Ahmad, S., Mu, X., Yang, F., Greenwald, E., Park, J. W., Jacob, E., Zhang, C. Z., Hur, S. (2018). Breaching self-tolerance to ALU duplex RNA underlies MDA5-mediated inflammation. Cell 172, 797-810.
Bao, W., Kojima, K., Kohany, O. (2015). Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob. DNA 6:11.
Bennett, J.M., Catovsky, D., Daniel, M.T., Flandrin, G., Galton, D.A., Gralnick, H.R., Sultan, C. (1985). Proposed revised criteria for the classification of acute myeloid leukemia. A report of the French-American-British Cooperative Group. Ann. Intern. Med. 103, 620–625.
Bersani, F., Lee, E., Kharchenko, P. V., Xu, A. W., Liu, M., Xega, K., MacKenzie, O. C., Brannigan, B. W., Wittner, B. S., Jung, H., Ramaswamy, S., Park, P. J., Maheswaran, S., Ting, D. T., Haber, D. A. (2015). Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. PNAS 112, 15148-15153.
Blagitko-Dorfs, N., Schlosser, P., Greve, G., Pfeifer, D., Meier, R., Baude, A., Brocks, D., Plass, C., Lübbert, M. (2019). Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation. Leukemia.
Brocks, D., Schmidt, C. R., Daskalakis, M., Jang, H. S., Shah, N. M., Li, D., Li, J., Zhang, B., Hou, Y., Laudato, S., Lipka, D. B., Schott, J., Bierhoff, H., Assenov, Y., Helf, M., Ressnerova, A., Islam, M. S., Lindroth, A. M., Haas, S., Essers, M., Imbusch, C. D., Brors, B., Oehme, I., Witt, O., Lübbert, M., Mallm, J. P., Rippe, K., Will, R., Weichenhan, D., Stoecklin, G., Gerhäuser, C., Oakes, C. C., Wang, T., Plass, C. (2017). DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repaeats. Nat. Genet. 49, 1052-1060.
Bulut-Karslioglu, A., De La Rosa-Velázquez, I. A., Ramirez, F., Barenboim, M., Onishi-Seebacher, M., Arand, J., Galán, C., Winter, G. E., Engist, B., Gerle, B., O'Sullivan, R. J., Martens, J. H., Walter, J., Manke, T., Lachner, M., Jenuwein, T. (2014). Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells. Mol. Cell 55, 277-290.
Burns, K. H. (2017). Transposable elements in cancer. Nat. Rev. Cancer 17, 415-424
Cancer Genome Atlas Research Network: Ley, T.J., Miller, C., Ding, L., Raphael, B.J., Mungall, A.J., Robertson, A.G., Hoadley, K., Triche, T.J., Laird, P.W., Baty, J.D., Fulton, L.L., Fulton, R., Heath, S.E., Kalicki-Veizer, J., Kandoth, C., Klco, J.M., Koboldt, D.C., Kanchi, K.-L., Kulkarni, S., Lamprecht, T.L., Larson, D.E., Lin, L., Lu, C., McLellan, M.D., McMichael, J.F., Payton, J., Schmidt, H., Spencer, D.H., Tomasson, M.H., Wallis, J.W., Wartman, L.D., Watson, M.A., Welch, J., Wendl, M.C., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Chiu, R., Chu, A., Chuah, E., Chun, H.-J., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R.A., Jones, S., Karsan, A., Lee, D., Li, H.I., Marra, M.A., Mayo, M., Moore, R.A., Mungall, K., Parker, J., Pleasance, E., Plettner, P., Schein, J., Stoll, D., Swanson, L., Tam, A., Thiessen, N., Varhol, R., Wye, N., Zhao, Y., Gabriel, S., Getz, G., Sougnez, C., Zou, L., Leiserson, M.D.M., Vandin, F., Wu, H.-T., Applebaum, F., Baylin, S.B., Akbani, R., Broom, B.M., Chen, K., Motter, T.C., Nguyen, K., Weinstein, J.N., Zhang, N., Ferguson, M.L., Adams, C., Black, A., Bowen, J., Gastier-Foster, J., Grossman, T., Lichtenberg, T., Wise, L., Davidsen, T., Demchok, J.A., Shaw, K.R.M., Sheth, M., Sofia, H.J., Yang, L., Downing, J.R., Eley, G. (2013). Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med. 368, 2059–2074.
