Author Correction: CTCF interacts with the lytic HSV-1 genome to promote viral transcription (Scientific Reports, (2017), 7, 1, (39861), 10.1038/srep39861);CTCF interacts with the lytic HSV-1 genome to promote viral transcription

Scientific Reports

Volumn 7, Issue , 2017, Pages

  Lang, Fengchao ^a,b   Li, Xin ^a,b   Vladimirova, Olga ^c   Hu, Benxia ^a,b   Chen, Guijun ^a   Xiao, Yu ^a   Singh, Vikrant ^c   Lu, Danfeng ^a,b   Li, Lihong ^a   Han, Hongbo ^d   Wickramasinghe, J M A S P ^c   Smith, Sheryl T ^e   Zheng, Chunfu ^f,g   Li, Qihan ^h   Lieberman, Paul M ^c   Fraser, Nigel W ⁱ   Zhou, Jumin ^a  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c WISTAR INSTITUTE   (United States)

^d PANZHIHUA UNIVERSITY   (China)

^e ARCADIA UNIVERSITY   (United States)

^f SOOCHOW UNIVERSITY   (China)

^g UNIVERSITY OF CALGARY   (Canada)

^h INSTITUTE OF MEDICAL BIOLOGY   (China)

ⁱ UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; PROTEIN BINDING; RNA POLYMERASE II; TRANSCRIPTION FACTOR CTCF; VIRUS RNA;

ANIMAL; CHLOROCEBUS AETHIOPS; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENETIC TRANSCRIPTION; GENETICS; HEK293 CELL LINE; HELA CELL LINE; HUMAN; HUMAN ALPHAHERPESVIRUS 1; METABOLISM; PATHOGENICITY; VERO CELL LINE; VIRUS GENOME; VIRUS REPLICATION;

ANIMALS; CCCTC-BINDING FACTOR; CERCOPITHECUS AETHIOPS; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENOME, VIRAL; HEK293 CELLS; HELA CELLS; HERPESVIRUS 1, HUMAN; HISTONES; HUMANS; PROTEIN BINDING; RNA POLYMERASE II; RNA, VIRAL; TRANSCRIPTION, GENETIC; VERO CELLS; VIRUS REPLICATION;

EID: 85007610427     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-021-84469-2     Document Type: Erratum

References (76)

