HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency

Abstract

BackgroundCertain post-translational modifications to histones, including H3K4me3, as well as binding sites for the transcription factor STAT1, predict the site of integration of exogenous gamma-retroviruses with great accuracy and cell-type specificity. Statistical methods that were used to identify chromatin features that predict exogenous gamma-retrovirus integration site selection were exploited here to determine whether cell type-specific chromatin markers are enriched in the vicinity of endogenous retroviruses (ERVs).ResultsAmong retro-elements in the human genome, the gamma-retrovirus HERV-H was highly associated with H3K4me3, though this association was only observed in embryonic stem (ES) cells (p < 10-300) and, to a lesser extent, in induced pluripotent stem (iPS) cells. No significant association was observed in nearly 40 differentiated cell types, nor was any association observed with other retro-elements. Similar strong association was observed between HERV-H and the binding sites within ES cells for the pluripotency transcription factors NANOG, OCT4, and SOX2. NANOG binding sites were located within the HERV-H 5′LTR itself. OCT4 and SOX2 binding sites were within 1 kB and 2 kB of the 5′LTR, respectively. In keeping with these observations, HERV-H RNA constituted 2% of all poly A RNA in ES cells. As ES cells progressed down a differentiation pathway, the levels of HERV-H RNA decreased progressively. RNA-Seq datasets showed HERV-H transcripts to be over 5 kB in length and to have the structure 5′LTR-gag-pro-3′LTR, with no evidence of splicing and no intact open reading frames.ConclusionThe developmental regulation of HERV-H expression, the association of HERV-H with binding sites for pluripotency transcription factors, and the extremely high levels of HERV-H RNA in human ES cells suggest that HERV-H contributes to pluripotency in human cells. Proximity of HERV-H to binding sites for pluripotency transcription factors within ES cells might be due to retention of the same chromatin features that determined the site of integration of the ancestral, exogenous, gamma-retrovirus that gave rise to HERV-H in the distant past. Retention of these markers, or, alternatively, recruitment of them to the site of the established provirus, may have acted post-integration to fix the provirus within the germ-line of the host species. Either way, HERV-H RNA provides a specific marker for pluripotency in human cells.

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses

“…However, ERV genes are unmethylated and expressed in embryonic stem cells (Santoni et al, 2012) and especially Syncytin-1 is epigenetically regulated throughout placentogenesis (Matouskova et al, 2006). Some tumors have ERV demethylation and increased expression such as the ERV-K (HML-2) 5'LTR-UTR in melanoma (Stengel et al, 2010) and the 5'-LTR region of several ERVs in testicular cancer (Gimenez et al, 2010).…”

HEMO, an ancestral endogenous retroviral envelope protein shed in the blood of pregnant women and expressed in pluripotent stem cells and tumors

“…An effect of HEMO in development should also be considered, taking into consideration that its expression is observed as early as at the eight-cell stage and persists at all of the subsequent embryonic stages. Of note, other ERVs-including HERV-H and HERV-K-have related profiles of expression, and abundant HERV-H RNA was recently shown to be a marker of cell "stemness" in humans and possibly play a role-via transcriptional effects and/or specific ERV-driven transcripts-in the maintenance of pluripotency in human stem cells (45)(46)(47)(48)(49) (reviewed in refs. [50][51][52].…”

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

“…If LTR promoters were randomly activated in unusual conditions such as long-term inflammation, the numbers of upregulated LTRs should correlate with copy numbers in the genome. If, on the contrary, they were activated through a selective process, one should observe the activation of specific subfamilies, such as LTR7 and HERVH-int, which are markers for pluripotent cells (Santoni et al 2012;Fort et al 2014). Figure 2F shows that some subfamilies with relatively small numbers of copies per genome were preferentially activated in HCC tumors compared to the random distribution (Supplemental Fig.…”