Casa, V., Gabellini, D. (2012). A repetitive elements perspective in Polycomb epigenetics. Front. Genet. 3, 1–16.
Chen, L., Kostadima, M., Martens, J.H.A., Canu, G., Garcia, S.P., Turro, E., Downes, K., Macaulay, I.C., Bielczyk-Maczynska, E., Coe, S., Farrow, S., Poudel, P., Burden, F., Jansen, S.B.G., Astle, W.J., Attwood, A., Bariana, T., de Bono, B., Breschi, A., Chambers, J.C., Choudry, F.A., Clarke, L., Coupland, P., van der Ent, M., Erber, W.N., Jansen, J.H., Favier, R., Fenech, M.E., Foad, N., Freson, K., van Geet, C., Gomez, K., Guigo, R., Hampshire, D., Kelly, A.M., Kerstens, H.H.D., Kooner, J.S., Laffan, M., Lentaigne, C., Labalette, C., Martin, T., Meacham, S., Mumford, A., Nurnberg, S.T., Palumbo, E., van der Reijden, B.A., Richardson, D., Sammut, S.J., Slodkowicz, G., Tamuri, A.U., Vasquez, L., Voss, K., Watt, S., Westbury, S., Flicek, P., Loos, R., Goldman, N., Bertone, P., Read, R.J., Richardson, S., Cvejic, A., Soranzo, N., Ouwehand, W.H., Stunnenberg, H.G., Frontini, M., Rendon, A. (2014). Transcriptional diversity during lineage commitment of human blood progenitors. Science 345:1251033.
Chiappinelli, K. B., Strissel, P. L., Desrichard, A., Li, H., Henke, C., Akman, B., Hein, A., Rote, N. S., Cope, L. M., Snyder, A., Makarov, V., Budhu, S., Slamon, D.J., Wolchok, J. D., Pardoll, D. M. , Beckmann, M. W., Zahnow, C. A., Merghoub, T., Chan, T. A., Baylin, S. B., Strick, R. (2015). Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. Cell 162, 974–986.
Chuong, E. B., Elde, N. C., Feschotte, C. (2016). Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351, 1083-1087.
Colombo, A.R., Zubair, A., Thiagarajan, D., Nuzhdin, S., Triche, T.J., Ramsingh, G. (2017). Suppression of transposable elements in leukemic stem cells. Sci. Rep. 7:7029.
Colombo, A.R., Triche, T., Ramsingh, G. (2018). Transposable element expression in acute myeloid leukemia transcriptome and prognosis. Sci. Rep. 8:16449.
Cuellar, T.L., Herzner, A.-M., Zhang, X., Goyal, Y., Watanabe, C., Friedman, B.A., Janakiraman, V., Durinck, S., Stinson, J., Arnott, D., Cheung, T.K., Chaudhuri, S., Modrusan, Z., Doerr, J.M., Classon, M., Haley, B. (2017). Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia. J. Cell Biol. 216, 3535–3549.
Ecco, G., Cassano, M., Kauzlaric, A., Duc, J., Coluccio, A., Offner, S., Imbeault, M., Rowe, H. M., Turelli, P., Trono, D. (2016). Transposable elements and their KRAB-ZFP controllers regulate gene expression in adult tissues. Dev Cell 36, 611-623.
Efroni, S., Duttagupta, R., Cheng, J., Dehghani, H., Hoeppner, D. J., Dash, C., Bazett-Jones, D. P., Le Grice, S., McKay, R. D., Buetow, K. H., Gingeras, T. R., Misteli, T., Meshorer, E. (2008). Global transcription in pluripotent embryonic stem cells. Cell Stem Cell, 2, 437-447.
Elsässer, S.J., Noh, K.-M., Diaz, N., Allis, C.D., Banaszynski, L.A. (2015). Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature 522, 240–244.
Faulkner, G. J., Kimura, Y., Daub, C. O., Wani, S., Plessy, C., Irvine, K. M., Schroder, K., Cloonan, N., Steptoe, A. L., Lassmann, T., Waki, K., Hornig, N., Arakawa, T., Takahashi, H., Kawai, J., Forrest, A. R., Suzuki, H., Hayashizaki, Y., Hume, D. A., Orlando, V., Grimmond, S. M., Carninci, P. (2009). The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 41, 563-571.
