{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T15:26:11Z","timestamp":1783524371303,"version":"3.55.0"},"reference-count":68,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2023,6,3]],"date-time":"2023-06-03T00:00:00Z","timestamp":1685750400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,6,3]],"date-time":"2023-06-03T00:00:00Z","timestamp":1685750400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100009193","name":"Marsden Fund","doi-asserted-by":"publisher","award":["16-UOO-178"],"award-info":[{"award-number":["16-UOO-178"]}],"id":[{"id":"10.13039\/501100009193","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008247","name":"University of Otago","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008247","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Genet Genomics"],"published-print":{"date-parts":[[2023,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Transposable elements (TEs) are genetic elements that have evolved as crucial regulators of human development and cancer, functioning as both genes and regulatory elements. When TEs become dysregulated in cancer cells, they can serve as alternate promoters to activate oncogenes, a process known as onco-exaptation. This study aimed to explore the expression and epigenetic regulation of onco-exaptation events in early human developmental tissues. We discovered co-expression of some TEs and oncogenes in human embryonic stem cells and first trimester and term placental tissues. Previous studies identified onco-exaptation events in various cancer types, including an AluJb SINE element\u2013<jats:italic>LIN28B<\/jats:italic> interaction in lung cancer cells, and showed that the TE-derived <jats:italic>LIN28B<\/jats:italic> transcript is associated with poor patient prognosis in hepatocellular carcinoma. This study further characterized the AluJb\u2013<jats:italic>LIN28B<\/jats:italic> transcript and confirmed that its expression is restricted to the placenta. Targeted DNA methylation analysis revealed differential methylation of the two <jats:italic>LIN28B<\/jats:italic> promoters between placenta and healthy somatic tissues, indicating that some TE\u2013oncogene interactions are not cancer-specific but arise from the epigenetic reactivation of developmental TE-derived regulatory events. In conclusion, our findings provide evidence that some TE\u2013oncogene interactions are not limited to cancer and may originate from the epigenetic reactivation of TE-derived regulatory events that are involved in early development. These insights broaden our understanding of the role of TEs in gene regulation and suggest the potential importance of targeting TEs in cancer therapy beyond their conventional use as cancer-specific markers.<\/jats:p>","DOI":"10.1007\/s00438-023-02033-1","type":"journal-article","created":{"date-parts":[[2023,6,3]],"date-time":"2023-06-03T15:01:23Z","timestamp":1685804483000},"page":"1045-1058","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["The transposable element-derived transcript of LIN28B has a placental origin and is not specific to tumours"],"prefix":"10.1007","volume":"298","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0395-1878","authenticated-orcid":false,"given":"Chiemi F.","family":"Lynch-Sutherland","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorissa I.","family":"McDougall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter A.","family":"Stockwell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzan N.","family":"Almomani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert J.","family":"Weeks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jackie L.","family":"Ludgate","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teena K. J. B.","family":"Gamage","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aniruddha","family":"Chatterjee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanna L.","family":"James","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R.","family":"Eccles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin