Mc CB. The origin and behavior of mutable loci in maize. Proc Natl Acad Sci U S A. 1950;36(6):344–55.
Article
Google Scholar
Mills RE, et al. Which transposable elements are active in the human genome? Trends Genet. 2007;23(4):183–91.
Article
CAS
PubMed
Google Scholar
Kokosar J, Kordis D. Genesis and regulatory wiring of retroelement-derived domesticated genes: a phylogenomic perspective. Mol Biol Evol. 2013;30(5):1015–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Franke V, et al. Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. Genome Res. 2017;27(8):1384–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anwar SL, Wulaningsih W, Lehmann U. Transposable elements in human cancer: causes and consequences of deregulation. Int J Mol Sci. 2017;18(5):974.
Article
PubMed Central
CAS
Google Scholar
Liu J, et al. LINE-I element insertion at the t(11;22) translocation breakpoint of a desmoplastic small round cell tumor. Genes Chromosomes Cancer. 1997;18(3):232–9.
Article
PubMed
Google Scholar
Daskalos A, et al. Hypomethylation of retrotransposable elements correlates with genomic instability in non-small cell lung cancer. Int J Cancer. 2009;124(1):81–7.
Article
CAS
PubMed
Google Scholar
Molaro A, Malik HS. Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline. Curr Opin Genet Dev. 2016;37:51–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hancks DC, Kazazian HH Jr. Roles for retrotransposon insertions in human disease. Mob DNA. 2016;7:9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Amarasinghe SL, et al. Opportunities and challenges in long-read sequencing data analysis. Genome Biol. 2020;21(1):30.
Article
PubMed
PubMed Central
Google Scholar
Turelli P, et al. Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons. Sci Adv. 2020;6(35): eaba3200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woodcock DM, et al. Asymmetric methylation in the hypermethylated CpG promoter region of the human L1 retrotransposon. J Biol Chem. 1997;272(12):7810–6.
Article
CAS
PubMed
Google Scholar
Walsh CP, Chaillet JR, Bestor TH. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet. 1998;20(2):116–7.
Article
CAS
PubMed
Google Scholar
Martens JH, et al. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 2005;24(4):800–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guelen L, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature. 2008;453(7197):948–51.
Article
CAS
PubMed
Google Scholar
Wallace MR, et al. A de novo Alu insertion results in neurofibromatosis type 1. Nature. 1991;353(6347):864–6.
Article
CAS
PubMed
Google Scholar
Miki Y, et al. Mutation analysis in the BRCA2 gene in primary breast cancers. Nat Genet. 1996;13(2):245–7.
Article
CAS
PubMed
Google Scholar
Lapp HE, Hunter RG. Early life exposures, neurodevelopmental disorders, and transposable elements. Neurobiol Stress. 2019;11: 100174.
Article
PubMed
PubMed Central
Google Scholar
Tam OH, et al. Postmortem cortex samples identify distinct molecular subtypes of ALS: retrotransposon activation, oxidative stress, and activated glia. Cell Rep. 2019;29(5):1164-1177 e5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu EY, et al. Loss of nuclear TDP-43 is associated with decondensation of LINE retrotransposons. Cell Rep. 2019;27(5):1409-1421 e6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thomas CA, et al. Modeling of TREX1-dependent autoimmune disease using human stem cells highlights L1 accumulation as a source of neuroinflammation. Cell Stem Cell. 2017;21(3):319-331 e8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jang HS, et al. Transposable elements drive widespread expression of oncogenes in human cancers. Nat Genet. 2019;51(4):611–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gasior SL, et al. The human LINE-1 retrotransposon creates DNA double-strand breaks. J Mol Biol. 2006;357(5):1383–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gilbert N, Lutz-Prigge S, Moran JV. Genomic deletions created upon LINE-1 retrotransposition. Cell. 2002;110(3):315–25.
Article
CAS
PubMed
Google Scholar
Han K, et al. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res. 2005;33(13):4040–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sorek R, Ast G, Graur D. Alu-containing exons are alternatively spliced. Genome Res. 2002;12(7):1060–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Belancio VP, Hedges DJ, Deininger P. LINE-1 RNA splicing and influences on mammalian gene expression. Nucleic Acids Res. 2006;34(5):1512–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lev-Maor G, et al. Intronic Alus influence alternative splicing. PLoS Genet. 2008;4(9): e1000204.
