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

Nature Structural & Molecular Biology volume 18, pages 735–741 (2011)Cite this article

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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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Figure 1: Characterization of parthenogenetic HiPSCs showing normal diploid homozygote genome.
Figure 2: Global expression and DNA methylation analysis of imprinted genes in parthenogenetic HiPSCs.
Figure 3: Small noncoding imprinted RNAs in parthenogenetic HiPSCs.
Figure 4: Differentiation potential of human parthenogenesis.

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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).

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Authors and Affiliations

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

    Yonatan Stelzer, Ofra Yanuka & Nissim Benvenisty

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  1. Yonatan Stelzer
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  2. Ofra Yanuka
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  3. 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.

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Correspondence to Nissim Benvenisty.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Figures 1–8

Supplementary Figures 1–8 (PDF 7072 kb)

Supplementary Table 1

Expression profile of differentially expressed genes and mirRNAs (XLS 435 kb)

Supplementary Table 2

Tissue specific gene expression analysis (XLS 568 kb)

Supplementary Table 3

Gene expression analysis following 7 days of treatment with BMP4 (XLS 25 kb)

Supplementary Table 4

Full list of primers (DOC 39 kb)

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Stelzer, Y., Yanuka, O. & Benvenisty, N. Global analysis of parental imprinting in human parthenogenetic induced pluripotent stem cells. Nat Struct Mol Biol 18, 735–741 (2011). https://doi.org/10.1038/nsmb.2050

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