Display options
Cite
Zhang X, Justice AC, Hu Y, et al. Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics. 2016;11(10):750-760doi: 10.1080/15592294.2016.1221569.
Zhang, X., Justice, A. C., Hu, Y., Wang, Z., Zhao, H., Wang, G., Johnson, E. O., Emu, B., Sutton, R. E., Krystal, J. H., & Xu, K. (2016). Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics, 11(10), 750-760. https://doi.org/10.1080/15592294.2016.1221569
Zhang, Xinyu, et al. "Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals." Epigenetics vol. 11,10 (2016): 750-760. doi: https://doi.org/10.1080/15592294.2016.1221569
Zhang X, Justice AC, Hu Y, Wang Z, Zhao H, Wang G, Johnson EO, Emu B, Sutton RE, Krystal JH, Xu K. Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics. 2016 Oct 02;11(10):750-760. doi: 10.1080/15592294.2016.1221569. Epub 2016 Sep 27. PMID: 27672717; PMCID: PMC5094631.
Copy Download .nbib Format: NLM
Share it on

Epigenetics. 2016 Oct 02;11(10):750-760. doi: 10.1080/15592294.2016.1221569. Epub 2016 Sep 27.

Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals.

Epigenetics

Xinyu Zhang, Amy C Justice, Ying Hu, Zuoheng Wang, Hongyu Zhao, Guilin Wang, Eric O Johnson, Brinda Emu, Richard E Sutton, John H Krystal, Ke Xu

Affiliations

  1. a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.
  2. b Connecticut Veteran Health System , West Haven , CT , USA.
  3. c Yale University School of Medicine, New Haven Veterans Affairs Connecticut Healthcare System , West Haven , CT , USA.
  4. d Center for Biomedical Informatics & Information Technology, National Cancer Institute , Bethesda , MD , USA.
  5. e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA.
  6. f Department of Biostatistics , Yale School of Public Health , New Haven , CT , USA.
  7. g Yale Center of Genomic Analysis, West Campus , Orange , CT , USA.
  8. h Fellow Program and Behavioral Health and Criminal Justice Division, RTI International , Research Triangle Park, NC , USA.

PMID: 27672717 PMCID: PMC5094631 DOI: 10.1080/15592294.2016.1221569

Abstract

Epigenetic control of human immunodeficiency virus-1 (HIV-1) genes is critical for viral integration and latency. However, epigenetic changes in the HIV-1-infected host genome have not been well characterized. Here, we report the first large-scale epigenome-wide association study of DNA methylation for HIV-1 infection. We recruited HIV-infected (n = 261) and uninfected (n = 117) patients from the Veteran Aging Cohort Study (VACS) and all samples were profiled for 485,521 CpG sites in DNA extracted from the blood. After adjusting for cell type and clinical confounders, we identified 20 epigenome-wide significant CpGs for HIV-1 infection. Importantly, 2 CpGs in the promoter of the NLR family, CARD domain containing gene 5 (NLRC5), a key regulator of major histocompatibility complex class I gene expression, showed significantly lower methylation in HIV-infected subjects than in uninfected subjects (cg07839457: t = -6.03, P

Keywords: ; DNA methylation; Epigenome-wide association; HIV-1 infection; viral load

References

  1. Retrovirology. 2014 Dec 13;11:118 - PubMed
  2. Epigenomics. 2015 Aug;7(5):745-55 - PubMed
  3. Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13794-9 - PubMed
  4. Nat Commun. 2014 Nov 18;5:5366 - PubMed
  5. Cell. 2010 Apr 30;141(3):483-96 - PubMed
  6. Epigenetics. 2015;10(10):922-30 - PubMed
  7. J Biol Chem. 2008 Apr 25;283(17):11097-106 - PubMed
  8. Aging Cell. 2012 Dec;11(6):1132-4 - PubMed
  9. Methods Mol Biol. 2015;1238:381-403 - PubMed
  10. Genome Biol. 2015 Feb 15;16:37 - PubMed
  11. J Virol. 2001 Oct;75(20):9753-61 - PubMed
  12. J Immunol. 2012 May 15;188(10):4940-50 - PubMed
  13. EMBO J. 1990 Apr;9(4):1157-64 - PubMed
  14. J Immunol. 2012 Jul 15;189(2):516-20 - PubMed
  15. J Immunol. 2012 May 15;188(10 ):4951-8 - PubMed
  16. Genome Biol. 2014 Feb 04;15(2):R31 - PubMed
  17. Mol Cell. 2016 Apr 21;62(2):157-68 - PubMed
  18. Mol Cell Biol. 1998 Sep;18(9):5166-77 - PubMed
  19. Epigenomics. 2012 Feb;4(1):41-9 - PubMed
  20. Med Care. 2006 Aug;44(8 Suppl 2):S25-30 - PubMed
  21. Immunol Cell Biol. 2015 Mar;93(3):233-44 - PubMed
  22. Epigenomics. 2016 May;8(5):587-91 - PubMed
  23. Epigenetics. 2014 Jun;9(6):884-95 - PubMed
  24. AIDS. 2014 Jul 31;28(12):1719-28 - PubMed
  25. Genomics. 2000 Feb 1;63(3):384-90 - PubMed
  26. Trends Mol Med. 2014 Oct;20(10):541-3 - PubMed
  27. PLoS Pathog. 2014 Mar 20;10(3):e1003997 - PubMed
  28. J Infect Dis. 2015 Jan 1;211(1):28-39 - PubMed
  29. Cold Spring Harb Symp Quant Biol. 1994;59:109-16 - PubMed
  30. Clin Epigenetics. 2015 Sep 24;7:103 - PubMed
  31. PLoS Pathog. 2009 Aug;5(8):e1000554 - PubMed
  32. AIDS. 2013 Aug 24;27(13):2019-29 - PubMed
  33. BMC Biochem. 2012 Jun 07;13:8 - PubMed
  34. Nat Neurosci. 2014 Sep;17(9):1156-63 - PubMed
  35. Immunity. 2007 Sep;27(3):406-16 - PubMed
  36. Sci Rep. 2015 Jun 03;5:10806 - PubMed
  37. Aging (Albany NY). 2015 Feb;7(2):97-109 - PubMed
  38. Cell Res. 2012 May;22(5):822-35 - PubMed
  39. J Immunol. 2012 Apr 15;188(8):3820-8 - PubMed
  40. PLoS Pathog. 2009 Jun;5(6):e1000495 - PubMed
  41. Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17225-30 - PubMed
  42. AIDS Rev. 2013 Jul-Sep;15(3):181-8 - PubMed
  43. Proc Natl Acad Sci U S A. 2016 May 24;113(21):5999-6004 - PubMed
  44. Nat Rev Immunol. 2012 Dec;12(12):813-20 - PubMed
  45. Nature. 2015 Apr 30;520(7549):670-4 - PubMed
  46. BMC Bioinformatics. 2012 May 08;13:86 - PubMed
  47. Epigenomics. 2011 Aug;3(4):487-502 - PubMed
  48. Cell Res. 2012 May;22(5):836-47 - PubMed
  49. Trends Microbiol. 2010 Oct;18(10):439-47 - PubMed
  50. Immunobiology. 2012 Jan;217(1):13-6 - PubMed
  51. J Infect Dis. 2015 Nov 15;212(10):1563-73 - PubMed
  52. Nat Biotechnol. 2013 Feb;31(2):142-7 - PubMed
  53. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7609-13 - PubMed

Publication Types

Grant support