{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T01:44:36Z","timestamp":1792028676044,"version":"4.4.0"},"reference-count":53,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T00:00:00Z","timestamp":1765152000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T00:00:00Z","timestamp":1768176000000},"content-version":"vor","delay-in-days":35,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"JST SPRING","award":["JPMJSP2127"],"award-info":[{"award-number":["JPMJSP2127"]}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["20cm0106306h0005"],"award-info":[{"award-number":["20cm0106306h0005"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["20fk0108088h0002"],"award-info":[{"award-number":["20fk0108088h0002"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["24fk0108629h0003"],"award-info":[{"award-number":["24fk0108629h0003"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["19H03689"],"award-info":[{"award-number":["19H03689"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["25K11650"],"award-info":[{"award-number":["25K11650"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Retrovirology"],"DOI":"10.1186\/s12977-025-00671-4","type":"journal-article","created":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T05:22:52Z","timestamp":1765171372000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Intra-pol proviral open region of HTLV-1 controls the transcription from both long terminal repeats"],"prefix":"10.1186","volume":"23","author":[{"given":"Miyu","family":"Sonoda","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Azusa","family":"Tanaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueda","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenyi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen","family":"Kiik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saumya","family":"Ramanayake","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kisato","family":"Nosaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norihiro","family":"Takenouchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masanori","family":"Nakagawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akihiro","family":"Fujimoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles R. M.","family":"Bangham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masao","family":"Matsuoka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun-ichirou","family":"Yasunaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,8]]},"reference":[{"key":"671_CR1","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/nrc2111","volume":"7","author":"M Matsuoka","year":"2007","unstructured":"Matsuoka M, Jeang KT. Human T-cell leukaemia virus type 1 (HTLV-1) infectivity and cellular transformation. Nat Rev Cancer. 2007;7:270\u201380. https:\/\/doi.org\/10.1038\/nrc2111.","journal-title":"Nat Rev Cancer"},{"key":"671_CR2","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1016\/0167-4781(89)90114-0","volume":"1009","author":"J Kypr","year":"1989","unstructured":"Kypr J, Mrazek J, Reich J. Nucleotide composition bias and CpG dinucleotide content in the genomes of HIV and HTLV 1\/2. Biochim Biophys Acta. 1989;1009:280\u20132. https:\/\/doi.org\/10.1016\/0167-4781(89)90114-0.","journal-title":"Biochim Biophys Acta"},{"key":"671_CR3","doi-asserted-by":"publisher","first-page":"e1009271","DOI":"10.1371\/journal.ppat.1009271","volume":"17","author":"M Izaki","year":"2021","unstructured":"Izaki M, Yasunaga JI, Nosaka K, Sugata K, Utsunomiya H, Suehiro Y, Shichijo T, Yamada A, Sugawara Y, Hibi T, et al. In vivo dynamics and adaptation of HTLV-1-infected clones under different clinical conditions. PLoS Pathog. 