دورية أكاديمية
Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states.
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. |
References: | Exp Cell Res. 1999 Apr 10;248(1):18-24. (PMID: 10094809) Cancer Res. 1999 Apr 1;59(7 Suppl):1743s-1746s. (PMID: 10197590) Genes Dev. 1999 Dec 1;13(23):3115-24. (PMID: 10601037) Nat Genet. 2000 Feb;24(2):109-10. (PMID: 10655052) Mamm Genome. 2000 May;11(5):405-8. (PMID: 10790543) Curr Biol. 2000 Aug 24;10(16):989-92. (PMID: 10985386) Proc Natl Acad Sci U S A. 1975 Dec;72(12):5099-102. (PMID: 1108013) Mol Reprod Dev. 2001 Apr;58(4):376-83. (PMID: 11241773) Proc Natl Acad Sci U S A. 2001 May 22;98(11):6209-14. (PMID: 11331774) Science. 2001 Jul 6;293(5527):95-7. (PMID: 11441181) Mol Reprod Dev. 2003 Oct;66(2):126-33. (PMID: 12950099) Proc Natl Acad Sci U S A. 1962 Jan 15;48:9-16. (PMID: 13868717) Biol Reprod. 2004 Apr;70(4):1162-70. (PMID: 14681201) Reproduction. 2005 Jan;129(1):27-38. (PMID: 15615896) Cancer Cell. 2005 Oct;8(4):275-85. (PMID: 16226703) Nat Genet. 2005 Nov;37(11):1274-9. (PMID: 16244654) Cell. 2006 Apr 21;125(2):315-26. (PMID: 16630819) J Transl Med. 2006 May 08;4:20. (PMID: 16681851) Stem Cells. 2006 Sep;24(9):2023-33. (PMID: 16690779) Cell. 2006 Aug 25;126(4):663-76. (PMID: 16904174) Science. 2007 Jan 26;315(5811):482-6. (PMID: 17170255) Nat Biotechnol. 2007 Jul;25(7):803-16. (PMID: 17572666) Nature. 2007 Jul 12;448(7150):196-9. (PMID: 17597760) Nature. 2007 Jul 12;448(7150):191-5. (PMID: 17597762) Nature. 2007 Aug 2;448(7153):553-60. (PMID: 17603471) Nature. 2007 Aug 30;448(7157):1050-3. (PMID: 17660834) Nat Biotechnol. 2007 Sep;25(9):1045-50. (PMID: 17704765) Hum Mol Genet. 2007 Oct 15;16 Spec No. 2:R243-51. (PMID: 17911167) Stem Cells. 2008 Jan;26(1):79-88. (PMID: 17962706) Cell. 2008 Feb 22;132(4):527-31. (PMID: 18295568) Cell Stem Cell. 2007 Sep 13;1(3):346-52. (PMID: 18371368) Genes Dev. 2008 May 1;22(9):1141-6. (PMID: 18451104) Nature. 2008 May 22;453(7194):519-23. (PMID: 18497825) Genome Biol. 2008;9(9):R137. (PMID: 18798982) Development. 2009 Feb;136(3):437-48. (PMID: 19141673) Development. 2009 Apr;136(7):1063-9. (PMID: 19224983) Hum Mol Genet. 2009 Jun 15;18(12):2177-87. (PMID: 19324901) Cell Reprogram. 2010 Feb;12(1):105-13. (PMID: 20132018) Bioinformatics. 2010 Apr 1;26(7):873-81. (PMID: 20147302) Stem Cells. 2010 Apr;28(4):743-52. (PMID: 20201062) Nature. 1991 May 23;351(6324):325-9. (PMID: 2034278) Nature. 1991 May 23;351(6324):329-31. (PMID: 2034279) Nature. 2010 May 13;465(7295):175-81. (PMID: 20418860) Nature. 2010 Sep 16;467(7313):285-90. (PMID: 20644535) Epigenetics. 2011 Jan;6(1):52-62. (PMID: 20864803) Cold Spring Harb Perspect Biol. 2011 Jul 01;3(7):null. (PMID: 21576252) Nat Rev Genet. 2011 Jun;12(6):429-42. (PMID: 21587299) Nat Genet. 2011 May 29;43(7):648-55. (PMID: 21623374) Nat Rev Genet. 