Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states

René A.M. Dirks, Guido van Mierlo, Hindrik H.D. Kerstens, Andreia S. Bernardo, Julianna Kobolák, István Bock, Julien Maruotti, Roger A. Pedersen, A. Dinnyés, Martijn A. Huynen, Alice Jouneau, Hendrik Marks

Research output: Article

Abstract

BACKGROUND: Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we apply allele-specific RNA-seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic tissues between E3.5 and E7.25 and in pluripotent cell lines to evaluate maintenance of imprinted gene expression. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos and from embryos obtained after nuclear transfer (NT) or parthenogenetic activation (PGA). RESULTS: As homozygous genomic regions of PGA-derived cells are not compatible with allele-specific RNA-seq, we developed an RNA-seq-based genotyping strategy allowing identification of informative heterozygous regions. Global analysis shows that proper imprinted gene expression as observed in embryonic tissues is largely lost in the ESC lines included in this study, which mainly consisted of female ESCs. Differentiation of ESC lines to embryoid bodies or NPCs does not restore monoallelic expression of imprinted genes, neither did reprogramming of the serum-cultured ESCs to the pluripotent ground state by the use of 2 kinase inhibitors. Fertilized EpiSC and EpiSC-NT lines largely maintain imprinted gene expression, as did EpiSC-PGA lines that show known paternally expressed genes being silent and known maternally expressed genes consistently showing doubled expression. Notably, two EpiSC-NT lines show aberrant silencing of Rian and Meg3, two critically imprinted genes in mouse iPSCs. With respect to female EpiSC, most of the lines displayed completely skewed X inactivation suggesting a (near) clonal origin. CONCLUSIONS: Altogether, our analysis provides a comprehensive overview of imprinted gene expression in pluripotency and provides a benchmark to allow identification of cell lines that faithfully maintain imprinted gene expression and therefore retain full developmental potential.

Original languageEnglish
Number of pages1
JournalEpigenetics & chromatin
Volume12
Issue number1
DOIs
Publication statusPublished - febr. 15 2019

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Gene Expression Profiling
Alleles
RNA
Gene Expression
Embryonic Stem Cells
Cell Line
Genes
Embryonic Structures
Genomic Imprinting
Embryoid Bodies
Benchmarking
Germ Layers
X Chromosome Inactivation
Phosphotransferases
Stem Cells
Maintenance
Serum

Keywords

    ASJC Scopus subject areas

    • Molecular Biology
    • Genetics

    Cite this

    Dirks, R. A. M., van Mierlo, G., Kerstens, H. H. D., Bernardo, A. S., Kobolák, J., Bock, I., ... Marks, H. (2019). Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states. Epigenetics & chromatin, 12(1). https://doi.org/10.1186/s13072-019-0259-8

    Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states. / Dirks, René A.M.; van Mierlo, Guido; Kerstens, Hindrik H.D.; Bernardo, Andreia S.; Kobolák, Julianna; Bock, István; Maruotti, Julien; Pedersen, Roger A.; Dinnyés, A.; Huynen, Martijn A.; Jouneau, Alice; Marks, Hendrik.

    In: Epigenetics & chromatin, Vol. 12, No. 1, 15.02.2019.

    Research output: Article

    Dirks, RAM, van Mierlo, G, Kerstens, HHD, Bernardo, AS, Kobolák, J, Bock, I, Maruotti, J, Pedersen, RA, Dinnyés, A, Huynen, MA, Jouneau, A & Marks, H 2019, 'Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states' Epigenetics & chromatin, vol. 12, no. 1. https://doi.org/10.1186/s13072-019-0259-8
    Dirks, René A.M. ; van Mierlo, Guido ; Kerstens, Hindrik H.D. ; Bernardo, Andreia S. ; Kobolák, Julianna ; Bock, István ; Maruotti, Julien ; Pedersen, Roger A. ; Dinnyés, A. ; Huynen, Martijn A. ; Jouneau, Alice ; Marks, Hendrik. / Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states. In: Epigenetics & chromatin. 2019 ; Vol. 12, No. 1.
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    AU - van Mierlo, Guido

    AU - Kerstens, Hindrik H.D.

    AU - Bernardo, Andreia S.

    AU - Kobolák, Julianna

    AU - Bock, István

    AU - Maruotti, Julien

    AU - Pedersen, Roger A.

    AU - Dinnyés, A.

    AU - Huynen, Martijn A.

    AU - Jouneau, Alice

    AU - Marks, Hendrik

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    N2 - BACKGROUND: Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we apply allele-specific RNA-seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic tissues between E3.5 and E7.25 and in pluripotent cell lines to evaluate maintenance of imprinted gene expression. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos and from embryos obtained after nuclear transfer (NT) or parthenogenetic activation (PGA). RESULTS: As homozygous genomic regions of PGA-derived cells are not compatible with allele-specific RNA-seq, we developed an RNA-seq-based genotyping strategy allowing identification of informative heterozygous regions. Global analysis shows that proper imprinted gene expression as observed in embryonic tissues is largely lost in the ESC lines included in this study, which mainly consisted of female ESCs. Differentiation of ESC lines to embryoid bodies or NPCs does not restore monoallelic expression of imprinted genes, neither did reprogramming of the serum-cultured ESCs to the pluripotent ground state by the use of 2 kinase inhibitors. Fertilized EpiSC and EpiSC-NT lines largely maintain imprinted gene expression, as did EpiSC-PGA lines that show known paternally expressed genes being silent and known maternally expressed genes consistently showing doubled expression. Notably, two EpiSC-NT lines show aberrant silencing of Rian and Meg3, two critically imprinted genes in mouse iPSCs. With respect to female EpiSC, most of the lines displayed completely skewed X inactivation suggesting a (near) clonal origin. CONCLUSIONS: Altogether, our analysis provides a comprehensive overview of imprinted gene expression in pluripotency and provides a benchmark to allow identification of cell lines that faithfully maintain imprinted gene expression and therefore retain full developmental potential.

    AB - BACKGROUND: Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we apply allele-specific RNA-seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic tissues between E3.5 and E7.25 and in pluripotent cell lines to evaluate maintenance of imprinted gene expression. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos and from embryos obtained after nuclear transfer (NT) or parthenogenetic activation (PGA). RESULTS: As homozygous genomic regions of PGA-derived cells are not compatible with allele-specific RNA-seq, we developed an RNA-seq-based genotyping strategy allowing identification of informative heterozygous regions. Global analysis shows that proper imprinted gene expression as observed in embryonic tissues is largely lost in the ESC lines included in this study, which mainly consisted of female ESCs. Differentiation of ESC lines to embryoid bodies or NPCs does not restore monoallelic expression of imprinted genes, neither did reprogramming of the serum-cultured ESCs to the pluripotent ground state by the use of 2 kinase inhibitors. Fertilized EpiSC and EpiSC-NT lines largely maintain imprinted gene expression, as did EpiSC-PGA lines that show known paternally expressed genes being silent and known maternally expressed genes consistently showing doubled expression. Notably, two EpiSC-NT lines show aberrant silencing of Rian and Meg3, two critically imprinted genes in mouse iPSCs. With respect to female EpiSC, most of the lines displayed completely skewed X inactivation suggesting a (near) clonal origin. CONCLUSIONS: Altogether, our analysis provides a comprehensive overview of imprinted gene expression in pluripotency and provides a benchmark to allow identification of cell lines that faithfully maintain imprinted gene expression and therefore retain full developmental potential.

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    KW - Genomic imprinting

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    KW - Mouse embryo

    KW - Nuclear transfer (NT)

    KW - Parthenogenetic activation (PGA)

    KW - Pluripotency

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