Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 560842
Title Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states
Author(s) Dirks, René A.M.; Mierlo, Guido Van; Kerstens, Hindrik H.D.; Bernardo, Andreia S.; Kobolák, Julianna; Bock, István; Maruotti, Julien; Pedersen, Roger A.; Dinnyés, András; Huynen, Martijn A.; Jouneau, Alice; Marks, Hendrik
Source Epigenetics and Chromatin 12 (2019)1. - ISSN 1756-8935
DOI https://doi.org/10.1186/s13072-019-0259-8
Publication type Refereed Article in a scientific journal
Publication year 2019
Keyword(s) Allele-specific RNA-seq - Embryonic stem cells - EpiSCs - ESCs - Genomic imprinting - Genotyping - Mouse embryo - Nuclear transfer (NT) - Parthenogenetic activation (PGA) - Pluripotency
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.

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