, including both protein transcription factors and DNA regulatory elements. CRISPR-based screens of both protein coding genes and non-coding regions have allowed identification of these transcriptional networks in human cells. Double-stranded DNA viruses also invoke human-like regulation to control transcription of viral genes that are required at different stages of the viral lifecycle. Here, we applied CRISPR-based tools to dissect regulation of a viral gene at high resolution in the oncogenic human herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV), whose compact, densely encoded genome provides unique challenges and opportunities for studying transcriptional networks. Through a combination of CRISPR-interference (CRISPRi) and Cas9 nuclease screening, we mapped a novel regulatory network comprised of coding and noncoding elements that influence expression of the essential KSHV protein ORF68 at early and late stages of the viral lifecycle. ORF68 encodes an essential protein involved in packaging the replicated viral DNA into nascent capsids. Although ORF68 expression initiates early in the viral lifecycle, we found that it is primarily required at later times. This work demonstrates the ability to exhaustively identify features controlling a given locus, capturing a complete viral regulatory circuit that functions within the human nucleus to control transcription.

RNA polymerase II subunit modulation during viral infection and cellular stress.

Control of gene expression, including transcription, is central in dictating the outcome of viral infection. One of the profound alterations induced by viruses is modification to the integrity and function of eukaryotic RNA polymerase II (Pol II). Here, we discuss how infection perturbs the Pol II complex by altering subunit phosphorylation and turnover, as well as how cellular genotoxic stress (e.g. DNA damage) elicits similar outcomes. By highlighting emerging parallels and differences in Pol II control during viral infection and abiotic stress, we hope to bolster identification of pathways that target Pol II and regulate the transcriptome.

Cold shock induces a terminal investment reproductive response in C. elegans.

Challenges from environmental stressors have a profound impact on many life-history traits of an organism, including reproductive strategy. Examples across multiple taxa have demonstrated that maternal reproductive investment resulting from stress can improve offspring survival; a form of matricidal provisioning when death appears imminent is known as terminal investment. Here we report a reproductive response in the nematode Caenorhabditis elegans upon exposure to acute cold shock at 2 °C, whereby vitellogenic lipid movement from the soma to the germline appears to be massively upregulated at the expense of parental survival. This response is dependent on functional TAX-2; TAX-4 cGMP-gated channels that are part of canonical thermosensory mechanisms in worms and can be prevented in the presence of activated SKN-1/Nrf2, the master stress regulator. Increased maternal provisioning promotes improved embryonic cold shock survival, which is notably suppressed in animals with impaired vitellogenesis. These findings suggest that cold shock in C. elegans triggers terminal investment to promote progeny fitness at the expense of parental survival and may serve as a tractable model for future studies of stress-induced progeny plasticity.

Predicting the Future: Parental Progeny Investment in Response to Environmental Stress Cues.

Environmental stressors can severely limit the ability of an organism to reproduce as lifespan is decreased and resources are shifted away from reproduction to survival. Although this is often detrimental to the organism's reproductive fitness, certain other reproductive stress responses may mitigate this effect by increasing the likelihood of progeny survival in the F1 and subsequent generations. Here we review three means by which these progeny may be conferred a competitive edge as a result of stress encountered in the parental generation: heritable epigenetic modifications to nucleotides and histones, simple maternal investments of cytosolic components, and the partially overlapping phenomenon of terminal investment, which can entail extreme parental investment strategies in either cytosolic components or gamete production. We examine instances of these categories and their ability to subsequently impact offspring fitness and reproduction. Ultimately, without impacting nucleotide sequence, these more labile alterations may shape development, evolution, ecology and even human health, necessitating further understanding and research into the specific mechanisms by which environmental stressors are sensed and elicit a corresponding response in the parental germline.