Ferguson, F. M., Fedorov, O., Chaikuad, A., Philpott, M., Muniz, J. R., Felletar, I., von Delft, F., Heightman, T., Knapp, S., Abell, C., Ciulli, A. (2013). Targeting low-druggability bromodomains: fragment based screening and inhibitor design against the BAZ2B bromodomain. J. Med. Chem. 56, 10183-10187.
Fort, A., Hashimoto, K., Yamada, D., Salimullah, M., Keya, C. A., Saxena, A., Bonetti, A., Voineagu, I., Bertin, N., Kratz, A., Noro, Y., Wong, C. H., de Hoon, M., Andersson, R., Sandelin, A., Suzuki, H., Wei, C. L., Koseki, H. FANTOM Consortium, Hasegawa, Y., Forrest, A. R., Carninci, P. (2013). Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat. Genet. 46, 558-566.
Garrido-Ramos, M. A. (ed) (2012). 'Repetitive DNA'. Karger AG, Basel
Gregory, G. D., Vakoc, C. R., Rozovskaia, T., Zheng, X., Patel, S., Nakamura, T., Canaani, E., Blobel, G. A. (2007). Mammalian ASH1L is a histone methyltransferase that occupies the transcribed region of active genes. Mol. Cell Biol. 27, 8466-8479.
Grishina, O., Schmoor, C., Döhner, K., Hackanson, B., Lubrich, B., May, A. M., Cieslik, C., Müller, M. J., Lübbert, M. (2015). DECIDER: prospective randomized multicenter phase II trial of low-dose decitabine (DAC) administered alone or in combination with the histone deacetylase inhibitor valproic acid (VPA) and all-trans retinoic acid (ATRA) in patients >60 years with acute myeloid leukemia who are ineligible for induction chemotherapy. BMC Cancer 15:430.
Guler, G. D., Tindell, C. A., Pitti, R., Wilson, C., Nichols, K., KaiWai Cheung, T., Kim, H. J., Wongchenko, M., Yan, Y., Haley, B., Cuellar, T., Webster, J., Alag, N., Hegde, G., Jackson, E., Nance, T. L., Giresi, P. G., Chen, K. B., Liu, J., Jhunjhunwala, S., Settleman, J., Stephan, J. P., Arnott, D., Classon, M. (2017). Repression of stress-induced LINE-1 expression protects cancer cell subpopulations from lethal drug exposure. Cancer Cell 32, 221-237.
Hall, L.L., Byron, M., Carone, D.M., Whitfield, T.W., Pouliot, G.P., Fischer, A., Jones, P., Lawrence, J. B. (2017). Demethylated HSATII DNA and HSATII RNA foci sequester PRC1 and MeCP2 into cancer-specific nuclear bodies. Cell Rep. 18, 2943–2956.
Hoelper, D., Huang, H., Jain, A.Y., Patel, D.J., Lewis, P.W. (2017). Structural and mechanistic insights into ATRX-dependent and -independent functions of the histone chaperone DAXX. Nat. Commun. 8:1193.
Jachowicz, J. W,, Bing, X., Pontabry, J., Bošković, A., Rando, O. J., Torres-Padilla, M. E. (2017). LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo. Nat. Genet. 49, 1502-1510.
Jin, Y., Tam, O. H., Paniagua, E., Hammell, M. (2015). TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics 31, 3593–3599.
Kazazian, H. H. (2004). Mobile elements: drivers of genome evolution. Science 303, 1626-1632.
Kishikawa, T., Otsuka, M., Yoshikawa, T., Ohno, M., Ijichi, H., Koike, K. (2016). Satellite RNAs promote pancreatic oncogenic processes via the dysfunction of YBX1. Nat. Commun. 7:13006.
Kishikawa, T., Otsuka, M., Yoshikawa, T., Ohno, M., Yamamoto, K., Yamamoto, N., Kotani, A., Koike, K. (2016). Quantitation of circulating satellite RNAs in pancreatic cancer patients. JCI Insight 1, 1–13.
Kondratova, V.N., Botezatu, I. V., Shelepov, V.P., Lichtenstein, A. V. (2014). Satellite DNA transcripts in blood plasma as potential markers of tumor growth. Mol. Biol. 48, 878–885.