2021;17:e1009271. https:\/\/doi.org\/10.1371\/journal.ppat.1009271.","journal-title":"PLoS Pathog"},{"key":"671_CR4","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1146\/annurev-virology-092818-015501","volume":"6","author":"CRM Bangham","year":"2019","unstructured":"Bangham CRM, Miura M, Kulkarni A, Matsuoka M. Regulation of latency in the human T cell leukemia Virus, HTLV-1. Annu Rev Virol. 2019;6:365\u201385. https:\/\/doi.org\/10.1146\/annurev-virology-092818-015501.","journal-title":"Annu Rev Virol"},{"key":"671_CR5","doi-asserted-by":"publisher","first-page":"E1269","DOI":"10.1073\/pnas.1715724115","volume":"115","author":"M Mahgoub","year":"2018","unstructured":"Mahgoub M, Yasunaga JI, Iwami S, Nakaoka S, Koizumi Y, Shimura K, Matsuoka M. Sporadic on\/off switching of HTLV-1 tax expression is crucial to maintain the whole population of virus-induced leukemic cells. Proc Natl Acad Sci U S A. 2018;115:E1269\u201378. https:\/\/doi.org\/10.1073\/pnas.1715724115.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"671_CR6","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1742-4690-6-19","volume":"6","author":"M Saito","year":"2009","unstructured":"Saito M, Matsuzaki T, Satou Y, Yasunaga J, Saito K, Arimura K, Matsuoka M, Ohara Y. In vivo expression of the HBZ gene of HTLV-1 correlates with proviral load, inflammatory markers and disease severity in HTLV-1 associated myelopathy\/tropical spastic paraparesis (HAM\/TSP). Retrovirology. 2009;6:19. https:\/\/doi.org\/10.1186\/1742-4690-6-19.","journal-title":"Retrovirology"},{"key":"671_CR7","doi-asserted-by":"publisher","first-page":"9359","DOI":"10.1128\/JVI.00242-08","volume":"82","author":"M Yoshida","year":"2008","unstructured":"Yoshida M, Satou Y, Yasunaga J, Fujisawa J, Matsuoka M. Transcriptional control of spliced and unspliced human T-cell leukemia virus type 1 bZIP factor (HBZ) gene. J Virol. 2008;82:9359\u201368. https:\/\/doi.org\/10.1128\/JVI.00242-08.","journal-title":"J Virol"},{"key":"671_CR8","doi-asserted-by":"publisher","first-page":"9070","DOI":"10.1128\/JVI.00661-12","volume":"86","author":"H Gazon","year":"2012","unstructured":"Gazon H, Lemasson I, Polakowski N, Cesaire R, Matsuoka M, Barbeau B, Mesnard JM, Peloponese JM. Jr. Human T-cell leukemia virus type 1 (HTLV-1) bZIP factor requires cellular transcription factor JunD to upregulate HTLV-1 antisense transcription from the 3\u2019 long terminal repeat. J Virol. 2012;86:9070\u20138. https:\/\/doi.org\/10.1128\/JVI.00661-12.","journal-title":"J Virol"},{"key":"671_CR9","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1186\/1742-4690-2-64","volume":"2","author":"Y Taniguchi","year":"2005","unstructured":"Taniguchi Y, Nosaka K, Yasunaga J, Maeda M, Mueller N, Okayama A, Matsuoka M. Silencing of human T-cell leukemia virus type I gene transcription by epigenetic mechanisms. Retrovirology. 2005;2:64. https:\/\/doi.org\/10.1186\/1742-4690-2-64.","journal-title":"Retrovirology"},{"key":"671_CR10","doi-asserted-by":"publisher","first-page":"3054","DOI":"10.1073\/pnas.1423199113","volume":"113","author":"Y Satou","year":"2016","unstructured":"Satou Y, Miyazato P, Ishihara K, Yaguchi H, Melamed A, Miura M, Fukuda A, Nosaka K, Watanabe T, Rowan AG, et al. The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome. Proc Natl Acad Sci U S A. 2016;113:3054\u20139. https:\/\/doi.org\/10.1073\/pnas.1423199113.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"671_CR11","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1016\/s0092-8674(00)81794-8","volume":"87","author":"K Ryan","year":"1996","unstructured":"Ryan K, Garrett N, Mitchell A, Gurdon JB. Eomesodermin, a key early gene in xenopus mesoderm differentiation. Cell. 1996;87:989\u20131000. https:\/\/doi.org\/10.1016\/s0092-8674(00)81794-8.","journal-title":"Cell"},{"key":"671_CR12","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/35003601","volume":"404","author":"AP Russ","year":"2000","unstructured":"Russ AP, Wattler S, Colledge WH, Aparicio SA, Carlton MB, Pearce JJ, Barton SC, Surani MA, Ryan K, Nehls MC, et al. Eomesodermin is required for mouse trophoblast development and mesoderm formation. Nature. 