Coxsackievirus B3 infection induces changes in the expression of numerous piRNAs

go back to reference Liu PP, Mason JWJC (2001) Advances in the understanding of myocarditis. Circulation 104(9):1076–1082PubMed Liu PP, Mason JWJC (2001) Advances in the understanding of myocarditis. Circulation 104(9):1076–1082PubMed

go back to reference Liu Q, Paroo ZJARoB (2010) Biochemical principles of small RNA pathways. Annu Rev Biochem 79(1):295–319PubMed Liu Q, Paroo ZJARoB (2010) Biochemical principles of small RNA pathways. Annu Rev Biochem 79(1):295–319PubMed

go back to reference Siomi MC, Sato K, Pezic D, Aravin AAJNRMCB (2011) PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12(4):246–258PubMed Siomi MC, Sato K, Pezic D, Aravin AAJNRMCB (2011) PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12(4):246–258PubMed

go back to reference Pillai RS, Chuma SJ (2012) piRNAs and their involvement in male germline development in mice. Dev Growth Differ 54(1):78–92PubMed Pillai RS, Chuma SJ (2012) piRNAs and their involvement in male germline development in mice. Dev Growth Differ 54(1):78–92PubMed

go back to reference Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442(7099):199–202PubMed Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442(7099):199–202PubMed

go back to reference Ernst C, Odom DT, Kutter C (2017) The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity. Nat Commun 8:1411–1421PubMedPubMedCentral Ernst C, Odom DT, Kutter C (2017) The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity. Nat Commun 8:1411–1421PubMedPubMedCentral

go back to reference Esposito T, Magliocca S, Formicola D, Gianfrancesco F (2011) piR_015520 belongs to Piwi-associated RNAs regulates expression of the human melatonin receptor 1A gene. PLoS One 6(7):e22727–e22734PubMedPubMedCentral Esposito T, Magliocca S, Formicola D, Gianfrancesco F (2011) piR_015520 belongs to Piwi-associated RNAs regulates expression of the human melatonin receptor 1A gene. PLoS One 6(7):e22727–e22734PubMedPubMedCentral

go back to reference Watanabe T, Cheng E, Mei Z, Lin HJGR (2015) Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline. Genome Res 25(3):368–380PubMedPubMedCentral Watanabe T, Cheng E, Mei Z, Lin HJGR (2015) Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline. Genome Res 25(3):368–380PubMedPubMedCentral

go back to reference Czech B, Munafo M, Ciabrelli F, Eastwood EL, Fabry MH, Kneuss E, Hannon GJ (2018) piRNA-guided genome defense: from biogenesis to silencing. Annu Rev Genet 52:131–157PubMed Czech B, Munafo M, Ciabrelli F, Eastwood EL, Fabry MH, Kneuss E, Hannon GJ (2018) piRNA-guided genome defense: from biogenesis to silencing. Annu Rev Genet 52:131–157PubMed

go back to reference Yin H, Lin H (2007) An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature 450(7167):304–308PubMed Yin H, Lin H (2007) An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature 450(7167):304–308PubMed

go back to reference Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, Kandel ER (2012) A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 149(3):693–707PubMedPubMedCentral Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, Kandel ER (2012) A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 149(3):693–707PubMedPubMedCentral

go back to reference Huang G, Hu H, Xue X, Shen S, Gao E, Guo G, Shen X, Zhang X (2013) Altered expression of piRNAs and their relation with clinicopathologic features of breast cancer. Clin Transl Oncol 15(7):563–568PubMed Huang G, Hu H, Xue X, Shen S, Gao E, Guo G, Shen X, Zhang X (2013) Altered expression of piRNAs and their relation with clinicopathologic features of breast cancer. Clin Transl Oncol 15(7):563–568PubMed

go back to reference Law PT, Qin H, Ching AK, Lai KP, Co NN, He M, Lung RW, Chan AW, Chan TF, Wong N (2013) Deep sequencing of small RNA transcriptome reveals novel non-coding RNAs in hepatocellular carcinoma. J Hepatol 58(6):1165–1173PubMed Law PT, Qin H, Ching AK, Lai KP, Co NN, He M, Lung RW, Chan AW, Chan TF, Wong N (2013) Deep sequencing of small RNA transcriptome reveals novel non-coding RNAs in hepatocellular carcinoma. J Hepatol 58(6):1165–1173PubMed

