Regulation of endogenous retroelements
Yang J, Cook L, Chen Z. Systematic evaluation of retroviral LTRs as cis-regulatory elements in mouse embryos. Cell Reports. 2024 Mar;43(3):113775. doi: 10.1016/j.celrep.2024.113775.; Garza R, Atacho DAM, Adami A, Gerdes P, Vinod M, Hsieh P, Karlsson O, Horvath V, Johansson PA, Pandiloski N, Matas-Fuentes J, Quaegebeur A, Kouli A, Sharma Y, Jönsson ME, Monni E, Englund E, Eichler EE, Gale Hammell M, Barker RA, Kokaia Z, Douse CH, Jakobsson J. LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification. Sci Adv. 2023 Nov 03;9(44):eadh9543. PMID: 37910626; PMCID: PMC10619931.; Carotti E, Carducci F, Barucca M, Canapa A, Biscotti MA. Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin. Int J Mol Sci. 2023 Jul 18;24(14). PMID: 37511347; PMCID: PMC10380595.; Gholami Barzoki M, Shatizadeh Malekshahi S, Heydarifard Z, Mahmodi MJ, Soltanghoraee H. The important biological roles of Syncytin-1 of human endogenous retrovirus W (HERV-W) and Syncytin-2 of HERV-FRD in the human placenta development. Mol Biol Rep. 2023 Sep;50(9):7901–7. doi: 10.1007/s11033-023-08658-0. PMID: 37421503.; Osmanski AB, Paulat NS, Korstian J, Grimshaw JR, Halsey M, Sullivan KAM, Moreno-Santillán DD, Crookshanks C, Roberts J, Garcia C, Johnson MG, Densmore LD, Stevens RD, , Rosen J, Storer JM, Hubley R, Smit AFA, Dávalos LM, Karlsson EK, Lindblad-Toh K, Ray DA, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli K, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot J, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science. 2023 Apr 28;380(6643). doi: 10.1126/science.abn1430.; Seczynska M, Lehner PJ. The sound of silence: mechanisms and implications of HUSH complex function. Trends Genet. 2023 Apr;39(4):251–67. doi: 10.1016/j.tig.2022.12.005. PMID: 36754727.; Sakashita A, Kitano T, Ishizu H, Guo Y, Masuda H, Ariura M, Murano K, Siomi H. Transcription of MERVL retrotransposons is required for preimplantation embryo development. Nat Genet. 2023 Mar;55(3):484–95. PMID: 36864102; PMCID: PMC10011141.; Stamidis N, Zylicz JJ. RNA -mediated heterochromatin formation at repetitive elements in mammals. The EMBO Journal. 2023 Feb 27;42(8). doi: 10.15252/embj.2022111717.; Pontis J, Pulver C, Playfoot CJ, Planet E, Grun D, Offner S, Duc J, Manfrin A, Lutolf MP, Trono D. Primate-specific transposable elements shape transcriptional networks during human development. Nat Commun. 2022 Nov 23;13(1):7178. PMID: 36418324; PMCID: PMC9684439.; Almeida MV, Vernaz G, Putman ALK, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet. 2022 Jun;38(6):529–53. doi: 10.1016/j.tig.2022.02.009. PMID: 35307201.; Fueyo R, Judd J, Feschotte C, Wysocka J. Roles of transposable elements in the regulation of mammalian transcription. Nature Reviews Molecular Cell Biology. 2022 Feb 28;23(7):481–97. doi: 10.1038/s41580-022-00457-y.; Xiang X, Tao Y, DiRusso J, Hsu F, Zhang J, Xue Z, Pontis J, Trono D, Liu W, Clark AT. Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. Nature Communications. 2022 Jan 24;13(1):463. doi: 10.1038/s41467-022-28105-1.; Low Y, Tan DEK, Hu Z, Tan SYX, Tee W. Transposable Element Dynamics and Regulation during Zygotic Genome Activation in Mammalian Embryos and Embryonic Stem Cell Model Systems. Stem Cells International. 2021 Oct 15;2021():1–17. doi: 10.1155/2021/1624669.; Xiong F, Wang R, Lee J, Li S, Chen S, Liao Z, Hasani LA, Nguyen PT, Zhu X, Krakowiak J, Lee D, Han L, Tsai K, Liu Y, Li W. RNA m6A modification orchestrates a LINE-1–host interaction that facilitates retrotransposition and contributes to long gene vulnerability. Cell Research. 