NP220 mediates silencing of unintegrated retroviral DNA
Open accessAbstract
The entry of foreign DNA into many mammalian cell types triggers the innate immune system, a complex set of responses to prevent infection by pathogens. One aspect of the response is the potent epigenetic silencing of incoming viral DNAs 1, including the extrachromosomal DNAs that are formed immediately after infection by retroviruses. These unintegrated viral DNAs are very poorly transcribed in all cells, even in permissive cells, in contrast to the robust expression that is observed after viral integration 2-5. The factors that are responsible for this low expression have not yet been identified. Here we performed a genome-wide CRISPR-Cas9 screen for genes that are required for silencing an integrase-deficient MLV-GFP reporter virus to explore the mechanisms responsible for repression of unintegrated viral DNAs in human cells. Our screen identified the DNA-binding protein NP220, the three proteins (MPP8, TASOR and PPHLN1) that comprise the HUSH complex-which silences proviruses in heterochromatin 6 and retrotransposons 7,8-the histone methyltransferase SETDB1, and other host factors that are required for silencing. Further tests by chromatin immunoprecipitation showed that NP220 is the key protein that recruits the HUSH complex, SETDB1 and the histone deacetylases HDAC1 and HDAC4 to silence the unintegrated retroviral DNA. Knockout of NP220 accelerates the replication of retroviruses. These experiments identify the molecular machinery that silences extrachromosomal retroviral DNA.
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DYSF is implicated in membrane repair; ZNF638 mediates the silencing of unintegrated viral DNA.
“DYSF is implicated in membrane repair22; ZNF638 mediates the silencing of unintegrated viral DNA23.”
From Locus for severity implicates CNS resilience in progression of multiple sclerosis (2023) · cites this paper as [23]
ZNF638 encodes the DNA-binding zinc finger protein 638, which mediates transcriptional repression of unintegrated retroviral DNA through recruitment of the HUSH complex and SETDB1.
“ZNF638 encodes the DNA-binding zinc finger protein 638, which mediates transcriptional repression of unintegrated retroviral DNA through recruitment of the human silencing hub (HUSH) complex and the histone methyltransferase SETDB123.”
From Locus for severity implicates CNS resilience in progression of multiple sclerosis (2023) · cites this paper as [23]
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Research works printed but not linked: 22
- [1]Orzalli MH & Knipe DM Cellular sensing of viral DNA and viral evasion mechanisms. Annu Rev Microbiol 68, 477– 492, doi: 10.1146/annurev-micro-091313-103409 (2014). 25002095 PMC4348004 · DOI
- [2]Schwartzberg P, Colicelli J & Goff SP Construction and analysis of deletion mutations in the pol gene of Moloney murine leukemia virus: a new viral function required for productive infection. Cell 37, 1043– 1052 (1984). 6204767
- [3]Schneider WM, Wu DT, Amin V, Aiyer S & Roth MJ MuLV IN mutants responsive to HDAC inhibitors enhance transcription from unintegrated retroviral DNA. Virology 426, 188– 196, doi: 10.1016/j.virol.2012.01.034 (2012). 22365328 PMC3294019 · DOI
- [4]Sakai H Integration is essential for efficient gene expression of human immunodeficiency virus type 1. Journal of virology 67, 1169– 1174 (1993). 8437208 PMC237481
- [5]Nakajima N, Lu R & Engelman A Human immunodeficiency virus type 1 replication in the absence of integrase-mediated dna recombination: definition of permissive and nonpermissive T-cell lines. Journal of virology 75, 7944– 7955 (2001). 11483739 PMC115038
- [6]Tchasovnikarova IA GENE SILENCING. Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells. Science 348, 1481– 1485, doi: 10.1126/science.aaa7227 (2015). 26022416 PMC4487827 · DOI
- [7]Liu N Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Nature 553, 228– 232, doi: 10.1038/nature25179 (2018). 29211708 PMC5774979 · DOI
- [8]Robbez-Masson L The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes. Genome Res 28, 836– 845, doi: 10.1101/gr.228171.117 (2018). 29728366 PMC5991525 · DOI · Paper page