C.","family":"Macaulay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,6,3]]},"reference":[{"issue":"3","key":"2033_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/cancers11030345","volume":"11","author":"SM Afify","year":"2019","unstructured":"Afify SM, Seno M (2019) Conversion of stem cells to cancer stem cells: undercurrent of cancer initiation. Cancers 11(3):1\u201319. https:\/\/doi.org\/10.3390\/cancers11030345","journal-title":"Cancers"},{"key":"2033_CR2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21103637","author":"A Ali","year":"2020","unstructured":"Ali A, Bouma GJ, Anthony R, Winger QA (2020a) The role of LIN28-let-7-ARID3B pathway in placental development. Int J Mol Sci. https:\/\/doi.org\/10.3390\/ijms21103637","journal-title":"Int J Mol Sci"},{"key":"2033_CR3","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21072549","author":"A Ali","year":"2020","unstructured":"Ali A, Stenglein MD, Spencer TE, Bouma GJ, Anthony RV, Winger QA (2020b) Trophectoderm-specific knockdown of LIN28 decreases expression of genes necessary for cell proliferation and reduces elongation of sheep conceptus. Int J Mol Sci. https:\/\/doi.org\/10.3390\/ijms21072549","journal-title":"Int J Mol Sci"},{"issue":"1","key":"2033_CR4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/jcb.22374","volume":"109","author":"G Altun","year":"2010","unstructured":"Altun G, Loring JF, Laurent LC (2010) DNA methylation in embryonic stem cells. J Cell Biochem 109(1):1\u20136. https:\/\/doi.org\/10.1002\/jcb.22374","journal-title":"J Cell Biochem"},{"issue":"1","key":"2033_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13100-016-0080-x","volume":"7","author":"A Babaian","year":"2016","unstructured":"Babaian A, Mager DL (2016) Endogenous retroviral promoter exaptation in human cancer. Mob DNA 7(1):1\u201321. https:\/\/doi.org\/10.1186\/s13100-016-0080-x","journal-title":"Mob DNA"},{"issue":"19","key":"2033_CR6","doi-asserted-by":"publisher","first-page":"2542","DOI":"10.1038\/onc.2015.308","volume":"35","author":"A Babaian","year":"2016","unstructured":"Babaian A, Romanish MT, Gagnier L, Kuo LY, Karimi MM, Steidl C, Mager DL (2016) Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma. Oncogene 35(19):2542\u20132546. https:\/\/doi.org\/10.1038\/onc.2015.308","journal-title":"Oncogene"},{"issue":"1","key":"2033_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-018-1577-z","volume":"19","author":"G Bourque","year":"2018","unstructured":"Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsv\u00e1k Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C (2018) Ten things you should know about transposable elements. Genome Biol 19(1):1\u201312. https:\/\/doi.org\/10.1186\/s13059-018-1577-z","journal-title":"Genome Biol"},{"key":"2033_CR8","doi-asserted-by":"publisher","DOI":"10.21203\/rs.3.rs-1648736\/v1","author":"M Branco","year":"2022","unstructured":"Branco M, Frost J, Amante S, Okae H, Jones E, Ashley B, Lewis R, Cleal J, Arima T, Maffucci T, Caley M (2022) Regulation of human trophoblast gene expression by endogenous retroviruses. Nat Struct Mol Biol. https:\/\/doi.org\/10.21203\/rs.3.rs-1648736\/v1","journal-title":"Nat Struct Mol Biol"},{"key":"2033_CR9","doi-asserted-by":"publisher","DOI":"10.3332\/ecancer.2018.840","author":"MH Bronchud","year":"2018","unstructured":"Bronchud MH (2018) Are aggressive epithelial cancers \u2018a disease\u2019 of Eutherian mammals? Ecancermedicalscience. https:\/\/doi.org\/10.3332\/ecancer.2018.840","journal-title":"Ecancermedicalscience"},{"issue":"7","key":"2033_CR10","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nrc.2017.35","volume":"17","author":"KH Burns","year":"2017","unstructured":"Burns KH (2017) Transposable elements in cancer. Nat Rev Cancer 17(7):415\u2013424. https:\/\/doi.org\/10.1038\/nrc.2017.35","journal-title":"Nat Rev Cancer"},{"issue":"2","key":"2033_CR11","doi-asserted-by":"publisher","first-page":"2759","DOI":"10.1096\/fj.201801163R","volume":"33","author":"J Canfield","year":"2019","unstructured":"Canfield J, Arlier S, Mong EF, Lockhart J, VanWye J, Guzeloglu-Kayisli O, Schatz F, Magness