Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Ábel Vértesy, Wibowo Arindrarto, Matthias S. Roost, Björn Reinius, Vanessa Torrens-Juaneda, Monika Bialecka, Ioannis Moustakas, Yavuz Ariyurek, Ewart Kuijk, Hailiang Mei, Rickard Sandberg, Alexander van Oudenaarden () and Susana M. Chuva de Sousa Lopes ()
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Ábel Vértesy: Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center
Wibowo Arindrarto: Leiden University Medical Center
Matthias S. Roost: Leiden University Medical Center
Björn Reinius: Karolinska Institutet
Vanessa Torrens-Juaneda: Leiden University Medical Center
Monika Bialecka: Leiden University Medical Center
Ioannis Moustakas: Leiden University Medical Center
Yavuz Ariyurek: Leiden University Medical Center
Ewart Kuijk: University Medical Center Utrecht
Hailiang Mei: Leiden University Medical Center
Rickard Sandberg: Karolinska Institutet
Alexander van Oudenaarden: Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center
Susana M. Chuva de Sousa Lopes: Leiden University Medical Center

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract In contrast to mouse, human female germ cells develop asynchronously. Germ cells transition to meiosis, erase genomic imprints, and reactivate the X chromosome. It is unknown if these events all appear asynchronously, and how they relate to each other. Here we combine exome sequencing of human fetal and maternal tissues with single-cell RNA-sequencing of five donors. We reconstruct full parental haplotypes and quantify changes in parental allele-specific expression, genome-wide. First we distinguish primordial germ cells (PGC), pre-meiotic, and meiotic transcriptional stages. Next we demonstrate that germ cells from various stages monoallelically express imprinted genes and confirm this by methylation patterns. Finally, we show that roughly 30% of the PGCs are still reactivating their inactive X chromosome and that this is related to transcriptional stage rather than fetal age. Altogether, we uncover the complexity and cell-to-cell heterogeneity of transcriptional and epigenetic remodeling in female human germ cells.

Date: 2018
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DOI: 10.1038/s41467-018-04215-7

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