Abstract
Recent studies have boosted our understanding of long noncoding RNAs (lncRNAs) in numerous biological processes, but few have examined their roles in somatic cell reprogramming. Through expression profiling and functional screening, we have identified that the large intergenic noncoding RNA p21 (lincRNA-p21) impairs reprogramming. Notably, lincRNA-p21 is induced by p53 but does not promote apoptosis or cell senescence in reprogramming. Instead, lincRNA-p21 associates with the H3K9 methyltransferase SETDB1 and the maintenance DNA methyltransferase DNMT1, which is facilitated by the RNA-binding protein HNRNPK. Consequently, lincRNA-p21 prevents reprogramming by sustaining H3K9me3 and/or CpG methylation at pluripotency gene promoters. Our results provide insight into the role of lncRNAs in reprogramming and establish a novel link between p53 and heterochromatin regulation.
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Acknowledgements
We thank all members of the Esteban Lab for their support. This work was supported by the National Basic Research Program of China (973 Program; 2011CB965201 and 2011CBA01106), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA01020106), the National Natural Science Foundation of China (31371513 and 81202010), the Cooperation Program of the Research Grants Council (RGC) of the Hong Kong Special Administrative Region and the National Natural Science Foundation of China (81261160506), the RGC of the Hong Kong Special Administrative Region, China (476310), the Natural Science Foundation of Guangdong Province (S2013010015487), the Bureau of Science, Technology and Information of Guangzhou Municipality (2012J5100040) and the International Science and Technology Cooperation Program of China (2013DFE33080).
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( Supplementary information is linked to the online version of the paper on the Cell Research website.)
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Supplementary information, Table S1
LincRNA expression in 4 cell types and reprogramming (related to Figure 1 and 2, Supplementary information, Figure S1 and S2) (XLSX 29 kb)
Supplementary information, Table S2
RNA-seq gene list (fold change higher than 1.5) at the indicated time points with lincRNA-p21 or Hnrnpk knockdown (related to Figure 5, Supplementary information, Figure S5 and S6). (XLSX 569 kb)
Supplementary information, Table S3
shRNA sequences, primers and antibodies used in this study (XLSX 29 kb)
Supplementary information, Figure S1
Expression of lincRNAs in reprogramming (related to Figure 1) (PDF 153 kb)
Supplementary information, Figure S2
LincRNA-p21 is induced by p53 (related to Figure 2) (PDF 321 kb)
Supplementary information, Figure S3
Comparison of cell proliferation and reprogramming efficiency in reprogrammed MEFs with lincRNA-p21 or/and p53 knockdown and iPSC clone characterization (related to Figure 2) (PDF 455 kb)
Supplementary information, Figure S5
LincRNA-p21 is a subset of HNRNPK function in reprogramming (related to Figure 5) (PDF 1289 kb)
Supplementary information, Figure S6
LincRNA-p21 influences the maturation of let-7 miRNAs but not the expression of mesenchymal or epithelial genes (related to Figure 5) (PDF 391 kb)
Supplementary information, Figure S7
HNRNPK binds to pluripotency genes in reprogramming and lincRNA-p21 regulates CpG methylation at the Nanog promoter (related to Figure 6) (PDF 479 kb)
Supplementary information, Data S1
Extended Materials and Methods (PDF 261 kb)
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Bao, X., Wu, H., Zhu, X. et al. The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Res 25, 80–92 (2015). https://doi.org/10.1038/cr.2014.165
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DOI: https://doi.org/10.1038/cr.2014.165
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