go back to reference Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DPJN (2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455(7217):1193–1197PubMed Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DPJN (2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455(7217):1193–1197PubMed

go back to reference Juliano CE, Reich A, Liu N, Götzfried J, Zhong M, Uman S, Reenan RA, Wessel GM, Steele RE, Lin HJPNASUSA (2014) PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells. Proc Natl Acad Sci USA 111(1):337–342PubMed Juliano CE, Reich A, Liu N, Götzfried J, Zhong M, Uman S, Reenan RA, Wessel GM, Steele RE, Lin HJPNASUSA (2014) PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells. Proc Natl Acad Sci USA 111(1):337–342PubMed

go back to reference Lim RSM, Anand A, Nishimiya-Fujisawa C, Kobayashi S, Kai TJDB (2014) Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway. Dev Biol 386(1):237–251PubMed Lim RSM, Anand A, Nishimiya-Fujisawa C, Kobayashi S, Kai TJDB (2014) Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway. Dev Biol 386(1):237–251PubMed

go back to reference Cong F, Cheung AK, Huang SMJ (2012) Chemical genetics-based target identification in drug discovery. Annu Rev Pharmacol Toxicol 52:57–58PubMed Cong F, Cheung AK, Huang SMJ (2012) Chemical genetics-based target identification in drug discovery. Annu Rev Pharmacol Toxicol 52:57–58PubMed

go back to reference Kirino Y, Mourelatos Z (2007) Mouse Piwi-interacting RNAs are 2’-O-methylated at their 3’ termini. Nat Struct Mol Biol 14(4):347–348PubMed Kirino Y, Mourelatos Z (2007) Mouse Piwi-interacting RNAs are 2’-O-methylated at their 3’ termini. Nat Struct Mol Biol 14(4):347–348PubMed

go back to reference Ha H, Song J, Wang S, Kapusta A, Feschotte C, Chen KC, Xing J (2014) A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements. BMC Genom 15(1):545–561 Ha H, Song J, Wang S, Kapusta A, Feschotte C, Chen KC, Xing J (2014) A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements. BMC Genom 15(1):545–561

go back to reference Wang K, Liang C, Liu J, Xiao H, Huang S, Xu J, Li FJBB (2014) Prediction of piRNAs using transposon interaction and a support vector machine. BMC Bioinform 15(1):419 Wang K, Liang C, Liu J, Xiao H, Huang S, Xu J, Li FJBB (2014) Prediction of piRNAs using transposon interaction and a support vector machine. BMC Bioinform 15(1):419

go back to reference Love MI, Wolfgang H, Simon AJGB (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550–571PubMedPubMedCentral Love MI, Wolfgang H, Simon AJGB (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550–571PubMedPubMedCentral

go back to reference Tim C, Markus K, Robert H, Michael EJNRMCB (2011) HTRA proteases: regulated proteolysis in protein quality control. Nat Rev Mol Cell Biol 12(3):152–162 Tim C, Markus K, Robert H, Michael EJNRMCB (2011) HTRA proteases: regulated proteolysis in protein quality control. Nat Rev Mol Cell Biol 12(3):152–162

go back to reference Li Z, Wang Z, Xu S, Liang W, Fan W (2017) Proteomic analysis reveals a new benefit of periodic mechanical stress on chondrocytes. Cell Physiol Biochem 44(4):1578–1590PubMed Li Z, Wang Z, Xu S, Liang W, Fan W (2017) Proteomic analysis reveals a new benefit of periodic mechanical stress on chondrocytes. Cell Physiol Biochem 44(4):1578–1590PubMed

go back to reference Liu J, Zhang S, Cheng B (2018) Epigenetic roles of PIWI interacting RNAs (piRNAs) in cancer metastasis (review). Oncol Rep 40(5):2423–2434PubMed Liu J, Zhang S, Cheng B (2018) Epigenetic roles of PIWI interacting RNAs (piRNAs) in cancer metastasis (review). Oncol Rep 40(5):2423–2434PubMed

go back to reference Yan Z, Hu HY, Jiang X, Maierhofer V, Neb E, He L, Hu Y, Hu H, Li N, Chen W, Khaitovich P (2011) Widespread expression of piRNA-like molecules in somatic tissues. Nucleic acids Res 39(15):6596–6607PubMedPubMedCentral Yan Z, Hu HY, Jiang X, Maierhofer V, Neb E, He L, Hu Y, Hu H, Li N, Chen W, Khaitovich P (2011) Widespread expression of piRNA-like molecules in somatic tissues. Nucleic acids Res 39(15):6596–6607PubMedPubMedCentral

