title: HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency.
abstract: BACKGROUND
  Certain 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).
  
  
  RESULTS
  Among 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland. federico.santoni@unige.ch
authors.forename: Federico A
authors.initials: FA
authors.lastname: Santoni
authors.forename: Jessica
authors.initials: J
authors.lastname: Guerra
authors.forename: Jeremy
authors.initials: J
authors.lastname: Luban
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D015415:Biomarkers / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism* / Q000821:virology; D020077:Endogenous Retroviruses / Q000235:genetics*; D005786:Gene Expression Regulation; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism* / Q000821:virology; D000071317:Nanog Homeobox Protein; D050814:Octamer Transcription Factor-3 / Q000235:genetics / Q000378:metabolism; D009928:Organ Specificity; D011485:Protein Binding; D011499:Protein Processing, Post-Translational; D012367:RNA, Viral / Q000235:genetics*; D055748:SOXB1 Transcription Factors / Q000235:genetics / Q000378:metabolism; D050794:STAT1 Transcription Factor / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D020079:Terminal Repeat Sequences
chemical_list: D015415:Biomarkers; D002843:Chromatin; D006657:Histones; D018398:Homeodomain Proteins; C486780:NANOG protein, human; D000071317:Nanog Homeobox Protein; D050814:Octamer Transcription Factor-3; C494173:POU5F1 protein, human; D012367:RNA, Viral; C527782:SOX2 protein, human; D055748:SOXB1 Transcription Factors; D050794:STAT1 Transcription Factor; C494079:STAT1 protein, human