Distributed genome network innovations attributed to transposable DNA elements

Organism

Transposable DNA-Modified System(s)

References

18 Fungal Genomes

“Whole-Genome Architecture and Transcriptional Profiles”

(Castanera, Lopez-Varas et al. 2016)

Diatom Phaeodactylum tricornutum

Responses to nitrate starvation and exposure to diatom-derived reactive aldehyde-induced stress

(Maumus, Allen et al. 2009; Oliver, Schofield et al. 2010)

Leishmania

Post-transcriptional regulation

(Bringaud, Muller et al. 2007)

Plants

Plants

Genome evolution

(Bennetzen and Wang 2014; Qiu and Köhler 2020)

Plants

Epigenetic Controls

(Lisch and Bennetzen 2011)

Plants

Stress Responses

(Negi, Rai et al. 2016; Hou, Lu et al. 2019)

Peaches, almonds

Evolutionary genome differences

(Alioto, Alexiou et al. 2020)

Grasses

C4 photosynthesis

(Cao, Xu et al. 2016)

Maize

Abiotic Stress Response

(Makarevitch, Waters et al. 2015; Lv, Hu et al. 2019; Ramachandran, McKain et al. 2020)

Maize

Helitron transposons “reshuffle the transcriptome”

(Barbaglia, Klusman et al. 2012)

Maize

25% of DNAse1-hypersensitive sites (actively transcribed loci) evolved from mobile DNA inseertions

(Zhao, Zhang et al. 2018)

Cotton

Fiber cell development

(Wang, Ai et al. 2016)

Tomato

Ripening

(Jouffroy, Saha et al. 2016)

Coffea

Drought stress response

(Lopes, Jjingo et al. 2013)

Arabidopsis

Abiotic stress (phosphate limitation, high salt, freezing temperatures, arsenic toxicity)

(Joly-Lopez, Hoen et al. 2016; Joly-Lopez, Forczek et al. 2017)

Arabidopsis

Flower development

(Muino, de Bruijn et al. 2016; Baud, Wan et al. 2020)

Arabidopsis

Endosperm development (functionally comparable to mammalian placenta)

(Batista, Moreno-Romero et al. 2019; Qiu and Köhler 2020)

Pine

“Transposable element interconnected gene networks”

(Voronova, Rendón-Anaya et al. 2020)

Animals

Metazoa

Evolutionary innovation

(Piskurek and Jackson 2012; Nishihara 2020)

Drosophila

Malathion insecticide resistance

(Salces-Ortiz, Vargas-Chavez et al. 2020)

Drosophila

X chromosome dosage compensation

(Ellison and Bachtrog 2013; Ellison and Bachtrog 2019)

Drosophila

Early embryonic development

(Spirov, Zagriychuk et al. 2014)

Vertebrates

Evolutionary innovation

(Warren, Naville et al. 2015; Etchegaray, Naville et al. 2021)

Vertebrates

Body plan development

(Woolfe and Elgar 2008; McEwen, Goode et al. 2009)

Zebrafish

p53 response network

(Micale, Loviglio et al. 2012)

Fish

Migratory behavior

(Carotti, Carducci et al. 2021)

Mammals

TET-controlled passive DNA demethylation

(Mulholland, Nishiyama et al. 2020)

Mammals

Estrogen receptor network

(Testori, Caizzi et al. 2012)

Mammals

Uterine development, pregnancy

(Lynch, Leclerc et al. 2011; Lynch, Nnamani et al. 2015)

Mammals

Placental development (species-specific elements in mouse and humans)

(Chuong 2013; Chuong and Feschotte 2013; Chuong, Rumi et al. 2013; Frank and Feschotte 2017; Sakurai, Nakagawa et al. 2017; Chuong 2018; Dunn-Fletcher, Muglia et al. 2018; Sun, Wolf et al. 2021; Zhang and Muglia 2021)

Mammals

Convergent evolution of prolactin expression with different mobile DNA insertions

(Emera, Casola et al. 2012)

Mammals

Mammary gland development

(Nishihara 2019)

Mammals

X-inactivation in females

(Lyon 2000; Lyon 2003; Elisaphenko, Kolesnikov et al. 2008; Kannan, Chernikova et al. 2015)

Mammals

Innate immunity

(Chuong, Elde et al. 2016; Chen, Wang et al. 2019; Srinivasachar Badarinarayan and Sauter 2021)

