title: Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells.
abstract: About half of the human genome consists of highly repetitive elements, most of which are considered dispensable for human life. Here, we report that repetitive elements originating from endogenous retroviruses (ERVs) are systematically transcribed during human early embryogenesis in a stage-specific manner. Our analysis highlights that the long terminal repeats (LTRs) of ERVs provide the template for stage-specific transcription initiation, thereby generating hundreds of co-expressed, ERV-derived RNAs. Conversion of human embryonic stem cells (hESCs) to an epiblast-like state activates blastocyst-specific ERV elements, indicating that their activity dynamically reacts to changes in regulatory networks. In addition to initiating stage-specific transcription, many ERV families contain preserved splice sites that join the ERV segment with non-ERV exons in their genomic vicinity. In summary, we find that ERV expression is a hallmark of cellular identity and cell potency that characterizes the cell populations in early human embryos.
authors: Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore. Electronic address: gokej@gis.a-star.edu.sg.
authors: Jonathan
authors: J
authors: Göke
authors: Gene Regulation Laboratory, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.
authors: Xinyi
authors: X
authors: Lu
authors: Gene Regulation Laboratory, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.
authors: Yun-Shen
authors: YS
authors: Chan
authors: Gene Regulation Laboratory, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117559, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
authors: Huck-Hui
authors: HH
authors: Ng
authors: Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.
authors: Lam-Ha
authors: LH
authors: Ly
authors: Gene Regulation Laboratory, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117559, Singapore.
authors: Friedrich
authors: F
authors: Sachs
authors: Gene Regulation Laboratory, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117559, Singapore.
authors: Iwona
authors: I
authors: Szczerbinska
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics*; D053595:Embryonic Stem Cells / Q000378:metabolism*; D020077:Endogenous Retroviruses / Q000235:genetics*; D006801:Humans; D020079:Terminal Repeat Sequences / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements