Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

Alan M. O'Doherty, Paul McGettigan, Rachelle E. Irwin, David A. Magee, Dominic Gagne, Eric Fournier, Abdullah Al-Naib, Marc André Sirard, Colum P. Walsh, Claude Robert, Trudee Fair

    Research output: Contribution to journalArticle

    3 Citations (Scopus)

    Abstract

    Background: Assisted reproductive technologies (ART) are widely used to treat fertility issues in humans and for the production of embryos in mammalian livestock. The use of these techniques, however, is not without consequence as they are often associated with inauspicious pre- and postnatal outcomes including premature birth, intrauterine growth restriction and increased incidence of epigenetic disorders in human and large offspring syndrome in cattle. Here, global DNA methylation profiles in the trophectoderm and embryonic discs of in vitro produced (IVP), superovulation-derived (SOV) and unstimulated, synchronised control day 17 bovine conceptuses (herein referred to as AI) were interrogated using the EmbryoGENE DNA Methylation Array (EDMA). Pyrosequencing was used to validate four loci identified as differentially methylated on the array and to assess the differentially methylated regions (DMRs) of six imprinted genes in these conceptuses. The impact of embryo-production induced DNA methylation aberrations was determined using Ingenuity Pathway Analysis, shedding light on the potential functional consequences of these differences. Results: Of the total number of differentially methylated loci identified (3140) 77.3 and 22.7% were attributable to SOV and IVP, respectively. Differential methylation was most prominent at intragenic sequences within the trophectoderm of IVP and SOV-derived conceptuses, almost a third (30.8%) of the differentially methylated loci mapped to intragenic regions. Very few differentially methylated loci were detected in embryonic discs (ED); 0.16 and 4.9% of the differentially methylated loci were located in the ED of SOV-derived and IVP conceptuses, respectively. The overall effects of SOV and IVP on the direction of methylation changes were associated with increased methylation; 70.6% of the differentially methylated loci in SOV-derived conceptuses and 57.9% of the loci in IVP-derived conceptuses were more methylated compared to AI-conceptuses. Ontology analysis of probes associated with intragenic sequences suggests enrichment for terms associated with cancer, cell morphology and growth. Conclusion: By examining (1) the effects of superovulation and (2) the effects of an in vitro system (oocyte maturation, fertilisation and embryo culture) we have identified that the assisted reproduction process of superovulation alone has the largest impact on the DNA methylome of subsequent embryos.

    LanguageEnglish
    Article number438 (2018)
    Pages1-15
    Number of pages15
    JournalBMC Genomics
    Volume19
    Issue number1
    DOIs
    Publication statusPublished - 5 Jun 2018

    Fingerprint

    Superovulation
    Assisted Reproductive Techniques
    Methylation
    DNA Methylation
    Embryonic Structures
    Mammalian Embryo
    In Vitro Oocyte Maturation Techniques
    Premature Birth
    Livestock
    Growth
    Oligonucleotide Array Sequence Analysis
    Fertilization
    Epigenomics
    Reproduction
    Fertility
    In Vitro Techniques
    DNA
    Incidence

    Keywords

    • Assisted reproduction technologies (ART)
    • Bovine
    • Development
    • DNA methylation
    • Embryo
    • Epigenetics
    • Gene body
    • Genomic imprinting
    • Reproduction

