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Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors.

Planello AC, Ji J, Sharma V, Singhania R, Mbabaali F, Müller F, Alfaro JA, Bock C, De Carvalho DD, Batada NN - Cell Regen (Lond) (2014)

Bottom Line: Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs.Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs.These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.

View Article: PubMed Central - PubMed

Affiliation: Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2 M9 Canada ; Department of Morphology, Piracicaba Dental School, University of Campinas, Piracicaba, SP Brazil.

ABSTRACT
The conversion of somatic cells into pluripotent stem cells via overexpression of reprogramming factors involves epigenetic remodeling. DNA methylation at a significant proportion of CpG sites in induced pluripotent stem cells (iPSCs) differs from that of embryonic stem cells (ESCs). Whether different sets of reprogramming factors influence the type and extent of aberrant DNA methylation in iPSCs differently remains unknown. In order to help resolve this critical question, we generated human iPSCs from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and cMYC) or the Thomson factors (OCT4, SOX2, NANOG and LIN28), and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our iPSCs, we identified Yamanaka-iPSC (Y-iPSC)-specific and Thomson-iPSC (T-iPSC)-specific recurrent aberrations. Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs. Differences in the level of transcripts encoding DNMT3b and TET3 between Y-iPSCs and T-iPSCs may contribute partially to the distinct types of aberrations. Finally, de novo aberrantly methylated genes in Y-iPSCs were enriched for NANOG targets that are also aberrantly methylated in some cancers. Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs. These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.

No MeSH data available.


Related in: MedlinePlus

Model relating reprogramming factors and types of DNA methylation aberrations. A hypothetical genomic region showing four CpGs. White disk represent unmethylated CpG and black disk represent methylated CpG. Reprogramming with the Yamanaka factors leads to proper methylation but failure to demethylate, leading to enrichment of DNA demethylation aberrations in these iPSCs relative to ESCs. Similarly, reprogramming with the Thomson factors leads to proper demethylation but failure to methylate, leading to enrichment of DNA methylation aberrations in these iPSCs relative to ESCs.
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Fig6: Model relating reprogramming factors and types of DNA methylation aberrations. A hypothetical genomic region showing four CpGs. White disk represent unmethylated CpG and black disk represent methylated CpG. Reprogramming with the Yamanaka factors leads to proper methylation but failure to demethylate, leading to enrichment of DNA demethylation aberrations in these iPSCs relative to ESCs. Similarly, reprogramming with the Thomson factors leads to proper demethylation but failure to methylate, leading to enrichment of DNA methylation aberrations in these iPSCs relative to ESCs.

Mentions: In conclusion, our study has revealed that different reprogramming factor combinations lead to differences in the type and extent of DNA methylation aberrations observed in iPSCs (Figure 6). It is possible that the differences in the DNA methylation landscape between Y-iPSCs and T-iPSCs may lead to subtle phenotypic consequences even when starting with the exact same donor cell type. We suggest that the differences between T-iPSCs and Y-iPSCs highlighted above might be advantageously used for achieving optimal reprogramming of various donor cell types depending on their overall levels of DNA methylation of their genome.Figure 6


Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors.

Planello AC, Ji J, Sharma V, Singhania R, Mbabaali F, Müller F, Alfaro JA, Bock C, De Carvalho DD, Batada NN - Cell Regen (Lond) (2014)

Model relating reprogramming factors and types of DNA methylation aberrations. A hypothetical genomic region showing four CpGs. White disk represent unmethylated CpG and black disk represent methylated CpG. Reprogramming with the Yamanaka factors leads to proper methylation but failure to demethylate, leading to enrichment of DNA demethylation aberrations in these iPSCs relative to ESCs. Similarly, reprogramming with the Thomson factors leads to proper demethylation but failure to methylate, leading to enrichment of DNA methylation aberrations in these iPSCs relative to ESCs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230737&req=5

Fig6: Model relating reprogramming factors and types of DNA methylation aberrations. A hypothetical genomic region showing four CpGs. White disk represent unmethylated CpG and black disk represent methylated CpG. Reprogramming with the Yamanaka factors leads to proper methylation but failure to demethylate, leading to enrichment of DNA demethylation aberrations in these iPSCs relative to ESCs. Similarly, reprogramming with the Thomson factors leads to proper demethylation but failure to methylate, leading to enrichment of DNA methylation aberrations in these iPSCs relative to ESCs.
Mentions: In conclusion, our study has revealed that different reprogramming factor combinations lead to differences in the type and extent of DNA methylation aberrations observed in iPSCs (Figure 6). It is possible that the differences in the DNA methylation landscape between Y-iPSCs and T-iPSCs may lead to subtle phenotypic consequences even when starting with the exact same donor cell type. We suggest that the differences between T-iPSCs and Y-iPSCs highlighted above might be advantageously used for achieving optimal reprogramming of various donor cell types depending on their overall levels of DNA methylation of their genome.Figure 6

Bottom Line: Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs.Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs.These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.

View Article: PubMed Central - PubMed

Affiliation: Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2 M9 Canada ; Department of Morphology, Piracicaba Dental School, University of Campinas, Piracicaba, SP Brazil.

ABSTRACT
The conversion of somatic cells into pluripotent stem cells via overexpression of reprogramming factors involves epigenetic remodeling. DNA methylation at a significant proportion of CpG sites in induced pluripotent stem cells (iPSCs) differs from that of embryonic stem cells (ESCs). Whether different sets of reprogramming factors influence the type and extent of aberrant DNA methylation in iPSCs differently remains unknown. In order to help resolve this critical question, we generated human iPSCs from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and cMYC) or the Thomson factors (OCT4, SOX2, NANOG and LIN28), and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our iPSCs, we identified Yamanaka-iPSC (Y-iPSC)-specific and Thomson-iPSC (T-iPSC)-specific recurrent aberrations. Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs. Differences in the level of transcripts encoding DNMT3b and TET3 between Y-iPSCs and T-iPSCs may contribute partially to the distinct types of aberrations. Finally, de novo aberrantly methylated genes in Y-iPSCs were enriched for NANOG targets that are also aberrantly methylated in some cancers. Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs. These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.

No MeSH data available.


Related in: MedlinePlus