RR, Lockwood CJ, Tsibris JCM, Kayisli UA, Totary-Jain H (2019) Decreased LIN28B in preeclampsia impairs human trophoblast differentiation and migration. FASEB J 33(2):2759\u20132769. https:\/\/doi.org\/10.1096\/fj.201801163R","journal-title":"FASEB J"},{"key":"2033_CR12","doi-asserted-by":"publisher","DOI":"10.3390\/genes9010023","author":"T Chishima","year":"2018","unstructured":"Chishima T, Iwakiri J, Hamada M (2018) Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs. Genes. https:\/\/doi.org\/10.3390\/genes9010023","journal-title":"Genes"},{"issue":"3","key":"2033_CR13","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1038\/ng.2553","volume":"45","author":"EB Chuong","year":"2013","unstructured":"Chuong EB, Rumi MAK, Soares MJ, Baker JC (2013) Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet 45(3):325\u2013329. https:\/\/doi.org\/10.1038\/ng.2553","journal-title":"Nat Genet"},{"issue":"2","key":"2033_CR14","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nrg.2016.139","volume":"18","author":"EB Chuong","year":"2017","unstructured":"Chuong EB, Elde NC, Feschotte C (2017) Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet 18(2):71\u201386. https:\/\/doi.org\/10.1038\/nrg.2016.139","journal-title":"Nat Rev Genet"},{"issue":"5","key":"2033_CR15","doi-asserted-by":"publisher","first-page":"E487","DOI":"10.1073\/pnas.1417000112","volume":"112","author":"G Cornelis","year":"2015","unstructured":"Cornelis G, Vernochet C, Carradec Q, Souquere S, Mulot B, Catzeflis F, Nilsson MA, Menzies BR, Renfree MB, Pierron G, Zeller U, Heidmann O, Dupressoir A, Heidmann T (2015) Retroviral envelope gene captures and syncytin exaptation for placentation in marsupials. Proc Natl Acad Sci USA 112(5):E487\u2013E496. https:\/\/doi.org\/10.1073\/pnas.1417000112","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"2033_CR16","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15\u201321. https:\/\/doi.org\/10.1093\/bioinformatics\/bts635","journal-title":"Bioinformatics"},{"key":"2033_CR17","doi-asserted-by":"publisher","DOI":"10.1101\/gr.277150.122","author":"C Du","year":"2023","unstructured":"Du C, Jiang J, Li Y, Yu M, Jin J, Chen S, Fan H, Macfarlan TS, Cao B, Sun M (2023) Regulation of endogenous retrovirus\u2013derived regulatory elements by GATA2\/3 and MSX2 in human trophoblast stem cells. Genome Res. https:\/\/doi.org\/10.1101\/gr.277150.122","journal-title":"Genome Res"},{"issue":"3","key":"2033_CR18","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1080\/19336918.2016.1170258","volume":"10","author":"J E. Davies","year":"2016","unstructured":"E. Davies J, Pollheimer J, Yong HEJ, Kokkinos MI, Kalionis B, Kn\u00f6fler M, Murthi P (2016) Epithelial-mesenchymal transition during extravillous trophoblast differentiation. Cell Adh Migr 10(3):310\u2013321. https:\/\/doi.org\/10.1080\/19336918.2016.1170258","journal-title":"Cell Adh Migr"},{"key":"2033_CR19","doi-asserted-by":"publisher","first-page":"5400","DOI":"10.1038\/sj.onc.1205651","volume":"21","author":"M Ehrlich","year":"2002","unstructured":"Ehrlich M (2002) DNA methylation in cancer: too much, but also too little. Oncogene 21:5400\u20135413. https:\/\/doi.org\/10.1038\/sj.onc.1205651","journal-title":"Oncogene"},{"issue":"5","key":"2033_CR20","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/ng.368","volume":"41","author":"GJ Faulkner","year":"2009","unstructured":"Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest ARR, Suzuki H, Hayashizaki Y, Hume DA, Carninci P (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41(5):563\u2013571. https:\/\/doi.org\/10.1038\/ng.368","journal-title":"Nat Genet"},{"issue":"2","key":"2033_CR21","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1093\/humupd\/dml048","volume":"13","author":"C Ferretti","year":"2007","unstructured":"Ferretti C, Bruni L, Dangles-Marie V, Pecking AP, Bellet D (2007) Molecular circuits shared by placental and cancer cells, and their implications in the proliferative, invasive and migratory capacities of trophoblasts. Hum Reprod Update 13(2):121\u2013141. https:\/\/doi.org\/10.1093\/humupd\/dml048","journal-title":"Hum