Ayarpadikannan, S and Kim, HS (2014). The impact of transposable elements in genome evolution and genetic instability and their implications in various diseases. Genomics and Informatics 12: 98-104.
Bao, W, Kojima, KK and Kohany, O (2015). Repbase Update, a database of repetitive elements in eukaryotics genomes. Mobile DNA 6: 11.
Batzer, MA, Deininger, PL, Hellmann-Blumberg, U, Jurka, J, Labuda, D, Rubin, CM, Schmid, CW, Ziętkiewicz, E and Zuckerkandl, E (1996). Standardized nomenclature for Alu repeats. Journal of Molecular Evolution 42: 3-6.
Bourque, G, Burns, KH, Gehring, M, Gorbunova, V, Seluanov, A, Hammell, M, Imbeault, M, Izsvák, Z, Levin, HL, Macfarlan, TS, Mager, DL and Feschotte, C (2018). Ten things you should know about transposable elements. Genome Biology 19: 199.
Branco, MR and Chuong, EB (2020). Crossroads between transposons and gene regulation. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 375: 20190330.
Burnett, BG, Muñoz, E, Tandon, A, Kwon, DY, Sumner, CJ and Fischbeck, KH (2009). Regulation of SMN protein stability. Molecular and Cellular Biology 29: 1107-1115.
Burns, KH (2020). Our conflict with transposable elements and its implications for human disease. Annual Review of Pathology: Mechanisms of Disease 15: 51-70.
Butchbach, MER (2016). Copy number variations in the Survival Motor Neuron genes: implications for spinal muscular atrophy and other neurodegenerative diseases. Frontiers in Molecular Biosciences 3: 7.
Butchbach, MER (2021). Genomic variability in the Survival Motor Neuron genes (SMN1 and SMN2): implications for spinal muscular atrophy phenotype and therapeutics development. International Journal of Molecular Sciences 22: 7896.
Campbell, L, Potter, A, Ignatius, J, Dubowitz, V and Davies, K (1997). Genomic variation and gene conversion in spinal muscular atrophy: implications for disease process and clinical phenotype. American Journal of Human Genetics 61: 40-50.
Chaves, Raquel, Ferreira, Daniela, Mendes-da-Silva, Ana, Meles, Susana and Adega, Filomena (2017). FA-SAT Is an Old Satellite DNA Frozen in Several Bilateria Genomes. Genome Biology and Evolution 9(11): 3073-3087.
Chen, LL and Yang, L (2017). ALUternative regulation for gene expression. Trends in Cell Biology 27: 480-490.
Chen, X, Sanchis-Juan, A, French, CE, Connell, AJ, Delon, I, Kingsbury, Z, Chawla, A, Halpern, AL, Taft, RJ, BioResource, NIHR, Bentley, DR, Butchbach, MER, Raymond, FL and Eberle, MA (2020a). Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genetics in Medicine 22: 945-953.
Chen, YJ, Chen, CY, Mai, TL, Chuang, CF, Chen, YC, Gupta, SK, Yen, L, Wang, YD and Chuang, TJ (2020b). Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axis in autism. Genome Research 30: 375-391.
Cho, S and Dreyfuss, G (2010). A degron created by SMN2 exon 7 skipping is a principal contributor to spinal muscular atrophy severity. Genes and Development 24: 438-442.
Chuong, EB, Elde, NC and Feschotte, C (2017). Regulatory activities of transposable elements: from conflicts to benefits. Nature Reviews Genetics 18: 71-86.
Consortium, 1000 Genomes Project, Abescasis, GR, Altshuler, D, Auton, A, Brooks, KD, Durbin, RM, Gibbs, RA, Hurles, ME and McVean, GA (2010). A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
Cosby, RL, Chang, NC and Feschotte, C (2019). Host-transposon interactions: conflict, cooperation and cooption. Genes and Development 33: 1098-1116.
Courseaux, A, Richard, F, Grosgeorge, J, Ortola, C, Viale, A, Turc-Carel, C, Dutrillaux, B, Gaudray, P and Nahon, JL (2003). Segmental duplications in euchromatic regions of human chromosome 5: a source of evolutionary instability and transcriptional innovation. Genome Research 13: 369-381.
Cowley, M and Oakey, RJ (2013). Transposable elements: re-wire and fine-tune the transcriptome. Plos Genetics 9: e1003234.
Crawford, TO and Pardo, CA (1996). The neurobiology of childhood spinal muscular atrophy. Neurobiology of Disease 3: 97-110.