Mammals

Wnt5a expression in mammalian secondary palate controlled by complex enhancer evolved from “coordinately co-opted” transposable elements

(Nishihara, Kobayashi et al. 2016)

Mammals

Basic mammalian morphology and body plan development

(Hirakawa, Nishihara et al. 2009; Okada, Sasaki et al. 2010)

Mammals

Brain and nervous system development

(Bejerano, Lowe et al. 2006; Santangelo, de Souza et al. 2007; Sasaki, Nishihara et al. 2008; McEwen, Goode et al. 2009; Tashiro, Teissier et al. 2011; Nakanishi, Kobayashi et al. 2012; Notwell, Chung et al. 2015; Lapp and Hunter 2016; Policarpi, Crepaldi et al. 2017; Ferrari, Grandi et al. 2021)

Eutherian mammals

Eutherian-specific morphology and neural development

(Polychronopoulos, King et al. 2017)

Eutherian mammals

“at least 16% of eutherian-specific CNEs overlap currently recognized transposable elements in human”

(Mikkelsen, Wakefield et al. 2007)

Bat Myotis velifer

Cell migration, gastrulation (weaker signals for Wnt signalling, artery and heart valve morphogenesis, neural crest differentiation)

(Cosby, Judd et al. 2021)

Mouse

RNA polymerase PolII- or PolIII-specific insulator-bounded subnuclear domains

(Roman, Gonzalez-Rico et al. 2011; Roman, Gonzalez-Rico et al. 2011)

Mouse

Circadian rhythms

(Cosby, Judd et al. 2021)

Mouse

Mouse germline development and specificity

(Maezawa, Sakashita et al. 2020)

Mouse

Visual cortex development

(Lennartsson, Arner et al. 2015)

Primates

Primate-specific innovations arose chiefly by positively selected mobile DNA element insertions

(Jacques, Jeyakani et al. 2013; Trizzino, Park et al. 2017; Rishishwar, Wang et al. 2018)

Anthropoids

Brain and eye development

(del Rosario, Rayan et al. 2014)

Human

Insulator-bound subnuclear domains

(Wang, Vicente-Garcia et al. 2015)

Human

c-Myc regulatory subnetwork

(Wang, Bowen et al. 2009)

Human

P53 response network

(Cui, Sirotin et al. 2011)

Human

Germline development

(Liu and Eiden 2011; Sakashita, Maezawa et al. 2020)

Human

Embryonic development

(Kunarso, Chia et al. 2010; Wang, Xie et al. 2014; Xiang and Liang 2021)

Human

Stem cell pluripotency

(Santoni, Guerra et al. 2012; Lu, Sachs et al. 2014; Izsvak, Wang et al. 2016; Römer, Singh et al. 2017; Torres-Padilla 2020; Sexton, Tillett et al. 2021)

Human

Zygotic genome activation and preimplantation embryonic development

(Grow, Flynn et al. 2015; Fu, Ma et al. 2019; Fu, Zhang et al. 2021)

Human

Cell type- and tissue-specific expression

(Huda, Bowen et al. 2011; Huda, Tyagi et al. 2011; Jjingo, Huda et al. 2011)

Human

Tissue-specific expression of regulatory long non-coding lncRNAs

(Chishima, Iwakiri et al. 2018)

 

 

REFERENCES

 

Alioto, T., K. G. Alexiou, et al. (2020). "Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence." Plant J 101(2): 455-472. https://pubmed.ncbi.nlm.nih.gov/31529539/

Barbaglia, A. M., K. M. Klusman, et al. (2012). "Gene capture by Helitron transposons reshuffles the transcriptome of maize." Genetics 190(3): 965-975. https://pubmed.ncbi.nlm.nih.gov/22174072/

Batista, R. A., J. Moreno-Romero, et al. (2019). "The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons." Elife 8. https://pubmed.ncbi.nlm.nih.gov/31789592/

Baud, A., M. Wan, et al. (2020). "Traces of transposable elements in genome dark matter coopted by flowering gene regulation networks " BioRxiv. /

Bejerano, G., C. B. Lowe, et al. (2006). "A distal enhancer and an ultraconserved exon are derived from a novel retroposon." Nature 441(7089): 87-90. https://pubmed.ncbi.nlm.nih.gov/16625209/

Bennetzen, J. L. and H. Wang (2014). "The contributions of transposable elements to the structure, function, and evolution of plant genomes." Annu Rev Plant Biol 65: 505-530. https://pubmed.ncbi.nlm.nih.gov/24579996/