1. Bell, A. C., West, A. G. & Felsenfeld, G. The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 98, 387-96 (1999).
2. Didych, D. A., Kotova, E. S., Akopov, S. B., Nikolaev, L. G. & Sverdlov, E. D. DNA fragments binding CTCF in vitro and in vivo are capable of blocking enhancer activity. BMC Res Notes 5, 178 (2012).
3. Phillips, J. E. & Corces, V. G. CTCF: master weaver of the genome. Cell 137, 1194-211 (2009).
4. Yusufzai, T. M., Tagami, H., Nakatani, Y. & Felsenfeld, G. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol Cell 13, 291-8 (2004).
5. Cho, D. H. et al. Antisense transcription and heterochromatin at the DM1 CTG repeats are constrained by CTCF. Mol Cell 20, 483-9 (2005).
6. Guo, Y. et al. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell 162, 900-10 (2015).
7. Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74-9 (2011).
8. Chernukhin, I. et al. CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Mol Cell Biol 27, 1631-48 (2007).
9. Ong, C. T. & Corces, V. G. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 15, 234-46 (2014).
10. Rowley, M. J. & Corces, V. G. The three-dimensional genome: principles and roles of long-distance interactions. Current Opinion in Cell Biology 40, 8-14 (2016).
11. Kim, T. H. et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128, 1231-45 (2007).
12. Tang, Z. et al. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell 163, 1611-27 (2015).
13. Chen, H. S. et al. Epigenetic deregulation of the LMP1/LMP2 locus of Epstein-Barr virus by mutation of a single CTCF-cohesin binding site. J Virol 88, 1703-13 (2014).
14. Kang, H., Wiedmer, A., Yuan, Y., Robertson, E. & Lieberman, P. M. Coordination of KSHV Latent and Lytic Gene Control by CTCFCohesin Mediated Chromosome Conformation. PLoS Pathog 7 (2011).
15. Komatsu, T., Sekiya, T. & Nagata, K. DNA replication-dependent binding of CTCF plays a critical role in adenovirus genome functions. Sci Rep 3, 2187 (2013).
16. Li, D. J., Verma, D., Mosbruger, T. & Swaminathan, S. CTCF and Rad21 Act as Host Cell Restriction Factors for Kaposi's Sarcoma-Associated Herpesvirus ( KSHV) Lytic Replication by Modulating Viral Gene Transcription. PLoS Pathog 10 (2014).
17. Martinez, F. P. et al. CTCF Binding to the First Intron of the Major Immediate Early (MIE) Gene of Human Cytomegalovirus (HCMV) Negatively Regulates MIE Gene Expression and HCMV Replication. J Virol 88, 7389-7401 (2014).
18. Portal, D. et al. Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2. Proc Natl Acad Sci USA 110, 18537-42 (2013).
19. Holdorf, M. M., Cooper, S. B., Yamamoto, K. R. & Miranda, J. J. Occupancy of chromatin organizers in the Epstein-Barr virus genome. Virology 415, 1-5 (2011).
20. Chen, Q. et al. CTCF-dependent chromatin boundary element between the latency-associated transcript and ICP0 promoters in the herpes simplex virus type 1 genome. J Virol 81, 5192-201 (2007).
21. Amelio, A. L., McAnany, P. K. & Bloom, D. C. A chromatin insulator-like element in the herpes simplex virus type 1 latencyassociated transcript region binds CCCTC-binding factor and displays enhancer-blocking and silencing activities. Journal of Virology 80, 2358-68 (2006).
22. Ertel, M. K., Cammarata, A. L., Hron, R. J. & Neumann, D. M. CTCF occupation of the herpes simplex virus 1 genome is disrupted at early times postreactivation in a transcription-dependent manner. J Virol 86, 12741-59 (2012).
23. Tempera, I., Klichinsky, M. & Lieberman, P. M. EBV Latency Types Adopt Alternative Chromatin Conformations. PLoS Pathog 7 (2011).
24. Pentland, I. & Parish, J. L. Targeting CTCF to Control Virus Gene Expression: A Common Theme amongst Diverse DNA Viruses. Viruses 7, 3574-85 (2015).
25. Jenkins, H. L. & Spencer, C. A. RNA polymerase II holoenzyme modifications accompany transcription reprogramming in herpes simplex virus type 1-infected cells. J Virol 75, 9872-84 (2001).
26. Oh, H. S. et al. A Targeted RNA Interference Screen Reveals Novel Epigenetic Factors That Regulate Herpesviral Gene Expression. MBio 5 (2014).