go back to reference Martinez VD, Vucic EA, Thu KL, Hubaux R, Enfield KS, Pikor LA, Becker-Santos DD, Brown CJ, Lam S, Lam WL (2015) Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology. Sci Rep 5:10423–10441PubMedPubMedCentral Martinez VD, Vucic EA, Thu KL, Hubaux R, Enfield KS, Pikor LA, Becker-Santos DD, Brown CJ, Lam S, Lam WL (2015) Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology. Sci Rep 5:10423–10441PubMedPubMedCentral

go back to reference Gou LT, Kang JY, Dai P, Wang X, Li F, Zhao S, Zhang M, Hua MM, Lu Y, Zhu Y, Li Z, Chen H, Wu LG, Li D, Fu XD, Li J, Shi HJ, Liu MF (2017) Ubiquitination-deficient mutations in human Piwi cause male infertility by impairing histone-to-protamine exchange during spermiogenesis. Cell 169(6):1090–1104PubMedPubMedCentral Gou LT, Kang JY, Dai P, Wang X, Li F, Zhao S, Zhang M, Hua MM, Lu Y, Zhu Y, Li Z, Chen H, Wu LG, Li D, Fu XD, Li J, Shi HJ, Liu MF (2017) Ubiquitination-deficient mutations in human Piwi cause male infertility by impairing histone-to-protamine exchange during spermiogenesis. Cell 169(6):1090–1104PubMedPubMedCentral

go back to reference Busch J, Ralla B, Jung M, Wotschofsky Z, Trujillo-Arribas E, Schwabe P, Kilic E, Fendler A, Jung K (2015) Piwi-interacting RNAs as novel prognostic markers in clear cell renal cell carcinomas. J Exp Clin Cancer Res 34:61–72PubMedPubMedCentral Busch J, Ralla B, Jung M, Wotschofsky Z, Trujillo-Arribas E, Schwabe P, Kilic E, Fendler A, Jung K (2015) Piwi-interacting RNAs as novel prognostic markers in clear cell renal cell carcinomas. J Exp Clin Cancer Res 34:61–72PubMedPubMedCentral

go back to reference Martinez VD, Enfield KSS, Rowbotham DA, Lam WL (2016) An atlas of gastric PIWI-interacting RNA transcriptomes and their utility for identifying signatures of gastric cancer recurrence. Gastric Cancer 19(2):660–665PubMed Martinez VD, Enfield KSS, Rowbotham DA, Lam WL (2016) An atlas of gastric PIWI-interacting RNA transcriptomes and their utility for identifying signatures of gastric cancer recurrence. Gastric Cancer 19(2):660–665PubMed

go back to reference Krishnan P, Ghosh S, Graham K, Mackey JR, Kovalchuk O, Damaraju S (2016) Piwi-interacting RNAs and PIWI genes as novel prognostic markers for breast cancer. Oncotarget 7(25):37944–37956PubMedPubMedCentral Krishnan P, Ghosh S, Graham K, Mackey JR, Kovalchuk O, Damaraju S (2016) Piwi-interacting RNAs and PIWI genes as novel prognostic markers for breast cancer. Oncotarget 7(25):37944–37956PubMedPubMedCentral

go back to reference Qu A, Wang W, Yang Y, Zhang X, Dong Y, Zheng G, Wu Q, Zou M, Du L, Wang Y, Wang C (2019) A serum piRNA signature as promising non-invasive diagnostic and prognostic biomarkers for colorectal cancer. Cancer Manag Res 11:3703–3720PubMedPubMedCentral Qu A, Wang W, Yang Y, Zhang X, Dong Y, Zheng G, Wu Q, Zou M, Du L, Wang Y, Wang C (2019) A serum piRNA signature as promising non-invasive diagnostic and prognostic biomarkers for colorectal cancer. Cancer Manag Res 11:3703–3720PubMedPubMedCentral