Law, M. J., Lower, K. M., Voon, H. P., Hughes, J. R., Garrick, D., Viprakasit, V., Mitson, M., De Gobbi, M., Marra, M., Morris, A., Abbott, A., Wilder, S. P., Taylor, S., Santos, G. M., Cross, J., Ayyub, H., Jones, S., Ragoussis, J., Rhodes, D., Dunham, I., Higgs, D. R., Gibbons, R. J. (2010). ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner. Cell, 143, 367-378.
Leonova, K., Safina, A., Nesher, E., Sandlesh, P., Pratt, R., Burkhart, C., Lipchick, B., Gitlin, I., Frangou, C., Koman, I., Wang, J., Kirsanov, K., Yakubovskaya, M. G., Gudkov, A. V., Gurova, K. (2018). TRAIN (Transcription of Repeats Activates INterferon) in response to chromatin destabilization induced by small molecules in mammalian cells. eLife 7:e30842.
Liu, M., Ohtani, H., Zhou, W., Ørskov, A.D., Charlet, J., Zhang, Y.W., Shen, H., Baylin, S.B., Liang, G., Grønbæk, K., Jones, P.A. (2016). Vitamin C increases viral mimicry induced by 5-aza-2-deoxycytidine. Proc. Natl. Acad. Sci. 113, 10238–10244.
Lübbert, M., Grishina, O., Schmoor, C., Schlenk, R. F., Jost, E., Crysandt, M., Heuser, M., Thol, F., Germing, U. (). Valproate and Retinoic Acid in Combination With Decitabine in Elderly Nonfit Patients With Acute Myeloid Leukemia: Results of a Multicenter, Randomized, 2× 2, Phase II Trial. Journal of Clinical Oncology, JCO-19.
Mita, P. and Boeke, J. D. (2016). How retrotransposons shape genome regulation. Curr. Opin. Genet. Dev. 37, 90-100.
Percharde, M., Lin, C. J., Yin, Y., Guan, J., Peixoto, G. A., Bulut-Karslioglu, A., Biechele, S., Huang, B., Shen, X., Ramalho-Santo, M. (2018). A LINE1-nucleolin partnership regulates early development and ESC identity. Cell 174, 391-405.
Rebollo, R., Romanish, M. T., Mager, D. L. (2012). Transposable elements: an abundant and natural source of regulatory sequences for host genes. Ann. Rev. Genet. 46, 21-42.
Reed-Inderbitzin, E., Moreno-Miralles, I., Vanden-Eynden, S.K., Xie, J., Lutterbach, B., Durst-Goodwin, K.L., Luce, K.S., Irvin, B.J., Cleary, M.L., Brandt, S.J., Hiebert, S.W. (2006). RUNX1 associates with histone deacetylases and SUV39H1 to repress transcription. Oncogene 25, 5777–86.
Roulois, D., Loo Yau, H., Singhania, R., Wang, Y., Danesh, A., Shen, S. Y., Han, H., Liang, G., Jones, P. A., Pugh, T.J., O’Brien, C., De Carvalho, D. D. (2015). DNA-demethylating agents target colorectal cancer cells by inducing viral mimicry by endogenous transcripts. Cell 162, 961–973.
Rowe, H. M., Kapopoulou, A., Corsinotti, A., Fasching, L., Macfarlan, T. S., Tarabay, Y., Viville, S., Jakobsson, J., Pfaff, S. L., Trono, D. (2013). TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res. 23, 452-461.
Sadic, D., Schmidt, K., Groh, S., Kondofersky, I., Ellwart, J., Fuchs, C., Theis, F.J., Schotta, G. (2015). Atrx promotes heterochromatin formation at retrotransposons. EMBO Rep. 16, 836–850.
Sawitzki, Z. (2017) Characterization of repetitive element transcription and expression changes induced by epigenetic drug treatment in acute myeloid leukemia. PhD thesis, University of Freiburg.
Schmidt, D., Schwalie, P. C., Wilson, M. D., Ballester, B , Gonçalves, A., Kutter, C., Brown, G. D., Marshall, A., Flicek, P., Odom, D. T. (2012). Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148, 335-348.