Reprod Update"},{"issue":"5","key":"2033_CR22","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1038\/nrg2337.The","volume":"9","author":"C Feschotte","year":"2008","unstructured":"Feschotte C (2008) The contribution of transposable elements of the evolution of regulatory networks. Nat Rev Genet 9(5):397\u2013405. https:\/\/doi.org\/10.1038\/nrg2337.The","journal-title":"Nat Rev Genet"},{"issue":"1","key":"2033_CR23","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1146\/annurev-cellbio-100814-125514","volume":"31","author":"M Friedli","year":"2015","unstructured":"Friedli M, Trono D (2015) The developmental control of transposable elements and the evolution of higher species. Annu Rev Cell Dev Biol 31(1):429\u2013451. https:\/\/doi.org\/10.1146\/annurev-cellbio-100814-125514","journal-title":"Annu Rev Cell Dev Biol"},{"key":"2033_CR24","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0965-5","author":"P Gerdes","year":"2016","unstructured":"Gerdes P, Richardson SR, Mager DL, Faulkner GJ (2016) Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. Genome Biol. https:\/\/doi.org\/10.1186\/s13059-016-0965-5","journal-title":"Genome Biol"},{"key":"2033_CR25","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1016\/j.thromres.2004.06.038","volume":"114","author":"NM Gude","year":"2004","unstructured":"Gude NM, Roberts CT, Kalionis B, King RG (2004) Growth and function of the normal human placenta. Thrombosis Res 114:397\u2013407. https:\/\/doi.org\/10.1016\/j.thromres.2004.06.038","journal-title":"Thrombosis Res"},{"issue":"8","key":"2033_CR26","doi-asserted-by":"publisher","first-page":"2016","DOI":"10.1016\/j.celrep.2018.02.002","volume":"22","author":"W Guo","year":"2018","unstructured":"Guo W, Hu Z, Bao Y, Li Y, Li S, Zheng Q, Lyu D, Chen D, Yu T, Li Y, Zhu X, Ding J, Zhao Y, He X, Huang S (2018) A LIN28B tumor-specific transcript in cancer. Cell Rep 22(8):2016\u20132025. https:\/\/doi.org\/10.1016\/j.celrep.2018.02.002","journal-title":"Cell Rep"},{"issue":"7","key":"2033_CR27","doi-asserted-by":"publisher","first-page":"3307","DOI":"10.3390\/ijms140713307","volume":"14","author":"M Hadjiargyrou","year":"2013","unstructured":"Hadjiargyrou M, Delihas N (2013) The intertwining of transposable elements and non-coding RNAs. Int J Mol Sci 14(7):3307\u201313328. https:\/\/doi.org\/10.3390\/ijms140713307","journal-title":"Int J Mol Sci"},{"issue":"8","key":"2033_CR28","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.1101\/gr.091678.109","volume":"19","author":"JD Hollister","year":"2009","unstructured":"Hollister JD, Gaut BS (2009) Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res 19(8):1419\u20131428. https:\/\/doi.org\/10.1101\/gr.091678.109","journal-title":"Genome Res"},{"issue":"4","key":"2033_CR30","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1038\/s41588-019-0373-3","volume":"51","author":"HS Jang","year":"2019","unstructured":"Jang HS, Shah NM, Du AY, Dailey ZZ, Pehrsson EC, Godoy PM, Zhang D, Li D, Xing X, Kim S, O\u2019Donnell D, Gordon JI, Wang T (2019) Transposable elements drive widespread expression of oncogenes in human cancers. Nat Genet 51(4):611\u2013617. https:\/\/doi.org\/10.1038\/s41588-019-0373-3","journal-title":"Nat Genet"},{"issue":"6","key":"2033_CR31","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1042\/EBC20190039","volume":"63","author":"N Jansz","year":"2019","unstructured":"Jansz N (2019) DNA methylation dynamics at transposable elements in mammals. Essays Biochem 63(6):677\u2013689. https:\/\/doi.org\/10.1042\/EBC20190039","journal-title":"Essays Biochem"},{"issue":"11","key":"2033_CR32","doi-asserted-by":"publisher","first-page":"R107","DOI":"10.1186\/gb-2012-13-11-r107","volume":"13","author":"D Kelley","year":"2012","unstructured":"Kelley D, Rinn J (2012) Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol 13(11):R107. https:\/\/doi.org\/10.1186\/gb-2012-13-11-r107","journal-title":"Genome Biol"},{"issue":"7","key":"2033_CR33","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/ng.600","volume":"42","author":"G