    Cite this

    O'Doherty, Alan M. ; McGettigan, Paul ; Irwin, Rachelle E. ; Magee, David A. ; Gagne, Dominic ; Fournier, Eric ; Al-Naib, Abdullah ; Sirard, Marc André ; Walsh, Colum P. ; Robert, Claude ; Fair, Trudee. / Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies. In: BMC Genomics. 2018 ; Vol. 19, No. 1. pp. 1-15.
    @article{b9e0194c9d3d4638848b73ce06fe90e8,
    title = "Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies",
    abstract = "Background: Assisted reproductive technologies (ART) are widely used to treat fertility issues in humans and for the production of embryos in mammalian livestock. The use of these techniques, however, is not without consequence as they are often associated with inauspicious pre- and postnatal outcomes including premature birth, intrauterine growth restriction and increased incidence of epigenetic disorders in human and large offspring syndrome in cattle. Here, global DNA methylation profiles in the trophectoderm and embryonic discs of in vitro produced (IVP), superovulation-derived (SOV) and unstimulated, synchronised control day 17 bovine conceptuses (herein referred to as AI) were interrogated using the EmbryoGENE DNA Methylation Array (EDMA). Pyrosequencing was used to validate four loci identified as differentially methylated on the array and to assess the differentially methylated regions (DMRs) of six imprinted genes in these conceptuses. The impact of embryo-production induced DNA methylation aberrations was determined using Ingenuity Pathway Analysis, shedding light on the potential functional consequences of these differences. Results: Of the total number of differentially methylated loci identified (3140) 77.3 and 22.7{\%} were attributable to SOV and IVP, respectively. Differential methylation was most prominent at intragenic sequences within the trophectoderm of IVP and SOV-derived conceptuses, almost a third (30.8{\%}) of the differentially methylated loci mapped to intragenic regions. Very few differentially methylated loci were detected in embryonic discs (ED); 0.16 and 4.9{\%} of the differentially methylated loci were located in the ED of SOV-derived and IVP conceptuses, respectively. The overall effects of SOV and IVP on the direction of methylation changes were associated with increased methylation; 70.6{\%} of the differentially methylated loci in SOV-derived conceptuses and 57.9{\%} of the loci in IVP-derived conceptuses were more methylated compared to AI-conceptuses. Ontology analysis of probes associated with intragenic sequences suggests enrichment for terms associated with cancer, cell morphology and growth. Conclusion: By examining (1) the effects of superovulation and (2) the effects of an in vitro system (oocyte maturation, fertilisation and embryo culture) we have identified that the assisted reproduction process of superovulation alone has the largest impact on the DNA methylome of subsequent embryos.",
    keywords = "Assisted reproduction technologies (ART), Bovine, Development, DNA methylation, Embryo, Epigenetics, Gene body, Genomic imprinting, Reproduction",
    author = "O'Doherty, {Alan M.} and Paul McGettigan and Irwin, {Rachelle E.} and Magee, {David A.} and Dominic Gagne and Eric Fournier and Abdullah Al-Naib and Sirard, {Marc Andr{\'e}} and Walsh, {Colum P.} and Claude Robert and Trudee Fair",
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    Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies. / O'Doherty, Alan M.; McGettigan, Paul; Irwin, Rachelle E.; Magee, David A.; Gagne, Dominic; Fournier, Eric; Al-Naib, Abdullah; Sirard, Marc André; Walsh, Colum P.; Robert, Claude; Fair, Trudee.

    In: BMC Genomics, Vol. 19, No. 1, 438 (2018), 05.06.2018, p. 1-15.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies

    AU - O'Doherty, Alan M.

    AU - McGettigan, Paul

    AU - Irwin, Rachelle E.

    AU - Magee, David A.

    AU - Gagne, Dominic

    AU - Fournier, Eric

    AU - Al-Naib, Abdullah

    AU - Sirard, Marc André

    AU - Walsh, Colum P.

    AU - Robert, Claude

    AU - Fair, Trudee

    N1 - Acceptance date is listed on the final published version that has been uploaded