Article
PubMed
PubMed Central
CAS
Google Scholar
Teugels E, et al. De novo Alu element insertions targeted to a sequence common to the BRCA1 and BRCA2 genes. Hum Mutat. 2005;26(3):284.
Article
PubMed
Google Scholar
Miki Y, et al. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 1992;52(3):643–5.
CAS
PubMed
Google Scholar
Rodriguez-Martin C, et al. Familial retinoblastoma due to intronic LINE-1 insertion causes aberrant and noncanonical mRNA splicing of the RB1 gene. J Hum Genet. 2016;61(5):463–6.
Article
CAS
PubMed
Google Scholar
Park SY, et al. Alu and LINE-1 hypomethylation is associated with HER2 enriched subtype of breast cancer. PLoS ONE. 2014;9(6): e100429.
Article
PubMed
PubMed Central
Google Scholar
de Cubas AA, et al. DNA hypomethylation promotes transposable element expression and activation of immune signaling in renal cell cancer. JCI Insight. 2020. https://doi.org/10.1172/jci.insight.137569.
Article
PubMed
PubMed Central
Google Scholar
Kong Y, et al. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat Commun. 2019;10(1):5228.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lee E, et al. Landscape of somatic retrotransposition in human cancers. Science. 2012;337(6097):967–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Voineagu I, et al. Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. Proc Natl Acad Sci U S A. 2008;105(29):9936–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu S, et al. Short inverted repeats are hotspots for genetic instability: relevance to cancer genomes. Cell Rep. 2015;10(10):1674–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wolff EM, et al. Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet. 2010;6(4): e1000917.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hur K, et al. Hypomethylation of long interspersed nuclear element-1 (LINE-1) leads to activation of proto-oncogenes in human colorectal cancer metastasis. Gut. 2014;63(4):635–46.
Article
CAS
PubMed
Google Scholar
Ade C, Roy-Engel AM, Deininger PL. Alu elements: an intrinsic source of human genome instability. Curr Opin Virol. 2013;3(6):639–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang W, et al. Alu distribution and mutation types of cancer genes. BMC Genomics. 2011;12:157.
Article
CAS
PubMed
PubMed Central
Google Scholar
Elliott B, Richardson C, Jasin M. Chromosomal translocation mechanisms at intronic alu elements in mammalian cells. Mol Cell. 2005;17(6):885–94.
Article
CAS
PubMed
Google Scholar
Jeffs AR, et al. The BCR gene recombines preferentially with Alu elements in complex BCR-ABL translocations of chronic myeloid leukaemia. Hum Mol Genet. 1998;7(5):767–76.
Article
CAS
PubMed
Google Scholar
Cui F, Sirotin MV, Zhurkin VB. Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct. 2011;6:2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cruickshanks HA, et al. Senescent cells harbour features of the cancer epigenome. Nat Cell Biol. 2013;15(12):1495–506.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu YC, et al. Transient DNMT3L expression reinforces chromatin surveillance to halt senescence progression in mouse embryonic fibroblast. Front Cell Dev Biol. 2020;8:103.
Article
PubMed
PubMed Central
Google Scholar
Bourc’his D, Bestor TH. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature. 2004;431(7004):96–9.
Article
CAS
PubMed
Google Scholar
Zamudio N, et al. DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination. Genes Dev. 2015;29(12):1256–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robertson KD. DNA methylation and human disease. Nat Rev Genet. 2005;6(8):597–610.
Article
CAS
PubMed
Google Scholar
Egger G, et al. Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts suggests an essential role for DNMT1 in cell survival. Proc Natl Acad Sci U S A. 2006;103(38):14080–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robert MF, et al. DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells. Nat Genet. 2003;33(1):61–5.
Article
CAS
PubMed
Google Scholar
Li Y, et al. Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1. Nature. 2018;564(7734):136–40.
Article
CAS
PubMed
Google Scholar
Okano M, et al. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999;99(3):247–57.
Article
CAS
PubMed
Google Scholar
Chedin F. The DNMT3 family of mammalian de novo DNA methyltransferases. Prog Mol Biol Transl Sci. 2011;101:255–85.