Deininger, PL, Moran, JV, Batzer, MA and Kazazian Jr, HH (2003). Mobile elements and mammalian genome evolution. Current Opinion in Genetics and Development 13: 651-658.
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, Orlando, V, Grimmond, SM and Carninci, P (2009). The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics 41: 563-571.
Friedli, M and Trono, D (2015). The developmental control of transposable elements and the evolution of higher species. Annual Review of Cell and Developmental Biology 31: 429-451.
Garcia-Perez, JL, Widmann, TJ and Adams, IR (2016). The impact of transposable elements on mammalian development. Development 143: 4101-4114.
Germain-Desprez, D, Brun, T, Rochette, C, Semionov, A, Rouget, R and Simard, LR (2001). The SMN genes are subject to transcriptional regulation during cellular differentiation. Gene 279: 109-117.
Greene, J, Baird, AM, Brady, L, Lim, M, Gray, SG, McDermott, R and Finn, SP (2017). Circular RNAs: biogenesis, function and role in human diseases. Frontiers in Molecular Biosciences 4: 38.
Hancks, DC and Kazazian Jr, HH (2016). Roles for retrotransposon insertions in human disease. Mobile DNA 7: 9.
Haque, S and Harries, LW (2017). Circular RNAs (circRNAs) in health and disease. Genes 8: 353.
Hedges, DJ and Deininger, PL (2007). Inviting instability: transposable elements, double-strand breaks and the maintenance of genome integrity. Mutation Research 616: 46-59.
Hu, S, Wang, X and Shan, G (2016). Insertion of an Alu element in a lncRNA leads to primate-specific modulation of alternative splicing. Nature Structural & Molecular Biology 23: 1011-1019.
Hubley, R, Finn, RD, Clements, J, Eddy, SR, Jones, TA, Bao, W, Smit, AFA and Wheeler, TJ (2016). The Dfam database of repetitive DNA families. Nucleic Acids Research 44: D81-D89.
Hughes, TA (2006). Regulation of gene expression by alternative untranslated regions. Trends in Genetics 22: 119-122.
Huh, JW, Kim, DS, Ha, HS, Lee, JR, Kim, YJ, Ahn, K, Lee, SR, Chang, KT and Kim, HS (2008). Cooperative exonization of MaLR and AluJo elements contributed an alternative promoter and novel splice variants of RNF19. Gene 424: 63-70.
Jahic, A, Erichsen, AK, Deufel, T, Tallaksen, CM and Beetz, C (2016). A polymorphic Alu insertion that mediates distinct disease-associated deletions. European Journal of Human Genetics 24: 1371-1374.
Jangam, D, Feschotte, C and Betrán, E (2017). Transposable element domestication as an adaptation to evolutionary conflicts. Trends in Genetics 33: 817-831.
Jedličková, I, Přistoupilová, A, Nosková, L, Majer, F, Stránecký, V, Hartmannová, H, Hodaňová, K, Trešlová, H, Hýblová, M, Solár, P, Minárik, G, Giertlová, M and Kmoch, S (2020). Spinal muscular atrophy caused by a novel Alu-mediated deletion of exons 2a-5 in SMN1 undetectable with routine genetic testing. Molecular Genetics and Genomic Medicine 8: e1238.
Jiang, L, Lin, R, Gallagher, S, Zayac, A, Butchbach, MER and Hung, P (2020). Development and validation of a 4-color multiplexing spinal muscular atrophy (SMA) genotyping assay on a novel integrated digital PCR instrument. Scientific Reports 10: 19892.
Jjingo, D, Conley, AB, Wang, J, Mariño-Ramírez, L and Jordan, IK (2014). Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. Mobile DNA 5: 14.
Jjingo, D, Huda, A, Gundapuneni, M, Mariño-Ramírez, L and Jordan, IK (2011). Effect of transposable element environment of human genes on gene length and expression. Genome Biology and Evolution 3: 259-271.
Jönsson, ME, Garza, R, Johansson, PA and Jakobsson, J (2020). Transposable elements: a common feature of neurodevelopmental and neurodegenerative disorders. Trends in Genetics 36: 610-623.
Jordan, IK, Rogozin, IB, Glazko, GV and Koonin, EV (2003). Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends in Genetics 19: 68-72.
Kabelitz, T and Bäurle, I (2015). Get the jump--Do 3'UTRs protect transposable elements from silencing? Mobile Genetic Elements 5: 51-54.
Kearse, M, Moir, R, Wilson, A, Stones-Havas, S, Cheung, M, Sturrock, S, Buxton, S, Cooper, A, Markowitz, S, Duran, C, Thierer, T, Ashton, B, Meintjes, P and Drummond, A (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647-1649.
