The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters

Cell Research

Volumn 25, Issue 1, 2015, Pages 80-92

  Bao, Xichen ^a   Wu, Haitao ^a,b   Zhu, Xihua ^a,b   Guo, Xiangpeng ^a   Hutchins, Andrew P ^a   Luo, Zhiwei ^a   Song, Hong ^a   Chen, Yongqiang ^a   Lai, Keyu ^a   Yin, Menghui ^a   Xu, Lingxiao ^c   Zhou, Liang ^d   Chen, Jiekai ^a   Wang, Dongye ^a,e   Qin, Baoming ^a,e,f   Frampton, Jon ^g   Tse, Hung Fat ^f,h   Pei, Duanqing ^a,f   Wang, Huating ⁱ   Zhang, Biliang ^a   Esteban, Miguel A ^a,f   more..

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c SHANDONG UNIVERSITY   (China)

^d SOUTHERN MEDICAL UNIVERSITY   (China)

^e GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH   (China)

^f UNIVERSITY OF HONG KONG   (Hong Kong)

^g UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^h UNIVERSITY OF HONG KONG   (China)

ⁱ CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

DNA methylation; H3K9 methylation; Heterochromatin; LincRNA p21; Long noncoding RNAs; p53; Somatic cell reprogramming

Indexed keywords

DNA (CYTOSINE 5) METHYLTRANSFERASE; DNA (CYTOSINE-5-)-METHYLTRANSFERASE 1; HETEROCHROMATIN; HISTONE; HISTONE LYSINE METHYLTRANSFERASE; LONG UNTRANSLATED RNA; PROTEIN P53; SETDB1 PROTEIN, MOUSE;

ANIMAL; APOPTOSIS; CELL PROLIFERATION; CPG ISLAND; CYTOLOGY; DNA METHYLATION; GENETICS; HETEROCHROMATIN; METABOLISM; MOUSE; NUCLEAR REPROGRAMMING; PLURIPOTENT STEM CELL; PROMOTER REGION;

ANIMALS; APOPTOSIS; CELL PROLIFERATION; CELLULAR REPROGRAMMING; CPG ISLANDS; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA METHYLATION; HETEROCHROMATIN; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; INDUCED PLURIPOTENT STEM CELLS; MICE; PROMOTER REGIONS, GENETIC; RNA, LONG NONCODING; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84920267059     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/cr.2014.165     Document Type: Article

References (36)

1. Takahashi K, Yamanaka S. Induced pluripotent stem cells in medicine and biology. Development 2013; 140:2457-2461.
2. Liang G, Zhang Y. Genetic and epigenetic variations in iPSCs: potential causes and implications for application. Cell Stem Cell 2013; 13:149-159.
3. Polo JM, Anderssen E, Walsh RM, et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 2012; 151:1617-1632.
4. Liu L, Xu Y, He M, et al. Transcriptional pause release is a rate-limiting step for somatic cell reprogramming. Cell Stem Cell 2014; 15:574-588.
5. Rais Y, Zviran A, Geula S, et al. Deterministic direct reprogramming of somatic cells to pluripotency. Nature 2013; 502:65-70.
6. Di Stefano B, Sardina JL, van Oevelen C, et al. C/EBPalpha poises B cells for rapid reprogramming into induced pluripotent stem cells. Nature 2014; 506:235-239.
7. Guo S, Zi X, Schulz VP, et al. Nonstochastic reprogramming from a privileged somatic cell state. Cell 2014; 156:649-662.
8. Tapia N, Schöler HR. p53 connects tumorigenesis and reprogramming to pluripotency. J Exp Med 2010; 207:2045-2048.
9. Soufi A, Donahue G, Zaret KS. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 2012; 151:994-1004.
10. Chen J, Liu H, Liu J, et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat Genet 2013; 45:34-42.
11. Sridharan R, Gonzales-Cope M, Chronis C, et al. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nat Cell Biol 2013; 15:872-882.
12. Mikkelsen TS, Hanna J, Zhang X, et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 2008; 454:49-55.
13. Subramanyam D, Blelloch R. From microRNAs to targets: pathway discovery in cell fate transitions. Curr Opin Genet Dev 2011; 21:498-503.
14. Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem 2012; 81:145-166.
15. Loewer S, Cabili MN, Guttman M, et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet 2010; 42 :1113-1117.
16. Wang Y, Xu Z, Jiang J, et al. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell 2013; 25:69-80.
17. Lin N, Chang KY, Li Z, et al. An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell 2014; 53:1005-1019.
18. Huarte M, Guttman M, Feldser D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010; 142:409-419.
19. Yoon JH, Abdelmohsen K, Srikantan S, et al. LincRNA-p21 suppresses target mRNA translation. Mol Cell 2012; 47:648-655.
20. Yang F, Zhang H, Mei Y, Wu M. Reciprocal regulation of HIF-1alpha and lincRNA-p21 modulates the Warburg effect. Mol Cell 2014; 53:88-100.
21. Silva J, Barrandon O, Nichols J, et al. Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol 2008; 6:e253.
22. Guttman M, Donaghey J, Carey BW, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011; 477:295-300.
23. Guo X, Liu Q, Wang G, et al. microRNA-29b is a novel mediator of Sox2 function in the regulation of somatic cell reprogramming. Cell Res 2013; 23:142-156.
24. Montserrat N, Nivet E, Sancho-Martinez I, et al. Reprogramming of human fibroblasts to pluripotency with lineage specifiers. Cell Stem Cell 2013; 13:341-350.
25. Shu J, Wu C, Wu Y, et al. Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell 2013; 153:963-975.
26. Choi YJ, Lin CP, Ho JJ, et al. miR-34 miRNAs provide a barrier for somatic cell reprogramming. Nat Cell Biol 2011; 13:1353-1360.
27. Lee HJ, Hore TA, Reik W. Reprogramming the methylome: erasing memory and creating diversity. Cell Stem Cell 2014; 14:710-719.
28. Bomsztyk K, Denisenko O, Ostrowski J. hnRNP K: one protein multiple processes. Bioessays 2004; 26:629-638.
29. Ng SY, Bogu GK, Soh BS, Stanton LW. The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis. Mol Cell 2013; 51:349-359.
30. Tuck AC, Tollervey D. A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell 2013; 154:996-1009.
31. Di Ruscio A, Ebralidze AK, Benoukraf T, et al. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 2013; 503:371-376.
32. Mohammad F, Mondal T, Guseva N, Pandey GK, Kanduri C. Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 2010; 137:2493-2499.
33. Dimitrova N, Zamudio JR, Jong RM, et al. LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint. Mol Cell 2014; 54:777-790.
34. Tsai MC, Manor O, Wan Y, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010; 329:689-693.
35. Pike KA, Hutchins AP, Vinette V, et al. Protein tyrosine phosphatase 1B is a regulator of the interleukin-10-induced transcriptional program in macrophages. Sci Signal 2014; 7:ra43.
36. Hutchins AP, Jauch R, Dyla M, Miranda-Saavedra D. glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data. Cell Regen 2014; 3:1. eCollection 2014.