Article
CAS
PubMed
Google Scholar
Kareta MS, et al. Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L. J Biol Chem. 2006;281(36):25893–902.
Article
CAS
PubMed
Google Scholar
Liao HF, et al. Functions of DNA methyltransferase 3-like in germ cells and beyond. Biol Cell. 2012;104(10):571–87.
Article
CAS
PubMed
Google Scholar
Zamudio N, Bourc’his D. Transposable elements in the mammalian germline: a comfortable niche or a deadly trap? Heredity (Edinb). 2010;105(1):92–104.
Article
CAS
Google Scholar
Rollins RA, et al. Large-scale structure of genomic methylation patterns. Genome Res. 2006;16(2):157–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou W, et al. DNA methylation enables transposable element-driven genome expansion. Proc Natl Acad Sci U S A. 2020;117(32):19359–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bestor TH. DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes. Philos Trans R Soc Lond B Biol Sci. 1990;326(1235):179–87.
Article
CAS
PubMed
Google Scholar
Rose NR, Klose RJ. Understanding the relationship between DNA methylation and histone lysine methylation. Biochim Biophys Acta. 2014;1839(12):1362–72.
Article
CAS
PubMed
Google Scholar
Walter M, et al. An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells. Elife. 2016. https://doi.org/10.7554/eLife.11418.
Article
PubMed
PubMed Central
Google Scholar
Maenohara S, et al. Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos. PLoS Genet. 2017;13(10): e1007042.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liu X, et al. UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9. Nat Commun. 2013;4:1563.
Article
PubMed
CAS
Google Scholar
Rothbart SB, et al. Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation. Nat Struct Mol Biol. 2012;19(11):1155–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jacobs FM, et al. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 2014;516(7530):242–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Karimi MM, et al. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell. 2011;8(6):676–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schultz DC, et al. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 2002;16(8):919–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quenneville S, et al. In embryonic stem cells, ZFP57/KAP1 recognize a methylated hexanucleotide to affect chromatin and DNA methylation of imprinting control regions. Mol Cell. 2011;44(3):361–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sasaki H, Matsui Y. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet. 2008;9(2):129–40.
Article
CAS
PubMed
Google Scholar
Svoboda P, et al. RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos. Dev Biol. 2004;269(1):276–85.
Article
CAS
PubMed
Google Scholar
Kabayama Y, et al. Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse growing oocytes. Nucleic Acids Res. 2017;45(9):5387–98.
CAS
PubMed
PubMed Central
Google Scholar
Houwing S, et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell. 2007;129(1):69–82.
Article
CAS
PubMed
Google Scholar
Ku HY, Lin H. PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression. Natl Sci Rev. 2014;1(2):205–18.
Article
CAS
PubMed
Google Scholar
Voronina E, et al. RNA granules in germ cells. Cold Spring Harb Perspect Biol. 2011. https://doi.org/10.1101/cshperspect.a002774.
Article
PubMed
PubMed Central
Google Scholar
Chang KW, et al. Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development. BMC Genomics. 2018;19(1):425.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ernst C, Odom DT, Kutter C. The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity. Nat Commun. 2017;8(1):1411.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sienski G, Donertas D, Brennecke J. Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell. 2012;151(5):964–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Watanabe T, et al. IWI2 targets RNAs transcribed from piRNA-dependent regions to drive DNA methylation in mouse prospermatogonia. EMBO J. 2018. https://doi.org/10.15252/embj.201695329.
Article
PubMed
PubMed Central
Google Scholar
Zoch A, et al. SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation. Nature. 2020;584(7822):635–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brandt J, et al. Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. Gene. 2005;345(1):101–11.
Article
CAS
PubMed
Google Scholar
Campillos M, et al. Computational characterization of multiple Gag-like human proteins. Trends Genet. 2006;22(11):585–9.
Article
CAS
PubMed
Google Scholar
Emerson RO, Thomas JH. Gypsy and the birth of the SCAN domain. J Virol. 2011;85(22):12043–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kapitonov VV, Jurka J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol. 2005;3(6): e181.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nikolaienko O, et al. Arc protein: a flexible hub for synaptic plasticity and cognition. Semin Cell Dev Biol. 2018;77:33–42.