Shanker, S., Paulson, A., Edenberg, H. J., Peak, A., Perera, A., Alekseyev, Y. O., Beckloff, N., Bivens, N. J., Donnelly, R., Gillaspy, A.F., Grove, D., Gu, W., Jafari, N., Kerley-Hamilton, J. S., Lyons, R. H., Tepper, C., Nicolet, C. M. (2015). Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA. J. Biomol. Tech. 26, 4–18.
Smit, A., Hubley, R., Green, P., n.d. Repeatmasker Open-4.0 2013-2015 <http://www.repeatmasker.org>.
Sze, C. C., and Shilatifard, A. (2016). MLL3/MLL4/COMPASS family on epigenetic regulation of enhancer function and cancer. Cold Spring Harbor Perspect Med.
Tachibana, M., Matsumura, Y., Fukuda, M., Kimura, H., Shinkai, Y. (2008). G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription. Embo J. 27, 2681-2690.
Tantin, D. (2013). Oct transcription factors in development and stem cells: insights and mechanisms. Development 140, 2857-2866.
Ting, D. T., Lipson, D., Paul, S., Brannigan, B. W., Akhavanfard, S., Coffman, E. J., Contino, G., Deshpande, V., Iafrate, A. J., Letovsky, S., Rivera, M. N., Bardeesy, N., Maheswaran, S., Haber, D. A. (2011). Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 331, 593–597.
Thompson, P. J., Dulberg, V., Moon, K. M., Foster, L. J., Chen, C., Karimi, M. M., Lorincz, M. C. (2015). hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells. Plos Genet. 11:e1004933.
Trizzino, M., Park, Y., Holsbach-Beltrame, M., Aracena, K., Mika, K., Caliskan, M., Perry, G. H., Lynch, V. J., Brown, C. D. (2017). Transposable elements are the primary source of novelty in primate gene regulation. Genome Res. 27, 1623-1633.
Warburton, P.E., Hasson, D., Guillem, F., Lescale, C., Jin, X., Abrusan, G. (2008). Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics 9:533.
Whitaker, J.W., Chen, Z., Wang, W. (2014). Predicting the human epigenome from DNA motifs. Nat. Methods 12, 265-272.
Wouters, B.J., Delwel, R. (2015). Epigenetics and approaches to targeted epigenetic therapy in acute myeloid leukemia. Blood 127, 42–53.
Yang, B. X., El Farran, C. A., Guo, H. C., Yu, T., Fang, H. T., Wang, H. F., Schlesinger, S., Seah, Y. F., Goh, G. Y., Neo, S. P., Li, Y., Lorincz, M. C., Tergaonkar, V., Lim, T. M., Chen, L., Gunaratne, J., Collins, J. J., Goff, S. P., Daley, G. Q., Li, H., Bard, F. A., Loh, Y. H. (2015). Systematic identification of factors for provirus silencing in embryonic stem cells. Cell 163, 230-245.
Yi, G., Wierenga, A. T. J., Petraglia, F., Narang, P., Janssen-Megens, E. M., Mandoli, A., Merkel, A., Berentsen, K., Kim, B., Matarese, F., Singh, A. A., Habibi, E., Prange, K. H. M., Mulder, A. B., Jansen, J. H., Clarke, L., Heath, S., van der Reijden, B. A., Flicek, P., Yaspo, M. L., Gut, I., Bock, C., Schuringa, J. J., Altucci, L., Vellenga, E., Stunnenberg, H. G., Martens, J. H. A. (2019). Chromatin-based classification of genetically heterogeneous AMLs into two distinct subtypes with diverse stemness phenotypes. Cell Rep. 26,1059-1069.
Zhu, Q., Pao, G. M., Huynh, A. M., Suh, H., Tonnu, N., Nederlof, P. M., Gage, F. H., Verma, I. M. (2011). BRCA1 tumour suppression occurs via heterochromatin-mediated silencing. Nature 477, 179–184.
Zhu, Q., Hoong, N., Aslanian, A., Hara, T., Benner, C., Heinz, S., Miga, K. H., Ke, E., Verma, S., Soroczynski, J., Yates, J. R. 3rd, Hunter, T., Verma, I. M. (2018) Heterochromatin-encoded satellite RNAs induce breast cancer. Mol. Cell 70, 842-853.