Publications
2025
Interferon Dependent Immune Memory during HSV-1 Neuronal Latency Results in Increased H3K9me3 and Restriction of Reactivation by ATRX.
Krakowiak PA, Flores ME, Cuddy SR, Whitford AL, Dochnal SA, Babnis A, Miyake T, Tigano M, Engel DA, Cliffe AR. Co-option of mitochondrial nucleic acid-sensing pathways by HSV-1 UL12.5 for reactivation from latent infection. Proc Natl Acad Sci U S A. 2025 Jan 28;122(4):e2413965122. doi: 10.1073/pnas.2413965122. Epub 2025 Jan 24. PMID: 39854226; PMCID: PMC11789124.
2024
Dochnal SA, Krakowiak PA, Whitford AL, Cliffe AR. Physiological oxygen concentration during sympathetic primary neuron culture improves neuronal health and reduces HSV-1 reactivation. Microbiol Spectr. 2024 Nov 11;12(12):e0203124. doi: 10.1128/spectrum.02031-24. Epub ahead of print. PMID: 39526754; PMCID: PMC11619363.
Francois AK, Rohani A, Loftus M, Dochnal S, Hrit J, McFarlane S, Whitford A, Lewis A, Krakowiak P, Boutell C, Rothbart SB, Kashatus D, Cliffe AR. Single-genome analysis reveals a heterogeneous association of the herpes simplex virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts. mBio. 2024 Feb 27:e0327823. doi: 10.1128/mbio.03278-23. Epub ahead of print. PMID: 38411116.
Dochnal SA, Whitford AL, Francois AK, Krakowiak PA, Cuddy S, Cliffe AR. c-Jun signaling during initial HSV-1 infection modulates latency to enhance later reactivation in addition to directly promoting the progression to full reactivation. J Virol. 2024 Jan 9:e0176423. doi: 10.1128/jvi.01764-23. Epub ahead of print. PMID: 38193709.
2023
Zubković A, Gomes C, Parchure A, Cesarec M, Ferenčić A, Rokić F, Jakovac H, Whitford AL, Dochnal SA, Cliffe AR, Cuculić D, Gallo A, Vugrek O, Hackenberg M, Jurak I. HSV-1 miRNAs are post-transcriptionally edited in latently infected human ganglia. J Virol. 2023 Oct 31;97(10):e0073023. doi: 10.1128/jvi.00730-23. Epub 2023 Sep 15. PMID: 37712701; PMCID: PMC10617394.
Cuddy SR, Cliffe AR. The Intersection of Innate Immune Pathways with the Latent Herpes Simplex Virus Genome. J Virol. 2023 May 31;97(5):e0135222. doi: 10.1128/jvi.01352-22. Epub 2023 Apr 27. PMID: 37129520; PMCID: PMC10231182.
2022
Whitford AL, Cliffe AR. Key questions on the epigenetics of herpes simplex virus latency. PLoS Pathog. 2022 Jun 30;18(6):e1010587. doi: 10.1371/journal.ppat.1010587. PMID: 35772067.
Dochnal S, Merchant HY, Schinlever AR, Babnis A, Depledge DP, Wilson AC, Cliffe AR. DLK-Dependent Biphasic Reactivation of Herpes Simplex Virus Latency Established in the Absence of Antivirals. J Virol. 2022 Jun 22;96(12):e0050822. doi: 10.1128/jvi.00508-22. Epub 2022 May 24. PMID: 35608347
Whitford AL, Clinton CA, Kennedy EBL, Dochnal SA, Suzich JB, Cliffe AR. Ex Vivo Herpes Simplex Virus Reactivation Involves a Dual Leucine Zipper Kinase-Dependent Wave of Lytic Gene Expression That Is Independent of Histone Demethylase Activity and Viral Genome Synthesis. J Virol. 2022 Jun 22;96(12):e0047522. doi: 10.1128/jvi.00475-22. Epub 2022 May 23. PMID: 35604215.
