This preprint reports that human lung epithelial A549 cells sustain intrinsic circadian clock rhythms and that infection with Sendai virus (SeV) progressively remodels circadian gene expression at the single-cell level. The authors identify copy-back viral genomes (cbVGs)—byproducts of negative-sense RNA virus replication—as primary drivers of this remodeling through innate immune signaling. Two separate sensing pathways mediate distinct components of the circadian response: the RIG-I adaptor MAVS is required for preferential induction of the BMAL1 paralog ARNTL2, whereas the double-stranded RNA sensor PKR is necessary for the cbVG-specific induction of the negative-feedback regulators NR1D1, NR1D2, and PER1. A similar cbVG-linked signature was observed with respiratory syncytial virus (RSV), indicating that cbVG-driven circadian reprogramming is not limited to SeV. Functional experiments show that ARNTL2 is required to amplify infection-driven transcriptional responses, selectively affecting expression of antiviral genes such as CCL5.
The authors show that A549 lung epithelial cells, a common in vitro model of airway epithelium, display sustained circadian rhythmicity when observed at single-cell resolution. Upon infection with SeV, these rhythms are progressively altered, indicating that viral infection can remodel the intrinsic timing machinery of individual epithelial cells. The remodeling is described as progressive and linked to innate immune activation rather than a generalized shutdown of clock function.
During replication of negative-sense RNA viruses, copy-back viral genomes (cbVGs) are generated and act as strong immunostimulatory species. In this work, cbVGs produced during SeV replication are implicated as the principal viral trigger that remodels circadian gene expression. The manuscript emphasizes that cbVG-driven innate immune signaling—not other forms of viral RNA or general replication stress—was primarily responsible for the observed circadian changes.
The circadian transcriptional changes driven by cbVGs depend on two mechanistically distinct innate sensing pathways. First, signaling through the RIG-I adaptor MAVS is required for the preferential induction of ARNTL2, a paralog of the core clock activator BMAL1. Second, detection by PKR, a double-stranded RNA sensor, is required for the cbVG-specific induction of negative-feedback clock regulators NR1D1, NR1D2, and PER1. These findings indicate a division of labor among innate sensors whereby different pathways selectively control subsets of clock genes in response to the same immunostimulatory viral species.
Using gain- and loss-of-function approaches, the authors demonstrate that ARNTL2 is functionally required to amplify the host transcriptional response to viral infection. ARNTL2 selectively affects the expression of specific antiviral genes; the study highlights CCL5 as one example of an antiviral effector whose induction depends on ARNTL2 activity. The data support a model in which cbVG-triggered MAVS signaling elevates ARNTL2, and ARNTL2 in turn potentiates subsets of antiviral transcriptional programs.
The authors report a similar cbVG-specific circadian gene signature during respiratory syncytial virus (RSV) infection, supporting the view that cbVG-driven circadian reprogramming is not unique to Sendai virus. This cross-virus observation suggests that cbVGs broadly produced during negative-sense RNA virus replication may commonly engage circadian regulatory pathways via innate immune sensing.
These results position innate immune signaling elicited by cbVGs as a selective driver of circadian clock gene expression during viral infection. The study identifies ARNTL2 as a previously unrecognized regulator of virus-induced host transcriptional responses and delineates distinct roles for MAVS and PKR in directing different arms of clock gene modulation. Together, the data suggest an integrated host response in which antiviral sensing reshapes circadian transcription in ways that may selectively modulate antiviral effector genes.
This summary is based on the preprint text provided. The article is explicitly noted as a preprint and has not been peer reviewed. Specific methodological details, quantitative metrics, sample sizes, exact time courses, and full experimental datasets are not included in the provided excerpt; those details are reported in the full preprint but are not reproduced here. Readers should consult the original preprint for experimental protocols, statistical analyses, and complete data before drawing definitive conclusions.