2021 Jun 09;31(8):861–85. doi: 10.1038/s41422-021-00515-8.; Chen C, Liu W, Guo J, Liu Y, Liu X, Liu J, Dou X, Le R, Huang Y, Li C, Yang L, Kou X, Zhao Y, Wu Y, Chen J, Wang H, Shen B, Gao Y, Gao S. Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos. Protein & Cell. 2021 Apr 22;12(6):455–74. doi: 10.1007/s13238-021-00837-8.; Liu J, Gao M, He J, Wu K, Lin S, Jin L, Chen Y, Liu H, Shi J, Wang X, Chang L, Lin Y, Zhao YL, Zhang X, Zhang M, Luo GZ, Wu G, Pei D, Wang J, Bao X, Chen J. The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity. Nature. 2021 Mar;591(7849):322–6. doi: 10.1038/s41586-021-03313-9. PMID: 33658714.; Hwang S, Jung H, Mun S, Lee S, Park K, Baek SC, Moon HC, Kim H, Kim B, Choi Y, Go Y, Tang W, Choi J, Choi JK, Cha H, Park HY, Liang P, Kim VN, Han K, Ahn K. L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force. Nature Communications. 2021 Feb 09;12(1):880. doi: 10.1038/s41467-021-21197-1.; Xu W, Li J, He C, Wen J, Ma H, Rong B, Diao J, Wang L, Wang J, Wu F, Tan L, Shi YG, Shi Y, Shen H. METTL3 regulates heterochromatin in mouse embryonic stem cells. Nature. 2021 Mar;591(7849):317–21. doi: 10.1038/s41586-021-03210-1. PMID: 33505026.; Chelmicki T, Roger E, Teissandier A, Dura M, Bonneville L, Rucli S, Dossin F, Fouassier C, Lameiras S, Bourc'his D. m6A RNA methylation regulates the fate of endogenous retroviruses. Nature. 2021 Mar;591(7849):312–6. doi: 10.1038/s41586-020-03135-1. PMID: 33442060.; Geis FK, Goff SP. Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview. Viruses. 2020 Aug 13;12(8). PMID: 32823517; PMCID: PMC7472088.; Sundaram V, Wysocka J. Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes. Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190347. PMID: 32075564; PMCID: PMC7061989.; Percharde M, Lin CJ, Yin Y, Guan J, Peixoto GA, Bulut-Karslioglu A, Biechele S, Huang B, Shen X, Ramalho-Santos M. A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity. Cell. 2018 Jul 12;174(2):391–405.e19. PMID: 29937225; PMCID: PMC6046266.; Yang P, Wang Y, Macfarlan TS. The Role of KRAB-ZFPs in Transposable Element Repression and Mammalian Evolution. Trends in Genetics. 2017 Nov;33(11):871–81. doi: 10.1016/j.tig.2017.08.006.; Wildschutte JH, Williams ZH, Montesion M, Subramanian RP, Kidd JM, Coffin JM. Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):E2326–34. PMID: 27001843; PMCID: PMC4843416.; Lupo A, Cesaro E, Montano G, Zurlo D, Izzo P, Costanzo P. KRAB-Zinc Finger Proteins: A Repressor Family Displaying Multiple Biological Functions. Curr Genomics. 2013 Jun;14(4):268–78. PMID: 24294107; PMCID: PMC3731817.; Macfarlan TS, Gifford WD, Driscoll S, Lettieri K, Rowe HM, Bonanomi D, Firth A, Singer O, Trono D, Pfaff SL. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature. 2012 Jul 05;487(7405):57–63. PMID: 22722858; PMCID: PMC3395470.; Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, Moran JV. LINE-1 retrotransposition activity in human genomes. Cell. 2010 Jun 25;141(7):1159–70. PMID: 20602998; PMCID: PMC3013285.; Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE. Active Alu retrotransposons in the human genome. Genome Res. 2008 Oct 03;18(12):1875–83. doi: 10.1101/gr.081737.108.; Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res. 2006 May;16(5):669–77. PMID: 16606702; PMCID: PMC1457042.; Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J; International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860–921. doi: 10.1038/35057062. PMID: 11237011.