Article
CAS
PubMed
Google Scholar
Matsui T, et al. SASPase regulates stratum corneum hydration through profilaggrin-to-filaggrin processing. EMBO Mol Med. 2011;3(6):320–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pang SW, et al. PNMA family: protein interaction network and cell signalling pathways implicated in cancer and apoptosis. Cell Signal. 2018;45:54–62.
Article
CAS
PubMed
Google Scholar
Edelstein LC, Collins T. The SCAN domain family of zinc finger transcription factors. Gene. 2005;359:1–17.
Article
CAS
PubMed
Google Scholar
Henke C, et al. Selective expression of sense and antisense transcripts of the sushi-ichi-related retrotransposon-derived family during mouse placentogenesis. Retrovirology. 2015;12:9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sundaram V, et al. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res. 2014;24(12):1963–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Faulkner GJ, et al. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet. 2009;41(5):563–71.
Article
CAS
PubMed
Google Scholar
Liang D, et al. Genomic analysis revealed a convergent evolution of LINE-1 in coat color: a case study in water buffaloes (Bubalus bubalis). Mol Biol Evol. 2021;38(3):1122–36.
Article
PubMed
Google Scholar
Medstrand P, Landry JR, Mager DL. Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans. J Biol Chem. 2001;276(3):1896–903.
Article
CAS
PubMed
Google Scholar
Goke J, et al. Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. Cell Stem Cell. 2015;16(2):135–41.
Article
CAS
PubMed
Google Scholar
Fort A, et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat Genet. 2014;46(6):558–66.
Article
CAS
PubMed
Google Scholar
Chuong EB, Elde NC, Feschotte C. Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet. 2017;18(2):71–86.
Article
CAS
PubMed
Google Scholar
Lynch VJ, et al. Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Rep. 2015;10(4):551–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chuong EB, et al. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet. 2013;45(3):325–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kunarso G, et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet. 2010;42(7):631–4.
Article
CAS
PubMed
Google Scholar
Spengler RM, Oakley CK, Davidson BL. Functional microRNAs and target sites are created by lineage-specific transposition. Hum Mol Genet. 2014;23(7):1783–93.
Article
CAS
PubMed
Google Scholar
Borchert GM, et al. Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive-element origins. Mob Genet Elements. 2011;1(1):8–17.
Article
PubMed
PubMed Central
Google Scholar
Piriyapongsa J, Marino-Ramirez L, Jordan IK. Origin and evolution of human microRNAs from transposable elements. Genetics. 2007;176(2):1323–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Petri R, et al. LINE-2 transposable elements are a source of functional human microRNAs and target sites. PLoS Genet. 2019;15(3): e1008036.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kang D, et al. TE composition of human long noncoding RNAs and their expression patterns in human tissues. Genes Genomics. 2015;37(1):87–95.
Article
CAS
Google Scholar
Kapusta A, et al. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet. 2013;9(4): e1003470.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kelley D, Rinn J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol. 2012;13(11):R107.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fort V, Khelifi G, Hussein SMI. Long non-coding RNAs and transposable elements: a functional relationship. Biochim Biophys Acta Mol Cell Res. 2021;1868(1): 118837.
Article
CAS
PubMed
Google Scholar
Profumo V, et al. LEADeR role of miR-205 host gene as long noncoding RNA in prostate basal cell differentiation. Nat Commun. 2019;10(1):307.
Article
PubMed
PubMed Central
CAS
Google Scholar
Grote P, Herrmann BG. The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis. RNA Biol. 2013;10(10):1579–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grote P, et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell. 2013;24(2):206–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, et al. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell. 2013;25(1):69–80.
Article
CAS
PubMed
Google Scholar
Bhattacharya A, et al. Multiple Alu exonization in 3’UTR of a primate-specific isoform of CYP20A1 creates a potential miRNA sponge. Genome Biol Evol. 2021. https://doi.org/10.1093/gbe/evaa233.
Article
PubMed
Google Scholar
Song W, et al. Long noncoding RNA BANCR mediates esophageal squamous cell carcinoma progression by regulating the IGF1R/Raf/MEK/ERK pathway via miR3383p. Int J Mol Med. 2020;46(4):1377–88.