- [9]Varmus H Retroviruses. Science 240, 1427– 1435 (1988). 3287617
- [10]Yoshimura FK & Weinberg RA Restriction endonuclease cleavage of linear and closed circular murine leukemia viral DNAs: discovery of a smaller circular form. Cell 16, 323– 332 (1979). 455438
- [11]Kilzer JM Roles of host cell factors in circularization of retroviral dna. Virology 314, 460– 467 (2003). 14517098
- [12]Inagaki H A large DNA-binding nuclear protein with RNA recognition motif and serine/arginine-rich domain. J Biol Chem 271, 12525– 12531 (1996). 8647861
- [13]Chang Y, Horton JR, Bedford MT, Zhang X & Cheng X Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding. Journal of molecular biology 408, 807– 814, doi: 10.1016/j.jmb.2011.03.018 (2011). 21419134 PMC3081990 · DOI
- [14]Kokura K, Sun L, Bedford MT & Fang J Methyl-H3K9-binding protein MPP8 mediates E-cadherin gene silencing and promotes tumour cell motility and invasion. The EMBO journal 29, 3673– 3687, doi: 10.1038/emboj.2010.239 (2010). 20871592 PMC2982762 · DOI
- [15]Chougui G HIV-2/SIV viral protein X counteracts HUSH repressor complex. Nat Microbiol, doi: 10.1038/s41564-018-0179-6 (2018). 29891865 · DOI
- [16]Yurkovetskiy L Primate immunodeficiency virus Vpx and Vpr counteract transcriptional repression of proviruses by the HUSH complex. bioRxiv, doi: 10.1101/293001 (2018). PMC6258279 30297740 · DOI
- [17]Gu H & Roizman B The two functions of herpes simplex virus 1 ICP0, inhibition of silencing by the CoREST/REST/HDAC complex and degradation of PML, are executed in tandem. Journal of virology 83, 181– 187, doi: 10.1128/JVI.01940-08 (2009). 18945770 PMC2612314 · DOI
- [18]Poon AP, Gu H & Roizman B ICP0 and the US3 protein kinase of herpes simplex virus 1 independently block histone deacetylation to enable gene expression. Proceedings of the National Academy of Sciences of the United States of America 103, 9993– 9998, doi: 10.1073/pnas.0604142103 (2006). 16785443 PMC1502567 · DOI
- [19]Wang GZ & Goff SP Postentry restriction of Mason-Pfizer monkey virus in mouse cells. Journal of virology 89, 2813– 2819, doi: 10.1128/JVI.03051-14 (2015). 25540373 PMC4325713 · DOI
- [20]Wolf D & Goff SP Embryonic stem cells use ZFP809 to silence retroviral DNAs. Nature 458, 1201– 1204, doi: 10.1038/nature07844 (2009). 19270682 PMC2676211 · DOI · Paper page
- [21]Joung J Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc 12, 828– 863, doi: 10.1038/nprot.2017.016 (2017). 28333914 PMC5526071 · DOI · Paper page
- [22]Diaz AA, Qin H, Ramalho-Santos M & Song JS HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis. Nucleic acids research 43, e16, doi: 10.1093/nar/gku1197 (2015). 25428347 PMC4330337 · DOI
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Self-citation
- Authors
- Zhu, Y., Wang, G. Z., Cingöz, O., & Goff, S. P.
- Affiliations
- Howard Hughes Medical Institute (US)
- Columbia University (US)
- Corresponding author
- Goff, Stephen P.
- Venue
- Nature
- Published
- 2018-11-28
- Volume
- 564
- Issue
- 7735
- Pages
- 278-282
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6349045
- OpenAlex
- W2902898030
- Cited by
- 123
- References
- 0
- Citations by year
- 2026: 8 · 2025: 13 · 2024: 24 · 2023: 19 · 2022: 14 · 2021: 18 · 2020: 15 · 2019: 10 · 2018: 2
- FWCI
- 4.00
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health
- National Cancer Institute (R01CA030488)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Keywords
- HUSH complex, SETDB1, histone deacetylase, HDAC1, HDAC4, extrachromosomal DNA, antiviral innate immunity, epigenetic silencing, mouse leukemia virus, CRISPR-Cas9 screen, histone methyltransferase
- MeSH terms
- CRISPR-Associated Protein 9, Antigens, Neoplasm, DNA-Binding Proteins, DNA, Viral, Histone Deacetylases, Humans, Nuclear Proteins, Phosphoproteins, Histone-Lysine N-Methyltransferase, Protein Methyltransferases, Proviruses, Repressor Proteins, Retroviridae, Transcription Factors, RNA-Binding Proteins, Virus Integration, Gene Silencing, Multiprotein Complexes, Chromatin Immunoprecipitation, Histone Deacetylase 1, Clustered Regularly Interspaced Short Palindromic Repeats
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