2021
Dochnal, SA, Francois, AK. Cliffe AR. De Novo Polycomb Recruitment: Lessons from Latent Herpesviruses. Viruses 2021 13(8), 1470. PMID: 34452335.
Suzich JB, Cuddy SR, Baidas H, Dochnal S, Ke E, Schinlever AR, Babnis A, Boutell C, Cliffe AR. PML-NB-dependent type I interferon memory results in a restricted form of HSV latency. EMBO Rep. 2021 Sep 6;22(9):e52547. doi: 10.15252/embr.202152547. Epub 2021 Jul 1. PMID: 34197022.
2020
Cuddy S, Schinlever AR, Dochnal S, Suzich J, Kundu P, Downs TK, Farah M, Desai B, Boutell C, Cliffe AR. Neuronal hyperexcitability is a DLK-dependent trigger of HSV-1 reactivation that can be induced by IL-1. eLife 2020 Dec 22;9:e58037. doi: 10.7554/eLife.58037. PMID: 33350386
2019
Cliffe AR. DNA Damage Meets Neurotrophin Signaling: A Delicate Balancing AKT to Maintain Virus Latency. Molecular Cell. 2019 May 2;74(3):411-413. doi: 10.1016/j.molcel.2019.04.015. PMID 31051136
2018
Suzich JB, Cliffe AR. Strength in diversity: Understanding the pathways to herpes simplex virus reactivation. Virology. 2018 Jul 14;522:81-91. PubMed PMID: 30014861
2016
Cliffe AR, Wilson AC. Restarting Lytic Gene Transcription at the Onset of Herpes Simplex Virus Reactivation., 2016; Journal of Virology. 91(2) . PMID: 27807236 | PMCID: PMC5215350
Pre-2016 Publications
Cliffe AR, Arbuckle JH, Vogel JL, Geden MJ, Rothbart SB, Cusack CL, Strahl BD, Kristie TM, Deshmukh M. Neuronal Stress Pathway Mediating a Histone Methyl/Phospho Switch Is Required for Herpes Simplex Virus Reactivation., 2015; Cell host & microbe. 18(6) 649-58. PMID: 26651941 | PMCID: PMC4681005
Gama V, Swahari V, Schafer J, Kole AJ, Evans A, Huang Y, Cliffe A, Golitz B, Sciaky N, Pei XH, Xiong Y, Deshmukh M. The E3 ligase PARC mediates the degradation of cytosolic cytochrome c to promote survival in neurons and cancer cells., 2014; Science signaling. 7(334) ra67. PMID: 25028717 | PMCID: PMC4182917
Cliffe AR, Coen DM, Knipe DM. Kinetics of facultative heterochromatin and polycomb group protein association with the herpes simplex viral genome during establishment of latent infection., 2013; mBio. 4(1) . PMID: 23322639 | PMCID: PMC3551550
Cliffe AR, Garber DA, Knipe DM. Transcription of the herpes simplex virus latency-associated transcript promotes the formation of facultative heterochromatin on lytic promoters., 2009; Journal of Virology. 83(16) 8182-90. PMID: 19515781 | PMCID: PMC2715743
Hancock MH, Cliffe AR, Knipe DM, Smiley JR. Herpes simplex virus VP16, but not ICP0, is required to reduce histone occupancy and enhance histone acetylation on viral genomes in U2OS osteosarcoma cells., 2009; Journal of Virology. 84(3) 1366-75. PMID: 19939931 | PMCID: PMC2812316
Knipe DM, Cliffe A. Chromatin control of herpes simplex virus lytic and latent infection., 2008; Nature reviews. Microbiology. 6(3) 211-21. PMID: 18264117
Cliffe AR, Knipe DM. Herpes simplex virus ICP0 promotes both histone removal and acetylation on viral DNA during lytic infection., 2008; Journal of virology. 82(24) 12030-8. PMID: 18842720 | PMCID: PMC2593313