Loss-of-function experiments in human pluripotent stem cells [hPSCs; comprising human embryonic stem cells (hESCs) or human induced pluripotent stem cells (hiPSCs)] provide a unique opportunity to study the mechanisms that regulate human development, physiology and disease (Avior et al., 2016; Pourquié et al., 2015; Zhu and Huangfu, 2013). However, functional genomic applications of hPSCs are currently limited by the lack of an easy and efficient method to conditionally manipulate gene expression in both hPSCs and hPSC-derived cells. Indeed, such a system is necessary both for the study of genes essential for hPSC self-renewal and for functional analyses at specific stages of differentiation.