Kunarso","year":"2010","unstructured":"Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, Chan YS, Ng HH, Bourque G (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42(7):631\u2013634. https:\/\/doi.org\/10.1038\/ng.600","journal-title":"Nat Genet"},{"issue":"12","key":"2033_CR35","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1038\/s41576-020-0251-y","volume":"21","author":"S Lanciano","year":"2020","unstructured":"Lanciano S, Cristofari G (2020) Measuring and interpreting transposable element expression. Nat Rev Genet 21(12):721\u2013736. https:\/\/doi.org\/10.1038\/s41576-020-0251-y","journal-title":"Nat Rev Genet"},{"issue":"16","key":"2033_CR36","doi-asserted-by":"publisher","first-page":"12194","DOI":"10.1074\/jbc.M607838200","volume":"282","author":"L Lande-Diner","year":"2007","unstructured":"Lande-Diner L, Zhang J, Ben-Porath I, Amariglio N, Keshet I, Hecht M, Azuara V, Fisher AG, Rechavi G, Cedar H (2007) Role of DNA methylation in stable gene repression. J Biol Chem 282(16):12194\u201312200. https:\/\/doi.org\/10.1074\/jbc.M607838200","journal-title":"J Biol Chem"},{"issue":"7","key":"2033_CR37","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao Y, Smyth GK, Shi W (2014) FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30(7):923\u2013930. https:\/\/doi.org\/10.1093\/bioinformatics\/btt656","journal-title":"Bioinformatics"},{"issue":"9","key":"2033_CR38","doi-asserted-by":"publisher","first-page":"483","DOI":"10.5732\/cjc.012.10282","volume":"32","author":"A Liu","year":"2013","unstructured":"Liu A, Yu X, Liu S (2013) Pluripotency transcription factors and cancer stem cells: Small genes make a big difference. Chin J Cancer 32(9):483\u2013487. https:\/\/doi.org\/10.5732\/cjc.012.10282","journal-title":"Chin J Cancer"},{"issue":"1","key":"2033_CR39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0087698","volume":"9","author":"T Lozoya","year":"2014","unstructured":"Lozoya T, Dom\u00ednguez F, Romero-Ruiz A, Steffani L, Mart\u00ednez S, Monterde M, Ferri B, N\u00fa\u00f1ez MJ, Romero-Espin\u00f3s A, Zamora O, Gurrea M, Sangiao-Alvarellos S, Vega O, Sim\u00f3n C, Pellicer A, Tena-Sempere M (2014) The Lin28\/Let-7 system in early human embryonic tissue and ectopic pregnancy. PLoS ONE 9(1):1\u20136. https:\/\/doi.org\/10.1371\/journal.pone.0087698","journal-title":"PLoS ONE"},{"key":"2033_CR40","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2020.00468","author":"CF Lynch-Sutherland","year":"2020","unstructured":"Lynch-Sutherland CF, Chatterjee A, Stockwell PA, Eccles MR, Macaulay EC (2020) Reawakening the developmental origins of cancer through transposable elements. Front Oncol. https:\/\/doi.org\/10.3389\/fonc.2020.00468","journal-title":"Front Oncol"},{"key":"2033_CR41","doi-asserted-by":"publisher","DOI":"10.1002\/bies.201700091","author":"EC Macaulay","year":"2017","unstructured":"Macaulay EC, Chatterjee A, Cheng X, Baguley BC, Eccles MR, Morison IM (2017) The genes of life and death: a potential role for placental-specific genes in cancer: active retrotransposons in the placenta encode unique functional genes that may also be used by cancer cells to promote malignancy. BioEssays. https:\/\/doi.org\/10.1002\/bies.201700091","journal-title":"BioEssays"},{"issue":"1","key":"2033_CR42","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1146\/annurev-cellbio-100913-013116","volume":"30","author":"G Martello","year":"2014","unstructured":"Martello G, Smith A (2014) The nature of embryonic stem cells. Annu Rev Cell Dev Biol 30(1):647\u2013675. https:\/\/doi.org\/10.1146\/annurev-cellbio-100913-013116","journal-title":"Annu Rev Cell Dev Biol"},{"key":"2033_CR43","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2014.00262","author":"JA Menendez","year":"2014","unstructured":"Menendez JA, Alarco\u00b4n T (2014) Metabostemness: a new cancer hallmark. Front Oncol. https:\/\/doi.org\/10.3389\/fonc.2014.00262","journal-title":"Front Oncol"},{"issue":"4","key":"2033_CR44","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/j.placenta.2010.01.009","volume":"31","author":"HK