2000;404:95\u20139. https:\/\/doi.org\/10.1038\/35003601.","journal-title":"Nature"},{"key":"671_CR13","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1126\/science.1090148","volume":"302","author":"EL Pearce","year":"2003","unstructured":"Pearce EL, Mullen AC, Martins GA, Krawczyk CM, Hutchins AS, Zediak VP, Banica M, DiCioccio CB, Gross DA, Mao CA, et al. Control of effector CD8\u2009+\u2009T cell function by the transcription factor eomesodermin. Science. 2003;302:1041\u20133. https:\/\/doi.org\/10.1126\/science.1090148.","journal-title":"Science"},{"key":"671_CR14","doi-asserted-by":"publisher","first-page":"2981","DOI":"10.3389\/fimmu.2018.02981","volume":"9","author":"J Li","year":"2018","unstructured":"Li J, He Y, Hao J, Ni L, Dong C. High levels of Eomes promote exhaustion of Anti-tumor CD8(+) T cells. Front Immunol. 2018;9:2981. https:\/\/doi.org\/10.3389\/fimmu.2018.02981.","journal-title":"Front Immunol"},{"key":"671_CR15","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1038\/s12276-021-00568-0","volume":"53","author":"W Seo","year":"2021","unstructured":"Seo W, Jerin C, Nishikawa H. Transcriptional regulatory network for the establishment of CD8(+) T cell exhaustion. Exp Mol Med. 2021;53:202\u20139. https:\/\/doi.org\/10.1038\/s12276-021-00568-0.","journal-title":"Exp Mol Med"},{"key":"671_CR16","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1038\/ni1268","volume":"6","author":"AM Intlekofer","year":"2005","unstructured":"Intlekofer AM, Takemoto N, Wherry EJ, Longworth SA, Northrup JT, Palanivel VR, Mullen AC, Gasink CR, Kaech SM, Miller JD, et al. Effector and memory CD8\u2009+\u2009T cell fate coupled by T-bet and eomesodermin. Nat Immunol. 2005;6:1236\u201344. https:\/\/doi.org\/10.1038\/ni1268.","journal-title":"Nat Immunol"},{"key":"671_CR17","doi-asserted-by":"publisher","first-page":"e10636","DOI":"10.1371\/journal.pone.0010636","volume":"5","author":"S Narayanan","year":"2010","unstructured":"Narayanan S, Silva R, Peruzzi G, Alvarez Y, Simhadri VR, Debell K, Coligan JE, Borrego F. Human Th1 cells that express CD300a are polyfunctional and after stimulation up-regulate the T-box transcription factor eomesodermin. PLoS ONE. 2010;5:e10636. https:\/\/doi.org\/10.1371\/journal.pone.0010636.","journal-title":"PLoS ONE"},{"key":"671_CR18","doi-asserted-by":"publisher","first-page":"e1008422","DOI":"10.1371\/journal.pcbi.1008422","volume":"16","author":"A Tanaka","year":"2020","unstructured":"Tanaka A, Ishitsuka Y, Ohta H, Fujimoto A, Yasunaga JI, Matsuoka M. Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells. PLoS Comput Biol. 2020;16:e1008422. https:\/\/doi.org\/10.1371\/journal.pcbi.1008422.","journal-title":"PLoS Comput Biol"},{"key":"671_CR19","doi-asserted-by":"publisher","first-page":"e1012690","DOI":"10.1371\/journal.pcbi.1012690","volume":"21","author":"A Tanaka","year":"2025","unstructured":"Tanaka A, Ishitsuka Y, Ohta H, Takenouchi N, Nakagawa M, Koh KR, Onishi C, Tanaka H, Fujimoto A, Yasunaga JI, Matsuoka M. Integrative analysis of ATAC-seq and RNA-seq for cells infected by human T-cell leukemia virus type 1. PLoS Comput Biol. 2025;21:e1012690. https:\/\/doi.org\/10.1371\/journal.pcbi.1012690.","journal-title":"PLoS Comput Biol"},{"key":"671_CR20","doi-asserted-by":"publisher","first-page":"2405","DOI":"10.1038\/s41467-022-30029-9","volume":"13","author":"M Matsuo","year":"2022","unstructured":"Matsuo M, Ueno T, Monde K, Sugata K, Tan BJY, Rahman A, Miyazato P, Uchiyama K, Islam S, Katsuya H, et al. Identification and characterization of a novel enhancer in the HTLV-1 proviral genome. Nat Commun. 