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Summary: Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) is accompanied by dramatic changes in epigenetic programs, including silencing of endogenous and exogenous retroviruses. Here, we utilized replication-defective and persistent Sendai virus (SeVdp)-based vectors to monitor retroviral silencing during reprogramming. We observed that retroviral silencing occurred at an early reprogramming stage without a requirement for KLF4 or the YY1-binding site in the retroviral genome. Insertional chromatin immunoprecipitation (iChIP) enabled us to isolate factors assembled on the silenced provirus, including components of inhibitor of histone acetyltransferase (INHAT), which includes the SET/TAF-I oncoprotein. Knockdown of SET/TAF-I in mouse embryonic fibroblasts (MEFs) diminished retroviral silencing during reprogramming, and overexpression of template activating factor-I α (TAF-Iα), a SET/TAF-I isoform predominant in embryonic stem cells (ESCs), reinforced retroviral silencing by an SeVdp-based vector that is otherwise defective in retroviral silencing. Our results indicate an important role for TAF-Iα in retroviral silencing during reprogramming. : Bui et al. use replication-defective and persistent Sendai virus (SeVdp)-based vectors to monitor retroviral silencing during reprogramming and find that the silencing occurs earlier than the acquisition of pluripotency. Insertional chromatin immunoprecipitation (iChIP) identifies TAF-Iα, a SET/TAF-I isoform predominant in ESCs, as a factor that facilitates retroviral silencing. Keywords: retroviral silencing, reprogramming, SeVdp vector, primer-binding site, insertional chromatin immunoprecipitation, TAF-Iα