Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern.
A large subset of mammalian imprinted genes show extra-embryonic lineage (EXEL) specific imprinted expression that is restricted to placental trophectoderm lineages and to visceral yolk sac endoderm (ysE). Isolated ysE provides a homogenous in vivo model of a mid-gestation extra-embryonic tissue to examine the mechanism of EXEL-specific imprinted gene silencing, but an in vitro model of ysE to facilitate more rapid and cost-effective experiments is not available. Reports indicate that ES cells differentiated into cystic embryoid bodies (EBs) contain ysE, so here we investigate if cystic EBs model ysE imprinted expression. The imprinted expression pattern of cystic EBs is shown to resemble fetal liver and not ysE. To investigate the reason for this we characterized the methylome and transcriptome of cystic EBs in comparison to fetal liver and ysE, by whole genome bisulphite sequencing and RNA-seq. Cystic EBs show a fetal liver pattern of global hypermethylation and low expression of repeats, while ysE shows global hypomethylation and high expression of IAPEz retroviral repeats, as reported for placenta. Transcriptome analysis confirmed that cystic EBs are more similar to fetal liver than ysE and express markers of early embryonic endoderm. Genome-wide analysis shows that ysE shares epigenetic and repeat expression features with placenta. Contrary to previous reports, we show that cystic EBs do not contain ysE, but are more similar to the embryonic endoderm of fetal liver. This explains why cystic EBs reproduce the imprinted expression seen in the embryo but not that seen in the ysE.
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria. Electronic address: tkulinski@ibb.waw.pl.
Tomasz M
TM
Kulinski
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria. Electronic address: rcasari@cemm.oeaw.ac.at.
M Rita T
MR
Casari
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria. Electronic address: pguenzl@cemm.oeaw.ac.at.
Philipp M
PM
Guenzl
IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, 1030 Vienna, Austria. Electronic address: daniel.wenzel@imba.oeaw.ac.at.
Daniel
D
Wenzel
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria. Electronic address: dandergassen@cemm.oeaw.ac.at.
Daniel
D
Andergassen
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria; Department of Medicine 1, Laboratory of Infection Biology, Medical University of Vienna, 1090 Vienna, Austria. Electronic address: ahladik@cemm.oeaw.ac.at.
Anastasiya
A
Hladik
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria. Electronic address: pdatlinger@cemm.oeaw.ac.at.
Paul
P
Datlinger
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria. Electronic address: mfarlik@cemm.oeaw.ac.at.
Matthias
M
Farlik
IMP/IMBA Transgenic Service, Institute of Molecular Pathology (IMP), Dr. Bohr Gasse 7, 1030 Vienna, Austria. Electronic address: christian.theussl@imp.ac.at.
H-Christian
HC
Theussl
IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, 1030 Vienna, Austria. Electronic address: josef.penninger@imba.oeaw.ac.at.
Josef M
JM
Penninger
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria; Department of Medicine 1, Laboratory of Infection Biology, Medical University of Vienna, 1090 Vienna, Austria. Electronic address: sknapp@cemm.oeaw.ac.at.
Sylvia
S
Knapp
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria. Electronic address: cbock@cemm.oeaw.ac.at.
Christoph
C
Bock
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria. Electronic address: dbarlow@cemm.oeaw.ac.at.
Denise P
DP
Barlow
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria. Electronic address: qhudson@cemm.oeaw.ac.at.
Quanah J
QJ
Hudson
D000818:Animals; D001483:Base Sequence; D002454:Cell Differentiation / Q000502:physiology; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology; D019175:DNA Methylation; D058732:Embryoid Bodies / Q000378:metabolism*; D004707:Endoderm / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D018392:Genomic Imprinting / Q000235:genetics*; D006652:Histological Techniques; D017403:In Situ Hybridization; D051379:Mice; D008954:Models, Biological; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA; D015017:Yolk Sac / Q000166:cytology / Q000378:metabolism
Cystic embryoid bodies (EBs); DNA methylation; Genomic imprinting; Visceral endoderm (VE); Visceral yolk sac (VYS); Visceral yolk sac Endoderm (ysE)