2022;13:2405. https:\/\/doi.org\/10.1038\/s41467-022-30029-9.","journal-title":"Nat Commun"},{"key":"671_CR21","doi-asserted-by":"publisher","first-page":"W39","DOI":"10.1093\/nar\/gkv416","volume":"43","author":"TL Bailey","year":"2015","unstructured":"Bailey TL, Johnson J, Grant CE, Noble WS. The MEME suite. Nucleic Acids Res. 2015;43:W39\u201349. https:\/\/doi.org\/10.1093\/nar\/gkv416.","journal-title":"Nucleic Acids Res"},{"key":"671_CR22","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1002\/ijc.20007","volume":"109","author":"S Takeda","year":"2004","unstructured":"Takeda S, Maeda M, Morikawa S, Taniguchi Y, Yasunaga J, Nosaka K, Tanaka Y, Matsuoka M. Genetic and epigenetic inactivation of tax gene in adult T-cell leukemia cells. Int J Cancer. 2004;109:559\u201367. https:\/\/doi.org\/10.1002\/ijc.20007.","journal-title":"Int J Cancer"},{"key":"671_CR23","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1073\/pnas.0507631103","volume":"103","author":"Y Satou","year":"2006","unstructured":"Satou Y, Yasunaga J, Yoshida M, Matsuoka M. HTLV-I basic leucine zipper factor gene mRNA supports proliferation of adult T cell leukemia cells. Proc Natl Acad Sci U S A. 2006;103:720\u20135. https:\/\/doi.org\/10.1073\/pnas.0507631103.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"671_CR24","doi-asserted-by":"publisher","first-page":"e1008164","DOI":"10.1371\/journal.ppat.1008164","volume":"15","author":"M Miura","year":"2019","unstructured":"Miura M, Dey S, Ramanayake S, Singh A, Rueda DS, Bangham CRM. Kinetics of HTLV-1 reactivation from latency quantified by single-molecule RNA FISH and stochastic modelling. PLoS Pathog. 2019;15:e1008164. https:\/\/doi.org\/10.1371\/journal.ppat.1008164.","journal-title":"PLoS Pathog"},{"key":"671_CR25","doi-asserted-by":"publisher","first-page":"5435","DOI":"10.1038\/s41467-023-41305-7","volume":"14","author":"N Witman","year":"2023","unstructured":"Witman N, Zhou C, Haneke T, Xiao Y, Huang X, Rohner E, Sohlmer J, Grote Beverborg N, Lehtinen ML, Chien KR, Sahara M. Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development. Nat Commun. 2023;14:5435. https:\/\/doi.org\/10.1038\/s41467-023-41305-7.","journal-title":"Nat Commun"},{"key":"671_CR26","doi-asserted-by":"publisher","first-page":"3234","DOI":"10.1128\/JVI.63.8.3234-3239.1989","volume":"63","author":"J Fujisawa","year":"1989","unstructured":"Fujisawa J, Toita M, Yoshida M. A unique enhancer element for the trans activator (p40tax) of human T-cell leukemia virus type I that is distinct from Cyclic AMP- and 12-O-tetradecanoylphorbol-13-acetate-responsive elements. J Virol. 1989;63:3234\u20139. https:\/\/doi.org\/10.1128\/JVI.63.8.3234-3239.1989.","journal-title":"J Virol"},{"key":"671_CR27","doi-asserted-by":"publisher","first-page":"e1006722","DOI":"10.1371\/journal.ppat.1006722","volume":"13","author":"R Furuta","year":"2017","unstructured":"Furuta R, Yasunaga JI, Miura M, Sugata K, Saito A, Akari H, Ueno T, Takenouchi N, Fujisawa JI, Koh KR, et al. Human T-cell leukemia virus type 1 infects multiple lineage hematopoietic cells in vivo. PLoS Pathog. 2017;13:e1006722. https:\/\/doi.org\/10.1371\/journal.ppat.1006722.","journal-title":"PLoS Pathog"},{"key":"671_CR28","doi-asserted-by":"publisher","unstructured":"Kulkarni A, Taylor GP, Klose RJ, Schofield CJ, Bangham CR. Histone H2A monoubiquitylation and p38-MAPKs regulate immediate-early gene-like reactivation of latent retrovirus HTLV-1. JCI Insight. 