Kim, S, Cho, CS, Han, KS and Lee, J (2016). Structural variation of Alu element and human disease. Genomics and Informatics 14: 70-77.
Klein, SJ and O'Neill, RJ (2018). Transposable elements: genome innovation, chromosome diversity and centromere conflict. Chromosome Research 26: 5-23.
Kolb, SJ and Kissel, JT (2015). Spinal muscular atrophy. Neurologic Clinics 33: 831-846.
Kristensen, LS, Andersen, MA, Stagsted, LVW, Ebbesen, KK, Hansen, TB and Kjems, J (2019). The biogenesis, biology and characterization of circular RNAs. Nature Reviews Genetics 20: 675-691.
Kryatova, MS, Steranka, JP, Burns, KH and Payer, LM (2017). Insertion and deletion polymorphisms of the ancient AluS family in the human genome. Mobile DNA 8: 6.
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, et al. (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921.
Lapp, HE and Hunter, RG (2019). Early life exposures, neurodevelopmental disorders and transposable elements. Neurobiology of Stress 11: 100174.
Lavi, E and Carmel, L (2018). Alu exaptation enriches the human transcriptome by introducing new gene ends. RNA Biology 15: 715-725.
Lee, JY, Ji, Z and Tian, B (2008). Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes. Nucleic Acids Research 36: 5581-5590.
Lefebvre, S, Bürglen, L, Reboullet, S, Clermont, O, Burlet, P, Viollet, L, Benichou, B, Cruaud, C, Millasseau, P, Zeviani, M, Le Paslier, D, Frézal, J, Cohen, D, Weissenbach, J, Munnich, A and Melki, J (1995). Identification and characterization of a spinal muscular atrophy-determining gene. Cell 80: 155-165.
Lorson, CL and Androphy, EJ (2000). An exonic enhancer is required for inclusion of an essential exon in the SMA-determining gene SMN. Human Molecular Genetics 9: 259-265.
Lorson, CL, Hahnen, E, Androphy, EJ and Wirth, B (1999). A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. Proceedings of the National Academy of Sciences of the United States of America 96: 6307-6311.
Marasca, F, Gasparotto, E, Polimeni, B, Vadalá, R, Ranzani, V and Bodega, B (2020). The sophicated transcriptional response governed by transposable elements in human health and disease. International Journal of Molecular Sciences 21: 3201.
Martinez-Gomez, L, Abascal, F, Jungreis, I, Pozo, F, Kellis, M, Mudge, JM and Tress, ML (2020). Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. NAR Genomics and Bioinformatics 2: lqz023.
Medstrand, P, van de Lagemaat, LN and Mager, DL (2002). Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Research 12: 1483-1495.
Monani, UR, Lorson, CL, Parsons, DW, Prior, TW, Androphy, EJ, Burghes, AHM and McPherson, JD (1999a). A single nucleotide difference that alters splicing patterns distinguishes the SMA gene SMN1 from the copy gene SMN2. Human Molecular Genetics 8: 1177-1183.
Monani, UR, McPherson, JD and Burghes, AHM (1999b). Promoter analysis of the human centromeric and telometic survival motor neuron genes (SMNc and SMNt). Biochimica et Biophysica Acta 1445: 330-336.
Nishihara, H (2019). Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation. Genes and Genetic Systems 94: 269-281.
O'Donnell, KA and Burns, KH (2010). Mobilizing diversity: transposable element insertions in genetic variation and disease. Mobile DNA 1: 21.
Ottesen, EW, Luo, D, Seo, J, Singh, NN and Singh, RN (2019). Human Survival Motor Neuron genes generate a vast repertoire of circular RNAs. Nucleic Acids Research 47: 2884-2905.
Ottesen, EW, Seo, J, Singh, NN and Singh, RN (2017). A multilayered control of the human Survival Motor Neuron gene expression by Alu elements. Frontiers in Microbiology 8: 2252.
Ottesen, EW and Singh, RN (2020). Characteristics of circular RNAs generated by human Survival Motor Neuron genes. Cellular Signalling 73: 109696.
Paço, Ana, Adega, Filomena and Chaves, Raquel (2015). LINE-1 retrotransposons: from ‘parasite’ sequences to functional elements. Journal of Applied Genetics 56(1): 133-145.
Pagliarini, V, Jolly, A, Bielli, P, Di Rosa, V, De la Grange, P and Sette, C (2020). Sam68 binds Alu-rich introns in SMN and promotes pre-mRNA circularization. Nucleic Acids Research 48: 633-645.
