Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

• Main Authors: Haifeng Fu, Weiyu Zhang, Niannian Li, Jiao Yang, Xiaoying Ye, Chenglei Tian, Xinyi Lu, Lin Liu
• Format: Article
• Language: English
• Published: BMC 2021-07-01
• Series: Genome Biology
• Subjects: Naïve and primed pluripotent state; Telomeres; 2C genes; Genome stability; Retrotransposons; Histone modifications
• Online Access: https://doi.org/10.1186/s13059-021-02417-9

Abstract Background Naïve and primed pluripotent stem cells (PSCs) represent two different pluripotent states. Primed PSCs following in vitro culture exhibit lower developmental potency as evidenced by failure in germline chimera assays, unlike mouse naïve PSCs. However, the molecular mechanisms underlying the lower developmental competency of primed PSCs remain elusive. Results We examine the regulation of telomere maintenance, retrotransposon activity, and genomic stability of primed PSCs and compare them with naïve PSCs. Surprisingly, primed PSCs only minimally maintain telomeres and show fragile telomeres, associated with declined DNA recombination and repair activity, in contrast to naïve PSCs that robustly elongate telomeres. Also, we identify LINE1 family integrant L1Md_T as naïve-specific retrotransposon and ERVK family integrant IAPEz to define primed PSCs, and their transcription is differentially regulated by heterochromatic histones and Dnmt3b. Notably, genomic instability of primed PSCs is increased, in association with aberrant retrotransposon activity. Conclusions Our data suggest that fragile telomere, retrotransposon-associated genomic instability, and declined DNA recombination repair, together with reduced function of cell cycle and mitochondria, increased apoptosis, and differentiation properties may link to compromised developmental potency of primed PSCs, noticeably distinguishable from naïve PSCs.