2018;3. https:\/\/doi.org\/10.1172\/jci.insight.123196.","DOI":"10.1172\/jci.insight.123196"},{"key":"671_CR29","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1038\/nchembio.138","volume":"5","author":"FV Subach","year":"2009","unstructured":"Subach FV, Subach OM, Gundorov IS, Morozova KS, Piatkevich KD, Cuervo AM, Verkhusha VV. Monomeric fluorescent timers that change color from blue to red report on cellular trafficking. Nat Chem Biol. 2009;5:118\u201326. https:\/\/doi.org\/10.1038\/nchembio.138.","journal-title":"Nat Chem Biol"},{"key":"671_CR30","doi-asserted-by":"publisher","first-page":"e1010387","DOI":"10.1371\/journal.ppat.1010387","volume":"18","author":"H Kiik","year":"2022","unstructured":"Kiik H, Ramanayake S, Miura M, Tanaka Y, Melamed A, Bangham CRM. Time-course of host cell transcription during the HTLV-1 transcriptional burst. PLoS Pathog. 2022;18:e1010387. https:\/\/doi.org\/10.1371\/journal.ppat.1010387.","journal-title":"PLoS Pathog"},{"key":"671_CR31","doi-asserted-by":"publisher","first-page":"1975","DOI":"10.1128\/JVI.71.3.1975-1983.1997","volume":"71","author":"I Lemasson","year":"1997","unstructured":"Lemasson I, Robert-Hebmann V, Hamaia S, Duc Dodon M, Gazzolo L, Devaux C. Transrepression of Lck gene expression by human T-cell leukemia virus type 1-encoded p40tax. J Virol. 1997;71:1975\u201383. https:\/\/doi.org\/10.1128\/JVI.71.3.1975-1983.1997.","journal-title":"J Virol"},{"key":"671_CR32","doi-asserted-by":"publisher","first-page":"e1006120","DOI":"10.1371\/journal.ppat.1006120","volume":"13","author":"H Kinosada","year":"2017","unstructured":"Kinosada H, Yasunaga JI, Shimura K, Miyazato P, Onishi C, Iyoda T, Inaba K, Matsuoka M. HTLV-1 bZIP factor enhances T-Cell proliferation by impeding the suppressive signaling of Co-inhibitory receptors. PLoS Pathog. 2017;13:e1006120. https:\/\/doi.org\/10.1371\/journal.ppat.1006120.","journal-title":"PLoS Pathog"},{"key":"671_CR33","doi-asserted-by":"publisher","unstructured":"Yukawa M, Jagannathan S, Vallabh S, Kartashov AV, Chen X, Weirauch MT, Barski A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. J Exp Med. 2020;217. https:\/\/doi.org\/10.1084\/jem.20182009.","DOI":"10.1084\/jem.20182009"},{"key":"671_CR34","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1128\/mcb.7.1.388-397.1987","volume":"7","author":"S Arrigo","year":"1987","unstructured":"Arrigo S, Yun M, Beemon K. cis-acting regulatory elements within gag genes of avian retroviruses. Mol Cell Biol. 1987;7:388\u201397. https:\/\/doi.org\/10.1128\/mcb.7.1.388-397.1987.","journal-title":"Mol Cell Biol"},{"key":"671_CR35","doi-asserted-by":"publisher","first-page":"4874","DOI":"10.1073\/pnas.87.12.4874","volume":"87","author":"E Verdin","year":"1990","unstructured":"Verdin E, Becker N, Bex F, Droogmans L, Burny A. Identification and characterization of an enhancer in the coding region of the genome of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A. 1990;87:4874\u20138. https:\/\/doi.org\/10.1073\/pnas.87.12.4874.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"671_CR36","doi-asserted-by":"publisher","first-page":"2632","DOI":"10.1128\/JVI.68.4.2632-2648.1994","volume":"68","author":"C Van Lint","year":"1994","unstructured":"Van Lint C, Ghysdael J, Paras P Jr., Burny A, Verdin E. A transcriptional regulatory element is associated with a nuclease-hypersensitive site in the pol gene of human immunodeficiency virus type 1. J Virol. 