B1 SINE-binding ZFP266 impedes reprogramming through suppression of chromatin opening by pioneering factors

Abstract: Successful generation of induced pluripotent stem cells (iPSCs) via the overexpression of Oct4 (Pou5f1), Sox2, Klf4 and c-Myc (OSKM) highlights the power of transcription factor (TF)-mediated cellular conversions. Nevertheless, iPSC reprogramming is inherently inefficient and understanding the molecular mechanisms underlying this inefficiency holds the key to control cellular identity successfully. Here, we report 16 novel reprogramming roadblock genes identified by CRISPR/Cas9-mediated genome-wide knockout (KO) screening. Of these, disruption of KRAB zinc finger protein (KRAB-ZFP) Zfp266 strongly and consistently enhanced iPSC generation in several iPSC reprogramming settings, emerging as the most robust roadblock. Further analyses revealed that ZFP266 bound Short Interspersed Nuclear Elements (SINEs) adjacent to OSK binding sites and impedes chromatin opening. This work serves as a resource for better understanding reprogramming mechanisms and proposes SINEs as a critical genetic element that regulates chromatin accessibility at enhancers for efficient pluripotency induction.