27. Abrisch, R. G., Eidem, T. M., Yakovchuk, P., Kugel, J. F. & Goodrich, J. A. Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. J Virol 90, 2503-13 (2015).
28. Fraser, K. A. & Rice, S. A. Herpes simplex virus immediate-early protein ICP22 triggers loss of serine 2-phosphorylated RNA polymerase II. J Virol 81, 5091-101 (2007).
29. Bastian, T. W. & Rice, S. A. Identification of Sequences in Herpes Simplex Virus Type 1 ICP22 That Influence RNA Polymerase II Modification and Viral Late Gene Expression. J Virol 83, 128-139 (2009).
30. Ou, M. & Sandri-Goldin, R. M. Inhibition of cdk9 during herpes simplex virus 1 infection impedes viral transcription. PLoS One 8, e79007 (2013).
31. Oh, J., Ruskoski, N. & Fraser, N. W. Chromatin assembly on herpes simplex virus 1 DNA early during a lytic infection is Asf1a dependent. J Virol 86, 12313-21 (2012).
32. Kent, J. R. et al. During lytic infection herpes simplex virus type 1 is associated with histones bearing modifications that correlate with active transcription. J Virol 78, 10178-86 (2004).
33. Placek, B. J. et al. The histone variant H3.3 regulates gene expression during lytic infection with herpes simplex virus type 1. J Virol 83, 1416-21 (2009).
34. Kalamvoki, M. & Roizman, B. The histone acetyltransferase CLOCK is an essential component of the herpes simplex virus 1 transcriptome that includes TFIID, ICP4, ICP27, and ICP22. J Virol 85, 9472-7 (2011).
35. Wang, L., Grossman, S. R. & Kieff, E. Epstein-Barr virus nuclear protein 2 interacts with p300, CBP, and PCAF histone acetyltransferases in activation of the LMP1 promoter. Proc Natl Acad Sci USA 97, 430-5 (2000).
36. Liang, Y. et al. A novel selective LSD1/KDM1A inhibitor epigenetically blocks herpes simplex virus lytic replication and reactivation from latency. MBio 4, e00558-12 (2013).
37. Phelan, A., Dunlop, J., Patel, A. H., Stow, N. D. & Clements, J. B. Nuclear sites of herpes simplex virus type 1 DNA replication and transcription colocalize at early times postinfection and are largely distinct from RNA processing factors. J Virol 71, 1124-32 (1997).
38. Chang, L. et al. Herpesviral replication compartments move and coalesce at nuclear speckles to enhance export of viral late mRNA. Proc Natl Acad Sci USA 108, E136-E144 (2011).
39. Everett, R. D. The spatial organization of DNA virus genomes in the nucleus. PLoS Pathog 9, e1003386 (2013).
40. Bloom, D. C., Giordani, N. V. & Kwiatkowski, D. L. Epigenetic regulation of latent HSV-1 gene expression. Biochim Biophys Acta 1799, 246-56 (2010).
41. Wagner, L. M., Bayer, A. & Deluca, N. A. Requirement of the N-terminal activation domain of herpes simplex virus ICP4 for viral gene expression. J Virol 87, 1010-8 (2013).
42. Mohni, K. N., Smith, S., Dee, A. R., Schumacher, A. J. & Weller, S. K. Herpes simplex virus type 1 single strand DNA binding protein and helicase/primase complex disable cellular ATR signaling. PLoS Pathog 9, e1003652 (2013).
43. Liu, X., Brutlag, D. L. & Liu, J. S. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput, 127-38 (2001).
44. Hou, C., Dale, R. & Dean, A. Cell type specificity of chromatin organization mediated by CTCF and cohesin. Proc Natl Acad Sci USA 107, 3651-6 (2010).
45. Mendez-Catala, C. F. et al. A novel mechanism for CTCF in the epigenetic regulation of Bax in breast cancer cells. Neoplasia 15, 898-912 (2013).
46. Lilley, C. E., Carson, C. T., Muotri, A. R., Gage, F. H. & Weitzman, M. D. DNA repair proteins affect the lifecycle of herpes simplex virus 1. Proc Natl Acad Sci USA 102, 5844-9 (2005).
47. Silva, L., Cliffe, A., Chang, L. & Knipe, D. M. Role for A-type lamins in herpesviral DNA targeting and heterochromatin modulation. PLoS Pathog 4, e1000071 (2008).
48. Lium, E. K., Panagiotidis, C. A., Wen, X. & Silverstein, S. Repression of the alpha0 gene by ICP4 during a productive herpes simplex virus infection. J Virol 70, 3488-96 (1996).
49. Shu, M., Taddeo, B., Zhang, W. R. & Roizman, B. Selective degradation of mRNAs by the HSV host shutoff RNase is regulated by the U(L)47 tegument protein. Proceedings of the National Academy of Sciences of the United States of America 110, E1669-E1675 (2013).