Ng","year":"2010","unstructured":"Ng HK, Novakovic B, Hiendleder S, Craig JM, Roberts CT, Saffery R (2010) Distinct patterns of gene-specific methylation in mammalian placentas: implications for placental evolution and function. Placenta 31(4):259\u2013268. https:\/\/doi.org\/10.1016\/j.placenta.2010.01.009","journal-title":"Placenta"},{"issue":"2","key":"2033_CR45","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1038\/nrc3184","volume":"12","author":"L Nguyen","year":"2012","unstructured":"Nguyen L, Vanner R, Dirks P, Eaves CJ (2012) Cancer stem cells: an evolving concept. Nat Rev Cancer 12(2):133\u2013143. https:\/\/doi.org\/10.1038\/nrc3184","journal-title":"Nat Rev Cancer"},{"issue":"2","key":"2033_CR46","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1016\/j.ccr.2014.06.018","volume":"26","author":"LH Nguyen","year":"2014","unstructured":"Nguyen LH, Robinton DA, Seligson MT, Wu L, Li L, Rakheja D, Comerford SA, Ramezani S, Sun X, Parikh MS, Yang EH, Powers JT, Shinoda G, Shah SP, Hammer RE, Daley GQ, Zhu H (2014) Lin28b is sufficient to drive liver cancer and necessary for its maintenance in murine models. Cancer Cell 26(2):248\u2013261. https:\/\/doi.org\/10.1016\/j.ccr.2014.06.018","journal-title":"Cancer Cell"},{"key":"2033_CR47","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2013.00285","author":"B Novakovic","year":"2013","unstructured":"Novakovic B, Saffery R (2013) Placental pseudo-malignancy from a DNA methylation perspective: unanswered questions and future directions. Front Genet. https:\/\/doi.org\/10.3389\/fgene.2013.00285","journal-title":"Front Genet"},{"key":"2033_CR48","doi-asserted-by":"publisher","first-page":"111286","DOI":"10.1016\/j.mad.2020.111286","volume":"189","author":"SK Patra","year":"2020","unstructured":"Patra SK (2020) Roles of OCT4 in pathways of embryonic development and cancer progression. Mech Ageing Dev 189:111286. https:\/\/doi.org\/10.1016\/j.mad.2020.111286","journal-title":"Mech Ageing Dev"},{"issue":"3","key":"2033_CR49","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","volume":"33","author":"M Pertea","year":"2015","unstructured":"Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33(3):290\u2013295. https:\/\/doi.org\/10.1038\/nbt.3122","journal-title":"Nat Biotechnol"},{"issue":"14","key":"2033_CR52","doi-asserted-by":"publisher","first-page":"4743","DOI":"10.1093\/nar\/gkm455","volume":"35","author":"D Reiss","year":"2007","unstructured":"Reiss D, Zhang Y, Mager DL (2007) Widely variable endogenous retroviral methylation levels in human placenta. Nucleic Acids Res 35(14):4743\u20134754. https:\/\/doi.org\/10.1093\/nar\/gkm455","journal-title":"Nucleic Acids Res"},{"key":"2033_CR53","doi-asserted-by":"publisher","DOI":"10.1016\/j.placenta.2021.01.006","author":"RM Roberts","year":"2021","unstructured":"Roberts RM, Ezashi T, Schulz LC, Sugimoto J, Schust DJ, Khan T, Zhou J (2021) Syncytins expressed in human placental trophoblast. Placenta. https:\/\/doi.org\/10.1016\/j.placenta.2021.01.006","journal-title":"Placenta"},{"key":"2033_CR54","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3005723","author":"S Rousseaux","year":"2013","unstructured":"Rousseaux S, Debernardi A, Jacquiau B, Vitte AL, Vesin A, Nagy-Mignotte H, Moro-Sibilot D, Brichon PY, Lantuejoul S, Hainaut P, Laffaire J, de Reyni\u00e8s A, Beer DG, Timsit JF, Brambilla C, Brambilla E, Khochbin S (2013) Ectopic activation of germline and placental genes identifies aggressive metastasis-prone lung cancers. Sci Transl Med. https:\/\/doi.org\/10.1126\/scitranslmed.3005723","journal-title":"Sci Transl Med"},{"issue":"15","key":"2033_CR55","doi-asserted-by":"publisher","first-page":"6037","DOI":"10.1073\/pnas.1215145110","volume":"110","author":"DI Schroeder","year":"2013","unstructured":"Schroeder DI, Blair JD, Lott P, Yu HOK, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, LaSalle JM (2013) The human placenta methylome. Proc Natl Acad Sci USA 110(15):6037\u20136042. https:\/\/doi.org\/10.1073\/pnas.1215145110","journal-title":"Proc Natl Acad Sci