Journal of RNAi and Gene Silencing (October 2005), 1(2), 66-78

Research Article

Prolonged transcriptional silencing and CpG methylation induced by siRNAs targeted to the HIV-1 promoter region

Kazuo Suzuki †, Toshiaki Shijuuku †, Toshihiko Fukamachi †, John Zaunders †, Gilles Guillemin ‡, David Cooper †,§ and Anthony Kelleher †,§

ABSTRACT

In addition to the degradation of homologous RNAs through the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) can in some systems induce cytosine methylation and transcriptional silencing of homologous promoters. Targeting of HIV-1 by RNAi results in transient suppression of the virus through degradation of viral transcripts. In an effort to prolong the suppressive effect of siRNAs on productive HIV-1 infection, we targeted conserved tandem NF- k B binding motifs in the viral LTR. A 21-nucleotide-RNA duplex induced marked and durable (at least 30 days) suppression of productive HIV-1 infection in chronically infected M agic-5 cells . This suppression is associated with CpG methylation within the 5’LTR and marked reduction of HIV-1 transcription in nuclear run-on assays. We then assessed three additional siRNAs targeting other sites within the HIV-1 promoter region. These siRNAs suppressed HIV-1 infection to different extents and degree of suppression correlated with the extent of de novo methylation of CpG motifs within the HIV-1 promoter region. These findings indicate that HIV-1 can be silenced by an RNA-directed mechanism that suppresses transcription and induces CpG methylation. In addition to providing evidence that this RNA-directed DNA methylation is active in mammalian cells, this is the first report of prolonged suppression of HIV-1 infection induced by siRNA.

KEYWORDS: siRNA, RNAi, gene-silencing, HIV-1, DNA-methylation, transcriptional silencing, TGS

† Centre for Immunology, Immunovirology Laboratory, St Vincent’s Hospital, Darlinghurst, NSW, 2010.

‡ Centre for Immunology, Neuroimmunology Dept, Darlinghurst, NSW, 2010.

§ National Centre in HIV Epidemiology and Clinical Research, UNSW, Darlinghurst, 2010, Australia.

*Correspondence to : Anthony Kelleher, Email: t.kelleher@cfi.unsw.edu.au, Tel: +612 83822094, Fax: +612 83822391

© Copyright Kazuo Suzuki et al

(Received 01 July 2005; Revised 20 September 2005; Accepted 26 September 2005)