title: Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State.
abstract: Human embryonic stem cells (hESCs) undergo epigenetic changes in vitro which may compromise function, so an epigenetic pluripotency "signature" would be invaluable for line validation. We assessed Cytosine-phosphate-Guanine Island (CGI) methylation in hESCs by genomic DNA hybridisation to a CGI array, and saw substantial variation in CGI methylation between lines. Comparison of hESC CGI methylation profiles to corresponding somatic tissue data and hESC mRNA expression profiles identified a conserved hESC-specific methylation pattern associated with expressed genes. Transcriptional repressors and activators were over-represented amongst genes whose associated CGIs were methylated or unmethylated specifically in hESCs, respectively. Knockdown of candidate transcriptional regulators (HMGA1, GLIS2, PFDN5) induced differentiation in hESCs, whereas ectopic expression in fibroblasts modulated iPSC colony formation. Chromatin immunoprecipitation confirmed interaction between the candidates and the core pluripotency transcription factor network. We thus identify novel pluripotency genes on the basis of a conserved and distinct epigenetic configuration in human stem cells.
authors.affiliation: MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom.
authors.forename: Steve
authors.initials: S
authors.lastname: Pells
authors.affiliation: MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom.
authors.forename: Eirini
authors.initials: E
authors.lastname: Koutsouraki
authors.affiliation: MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom.
authors.forename: Sofia
authors.initials: S
authors.lastname: Morfopoulou
authors.affiliation: MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom.
authors.forename: Sara
authors.initials: S
authors.lastname: Valencia-Cadavid
authors.affiliation: MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Tomlinson
authors.affiliation: Centre for Molecular and Structural Biomedicine, University of Algarve, 8005-139, Faro, Portugal.
authors.forename: Ravi
authors.initials: R
authors.lastname: Kalathur
authors.affiliation: Centre for Molecular and Structural Biomedicine, University of Algarve, 8005-139, Faro, Portugal.
authors.forename: Matthias E
authors.initials: ME
authors.lastname: Futschik
authors.affiliation: MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom.
authors.forename: Paul A
authors.initials: PA
authors.lastname: De Sousa
mesh_terms: D002454:Cell Differentiation / Q000235:genetics; D002460:Cell Line; D002478:Cells, Cultured; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics; D005260:Female; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D025741:HMGA1a Protein / Q000235:genetics / Q000378:metabolism; D000066449:Human Embryonic Stem Cells / Q000378:metabolism*; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D051741:Kruppel-Like Transcription Factors / Q000235:genetics / Q000378:metabolism; D008297:Male; D011485:Protein Binding; D034622:RNA Interference; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: C447919:GLIS2 protein, human; D051741:Kruppel-Like Transcription Factors; C115636:PFDN5 protein, human; D012097:Repressor Proteins; D025741:HMGA1a Protein