50. Cliffe, A. R., Garber, D. A. & Knipe, D. M. Transcription of the herpes simplex virus latency-associated transcript promotes the formation of facultative heterochromatin on lytic promoters. Journal of Virology 83, 8182-90 (2009).
51. Egloff, S. & Murphy, S. Cracking the RNA polymerase II CTD code. Trends Genet 24, 280-8 (2008).
52. Jonkers, I. & Lis, J. T. Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 16, 167-77 (2015).
53. Hsin, J. P. & Manley, J. L. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 26, 2119-37 (2012).
54. Moore, J. M. et al. Loss of Maternal CTCF Is Associated with Peri-Implantation Lethality of Ctcf Null Embryos. PLoS One 7 (2012).
55. Heath, H. et al. CTCF regulates cell cycle progression of alphabeta T cells in the thymus. EMBO J 27, 2839-50 (2008).
56. Xiao, T., Wongtrakoongate, P., Trainor, C. & Felsenfeld, G. CTCF Recruits Centromeric Protein CENP-E to the Pericentromeric/Centromeric Regions of Chromosomes through Unusual CTCF-Binding Sites. Cell Rep 12, 1704-14 (2015).
57. Zuin, J. et al. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci USA 111, 996-1001 (2014).
58. Hughes, D. J. et al. Contributions of CTCF and DNA methyltransferases DNMT1 and DNMT3B to Epstein-Barr virus restricted latency. J Virol 86, 1034-45 (2012).
59. Tempera, I. & Lieberman, P. M. Epigenetic regulation of EBV persistence and oncogenesis. Semin Cancer Biol 26, 22-9 (2014).
60. Liang, Y., Vogel, J. L., Narayanan, A., Peng, H. & Kristie, T. M. Inhibition of the histone demethylase LSD1 blocks alpha-herpesvirus lytic replication and reactivation from latency. Nat Med 15, 1312-7 (2009).
61. Roizman, B. & Whitley, R. J. An Inquiry into the Molecular Basis of HSV Latency and Reactivation. Annual Review of Microbiology 67, 355-374 (2013).
62. Dai-Ju, J. Q., Li, L., Johnson, L. A. & Sandri-Goldin, R. M. ICP27 interacts with the C-terminal domain of RNA polymerase II and facilitates its recruitment to herpes simplex virus 1 transcription sites, where it undergoes proteasomal degradation during infection. J Virol 80, 3567-81 (2006).
63. Kristie, T. M. Dynamic modulation of HSV chromatin drives initiation of infection and provides targets for epigenetic therapies. Virology 479-480, 555-61 (2015).
64. Lester, J. T. & DeLuca, N. A. Herpes simplex virus 1 ICP4 forms complexes with TFIID and mediator in virus-infected cells. J Virol 85, 5733-44 (2011).
65. Rice, S. A. & Davido, D. J. HSV-1 ICP22: hijacking host nuclear functions to enhance viral infection. Future Microbiol 8, 311-21 (2013).
66. Durand, L. O. & Roizman, B. Role of cdk9 in the optimization of expression of the genes regulated by ICP22 of herpes simplex virus 1. J Virol 82, 10591-9 (2008).
67. Liu, Z., Scannell, D. R., Eisen, M. B. & Tjian, R. Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell 146, 720-31 (2011).
68. Cuddapah, S. et al. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 19, 24-32 (2009).
69. Smith, S. T. et al. Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization. Dev Biol 328, 518-28 (2009).
70. Laitem, C. et al. CTCF regulates NELF, DSIF and P-TEFb recruitment during transcription. Transcription 6, 79-90 (2015).
71. Splinter, E. et al. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev 20, 2349-54 (2006).
72. Zhou, C. & Knipe, D. M. Association of herpes simplex virus type 1 ICP8 and ICP27 proteins with cellular RNA polymerase II holoenzyme. J Virol 76, 5893-904 (2002).
73. Showalter, S. D., Zweig, M. & Hampar, B. Monoclonal antibodies to herpes simplex virus type 1 proteins, including the immediateearly protein ICP 4. Infect Immun 34, 684-92 (1981).
74. Everett, R. D., Sourvinos, G., Leiper, C., Clements, J. B. & Orr, A. Formation of nuclear foci of the herpes simplex virus type 1 regulatory protein ICP4 at early times of infection: localization, dynamics, recruitment of ICP27, and evidence for the de novo induction of ND10-like complexes. Journal of Virology 78, 1903-17 (2004).
75. Hartig, S. M. Basic image analysis and manipulation in ImageJ. Curr Protoc Mol Biol Chapter 14, Unit14 15 (2013).
76. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).