USA"},{"issue":"11","key":"2033_CR56","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1038\/s41576-021-00385-1","volume":"22","author":"AD Senft","year":"2021","unstructured":"Senft AD, Macfarlan TS (2021) Transposable elements shape the evolution of mammalian development. Nat Rev Genet 22(11):691\u2013711. https:\/\/doi.org\/10.1038\/s41576-021-00385-1","journal-title":"Nat Rev Genet"},{"issue":"3","key":"2033_CR57","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1002\/wsbm.64","volume":"2","author":"Z Siegfried","year":"2010","unstructured":"Siegfried Z, Simon I (2010) DNA methylation and gene expression. Wiley Interdiscip Rev Syst Biol Med 2(3):362\u2013371. https:\/\/doi.org\/10.1002\/wsbm.64","journal-title":"Wiley Interdiscip Rev Syst Biol Med"},{"issue":"3","key":"2033_CR58","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1038\/nrg3354","volume":"14","author":"ZD Smith","year":"2013","unstructured":"Smith ZD, Meissner A (2013) DNA methylation: roles in mammalian development. Nat Rev Genet 14(3):204\u2013220. https:\/\/doi.org\/10.1038\/nrg3354","journal-title":"Nat Rev Genet"},{"issue":"7673","key":"2033_CR59","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1038\/nature23891","volume":"549","author":"ZD Smith","year":"2017","unstructured":"Smith ZD, Shi J, Gu H, Donaghey J, Clement K, Cacchiarelli D, Gnirke A, Michor F, Meissner A (2017) Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature 549(7673):543\u2013547. https:\/\/doi.org\/10.1038\/nature23891","journal-title":"Nature"},{"issue":"13","key":"2033_CR60","doi-asserted-by":"publisher","first-page":"1814","DOI":"10.1093\/bioinformatics\/btu126","volume":"30","author":"PA Stockwell","year":"2014","unstructured":"Stockwell PA, Chatterjee A, Rodger EJ, Morison IM (2014) DMAP: Differential methylation analysis package for RRBS and WGBS data. Bioinformatics 30(13):1814\u20131822. https:\/\/doi.org\/10.1093\/bioinformatics\/btu126","journal-title":"Bioinformatics"},{"key":"2033_CR61","doi-asserted-by":"publisher","DOI":"10.1002\/cpz1.206","author":"PA Stockwell","year":"2021","unstructured":"Stockwell PA, Lynch-Sutherland CF, Chatterjee A, Macaulay EC, Eccles MR (2021) RepExpress: a novel pipeline for the quantification and characterization of transposable element expression from RNA-seq data. Curr Protoc Bioinform. https:\/\/doi.org\/10.1002\/cpz1.206. (PMID: 34387946)","journal-title":"Curr Protoc Bioinform"},{"key":"2033_CR62","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2019.0347","author":"V Sundaram","year":"2020","unstructured":"Sundaram V, Wysocka J (2020) Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes. Phil Trans R Soc B. https:\/\/doi.org\/10.1098\/rstb.2019.0347","journal-title":"Phil Trans R Soc B"},{"issue":"6","key":"2033_CR63","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1038\/nrg2341","volume":"9","author":"MM Suzuki","year":"2008","unstructured":"Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9(6):465\u2013476. https:\/\/doi.org\/10.1038\/nrg2341","journal-title":"Nat Rev Genet"},{"issue":"2","key":"2033_CR64","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.gene.2016.02.019","volume":"584","author":"H Tatetsu","year":"2016","unstructured":"Tatetsu H, Kong NR, Chong G, Amabile G, Tenen DG, Chai L (2016) SALL4, the missing link between stem cells, development and cancer. Gene 584(2):111\u2013119. https:\/\/doi.org\/10.1016\/j.gene.2016.02.019","journal-title":"Gene"},{"issue":"1\u20132","key":"2033_CR65","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.mrrev.2008.02.004","volume":"659","author":"T Vaissi\u00e8re","year":"2008","unstructured":"Vaissi\u00e8re T, Sawan C, Herceg Z (2008) Epigenetic interplay between histone modifications and DNA methylation in gene silencing. Mutat Res 659(1\u20132):40\u201348. https:\/\/doi.org\/10.1016\/j.mrrev.2008.02.004","journal-title":"Mutat Res"},{"key":"2033_CR66","doi-asserted-by":"publisher","first-page":"1207","DOI":"10.2147\/OTT.S38114","volume":"6","author":"ML Wang","year":"2013","unstructured":"Wang ML, Chiou SH, Wu CW (2013) Targeting cancer stem cells: emerging role of Nanog transcription