The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency

Abstract

Human pluripotent stem cells (PSCs) express human endogenous retrovirus type-H (HERV-H), which exists as more than a thousand copies on the human genome and frequently produces chimeric transcripts as long-non-coding RNAs (lncRNAs) fused with downstream neighbor genes. Previous studies showed that HERV-H expression is required for the maintenance of PSC identity, and aberrant HERV-H expression attenuates neural differentiation potentials, however, little is known about the actual of function of HERV-H. In this study, we focused on ESRG, which is known as a PSC-related HERV-H-driven lncRNA. The global transcriptome data of various tissues and cell lines and quantitative expression analysis of PSCs showed that ESRG expression is much higher than other HERV-Hs and tightly silenced after differentiation. However, the loss of function by the complete excision of the entire ESRG gene body using a CRISPR/Cas9 platform revealed that ESRG is dispensable for the maintenance of the primed and naïve pluripotent states. The loss of ESRG hardly affected the global gene expression of PSCs or the differentiation potential toward trilineage. Differentiated cells derived from ESRG-deficient PSCs retained the potential to be reprogrammed into induced PSCs (iPSCs) by the forced expression of OCT3/4, SOX2, and KLF4. In conclusion, ESRG is dispensable for the maintenance and recapturing of human pluripotency.

ZBTB12 is a molecular barrier to dedifferentiation in human pluripotent stem cells

“…10k, l). These results are in agreement with a recent report showing that ESRG is dispensable for hPSC self-renewal 64 . Upon differentiation, however, ESRG KD boosted dissolution of the core pluripotency gene network (Fig.…”

“…5d-f). On the other hand, there is a discrepancy between studies on the role of ESRG in pluripotency 14,64 and the mechanism is underexplored. In the current study, we found that ESRG KD had no effect on the expression of core pluripotency genes in hESCs (Supplementary Fig.…”

Human endogenous retroviruses in development and disease

“…Although a general knockdown of HERV-H is sufficient to impair pluripotency, individual HERVH-derived lncRNAs with unique chimeric sequences also play specific roles in hPSCs, such as ESRG [42] , linc-ROR [44] , LINC00458 [45] , and HPAT [46] . However, a recent study showed that ESRG is dispensable for pluripotency maintenance by a complete excision of the entire ESRG region [47] . The disagreement between these studies could be attributed to the different methods, Wang et al using an RNAi knockdown [42] while Takahashi et al .…”

“…The disagreement between these studies could be attributed to the different methods, Wang et al using an RNAi knockdown [42] while Takahashi et al . using CRISPR/Cas9 knockout [47] . In addition, HERV-H LTRs contain binding sites for the LTR-binding protein 9 (LBP9) [42] , OCT4 [43] , and NANOG [48] to recruit these pluripotency factors.…”

Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells

“…For example, it has been reported that the knockdown of one specific HERV-H transcript, ESRG, leads to loss of pluripotency in hESC 55 . However, in a recent study from Shiyan Yamanaka’s group 80 , the authors showed that genetic depletion of the DNA sequence of the entire ESRG locus is dispensable for pluripotency or iPSC reprogramming 80 . These data suggest that HERV-H knockdown causes unknown off-target effects, which in turn results in hESC differentiation and loss of pluripotency.…”