2011 Jul 18;12(8):565-75. (PMID: 21765458) Nature. 2011 Sep 14;477(7364):289-94. (PMID: 21921910) Nature. 2011 Sep 14;477(7364):326-9. (PMID: 21921916) Stem Cells. 2012 Feb;30(2):161-8. (PMID: 22109880) Cell Reprogram. 2012 Feb;14(1):56-67. (PMID: 22204592) Nat Genet. 2012 Mar 04;44(4):398-405, S1-2. (PMID: 22387999) PLoS Genet. 2012;8(3):e1002600. (PMID: 22479196) Cell. 2012 Apr 27;149(3):590-604. (PMID: 22541430) BMC Res Notes. 2013 Apr 04;6:133. (PMID: 23557140) Am J Stem Cells. 2011 Aug 19;1(1):59-74. (PMID: 23671798) Cell Stem Cell. 2013 Sep 5;13(3):360-9. (PMID: 23850244) Cell Stem Cell. 2013 Sep 5;13(3):351-9. (PMID: 23850245) Biochim Biophys Acta. 2014 Mar;1839(3):129-37. (PMID: 24096207) Nature. 2013 Dec 12;504(7479):282-6. (PMID: 24172903) Cell Stem Cell. 2013 Dec 5;13(6):663-75. (PMID: 24315441) Nat Protoc. 2014 Mar;9(3):559-74. (PMID: 24504480) Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4484-9. (PMID: 24623855) Stem Cells Dev. 2014 Sep 1;23(17):2014-29. (PMID: 24738887) Development. 2014 May;141(9):1805-13. (PMID: 24757003) Nat Cell Biol. 2014 Jun;16(6):516-28. (PMID: 24859004) Annu Rev Genomics Hum Genet. 2014;15:93-126. (PMID: 24898037) Nat Rev Genet. 2014 Aug;15(8):517-30. (PMID: 24958438) Nature. 2014 Jul 10;511(7508):177-83. (PMID: 25008523) Cell Stem Cell. 2014 Oct 2;15(4):471-487. (PMID: 25090446) Cell. 2014 Sep 11;158(6):1254-1269. (PMID: 25215486) PLoS One. 2015 Mar 06;10(3):e0120033. (PMID: 25749170) Nat Genet. 2015 May;47(5):544-9. (PMID: 25848752) Genome Biol. 2015 Aug 03;16:149. (PMID: 26235224) Cell Stem Cell. 2016 Mar 3;18(3):323-329. (PMID: 26853856) Nature. 2016 Jul 06;535(7611):289-293. (PMID: 27383781) Nat Commun. 2016 Jul 07;7:12144. (PMID: 27385103) Cell Stem Cell. 2016 Oct 6;19(4):502-515. (PMID: 27424783) Cold Spring Harb Protoc. 2017 Jan 3;2017(1):. (PMID: 28049783) Cell. 1987 Nov 6;51(3):503-12. (PMID: 2822260) Cell Rep. 2017 May 2;19(5):957-968. (PMID: 28467909) Nature. 2017 Jul 27;547(7664):419-424. (PMID: 28723896) Nature. 2017 Aug 10;548(7666):224-227. (PMID: 28746308) Nature. 2017 Aug 10;548(7666):219-223. (PMID: 28746311) Elife. 2017 Aug 14;6:. (PMID: 28806168) Biol Open. 2018 Aug 17;7(8):null. (PMID: 30026265) Cell Stem Cell. 2019 Jan 3;24(1):123-137.e8. (PMID: 30472157) Nature. 1984 Sep 27-Oct 3;311(5984):374-6. (PMID: 6482961) Cell. 1984 May;37(1):179-83. (PMID: 6722870) J Embryol Exp Morphol. 1983 Apr;74:297-309. (PMID: 6886600) Proc Natl Acad Sci U S A. 1981 Dec;78(12):7634-8. (PMID: 6950406) Nature. 1981 Jul 9;292(5819):154-6. (PMID: 7242681) Mol Cell Biol. 1995 Jan;15(1):141-51. (PMID: 7799920) Development. 1994 Jun;120(6):1651-60. (PMID: 8050371) Nat Genet. 1997 Sep;17(1):12-3. (PMID: 9288087) Development. 1998 Jun;125(12):2273-82. (PMID: 9584126) |
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 |
تدمد: | 1756-8935 |
---|---|
DOI: | 10.1186/s13072-019-0259-8 |