title: Genome-wide characterization of the routes to pluripotency.
abstract: Somatic cell reprogramming to a pluripotent state continues to challenge many of our assumptions about cellular specification, and despite major efforts, we lack a complete molecular characterization of the reprograming process. To address this gap in knowledge, we generated extensive transcriptomic, epigenomic and proteomic data sets describing the reprogramming routes leading from mouse embryonic fibroblasts to induced pluripotency. Through integrative analysis, we reveal that cells transition through distinct gene expression and epigenetic signatures and bifurcate towards reprogramming transgene-dependent and -independent stable pluripotent states. Early transcriptional events, driven by high levels of reprogramming transcription factor expression, are associated with widespread loss of histone H3 lysine 27 (H3K27me3) trimethylation, representing a general opening of the chromatin state. Maintenance of high transgene levels leads to re-acquisition of H3K27me3 and a stable pluripotent state that is alternative to the embryonic stem cell (ESC)-like fate. Lowering transgene levels at an intermediate phase, however, guides the process to the acquisition of ESC-like chromatin and DNA methylation signature. Our data provide a comprehensive molecular description of the reprogramming routes and is accessible through the Project Grandiose portal at http://www.stemformatics.org.
authors.affiliation: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.
authors.forename: Samer M I
authors.initials: SM
authors.lastname: Hussein
authors.affiliation: 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5T 3H7, Canada.
authors.forename: Mira C
authors.initials: MC
authors.lastname: Puri
authors.affiliation: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Tonge
authors.affiliation: 1] Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands [2] Netherlands Proteomics Centre, Padualaan 8, 3584CH Utrecht, The Netherlands.
authors.forename: Marco
authors.initials: M
authors.lastname: Benevento
authors.affiliation: 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 3H7, Canada.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Corso
authors.affiliation: Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra), ACT 2601, Australia.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Clancy
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Rowland
authors.initials: R
authors.lastname: Mosbergen
authors.affiliation: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.
authors.forename: Mira
authors.initials: M
authors.lastname: Li
authors.affiliation: 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, South Korea [2] Department of Biomedical Sciences and Biochemistry, Seoul National University College of Medicine, Seoul 110-799, South Korea.
authors.forename: Dong-Sung
authors.initials: DS
authors.lastname: Lee
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.
authors.forename: Nicole
authors.initials: N
authors.lastname: Cloonan
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.
authors.forename: David L A
authors.initials: DL
authors.lastname: Wood
authors.affiliation: 1] Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands [2] Netherlands Proteomics Centre, Padualaan 8, 3584CH Utrecht, The Netherlands.
authors.forename: Javier
authors.initials: J
authors.lastname: Munoz
authors.affiliation: Gene and Stem Cell Therapy Program and Bioinformatics Lab, Centenary Institute, Camperdown 2050, NSW, Australia &Sydney Medical School, 31 University of Sydney 2006, New South Wales, Australia.
authors.forename: Robert
authors.initials: R
authors.lastname: Middleton
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Othmar
authors.initials: O
authors.lastname: Korn
authors.affiliation: 1] Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra), ACT 2601, Australia [2] Genome Discovery Unit, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra) 2601, ACT, Australia.
authors.forename: Hardip R
authors.initials: HR
authors.lastname: Patel
authors.affiliation: 1] Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto M5S-3G9, Canada [2] The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto M5S 3E1, Canada.
authors.forename: Carl A
authors.initials: CA
authors.lastname: White
authors.affiliation: 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, South Korea [2] Life Science Institute, Macrogen Inc., Seoul 153-781, South Korea.
authors.forename: Jong-Yeon
authors.initials: JY
authors.lastname: Shin
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.
authors.forename: Maely E
authors.initials: ME
authors.lastname: Gauthier
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.
authors.forename: Kim-Anh
authors.initials: KA
authors.lastname: Lê Cao
authors.affiliation: 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, South Korea [2] Department of Biomedical Sciences and Biochemistry, Seoul National University College of Medicine, Seoul 110-799, South Korea.
authors.forename: Jong-Il
authors.initials: JI
authors.lastname: Kim
authors.affiliation: Department of Systems &Computational Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA.
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Mar
authors.affiliation: Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto M5S-3G9, Canada.
authors.forename: Nika
authors.initials: N
authors.lastname: Shakiba
authors.affiliation: Gene and Stem Cell Therapy Program and Bioinformatics Lab, Centenary Institute, Camperdown 2050, NSW, Australia &Sydney Medical School, 31 University of Sydney 2006, New South Wales, Australia.
authors.forename: William
authors.initials: W
authors.lastname: Ritchie
authors.affiliation: 1] Gene and Stem Cell Therapy Program and Bioinformatics Lab, Centenary Institute, Camperdown 2050, NSW, Australia &Sydney Medical School, 31 University of Sydney 2006, New South Wales, Australia [2] Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, New South Wales, Australia.
authors.forename: John E J
authors.initials: JE
authors.lastname: Rasko
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.
authors.forename: Sean M
authors.initials: SM
authors.lastname: Grimmond
authors.affiliation: 1] Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto M5S-3G9, Canada [2] The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto M5S 3E1, Canada.
authors.forename: Peter W
authors.initials: PW
authors.lastname: Zandstra
authors.affiliation: 1] Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia [2] College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK.
authors.forename: Christine A
authors.initials: CA
authors.lastname: Wells
authors.affiliation: 1] Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra), ACT 2601, Australia [2] Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia.
authors.forename: Thomas
authors.initials: T
authors.lastname: Preiss
authors.affiliation: 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, South Korea [2] Department of Biomedical Sciences and Biochemistry, Seoul National University College of Medicine, Seoul 110-799, South Korea [3] Life Science Institute, Macrogen Inc., Seoul 153-781, South Korea.
authors.forename: Jeong-Sun
authors.initials: JS
authors.lastname: Seo
authors.affiliation: 1] Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands [2] Netherlands Proteomics Centre, Padualaan 8, 3584CH Utrecht, The Netherlands.
authors.forename: Albert J R
authors.initials: AJ
authors.lastname: Heck
authors.affiliation: 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada [3] Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario M5S 1E2, Canada.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Rogers
authors.affiliation: 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 3H7, Canada [3] Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario M5S 1E2, Canada.
authors.forename: Andras
authors.initials: A
authors.lastname: Nagy
mesh_terms: D000818:Animals; D065150:Cellular Reprogramming / Q000235:genetics*; D002843:Chromatin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D004843:Epistasis, Genetic / Q000235:genetics; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D016678:Genome / Q000235:genetics*; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D057026:Induced Pluripotent Stem Cells / Q000166:cytology* / Q000378:metabolism*; D020407:Internet; D051379:Mice; D020543:Proteome / Q000235:genetics; D040901:Proteomics; D062085:RNA, Long Noncoding / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics; D059467:Transcriptome / Q000235:genetics; D019076:Transgenes / Q000235:genetics
chemical_list: D002843:Chromatin; D006657:Histones; D020543:Proteome; D062085:RNA, Long Noncoding; D014157:Transcription Factors