Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells
Matthew M. Edwards,
Ning Wang,
Dashiell J. Massey,
Sakshi Bhatele,
Dieter Egli,
Amnon Koren
Affiliations
Matthew M. Edwards
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Ning Wang
Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
Dashiell J. Massey
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Sakshi Bhatele
Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
Dieter Egli
Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Corresponding author
Amnon Koren
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Corresponding author
Summary: Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.
