Transcription Factor Binding Sites Are Genetic Determinants of Retroviral Integration in the Human Genome

Abstract

Gamma-retroviruses and lentiviruses integrate non-randomly in mammalian genomes, with specific preferences for active chromatin, promoters and regulatory regions. Gene transfer vectors derived from gamma-retroviruses target at high frequency genes involved in the control of growth, development and differentiation of the target cell, and may induce insertional tumors or pre-neoplastic clonal expansions in patients treated by gene therapy. The gene expression program of the target cell is apparently instrumental in directing gamma-retroviral integration, although the molecular basis of this phenomenon is poorly understood. We report a bioinformatic analysis of the distribution of transcription factor binding sites (TFBSs) flanking >4,000 integrated proviruses in human hematopoietic and non-hematopoietic cells. We show that gamma-retroviral, but not lentiviral vectors, integrate in genomic regions enriched in cell-type specific subsets of TFBSs, independently from their relative position with respect to genes and transcription start sites. Analysis of sequences flanking the integration sites of Moloney leukemia virus (MLV)- and human immunodeficiency virus (HIV)-derived vectors carrying mutations in their long terminal repeats (LTRs), and of HIV vectors packaged with an MLV integrase, indicates that the MLV integrase and LTR enhancer are the viral determinants of the selection of TFBS-rich regions in the genome. This study identifies TFBSs as differential genomic determinants of retroviral target site selection in the human genome, and suggests that transcription factors binding the LTR enhancer may synergize with the integrase in tethering retroviral pre-integration complexes to transcriptionally active regulatory regions. Our data indicate that gamma-retroviruses and lentiviruses have evolved dramatically different strategies to interact with the host cell chromatin, and predict a higher risk in using gamma-retroviral vs. lentiviral vectors for human gene therapy applications.

Applications of DNA integrating elements: Facing the bias bully

“…10 Furthermore, contrary to HIV, MuLV demonstrated a strong preference for DNase I hypersensitive sites and regions rich in transcription factor binding site motifs. 17,18 Moreover, its bias appeared to be mostly determined by the MuLV-specific integrase 17,18 and the enhancer in the LTR. 17 HIV integrations associated with epigenetic marks such as H3K36me3, consistent with its reported bias for transcriptionally active genes.…”

“…17,18 Moreover, its bias appeared to be mostly determined by the MuLV-specific integrase 17,18 and the enhancer in the LTR. 17 HIV integrations associated with epigenetic marks such as H3K36me3, consistent with its reported bias for transcriptionally active genes. 19 These and other studies on retroviral integration biases were reviewed extensively in.…”

Retroviral integration profiles: their determinants and implications for gene therapy

“…The retroviral propensity for frequently targeting oncogenes and cell growth/survival genes and the integration preference for TSSs and CpG islands synergistically increase the malignant potential of retroviral vectors (21). In addition, MLV considerably prefers transcription factor binding sites (TFBSs) (22) and moderately genes, especially highly expressed genes, during integration (16,21). Another gamma-retrovirus, porcine endogenous retrovirus (PERV), shows a similar integration pattern, favoring TSSs and CpG islands (23).…”

“…In addition, HIV-1 targets oncogenes and the genes involved in cell growth and survival (21). In contrast, HIV-1 disfavors CpG islands and does not show any preference for TFBSs (16,22,26). Interestingly, integrated lentiviral vectors can both up-and down-regulate host gene expression, in contrast to MLV (20).…”

Retroviral Infection of hES Cells Produces Random-like Integration Patterns

“…It has been suggested that interactions among retroviral pre-integration complexes (PICs) and cellular proteins, such as transcription factors (TFs), determine viral integration sites via a mechanism in which cellular proteins tether PICs to certain genomic loci (Engelman and Cherepanov, 2008;Felice et al, 2009). However, only a fraction of host proteins associating with retroviral PICs have been identified, and other mechanisms that underlie such interactions are still poorly understood (Cattoglio et al, 2010).…”