CAS
PubMed
PubMed Central
Google Scholar
Wang J, et al. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res. 2010;38(16):5366–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Panzitt K, et al. Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. Gastroenterology. 2007;132(1):330–42.
Article
CAS
PubMed
Google Scholar
Toki N, et al. SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies. Nucleic Acids Res. 2020;48(20):11626–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carrieri C, et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature. 2012;491(7424):454–7.
Article
CAS
PubMed
Google Scholar
Schein A, et al. Identification of antisense long noncoding RNAs that function as SINEUPs in human cells. Sci Rep. 2016;6:33605.
Article
CAS
PubMed
PubMed Central
Google Scholar
Indrieri A, et al. Synthetic long non-coding RNAs [SINEUPs] rescue defective gene expression in vivo. Sci Rep. 2016;6:27315.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gowravaram M, et al. Insights into the assembly and architecture of a Staufen-mediated mRNA decay (SMD)-competent mRNP. Nat Commun. 2019;10(1):5054.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gong C, Maquat LE. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3’ UTRs via Alu elements. Nature. 2011;470(7333):284–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gong C, et al. SMD and NMD are competitive pathways that contribute to myogenesis: effects on PAX3 and myogenin mRNAs. Genes Dev. 2009;23(1):54–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cho H, et al. Staufen1-mediated mRNA decay functions in adipogenesis. Mol Cell. 2012;46(4):495–506.
Article
CAS
PubMed
Google Scholar
Wang J, Gong C, Maquat LE. Control of myogenesis by rodent SINE-containing lncRNAs. Genes Dev. 2013;27(7):793–804.
Article
CAS
PubMed
PubMed Central
Google Scholar
Elisaphenko EA, et al. A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements. PLoS ONE. 2008;3(6): e2521.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pintacuda G, Young AN, Cerase A. Function by structure: spotlights on Xist long non-coding RNA. Front Mol Biosci. 2017;4:90.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jacques PE, Jeyakani J, Bourque G. The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet. 2013;9(5): e1003504.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang T, et al. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A. 2007;104(47):18613–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei CL, et al. A global map of p53 transcription-factor binding sites in the human genome. Cell. 2006;124(1):207–19.
Article
CAS
PubMed
Google Scholar
Luo X, et al. 3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis. Cell. 2021;184(3):723-740 e21.
Article
CAS
PubMed
Google Scholar
Zhang W, et al. Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes. Nucleic Acids Res. 2019;47(16):8485–501.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang Y, et al. Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition. Elife. 2017. https://doi.org/10.7554/eLife.22345.
Article
PubMed
PubMed Central
Google Scholar
Wu J, et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016;534(7609):652–7.
Article
CAS
PubMed
Google Scholar
Yang F, et al. DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state. Cell Stem Cell. 2020;26(2):234-250 e7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Todd CD, et al. Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells. Elife. 2019. https://doi.org/10.7554/eLife.44344.
Article
PubMed
PubMed Central
Google Scholar
Macfarlan TS, et al. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature. 2012;487(7405):57–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sakashita A, et al. Endogenous retroviruses drive species-specific germline transcriptomes in mammals. Nat Struct Mol Biol. 2020;27(10):967–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maezawa S, et al. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Nat Struct Mol Biol. 2020;27(10):978–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chuong EB, Elde NC, Feschotte C. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science. 2016;351(6277):1083–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ye M, et al. Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers. Proc Natl Acad Sci U S A. 2020;117(14):7905–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heintzman ND, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007;39(3):311–8.
Article
CAS
PubMed
Google Scholar
Nishihara H. Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation. Genes Genet Syst. 2020;94(6):269–81.
Article
PubMed
CAS
Google Scholar
Lunyak VV, et al. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science. 2007;317(5835):248–51.
Article
CAS
PubMed
Google Scholar
Diehl AG, Ouyang N, Boyle AP. Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. Nat Commun. 2020;11(1):1796.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang J, et al. MIR retrotransposon sequences provide insulators to the human genome. Proc Natl Acad Sci U S A. 2015;112(32):E4428–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu JY, et al. Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome. Cell Res. 2021. https://doi.org/10.1038/s41422-020-00466-6.
Article
PubMed
PubMed Central
Google Scholar