دورية أكاديمية
أعرض في EDS

Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states.

التفاصيل البيبلوغرافية
العنوان: Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states.
المؤلفون: Dirks RAM; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6500 HB, Nijmegen, The Netherlands., van Mierlo G; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6500 HB, Nijmegen, The Netherlands.; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA, Nijmegen, The Netherlands., Kerstens HHD; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6500 HB, Nijmegen, The Netherlands., Bernardo AS; The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust- Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK.; Mill Hill Laboratory, The Ridgeway, The Francis Crick Institute, London, NW7 1AA, UK., Kobolák J; BioTalentum Ltd., Gödöllő, Hungary., Bock I; BioTalentum Ltd., Gödöllő, Hungary., Maruotti J; UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France.; Phenocell SAS, Evry, France., Pedersen RA; The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust- Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK., Dinnyés A; BioTalentum Ltd., Gödöllő, Hungary.; Molecular Animal Biotechnology Laboratory, Szent István University, Gödöllő, Hungary., Huynen MA; Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands., Jouneau A; UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France., Marks H; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6500 HB, Nijmegen, The Netherlands. H.Marks@ncmls.ru.nl.
المصدر: Epigenetics & chromatin [Epigenetics Chromatin] 2019 Feb 15; Vol. 12 (1), pp. 14. Date of Electronic Publication: 2019 Feb 15.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 101471619 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-8935 (Electronic) Linking ISSN: 17568935 NLM ISO Abbreviation: Epigenetics Chromatin Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : BioMed Central
مواضيع طبية MeSH: Alleles* , Genomic Imprinting*, Mouse Embryonic Stem Cells/*metabolism , RNA, Messenger/*genetics, Animals ; Cell Differentiation ; Cell Line ; Cells, Cultured ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Silencing ; Germ Layers/cytology ; Germ Layers/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred DBA ; Mouse Embryonic Stem Cells/cytology
مستخلص: 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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فهرسة مساهمة: Keywords: Allele-specific RNA-seq; ESCs; Embryonic stem cells; EpiSCs; Genomic imprinting; Genotyping; Mouse embryo; Nuclear transfer (NT); Parthenogenetic activation (PGA); Pluripotency
المشرفين على المادة: 0 (RNA, Messenger)
تواريخ الأحداث: Date Created: 20190216 Date Completed: 20190315 Latest Revision: 20200225
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC6376749
DOI: 10.1186/s13072-019-0259-8
PMID: 30767785
قاعدة البيانات: MEDLINE
الوصف
تدمد:1756-8935
DOI:10.1186/s13072-019-0259-8