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Pluripotency Regulation by HPAT5 - The Missing lincRNA?



Review of “The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming” from Nature Genetics by Stuart P. Atkinson

Long intergenic non-coding RNAs (lincRNAs) transcription takes place at tens of thousands of sites in non-coding DNA sequences which are frequently enriched for various classes of transposable elements (TEs). Researchers group lincRNAs into families based on the presence of these elements and some of these large families have been linked to human embryonic stem cell (hESC) pluripotency (HERV-H) [1] and human preimplantation embryo development (HERV-H and HERV-K) [2, 3]. However, any information on the roles of individual TE-derived lincRNAs in pluripotency and embryogenesis has, so far, been posted missing.

To rectify this “missing lincRNA” data, researchers from the groups of Vittorio Sebastiano and Renee A Reijo Pera sought to study 23 lincRNAs highly expressed in hESCs which had been previously identified using hybrid RNA sequencing [4]. Their new study, published in Nature Genetics, characterizes three individual TE-derived human lincRNAs associated with the acquisition of pluripotency and embryo development [5]. 

Of the 23 lincRNAs (human pluripotency-associated transcripts (HPAT) 1-23) identified in the previous study, the authors noted specifically elevated expression of HPAT2, 3, and 5 in the inner cell mass (ICM) but not in trophectoderm of human blastocysts, with HPAT5 expressed at the highest levels. Small interfering (si)RNA knockdown of all three HPATs in a single blastomere of a 2-cell stage embryo impeded said blastomere from contributing to the ICM of the developing embryo, so suggesting, for the first time, an important role for lincRNAs in human embryogenesis.

The authors then forged a strong link between HPAT2, 3, and 5 with the pluripotent state through various assessments in human induced pluripotent stem cell (hiPSCs) and hESCs. Specifically, they found that:

  • Gene transcription networks-generated at differing stages of iPSC-reprogramming found close links between the three HPATS to the core regulatory network of pluripotency (POU5F1, SOX2, SALL4, and NANOG)
  • siRNA-mediated knockdown of the three HPATs inhibited hiPSC reprogramming, with HPAT5 inhibition having the largest single effect
  • Expression of HPAT2, 3, and 5 alongside POU5F1 (OCT4) allowed the successful derivation of iPSCs
  • NANOG chromatin immunoprecipitation assays found that HPAT2, 3 and, 5 gene promoter regions were specifically bound by NANOG
  • HPAT5 overexpression effectively inhibited hESC-differentiation

But how exactly are these TE-derived-lincRNAs doing it all? A subsequent protein interaction assay indicated a strong interaction of HPAT5 with proteins involved in the microRNA (miRNA) processing pathway (TARBP2 and AGO2) and bioinformatics found that HPAT5 contained miRNA response elements (MREs) specific for the entire let-7 miRNA family (whose expression inhibits hiPSCs reprogramming [6]). Subsequent HPAT5 ablation using CRISPR/Cas9 in hESCs led to increased levels of let-7, although not to a level sufficient to induce differentiation, suggesting that HPAT5-mediated suppression of let-7 expression is only one means of let-7 regulation.

This intriguing study underlines the importance of single lincRNAs in pluripotency and embryo development and also highlights the importance that retroviral TEs have on human development and evolution. Hopefully future studies employing techniques such as CRISPR will lay bare the involvement of many more lincRNA and further our understanding of the beginnings of pluripotency and how these transposable elements have affected our development.


  1. Lu X, Sachs F, Ramsay L, et al. The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol 2014;21:423-425.
  2. Goke J, Lu X, Chan YS, et al. Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. Cell Stem Cell 2015;16:135-141.
  3. Grow EJ, Flynn RA, Chavez SL, et al. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature 2015;522:221-225.
  4. Au KF, Sebastiano V, Afshar PT, et al. Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A 2013;110:E4821-4830.
  5. Durruthy-Durruthy J, Sebastiano V, Wossidlo M, et al. The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming. Nat Genet 2016;48:44-52.
  6. Worringer KA, Rand TA, Hayashi Y, et al. The let-7/LIN-41 pathway regulates reprogramming to human induced pluripotent stem cells by controlling expression of prodifferentiation genes. Cell Stem Cell 2014;14:40-52.