go back to reference Bahn JH, Zhang Q, Li F, Chan TM, Lin X, Kim Y, Wong DT, Xiao X (2015) The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clin Chem 61(1):221–230PubMed Bahn JH, Zhang Q, Li F, Chan TM, Lin X, Kim Y, Wong DT, Xiao X (2015) The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clin Chem 61(1):221–230PubMed

go back to reference Krishnan P, Damaraju S (2018) The challenges and opportunities in the clinical application of noncoding RNAs: the road map for miRNAs and piRNAs in cancer diagnostics and prognostics. Int J Genom 2018:5848046–5848064 Krishnan P, Damaraju S (2018) The challenges and opportunities in the clinical application of noncoding RNAs: the road map for miRNAs and piRNAs in cancer diagnostics and prognostics. Int J Genom 2018:5848046–5848064

go back to reference Hashim A, Rizzo F, Marchese G, Ravo M, Tarallo R, Nassa G, Giurato G, Santamaria G, Cordella A, Cantarella C, Weisz A (2014) RNA sequencing identifies specific PIWI-interacting small non-coding RNA expression patterns in breast cancer. Oncotarget 5(20):9901–9910PubMedPubMedCentral Hashim A, Rizzo F, Marchese G, Ravo M, Tarallo R, Nassa G, Giurato G, Santamaria G, Cordella A, Cantarella C, Weisz A (2014) RNA sequencing identifies specific PIWI-interacting small non-coding RNA expression patterns in breast cancer. Oncotarget 5(20):9901–9910PubMedPubMedCentral

go back to reference Cheng J, Guo JM, Xiao BX, Miao Y, Jiang Z, Zhou H, Li QN (2011) piRNA, the new non-coding RNA, is aberrantly expressed in human cancer cells. Clinica Chimica Acta Int J Clin Chem 412(17–18):1621–1625 Cheng J, Guo JM, Xiao BX, Miao Y, Jiang Z, Zhou H, Li QN (2011) piRNA, the new non-coding RNA, is aberrantly expressed in human cancer cells. Clinica Chimica Acta Int J Clin Chem 412(17–18):1621–1625

go back to reference Cui L, Lou Y, Zhang X, Zhou H, Deng H, Song H, Yu X, Xiao B, Wang W, Guo J (2011) Detection of circulating tumor cells in peripheral blood from patients with gastric cancer using piRNAs as markers. Clin Biochem 44(13):1050–1057PubMed Cui L, Lou Y, Zhang X, Zhou H, Deng H, Song H, Yu X, Xiao B, Wang W, Guo J (2011) Detection of circulating tumor cells in peripheral blood from patients with gastric cancer using piRNAs as markers. Clin Biochem 44(13):1050–1057PubMed

go back to reference Cheng J, Deng H, Xiao B, Zhou H, Zhou F, Shen Z, Guo J (2012) piR-823, a novel non-coding small RNA, demonstrates in vitro and in vivo tumor suppressive activity in human gastric cancer cells. Cancer Lett 315(1):12–17PubMed Cheng J, Deng H, Xiao B, Zhou H, Zhou F, Shen Z, Guo J (2012) piR-823, a novel non-coding small RNA, demonstrates in vitro and in vivo tumor suppressive activity in human gastric cancer cells. Cancer Lett 315(1):12–17PubMed

go back to reference Assumpcao CB, Calcagno DQ, Araujo TM, Santos SE, Santos AK, Riggins GJ, Burbano RR, Assumpcao PP (2015) The role of piRNA and its potential clinical implications in cancer. Epigenomics 7(6):975–984PubMed Assumpcao CB, Calcagno DQ, Araujo TM, Santos SE, Santos AK, Riggins GJ, Burbano RR, Assumpcao PP (2015) The role of piRNA and its potential clinical implications in cancer. Epigenomics 7(6):975–984PubMed

go back to reference Imbeault M, Helleboid PY, Trono DJN (2017) KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks. Nature 543(7646):550–554PubMed Imbeault M, Helleboid PY, Trono DJN (2017) KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks. Nature 543(7646):550–554PubMed

go back to reference Rouget C, Papin C, Boureux A, Meunier AC, Franco B, Robine N, Lai EC, Pelisson A, Simonelig M (2010) Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467(7319):1128–1132PubMedPubMedCentral Rouget C, Papin C, Boureux A, Meunier AC, Franco B, Robine N, Lai EC, Pelisson A, Simonelig M (2010) Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467(7319):1128–1132PubMedPubMedCentral