Payer, LM and Burns, KH (2019). Transposable elements in human genetic disease. Nature Reviews Genetics 20: 760-772.
Percharde, M, Sultana, T and Ramalho Santos, M (2020). What doesn't kill you makes you stronger: transposons as dual players in chromatin regulation and genomic variation. Bioessays 42: 1900232.
Petri, R, Brattas, PL, Sharma, Y, Jönsson, ME, Pircs, K, Bengzon, J and Jakobsson, J (2019). LINE-2 transposable elements are a source of functional human microRNAs and target sites. Plos Genetics 15: e1008036.
Piégu, B, Bire, S, Arensburger, P and Bigot, Y (2015). A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity. Molecular Phylogenetics and Evolution 86: 90-109.
Piriyapongsa, J, Rutledge, MT, Patel, S, Borodovsky, M and Jordan, IK (2007). Evaluating the protein coding potential of exonized transposable element sequences. Biology Direct 2: 31.
Platt II, RN, Vangewege, MW and Ray, DA (2018). Mammalian transposable elements and their impacts on genome evolution. Chromosome Research 26: 25-43.
Pujar, S, O'Leary, NA, Farrell, CM, Loveland, JE, Mudge, JM, Wallin, C, Girón, CG, Diekhans, M, Barnes, I, Bennett, R, Berry, AE, Cox, E, Davidson, C, Goldfarg, T, Gonzalez, jM, Hunt, T, Jackson, JD, Joardar, V, Kay, MP, Kodali, VK, Martin, FJ, McAndrews, M, McGarvey, KM, Murphy, M, Rajput, B, et al. (2018). Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation. Nucleic Acids Research 46: D221-D228.
Rebollo, R, Farivar, S and Mager, DL (2012). C-GATE -- catalogue of gene affected by transposable elements. Mobile DNA 3: 9.
Rice, P, Longden, I and Bleasby, A (2000). EMBOSS: the European Molecular Biology Open Software Suite. Trends in Genetics 16: 276-277.
Robberecht, C, Voet, T, Zamani Esteki, M, Nowakowska, BA and Vermeesch, JR (2013). Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations. Genome Research 23: 411-418.
Roy-Engel, AM, El-Sawy, M, Farooq, L, Odom, GL, Perepelitsa-Belancio, V, Bruch, H, Oyeniran, OO and Deininger, PL (2005). Human retroelements may introduce intragenic polyadenylation signals. Cytogenetic and Genome Research 110: 365-371.
Ruhno, C, McGovern, VL, Avenarius, MR, Snyder, PJ, Prior, TW, Nery, FC, Muhtaseb, A, Roggenbuck, JS, Kissel, JT, Sansone, VA, Siranosian, JJ, Johnstone, AJ, Nwe, PH, Zhang, RZ, Swoboda, KJ and Burghes, AHM (2019). Complete sequencing of the SMN2 gene in SMA patients detect SMN gene deletion junctions and variants in SMN that modify the SMA phenotype. Human Genetics 138: 241-256.
Saleh, A, Marcia, A and Muotri, AR (2019). Transposable lements, inflammation and neurological disease. Frontiers in Neurology 10: 894.
Schmutz, J, Martin, J, Terry, A, Couronne, O, Grimwood, J, Lowry, S, Gordon, LA, Scott, D, Xie, G, Huang, W, Hellsten, U, Tran-Gyamfi, M, She, X, Prabhakar, S, Aerts, A, Altherr, M, Bajorek, E, Black, S, Branscomb, E, Caoile, C, Challacombe, JF, Chan, YM, Denys, M, Detter, JC, Escobar, J, et al. (2004). The DNA sequence and comparative analysis of human chromosome 5. Nature 431: 268-274.
Sela, N, Kim, E and Ast, G (2010). The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biology 11: R59.
Sela, N, Mersch, B, Gal-Mark, N, Lev-Maor, G, Hotz-Wagenblatt, A and Ast, G (2007). Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biology 8: R127.
Sen, SK, Han, KS, Wang, J, Lee, J, Wang, H, Callinan, PA, Dyer, M, Cordaux, R, Liang, P and Batzer, MA (2006). Human genomic deletions mediated by recombination between Alu elements. American Journal of Human Genetics 79: 41-53.
Seo, J, Singh, NN, Ottesen, EW, Lee, BM and Singh, RN (2016). A novel human-specific splice isoform alters the critical C-terminus of Survival Motor Neuron protein. Scientific Reports 6: 30778.