1994;68:2632\u201348. https:\/\/doi.org\/10.1128\/JVI.68.4.2632-2648.1994.","journal-title":"J Virol"},{"key":"671_CR37","doi-asserted-by":"publisher","first-page":"e19084","DOI":"10.1371\/journal.pone.0019084","volume":"6","author":"L Colin","year":"2011","unstructured":"Colin L, Vandenhoudt N, de Walque S, Van Driessche B, Bergamaschi A, Martinelli V, Cherrier T, Vanhulle C, Guiguen A, David A, et al. The AP-1 binding sites located in the pol gene intragenic regulatory region of HIV-1 are important for viral replication. PLoS ONE. 2011;6:e19084. https:\/\/doi.org\/10.1371\/journal.pone.0019084.","journal-title":"PLoS ONE"},{"key":"671_CR38","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1182\/blood-2015-04-641118","volume":"126","author":"K Sugata","year":"2015","unstructured":"Sugata K, Yasunaga J, Mitobe Y, Miura M, Miyazato P, Kohara M, Matsuoka M. Protective effect of cytotoxic T lymphocytes targeting HTLV-1 bZIP factor. Blood. 2015;126:1095\u2013105. https:\/\/doi.org\/10.1182\/blood-2015-04-641118.","journal-title":"Blood"},{"key":"671_CR39","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1093\/infdis\/jiq078","volume":"203","author":"S Hilburn","year":"2011","unstructured":"Hilburn S, Rowan A, Demontis MA, MacNamara A, Asquith B, Bangham CR, Taylor GP. In vivo expression of human T-lymphotropic virus type 1 basic leucine-zipper protein generates specific CD8\u2009+\u2009and CD4\u2009+\u2009T-lymphocyte responses that correlate with clinical outcome. J Infect Dis. 2011;203:529\u201336. https:\/\/doi.org\/10.1093\/infdis\/jiq078.","journal-title":"J Infect Dis"},{"key":"671_CR40","doi-asserted-by":"publisher","first-page":"979","DOI":"10.3389\/fmicb.2020.00979","volume":"11","author":"JI Yasunaga","year":"2020","unstructured":"Yasunaga JI. Strategies of human T-Cell leukemia virus type 1 for persistent infection: implications for leukemogenesis of adult T-Cell leukemia-Lymphoma. Front Microbiol. 2020;11:979. https:\/\/doi.org\/10.3389\/fmicb.2020.00979.","journal-title":"Front Microbiol"},{"key":"671_CR41","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1002\/ijc.2910540208","volume":"54","author":"O Shinzato","year":"1993","unstructured":"Shinzato O, Kamihira S, Ikeda S, Kondo H, Kanda T, Nagata Y, Nakayama E, Shiku H. Relationship between the anti-HTLV-1 antibody level, the number of abnormal lymphocytes and the viral-genome dose in HTLV-1-infected individuals. Int J Cancer. 1993;54:208\u201312. https:\/\/doi.org\/10.1002\/ijc.2910540208.","journal-title":"Int J Cancer"},{"key":"671_CR42","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1002\/ana.410260304","volume":"26","author":"M Yoshida","year":"1989","unstructured":"Yoshida M, Osame M, Kawai H, Toita M, Kuwasaki N, Nishida Y, Hiraki Y, Takahashi K, Nomura K, Sonoda S, et al. Increased replication of HTLV-I in HTLV-I-associated myelopathy. Ann Neurol. 1989;26:331\u20135. https:\/\/doi.org\/10.1002\/ana.410260304.","journal-title":"Ann Neurol"},{"key":"671_CR43","doi-asserted-by":"publisher","first-page":"1447","DOI":"10.1038\/s41564-025-02006-7","volume":"10","author":"K Sugata","year":"2025","unstructured":"Sugata K, Rahman A, Niimura K, Monde K, Ueno T, Rajib SA, Takatori M, Sakhor W, Hossain MB, Sithi SN, et al. Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment. Nat Microbiol. 2025;10:1447\u201362. https:\/\/doi.org\/10.1038\/s41564-025-02006-7.","journal-title":"Nat Microbiol"},{"key":"671_CR44","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1006\/viro.1997.8781","volume":"237","author":"D Derse","year":"1997","unstructured":"Derse D, Mikovits J, Ruscetti F. X-I and X-II open reading frames of HTLV-I are not required for virus replication or for immortalization of primary T-cells in vitro. Virology. 1997;237:123\u20138. https:\/\/doi.org\/10.1006\/viro.1997.8781.","journal-title":"Virology"},{"key":"671_CR45","first-page":"28","volume":"2","author":"TL Bailey","year":"1994","unstructured":"Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994;2:28\u201336.