go back to reference Teixeira FK, Okuniewska M, Malone CD, Coux RX, Rio DC, Lehmann R (2017) piRNA-mediated regulation of transposon alternative splicing in the soma and germ line. Nature 552(7684):268–272PubMedPubMedCentral Teixeira FK, Okuniewska M, Malone CD, Coux RX, Rio DC, Lehmann R (2017) piRNA-mediated regulation of transposon alternative splicing in the soma and germ line. Nature 552(7684):268–272PubMedPubMedCentral

go back to reference Le Thomas A, Rogers AK, Webster A, Marinov GK, Liao SE, Perkins EM, Hur JK, Aravin AA, Toth KF (2013) Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev 27(4):390–399PubMedPubMedCentral Le Thomas A, Rogers AK, Webster A, Marinov GK, Liao SE, Perkins EM, Hur JK, Aravin AA, Toth KF (2013) Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev 27(4):390–399PubMedPubMedCentral

go back to reference Sienski G, Donertas D, Brennecke J (2012) Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 151(5):964–980PubMedPubMedCentral Sienski G, Donertas D, Brennecke J (2012) Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 151(5):964–980PubMedPubMedCentral

go back to reference Watanabe T, Lin H (2014) Posttranscriptional regulation of gene expression by Piwi proteins and piRNAs. Mol Cell 56(1):18–27PubMedPubMedCentral Watanabe T, Lin H (2014) Posttranscriptional regulation of gene expression by Piwi proteins and piRNAs. Mol Cell 56(1):18–27PubMedPubMedCentral

go back to reference Iwasaki YW, Murano K, Ishizu H, Shibuya A, Iyoda Y, Siomi MC, Siomi H, Saito K (2016) Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons. Mol Cell 63(3):408–419PubMed Iwasaki YW, Murano K, Ishizu H, Shibuya A, Iyoda Y, Siomi MC, Siomi H, Saito K (2016) Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons. Mol Cell 63(3):408–419PubMed

go back to reference Aravin AA, Sachidanandam R, Bourc’his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ (2008) A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31(6):785–799PubMedPubMedCentral Aravin AA, Sachidanandam R, Bourc’his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ (2008) A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31(6):785–799PubMedPubMedCentral

go back to reference Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O’Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520–562PubMed Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O’Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520–562PubMed

go back to reference Leung DC, Lorincz MC (2012) Silencing of endogenous retroviruses: when and why do histone marks predominate? Trends Biochem Sci 37(4):127–133PubMed Leung DC, Lorincz MC (2012) Silencing of endogenous retroviruses: when and why do histone marks predominate? Trends Biochem Sci 37(4):127–133PubMed

go back to reference Brind’Amour J, Kobayashi H, Richard Albert J, Shirane K, Sakashita A, Kamio A, Bogutz A, Koike T, Karimi MM, Lefebvre L, Kono T, Lorincz MC (2018) LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation. Nat Commun 9(1):3331–3345PubMedPubMedCentral Brind’Amour J, Kobayashi H, Richard Albert J, Shirane K, Sakashita A, Kamio A, Bogutz A, Koike T, Karimi MM, Lefebvre L, Kono T, Lorincz MC (2018) LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation. Nat Commun 9(1):3331–3345PubMedPubMedCentral

go back to reference Lee JW, Kim HS (2006) Endogenous retrovirus HERV-I LTR family in primates: sequences, phylogeny, and evolution. Arch Virol 151(8):1651–1658PubMed Lee JW, Kim HS (2006) Endogenous retrovirus HERV-I LTR family in primates: sequences, phylogeny, and evolution. Arch Virol 151(8):1651–1658PubMed

go back to reference Chang NT, Yang WK, Huang HC, Yeh KW, Wu CW (2007) The transcriptional activity of HERV-I LTR is negatively regulated by its cis-elements and wild type p53 tumor suppressor protein. J Biomed Sci 14(2):211–222PubMed Chang NT, Yang WK, Huang HC, Yeh KW, Wu CW (2007) The transcriptional activity of HERV-I LTR is negatively regulated by its cis-elements and wild type p53 tumor suppressor protein. J Biomed Sci 14(2):211–222PubMed

go back to reference Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, Heidmann T (2006) Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res 16(12):1548–1556PubMedPubMedCentral Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, Heidmann T (2006) Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res 16(12):1548–1556PubMedPubMedCentral