Sievers, F, Wilm, A, Dineen, D, Gibson, TJ, Karplus, K, Li, W, Lopez, R, McWilliam, H, Remmert, M, Söding, J, Thompson, JD and Higgins, DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7: 539.
Singh, NN, Ottesen, EW and Singh, RN (2020). A survey of transcripts generated by spinal muscular atrophy genes. Biochimica et Biophysica Acta 1863: 194562.
Singh, RN, Howell, MD, Ottesen, EW and Singh, NN (2017). Diverse role of survival motor neuron protein. Biochimica et Biophysica Acta 1860: 299-315.
Song, X, Beck, CR, Du, R, Campbell, IM, Coban Akdemir, Z, Gu, S, Breman, AM, Stankiewicz, P, Ira, G, Shaw, CA and Lupski, JR (2018). Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements. Genome Research 28: 1228-1242.
Sorek, R, Ast, G and Graur, D (2002). Alu-containing exons are alternatively spliced. Genome Research 12: 1060-1067.
Stabley, DL, Harris, AW, Holbrook, J, Chubbs, NJ, Lozo, KW, Crawford, TO, Swoboda, KJ, Funanage, VL, Wang, W, Mackenzie, W, Scavina, M, Sol-Church, K and Butchbach, MER (2015). SMN1 and SMN2 copy numbers in cell lines derived from patients with spinal muscular atrophy as measured by array digital PCR. Molecular Genetics and Genomic Medicine 3: 248-257.
Stabley, DL, Holbrook, J, Scavina, M, Crawford, TO, Swoboda, KJ, Robbins, KM and Butchbach, MER (2021). Detection of SMN1 and SMN2 gene conversion events and partial SMN1 deletions using array digital PCR. Neurogenetics 22: 53-64.
Storer, J, Hubley, R, ROsen, J, Wheeler, TJ and Smit, AF (2021). The Dfam community resource of transposable element families, sequence models and genome annotations. Mobile DNA 12: 2.
Sundaram, V and Wysocka, J (2020). Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 375: 20190347.
Tam, OH, Ostrow, LW and Gale Hammell, M (2019). Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease. Mobile DNA 10: 32.
Thornburg, BG, Gotea, V and MakaLowski, W (2006). Transposable elements as a significant source of transcription regulating signals. Gene 365: 104-110.
van de Lagemaat, LN, Landry, JR, Mager, DL and Medstrand, P (2003). Transposable elements in mammals promote regulatory variation ande diversification of genes with specialized functions. Trends in Genetics 19: 530-536.
Voellenkle, C, Perfetti, A, Carrara, M, Fuschi, P, Renna, LV, Longo, M, Sain, SB, Cardani, R, Valaperta, R, Silverstri, G, Legnini, I, Bozzoni, I, Furling, D, Gaetano, C, Falcone, G, Meola, G and Martelli, F (2019). Dysregulation of circular RNAs in myotonic dystrophy type 1. International Journal of Molecular Sciences 20: 1938.
Vorechovsky, I (2010). Transposable elements in disease-associated cryptic exons. Human Genetics 127: 135-154.
Weber, P, Rausch, C, Scholl, A and Cardoso, MC (2019). Repli-FISH (fluorescence in situ hybridization): application of 3D-(immuno)-FISH for the study of DNA replication timing of genetic repeat elements. OBM Genetics 3: 1901062.
Wells, JN and Feschotte, C (2020). A field guide to eukaryotic transposable elements. Annual Review of Genetics 54: 539-561.
Wirth, B (2021). Spinal muscular atrophy: in the challenge lies a solution. Trends in Neurosciences 44: 306-322.
Wirth, B, Herz, M, Wetter, A, Moskau, S, Hahnen, E, Rudnik-Schöneborn, S, Wienker, T and Zerres, K (1999). Quantitative analysis of survival motor neuron copies: identification of subtle SMN1 mutations in patients with spinal muscular atrophy, genotype-phenotype correlation and implications for genetic counseling. American Journal of Human Genetics 64: 1340-1356.
Yoshimoto, S, Harahap, NIF, Hamamura, Y, Ar Rochmah, M, Shima, A, Morisada, N, Shinohara, M, Saito, T, Saito, K, Lai, PS, Matsuo, M, Awano, H, Morioka, I, Iijima, K and Nishio, H (2016). Alternative splicing of a cryptic exon embedded in intron 6 of SMN1 and SMN2. Human Genome Variation 3: 16040.
Zeng, L, Pederson, SM, Kortschak, RD and Adelson, DL (2018). Transposable elements and gene expression during the evolution of amniotes. Mobile DNA 9: 17.