Characterization of genetic-origin-dependent monoallelic expression in mouse embryonic stem cells.
Alleles
Animals
Cell Differentiation
/ genetics
Cell Line
DNA Methylation
/ genetics
Embryonic Stem Cells
/ metabolism
Epigenesis, Genetic
/ genetics
Epigenomics
/ methods
Female
Gene Expression
/ genetics
Gene Expression Profiling
/ methods
Gene Expression Regulation, Developmental
/ genetics
Genomic Imprinting
/ genetics
Male
Mice
Mice, Inbred Strains
Mouse Embryonic Stem Cells
/ metabolism
Pluripotent Stem Cells
/ metabolism
Transcriptome
/ genetics
embryonic stem cell
histone methylation
monoallelically expressed gene
retrotransposon
single nucleotide polymorphism
transcription factor binding site
Journal
Genes to cells : devoted to molecular & cellular mechanisms
ISSN: 1365-2443
Titre abrégé: Genes Cells
Pays: England
ID NLM: 9607379
Informations de publication
Date de publication:
Jan 2020
Jan 2020
Historique:
received:
22
10
2019
revised:
12
11
2019
accepted:
13
11
2019
pubmed:
17
11
2019
medline:
12
6
2020
entrez:
17
11
2019
Statut:
ppublish
Résumé
Monoallelic gene expression occurs in various mammalian cells and can be regulated genetically, epigenetically and/or stochastically. We identified 145 monoallelically expressed genes (MoEGs), including seven known imprinted genes, in mouse embryonic stem cells (ESCs) derived from reciprocal F1 hybrid blastocysts and cultured in 2i/LIF. As all MoEGs except for the imprinted genes were expressed in a genetic-origin-dependent manner, we focused on this class of MoEGs for mechanistic studies. We showed that a majority of the genetic-origin-dependent MoEGs identified in 2i/LIF ESCs remain monoallelically expressed in serum/LIF ESCs, but become more relaxed or even biallelically expressed upon differentiation. These MoEGs and their regulatory regions were highly enriched for single nucleotide polymorphisms. In addition, some MoEGs were associated with retrotransposon insertions/deletions, consistent with the fact that certain retrotransposons act as regulatory elements in pluripotent stem cells. Interestingly, most MoEGs showed allelic differences in enrichment of histone H3K27me and H3K4me marks, linking allelic epigenetic differences and monoallelic expression. In contrast, there was little or no allelic difference in CpG methylation or H3K9me. Taken together, our study highlights the impact of genetic variation including single nucleotide polymorphisms and retrotransposon insertions/deletions on monoallelic epigenetic marks and expression in ESCs.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
54-64Subventions
Organisme : Takeda Medical Research Foundation
Organisme : Japan Society for the Promotion of Science
ID : JP14J03854
Organisme : Japan Society for the Promotion of Science
ID : JP18H05214
Organisme : Japan Society for the Promotion of Science
ID : JP25112010
Informations de copyright
© 2019 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.
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