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RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells
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“In mouse embryonic stem (mES) cells, it was shown that TET2 binds to PSPC1, an RNA-binding protein, to mediate RNA 5-methylcytosine (m5C) oxidation16.”
From RNA m5C oxidation by TET2 regulates chromatin state and leukaemogenesis (2024) · cites this paper as [16]
In the citing paper
“Both proteins have been associated with additional functions beyond DNA modification.30,31,32,33,34,35,36,37”
From Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging (2024) · cites this paper as [34]
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Genome engineering using the CRISPR-Cas9 system
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
Tsai, M.-C., Manor, O., Wan, Y., Mosammaparast, N., Wang, J. K., Lan, F., Shi, Y., Segal, E., & Chang, H. Y. (2010) · Science · doi:10.1126/science.1192002 · Cited by 3,290
Self-citationGenome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., et al. (2015) · Nature · doi:10.1038/nature14136 · Cited by 2,825
Warren, L., Manos, P. D., Ahfeldt, T., Loh, Y.-H., Li, H., Lau, F., Ebina, W., Mandal, P. K., Smith, Z. D., Meissner, A., et al. (2010) · Cell Stem Cell · doi:10.1016/j.stem.2010.08.012 · Cited by 2,662
Role of TET enzymes in DNA methylation, development, and cancer
Rasmussen, K. D., & Helin, K. (2016) · Genes & Development · doi:10.1101/gad.276568.115 · Cited by 1,040
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity
Williams, K., Christensen, J., Pedersen, M. T., Johansen, J. V., Cloos, P. A. C., Rappsilber, J., & Helin, K. (2011) · Nature · doi:10.1038/nature10066 · Cited by 1,021
Regulatory evolution of innate immunity through co-option of endogenous retroviruses
Chuong, E. B., Elde, N. C., & Feschotte, C. (2016) · Science · doi:10.1126/science.aad5497 · Cited by 1,008
KAP1 controls endogenous retroviruses in embryonic stem cells
Rowe, H. M., Jakobsson, J., Mesnard, D., Rougemont, J., Reynard, S., Aktas, T., Maillard, P. V., Layard-Liesching, H., Verp, S., Marquis, J., et al. (2010) · Nature · doi:10.1038/nature08674 · Cited by 874
Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6
Zhang, Q., Zhao, K., Shen, Q., Han, Y., Gu, Y., Li, X., Zhao, D., Liu, Y., Wang, C., Zhang, X., et al. (2015) · Nature · doi:10.1038/nature15252 · Cited by 807
Research works printed but not linked: 46
- Wu, X. & Zhang, Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat. Rev. Genet. 18, 517–534 (2017). · DOI · Paper page
- Frye, M. & Blanco, S. Post-transcriptional modifications in development and stem cells. Development 143, 3871–3881 (2016). · DOI
- Masiello, I. & Biggiogera, M. Ultrastructural localization of 5-methylcytosine on DNA and RNA. Cell. Mol. Life Sci. 74, 3057–3064 (2017). · DOI
- Zhang, H. Y., Xiong, J., Qi, B. L., Feng, Y. Q. & Yuan, B. F. The existence of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA in mammals. Chem. Commun. (Camb.) 52, 737–740 (2016). · DOI
- Miao, Z. et al. 5-hydroxymethylcytosine is detected in RNA from mouse brain tissues. Brain Res. 1642, 546–552 (2016). · DOI
- Delatte, B. et al. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science 351, 282–285 (2016). · DOI · Paper page
- Fu, L. et al. Tet-mediated formation of 5-hydroxymethylcytosine in RNA. J. Am. Chem. Soc. 136, 11582–11585 (2014). · DOI · Paper page
- Schlesinger, S. & Goff, S. P. Retroviral transcriptional regulation and embryonic stem cells: war and peace. Mol. Cell. Biol. 35, 770–777 (2015). · DOI
- Macfarlan, T. S. et al. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487, 57–63 (2012). · DOI · Paper page
- Kim, J., Cantor, A. B., Orkin, S. H. & Wang, J. Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells. Nat. Protoc. 4, 506–517 (2009). · DOI
- Wang, J. et al. A protein interaction network for pluripotency of embryonic stem cells. Nature 444, 364–368 (2006). · DOI
- Huang, Y. et al. Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. Proc. Natl. Acad. Sci. USA 111, 1361–1366 (2014). · DOI
- Hon, G. C. et al. 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Mol. Cell 56, 286–297 (2014). · DOI · Paper page
- Fox, A. H., Bond, C. S. & Lamond, A. I. P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner. Mol. Biol. Cell 16, 5304–5315 (2005). · DOI
- Gilbert, S. L., Pehrson, J. R. & Sharp, P. A. XIST RNA associates with specific regions of the inactive X chromatin. J. Biol. Chem. 275, 36491–36494 (2000). · DOI
- Chen, Q., Chen, Y., Bian, C., Fujiki, R. & Yu, X. TET2 promotes histone O-GlcNAcylation during gene transcription. Nature 493, 561–564 (2013). · DOI · Paper page
- Knott, G. J., Bond, C. S. & Fox, A. H. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold. Nucleic Acids Res. 44, 3989–4004 (2016). · DOI
- Ma, C. et al. Nono, a bivalent domain factor, regulates Erk signaling and mouse embryonic stem cell pluripotency. Cell Rep. 17, 997–1007 (2016). · DOI
