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Background  Lentiviral vectors (LV) are widely used for various gene transfer or gene therapy applications. The effects of LV on target cells are expected to be limited to gene delivery. Yet, human hematopoietic CD34+ cells respond to functional LVs as well as several types of non-integrating LVs by genome-wide DNA methylation changes.    Results  A new algorithm for the analysis of 450K Illumina data showed that these changes were marked by de novo methylation. The same 4126 cytosines located in islands corresponding to 1059 genes were systematically methylated. This effect required cellular entry of the viral particle in the cells but not the genomic integration of the vector cassette. Some LV preparations induced only mild sporadic changes while others had strong effects suggesting that LV batch heterogeneity may be related to the extent of the epigenetic response.    Conclusion  These findings identify a previously uncharacterized but consistent cellular response to viral components and provide a novel example of environmentally modified epigenome.    Electronic supplementary material  The online version of this article (doi:10.1186/s13072-016-0077-1) contains supplementary material, which is available to authorized users.

Systemic epigenetic response to recombinant lentiviral vectors independent of proviral integration