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Global analysis of parental imprinting in human parthenogenetic induced pluripotent stem cells

Nature Structural & Molecular Biology volume 18, pages 735741 (2011) | Download Citation

Abstract

To study the role of parental imprinting in human embryogenesis, we generated parthenogenetic human induced pluripotent stem cells (iPSCs) with a homozygote diploid karyotype. Global gene expression and DNA methylation analyses of the parthenogenetic cells enabled the identification of the entire repertoire of paternally expressed genes. We thus demonstrated that the gene U5D, encoding a variant of the U5 small RNA component of the spliceosome, is an imprinted gene. Introduction of the U5D gene into parthenogenetic cells partially corrected their molecular phenotype. Our analysis also uncovered multiple miRNAs existing as imprinted clustered transcripts, whose putative targets we then studied further. Examination of the consequences of parthenogenesis on human development identified marked effects on the differentiation of extraembryonic trophectoderm and embryonic liver and muscle tissues. This analysis suggests that distinct regulatory imprinted small RNAs and their targets have substantial roles in human development.

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Acknowledgements

We thank M. Pick for her help with generating parthenogenetic iPSCs and O. Bar-Nur for providing WT-HiPSCs; U. Ben-David for his technical help with the teratoma formation experiments; T. Golan-Lev for her assistance with the graphic design and immunostaining assays; and A. Eden, D. Kitsberg, Y. Mayshar, D. Ronen and N. Sharon for critical reading of the manuscript. N.B. is the Herbert Cohn Chair in Cancer Research. This research was supported partially by the Israel Science Foundation–Morasha Foundation (grant no. 943/09).

Author information

Affiliations

  1. Stem Cell Unit, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel.

    • Yonatan Stelzer
    • , Ofra Yanuka
    •  & Nissim Benvenisty

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Contributions

Y.S.: conception and design, collection and assembly of data, data analysis and interpretation, and manuscript writing; O.Y.: conception and design, and collection and assembly of data; N.B.: conception and design, financial support, data analysis and interpretation, manuscript writing and final approval of the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nissim Benvenisty.

Supplementary information

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    Supplementary Figures 1–8

    Supplementary Figures 1–8

Excel files

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    Supplementary Table 1

    Expression profile of differentially expressed genes and mirRNAs

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    Supplementary Table 2

    Tissue specific gene expression analysis

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    Supplementary Table 3

    Gene expression analysis following 7 days of treatment with BMP4

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    Supplementary Table 4

    Full list of primers

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DOI

https://doi.org/10.1038/nsmb.2050

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