title: Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics.
abstract: Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines, some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine whether this aberrant methylation results from genetic variation or non-genetic mechanisms, we generated human iPSCs from monozygotic twins to investigate how genetic background, clone, and passage number contribute. We found that aberrantly methylated CpGs are enriched in regulatory regions associated with MYC protein motifs and affect gene expression. We classified differentially methylated CpGs as being associated with genetic and/or non-genetic factors (clone and passage), and we found that aberrant methylation preferentially occurs at CpGs associated with clone-specific effects. We further found that clone-specific effects play a strong role in recurrent aberrant methylation at specific CpG sites across different studies. Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming.
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
authors.forename: Athanasia D
authors.initials: AD
authors.lastname: Panopoulos
authors.affiliation: Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Erin N
authors.initials: EN
authors.lastname: Smith
authors.affiliation: Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Angelo D
authors.initials: AD
authors.lastname: Arias
authors.affiliation: Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; BioSpyder Technologies, Inc., Carlsbad, CA 92008, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Shepard
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Yuriko
authors.initials: Y
authors.lastname: Hishida
authors.affiliation: Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Veronica
authors.initials: V
authors.lastname: Modesto
authors.affiliation: Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Kenneth E
authors.initials: KE
authors.lastname: Diffenderfer
authors.affiliation: Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
authors.forename: Clay
authors.initials: C
authors.lastname: Conner
authors.affiliation: Human Longevity, Inc., San Diego, CA 92121, USA.
authors.forename: William
authors.initials: W
authors.lastname: Biggs
authors.affiliation: Human Longevity, Inc., San Diego, CA 92121, USA.
authors.forename: Efren
authors.initials: E
authors.lastname: Sandoval
authors.affiliation: Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: D'Antonio-Chronowska
authors.affiliation: Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: W Travis
authors.initials: WT
authors.lastname: Berggren
authors.affiliation: Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address: belmonte@salk.edu.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Izpisua Belmonte
authors.affiliation: Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: kafrazer@ucsd.edu.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Frazer
mesh_terms: D002999:Clone Cells; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D005347:Fibroblasts / Q000378:metabolism; D005786:Gene Expression Regulation; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D059372:Nucleotide Motifs / Q000235:genetics*; D016271:Proto-Oncogene Proteins c-myc / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000378:metabolism; D014430:Twins, Monozygotic / Q000235:genetics
chemical_list: D016271:Proto-Oncogene Proteins c-myc; D014157:Transcription Factors
keywords: MYC binding motifs; NHLBI NextGen; aberrant methylation; genetic background; iPSC; iPSCORE; induced pluripotent stem cells; methylation variation; reprogramming