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"671_CR46","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol. 2011;29:24\u20136. https:\/\/doi.org\/10.1038\/nbt.1754.","journal-title":"Nat Biotechnol"},{"key":"671_CR47","doi-asserted-by":"publisher","first-page":"R24","DOI":"10.1186\/gb-2007-8-2-r24","volume":"8","author":"S Gupta","year":"2007","unstructured":"Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Quantifying similarity between motifs. Genome Biol. 2007;8:R24. https:\/\/doi.org\/10.1186\/gb-2007-8-2-r24.","journal-title":"Genome Biol"},{"key":"671_CR48","doi-asserted-by":"publisher","first-page":"10683","DOI":"10.1128\/JVI.01009-06","volume":"80","author":"P Miyazato","year":"2006","unstructured":"Miyazato P, Yasunaga J, Taniguchi Y, Koyanagi Y, Mitsuya H, Matsuoka M. De Novo human T-cell leukemia virus type 1 infection of human lymphocytes in NOD-SCID, common gamma-chain knockout mice. J Virol. 2006;80:10683\u201391. https:\/\/doi.org\/10.1128\/JVI.01009-06.","journal-title":"J Virol"},{"key":"671_CR49","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1093\/brain\/awaa421","volume":"144","author":"K Kim","year":"2021","unstructured":"Kim K, Probstel AK, Baumann R, Dyckow J, Landefeld J, Kogl E, Madireddy L, Loudermilk R, Eggers EL, Singh S, et al. Cell type-specific transcriptomics identifies neddylation as a novel therapeutic target in multiple sclerosis. Brain. 2021;144:450\u201361. https:\/\/doi.org\/10.1093\/brain\/awaa421.","journal-title":"Brain"},{"key":"671_CR50","doi-asserted-by":"publisher","first-page":"80","DOI":"10.3390\/v8030080","volume":"8","author":"JM Fox","year":"2016","unstructured":"Fox JM, Hilburn S, Demontis MA, Brighty DW, Rios Grassi MF, Galvao-Castro B, Taylor GP, Martin F. Long terminal repeat circular DNA as markers of active viral replication of human T lymphotropic Virus-1 in vivo. Viruses. 2016;8:80. https:\/\/doi.org\/10.3390\/v8030080.","journal-title":"Viruses"},{"key":"671_CR51","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1023\/a:1025732728195","volume":"27","author":"Y Suzuki","year":"2003","unstructured":"Suzuki Y, Misawa N, Sato C, Ebina H, Masuda T, Yamamoto N, Koyanagi Y. Quantitative analysis of human immunodeficiency virus type 1 DNA dynamics by real-time PCR: integration efficiency in stimulated and unstimulated peripheral blood mononuclear cells. Virus Genes. 2003;27:177\u201388. https:\/\/doi.org\/10.1023\/a:1025732728195.","journal-title":"Virus Genes"},{"key":"671_CR52","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. 2025. https:\/\/www.R-project.org\/"},{"key":"671_CR53","unstructured":"Posit team. RStudio: Integrated Development Environment for R. Posit Software, PBC, Boston MA. 2025. http:\/\/www.posit.co\/"}],"container-title":["Retrovirology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12977-025-00671-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12977-025-00671-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12977-025-00671-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T22:10:20Z","timestamp":1768342220000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12977-025-00671-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,8]]},"references-count":53,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["671"],"URL":"https:\/\/doi.org\/10.1186\/s12977-025-00671-4","relation":{},"ISSN":["1742-4690"],"issn-type":[{"value":"1742-4690","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,8]]},"assertion":[{"value":"16 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 November 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Blood samples from ATL patients and HAM patients were collected after the written informed consent was obtained in accordance with the Declaration of Helsinki. These experiments were approved by the Institutional Ethics Committee of Kumamoto University (accession numbers: G489, G499, and E2214).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1"}}