- Cao, S. et al. Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing. BMC Genomics 15, 4 (2014). · DOI
- Peaston, A. E. et al. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7, 597–606 (2004). · DOI · Paper page
- Friedli, M. & Trono, D. The developmental control of transposable elements and the evolution of higher species. Annu. Rev. Cell Dev. Biol. 31, 429–451 (2015). · DOI
- Leeb, M. et al. Polycomb complexes act redundantly to repress genomic repeats and genes. Genes Dev. 24, 265–276 (2010). · DOI · Paper page
- Maksakova, I. A. et al. Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. Epigenetics Chromatin 6, 15 (2013). · DOI
- Kigami, D., Minami, N., Takayama, H. & Imai, H. MuERV-L is one of the earliest transcribed genes in mouse one-cell embryos. Biol. Reprod. 68, 651–654 (2003). · DOI
- Macfarlan, T. S. et al. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev. 25, 594–607 (2011). · DOI
- Rowe, H. M. & Trono, D. Dynamic control of endogenous retroviruses during development. Virology 411, 273–287 (2011). · DOI
- Kowalska, E. et al. Distinct roles of DBHS family members in the circadian transcriptional feedback loop. Mol. Cell. Biol. 32, 4585–4594 (2012). · DOI
- Li, Z. et al. Deletion of Tet2 in mice leads to dysregulated hematopoietic stem cells and subsequent development of myeloid malignancies. Blood 118, 4509–4518 (2011). · DOI · Paper page
- Huber, S. M. et al. Formation and abundance of 5-hydroxymethylcytosine in RNA. ChemBioChem 16, 752–755 (2015). · DOI
- Amort, T. et al. Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain. Genome Biol. 18, 1 (2017). · DOI
- Zhang, X. et al. The tRNA methyltransferase NSun2 stabilizes p16INK4 mRNA by methylating the 3′-untranslated region of p16. Nat. Commun. 3, 712 (2012). · DOI
- Vella, P. et al. Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells. Mol. Cell 49, 645–656 (2013). · DOI
- Deplus, R. et al. TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS. EMBO J. 32, 645–655 (2013). · DOI · Paper page
- Chen, L. L. & Carmichael, G. G. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol. Cell 35, 467–478 (2009). · DOI
- Fox, A. H. & Lamond, A. I. Paraspeckles. Cold Spring Harb. Perspect. Biol. 2, a000687 (2010).
- He, C. et al. High-resolution mapping of RNA-binding regions in the nuclear proteome of embryonic stem cells. Mol. Cell 64, 416–430 (2016). · DOI
- Lee, E. et al. Landscape of somatic retrotransposition in human cancers. Science 337, 967–971 (2012). · DOI · Paper page
- Choi, Y. J. et al. Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells. Science 355, eaag1927 (2017). · DOI
- Gerdes, P., Richardson, S. R. & Faulkner, G. J. TET enzymes: double agents in the transposable element-host genome conflict. Genome Biol. 17, 259 (2016). · DOI
- de la Rica, L. et al. TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells. Genome Biol. 17, 234 (2016). · DOI
- Ivanova, N. et al. Dissecting self-renewal in stem cells with RNA interference. Nature 442, 533–538 (2006). · DOI
- Lee, T. I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006). · DOI
- Ule, J., Jensen, K., Mele, A. & Darnell, R. B. CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37, 376–386 (2005). · DOI
- Elsässer, S. J., Noh, K. M., Diaz, N., Allis, C. D. & Banaszynski, L. A. Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature 522, 240–244 (2015). · DOI
- Ding, J. et al. Tex10 coordinates epigenetic control of super-enhancer activity in pluripotency and reprogramming. Cell Stem Cell 16, 653–668 (2015). · DOI
- Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012). · DOI · Paper page
Cited by
Ten things you should know about transposable elements
Bourque, G., Burns, K. H., Gehring, M., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvák, Z., Levin, H. L., Macfarlan, T. S., et al. (2018) · Genome Biology · doi:10.1186/s13059-018-1577-z · Cited by 1,430
Jakobsen, N. A., Turkalj, S., Zeng, A. G. X., Stoilova, B., Metzner, M., Rahmig, S., Nagree, M. S., Shah, S., Moore, R., Usukhbayar, B., et al. (2024) · Cell Stem Cell · doi:10.1016/j.stem.2024.05.010 · Cited by 130
RNA m5C oxidation by TET2 regulates chromatin state and leukaemogenesis
Zou, Z., Dou, X., Li, Y., Zhang, Z., Wang, J., Gao, B., Xiao, Y., Wang, Y., Zhao, L., Sun, C., et al. (2024) · Nature · doi:10.1038/s41586-024-07969-x · Cited by 103
Self-citation
Metadata
- Authors
- Guallar, D., Bi, X., Pardavila, J. A., Huang, X., Saenz, C., Shi, X., Zhou, H., Faiola, F., Ding, J., Haruehanroengra, P., Yang, F., Li, D., Sanchez-Priego, C., Saunders, A., Pan, F., Valdes, V. J., Kelley, K., Blanco, M. G., Chen, L., Wang, H., Sheng, J., Xu, M., Fidalgo, M., Shen, X., & Wang, J.
- Venue
- Nature Genetics
- Published
- 2018-02-26
- Volume
- 50
- Issue
- 3
- Pages
- 443-451
- ISSN
- 1061-4036
- 1546-1718
- PMC
- PMC5862756
- Cited by
- 190
- References
- 14
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
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