    PY - 2018/6/5

    Y1 - 2018/6/5

    N2 - Background: Assisted reproductive technologies (ART) are widely used to treat fertility issues in humans and for the production of embryos in mammalian livestock. The use of these techniques, however, is not without consequence as they are often associated with inauspicious pre- and postnatal outcomes including premature birth, intrauterine growth restriction and increased incidence of epigenetic disorders in human and large offspring syndrome in cattle. Here, global DNA methylation profiles in the trophectoderm and embryonic discs of in vitro produced (IVP), superovulation-derived (SOV) and unstimulated, synchronised control day 17 bovine conceptuses (herein referred to as AI) were interrogated using the EmbryoGENE DNA Methylation Array (EDMA). Pyrosequencing was used to validate four loci identified as differentially methylated on the array and to assess the differentially methylated regions (DMRs) of six imprinted genes in these conceptuses. The impact of embryo-production induced DNA methylation aberrations was determined using Ingenuity Pathway Analysis, shedding light on the potential functional consequences of these differences. Results: Of the total number of differentially methylated loci identified (3140) 77.3 and 22.7% were attributable to SOV and IVP, respectively. Differential methylation was most prominent at intragenic sequences within the trophectoderm of IVP and SOV-derived conceptuses, almost a third (30.8%) of the differentially methylated loci mapped to intragenic regions. Very few differentially methylated loci were detected in embryonic discs (ED); 0.16 and 4.9% of the differentially methylated loci were located in the ED of SOV-derived and IVP conceptuses, respectively. The overall effects of SOV and IVP on the direction of methylation changes were associated with increased methylation; 70.6% of the differentially methylated loci in SOV-derived conceptuses and 57.9% of the loci in IVP-derived conceptuses were more methylated compared to AI-conceptuses. Ontology analysis of probes associated with intragenic sequences suggests enrichment for terms associated with cancer, cell morphology and growth. Conclusion: By examining (1) the effects of superovulation and (2) the effects of an in vitro system (oocyte maturation, fertilisation and embryo culture) we have identified that the assisted reproduction process of superovulation alone has the largest impact on the DNA methylome of subsequent embryos.

    AB - Background: Assisted reproductive technologies (ART) are widely used to treat fertility issues in humans and for the production of embryos in mammalian livestock. The use of these techniques, however, is not without consequence as they are often associated with inauspicious pre- and postnatal outcomes including premature birth, intrauterine growth restriction and increased incidence of epigenetic disorders in human and large offspring syndrome in cattle. Here, global DNA methylation profiles in the trophectoderm and embryonic discs of in vitro produced (IVP), superovulation-derived (SOV) and unstimulated, synchronised control day 17 bovine conceptuses (herein referred to as AI) were interrogated using the EmbryoGENE DNA Methylation Array (EDMA). Pyrosequencing was used to validate four loci identified as differentially methylated on the array and to assess the differentially methylated regions (DMRs) of six imprinted genes in these conceptuses. The impact of embryo-production induced DNA methylation aberrations was determined using Ingenuity Pathway Analysis, shedding light on the potential functional consequences of these differences. Results: Of the total number of differentially methylated loci identified (3140) 77.3 and 22.7% were attributable to SOV and IVP, respectively. Differential methylation was most prominent at intragenic sequences within the trophectoderm of IVP and SOV-derived conceptuses, almost a third (30.8%) of the differentially methylated loci mapped to intragenic regions. Very few differentially methylated loci were detected in embryonic discs (ED); 0.16 and 4.9% of the differentially methylated loci were located in the ED of SOV-derived and IVP conceptuses, respectively. The overall effects of SOV and IVP on the direction of methylation changes were associated with increased methylation; 70.6% of the differentially methylated loci in SOV-derived conceptuses and 57.9% of the loci in IVP-derived conceptuses were more methylated compared to AI-conceptuses. Ontology analysis of probes associated with intragenic sequences suggests enrichment for terms associated with cancer, cell morphology and growth. Conclusion: By examining (1) the effects of superovulation and (2) the effects of an in vitro system (oocyte maturation, fertilisation and embryo culture) we have identified that the assisted reproduction process of superovulation alone has the largest impact on the DNA methylome of subsequent embryos.

    KW - Assisted reproduction technologies (ART)

    KW - Bovine

    KW - Development

    KW - DNA methylation

    KW - Embryo

    KW - Epigenetics

    KW - Gene body

    KW - Genomic imprinting

    KW - Reproduction

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    UR - https://pure.ulster.ac.uk/en/publications/intragenic-sequences-in-the-trophectoderm-harbour-the-greatest-pr

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