[en] Pluripotency can be induced in somatic cells by overexpressing transcription factors, including POU class 5 homeobox 1 (OCT3/4), sex determining region Y-box 2 (SOX2), Kruppel-like factor 4 (KLF4), and myelocytomatosis oncogene (c-MYC). However, some induced pluripotent stem cells (iPSCs) exhibit defective differentiation and inappropriate maintenance of pluripotency features. Here we show that dynamic regulation of human endogenous retroviruses (HERVs) is important in the reprogramming process toward iPSCs, and in re-establishment of differentiation potential. During reprogramming, OCT3/4, SOX2, and KLF4 transiently hyperactivated LTR7s--the long-terminal repeats of HERV type-H (HERV-H)--to levels much higher than in embryonic stem cells by direct occupation of LTR7 sites genome-wide. Knocking down LTR7s or long intergenic non-protein coding RNA, regulator of reprogramming (lincRNA-RoR), a HERV-H-driven long noncoding RNA, early in reprogramming markedly reduced the efficiency of iPSC generation. KLF4 and LTR7 expression decreased to levels comparable with embryonic stem cells once reprogramming was complete, but failure to resuppress KLF4 and LTR7s resulted in defective differentiation. We also observed defective differentiation and LTR7 activation when iPSCs had forced expression of KLF4. However, when aberrantly expressed KLF4 or LTR7s were suppressed in defective iPSCs, normal differentiation was restored. Thus, a major mechanism by which OCT3/4, SOX2, and KLF4 promote human iPSC generation and reestablish potential for differentiation is by dynamically regulating HERV-H LTR7s.
Disciplines :
Biotechnology
Author, co-author :
Ohnuki, Mari
Tanabe, Koji
Sutou, Kenta
Teramoto, Ito
Sawamura, Yuka
Narita, Megumi
Nakamura, Michiko
Tokunaga, Yumie ; Université de Liège - ULiège > Medical Genomics-Unit of Animal Genomics
Nakamura, Masahiro
Watanabe, Akira
Yamanaka, Shinya
Takahashi, Kazutoshi
Language :
English
Title :
Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential.
Publication date :
2014
Journal title :
Proceedings of the National Academy of Sciences of the United States of America
ISSN :
0027-8424
eISSN :
1091-6490
Publisher :
National Academy of Sciences, Washington, United States - District of Columbia
Thomson JA, et al. (1998) Embryonic stem cell lines derived from human blastocysts. Science 282(5391):1145-1147. (Pubitemid 28516247)
Takahashi K, et al. (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131(5):861-872. (Pubitemid 350138099)
Koyanagi-Aoi M, et al. (2013) Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells. Proc Natl Acad Sci USA 110(51):20569-20574.
Lander ES, et al.; International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860-921. (Pubitemid 32165345)
Santoni FA, Guerra J, Luban J (2012) HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Retrovirology 9:111.
Kunarso G, et al. (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42(7):631-634.
Takayama N, et al. (2010) Transient activation of c-MYC expression is critical for efficient platelet generation from human induced pluripotent stem cells. J Exp Med 207(13):2817-2830.
Okita K, et al. (2011) A more efficient method to generate integration-free human iPS cells. Nat Methods 8(5):409-412.
Morizane A, Doi D, Kikuchi T, Nishimura K, Takahashi J (2011) Small-molecule inhibitors of bone morphogenic protein and activin/nodal signals promote highly efficient neural induction from human pluripotent stem cells. J Neurosci Res 89(2):117-126.
Kelley D, Rinn J (2012) Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol 13(11):R107.
Tanabe K, Nakamura M, Narita M, Takahashi K, Yamanaka S (2013) Maturation, not initiation, is the major roadblock during reprogramming toward pluripotency from human fibroblasts. Proc Natl Acad Sci USA 110(30):12172-12179.
Takahashi K, et al. (2014) Induction of pluripotency in human somatic cells via a transient state resembling primitive streak-like mesendoderm. Nat Commun 5:3678.
Jern P, Sperber GO, Ahlsén G, Blomberg J (2005) Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H. J Virol 79(10):6325-6337. (Pubitemid 40617236)
Liang Q, Xu Z, Xu R, Wu L, Zheng S (2012) Expression patterns of non-coding spliced transcripts from human endogenous retrovirus HERV-H elements in colon cancer. PLoS ONE 7(1):e29950.
Lister R, et al. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471(7336):68-73.
Rowe HM, et al. (2013) De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development 140(3):519-529.
Woltjen K, et al. (2009) piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature 458(7239):766-770.
Kim H, et al. (2011) miR-371-3 expression predicts neural differentiation propensity in human pluripotent stem cells. Cell Stem Cell 8(6):695-706.
Darr H, Mayshar Y, Benvenisty N (2006) Overexpression of NANOG in human ES cells enables feeder-free growth while inducing primitive ectoderm features. Development 133(6):1193-1201.
Lu X, et al. (2014) The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol 21(4):423-425.
Quenneville S, et al. (2011) In embryonic stem cells, ZFP57/KAP1 recognize a methylated hexanucleotide to affect chromatin and DNA methylation of imprinting control regions. Mol Cell 44(3):361-372.
Loewer S, et al. (2010) Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet 42(12):1113-1117.
Wang Y, et al. (2013) Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell 25(1):69-80.
Zhang A, et al. (2013) The human long non-coding RNA-RoR is a p53 repressor in response to DNA damage. Cell Res 23(3):340-350.
Kawamura T, et al. (2009) Linking the p53 tumour suppressor pathway to somatic cell reprogramming. Nature 460(7259):1140-1144.
Hong H, et al. (2009) Suppression of induced pluripotent stem cell generation by the p53-p21 pathway. Nature 460(7259):1132-1135.
Banito A, et al. (2009) Senescence impairs successful reprogramming to pluripotent stem cells. Genes Dev 23(18):2134-2139.
Utikal J, et al. (2009) Immortalization eliminates a roadblock during cellular reprogramming into iPS cells. Nature 460(7259):1145-1148.
Marión RM, et al. (2009) A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity. Nature 460(7259):1149-1153.
Macfarlan TS, et al. (2012) Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487(7405):57-63.
Friedli M, et al. (2014) Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency. Genome Res.