factor. Onco Targets Ther 6:1207\u20131220. https:\/\/doi.org\/10.2147\/OTT.S38114","journal-title":"Onco Targets Ther"},{"issue":"7531","key":"2033_CR67","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/nature13804","volume":"516","author":"J Wang","year":"2014","unstructured":"Wang J, Xie G, Singh M, Ghanbarian AT, Rask\u00f3 T, Szvetnik A, Cai H, Besser D, Prigione A, Fuchs NV, Schumann GG, Chen W, Lorincz MC, Ivics Z, Hurst LD, Izsv\u00e1k Z (2014) Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature 516(7531):405\u2013409. https:\/\/doi.org\/10.1038\/nature13804","journal-title":"Nature"},{"issue":"1","key":"2033_CR68","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12943-015-0402-5","volume":"14","author":"T Wang","year":"2015","unstructured":"Wang T, Wang G, Hao D, Liu X, Wang D, Ning N, Li X (2015) Aberrant regulation of the LIN28A\/LIN28B and let-7 loop in human malignant tumors and its effects on the hallmarks of cancer. Mol Cancer 14(1):1\u201313. https:\/\/doi.org\/10.1186\/s12943-015-0402-5","journal-title":"Mol Cancer"},{"issue":"10","key":"2033_CR69","doi-asserted-by":"publisher","first-page":"1182","DOI":"10.5966\/sctm.2014-0090","volume":"3","author":"Y Yamada","year":"2014","unstructured":"Yamada Y, Haga H, Yamada Y (2014) Concise review: dedifferentiation meets cancer development: proof of concept for epigenetic cancer. Stem Cells Transl Med 3(10):1182\u20131187. https:\/\/doi.org\/10.5966\/sctm.2014-0090","journal-title":"Stem Cells Transl Med"},{"issue":"9","key":"2033_CR70","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1093\/carcin\/bgv085","volume":"36","author":"Z Zhang","year":"2015","unstructured":"Zhang Z, Zhang S, Ma P, Jing Y, Peng H, Gao WQ, Zhuang G (2015) Lin28B promotes melanoma growth by mediating a microRNA regulatory circuit. Carcinogenesis 36(9):937\u2013945. https:\/\/doi.org\/10.1093\/carcin\/bgv085","journal-title":"Carcinogenesis"},{"issue":"9","key":"2033_CR71","doi-asserted-by":"publisher","first-page":"1380","DOI":"10.1038\/s41588-019-0479-7","volume":"51","author":"Y Zhang","year":"2019","unstructured":"Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Ren B (2019) Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat Genet 51(9):1380\u20131388. https:\/\/doi.org\/10.1038\/s41588-019-0479-7","journal-title":"Nat Genet"},{"issue":"5","key":"2033_CR72","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1016\/j.biocel.2013.02.006","volume":"45","author":"J Zhou","year":"2013","unstructured":"Zhou J, Ng SB, Chng WJ (2013) LIN28\/LIN28B: An emerging oncogenic driver in cancer stem cells. Int J Biochem Cell Biol 45(5):973\u2013978. https:\/\/doi.org\/10.1016\/j.biocel.2013.02.006","journal-title":"Int J Biochem Cell Biol"}],"container-title":["Molecular Genetics and Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00438-023-02033-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00438-023-02033-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00438-023-02033-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,22]],"date-time":"2023-07-22T12:04:50Z","timestamp":1690027490000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00438-023-02033-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6,3]]},"references-count":68,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,9]]}},"alternative-id":["2033"],"URL":"https:\/\/doi.org\/10.1007\/s00438-023-02033-1","relation":{},"ISSN":["1617-4615","1617-4623"],"issn-type":[{"value":"1617-4615","type":"print"},{"value":"1617-4623","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,6,3]]},"assertion":[{"value":"5 July 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 May 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 June 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no conflicts of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"Collection of first trimester placentae used in this work were collected following informed consent with approval from the Northern X Health and Disability Ethics Committee (NTX\/12\/06\/057\/AM09).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}]}}