Bringaud, F., M. Muller, et al. (2007). "Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania." PLoS Pathog 3(9): 1291-1307. https://pubmed.ncbi.nlm.nih.gov/17907803/

Cao, C., J. Xu, et al. (2016). "Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis." BMC Genomics 17(1): 201. https://pubmed.ncbi.nlm.nih.gov/26955946/

Carotti, E., F. Carducci, et al. (2021). "Transposable Elements and Teleost Migratory Behaviour." Int J Mol Sci 22(2). https://pubmed.ncbi.nlm.nih.gov/33435333/

Castanera, R., L. Lopez-Varas, et al. (2016). "Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles." PLoS Genet 12(6): e1006108. https://pubmed.ncbi.nlm.nih.gov/27294409/

Chen, C., W. Wang, et al. (2019). "Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs." Mob DNA 10: 19. https://pubmed.ncbi.nlm.nih.gov/31080521/

Chishima, T., J. Iwakiri, et al. (2018). "Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs." Genes (Basel) 9(1). https://pubmed.ncbi.nlm.nih.gov/29315213/

Chuong, E. B. (2013). "Retroviruses facilitate the rapid evolution of the mammalian placenta." Bioessays 35(10): 853-861. https://pubmed.ncbi.nlm.nih.gov/23873343/

Chuong, E. B. (2018). "The placenta goes viral: Retroviruses control gene expression in pregnancy." PLoS Biol 16(10): e3000028. https://pubmed.ncbi.nlm.nih.gov/30300353/

Chuong, E. B., N. C. Elde, et al. (2016). "Regulatory evolution of innate immunity through co-option of endogenous retroviruses." Science 351(6277): 1083-1087. https://pubmed.ncbi.nlm.nih.gov/26941318/

Chuong, E. B. and C. Feschotte (2013). "Evolution. Transposons up the dosage." Science 342(6160): 812-813. https://pubmed.ncbi.nlm.nih.gov/24233714/

Chuong, E. B., M. A. Rumi, et al. (2013). "Endogenous retroviruses function as species-specific enhancer elements in the placenta." Nat Genet 45(3): 325-329. https://pubmed.ncbi.nlm.nih.gov/23396136/

Cosby, R. L., J. Judd, et al. (2021). "Recurrent evolution of vertebrate transcription factors by transposase capture." Science 371(6531). https://pubmed.ncbi.nlm.nih.gov/33602827/

Cui, F., M. V. Sirotin, et al. (2011). "Impact of Alu repeats on the evolution of human p53 binding sites." Biol Direct 6(1): 2. https://pubmed.ncbi.nlm.nih.gov/21208455/

del Rosario, R. C., N. A. Rayan, et al. (2014). "Noncoding origins of anthropoid traits and a new null model of transposon functionalization." Genome Res 24(9): 1469-1484. https://pubmed.ncbi.nlm.nih.gov/25043600/

Dunn-Fletcher, C. E., L. M. Muglia, et al. (2018). "Anthropoid primate-specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length." PLoS Biol 16(9): e2006337. https://pubmed.ncbi.nlm.nih.gov/30231016/

Elisaphenko, E. A., N. N. Kolesnikov, et al. (2008). "A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements." PLoS One 3(6): e2521. https://pubmed.ncbi.nlm.nih.gov/18575625/

Ellison, C. and D. Bachtrog (2019). "Recurrent gene co-amplification on Drosophila X and Y chromosomes." PLoS Genet 15(7): e1008251. https://pubmed.ncbi.nlm.nih.gov/31329593/

Ellison, C. E. and D. Bachtrog (2013). "Dosage compensation via transposable element mediated rewiring of a regulatory network." Science 342(6160): 846-850. https://pubmed.ncbi.nlm.nih.gov/24233721/

Emera, D., C. Casola, et al. (2012). "Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements." Mol Biol Evol 29(1): 239-247. https://pubmed.ncbi.nlm.nih.gov/21813467/

Etchegaray, E., M. Naville, et al. (2021). "Transposable element-derived sequences in vertebrate development." Mob DNA 12(1): 1. https://pubmed.ncbi.nlm.nih.gov/33407840/

Ferrari, R., N. Grandi, et al. (2021). "Retrotransposons as Drivers of Mammalian Brain Evolution." Life (Basel) 11(5). https://pubmed.ncbi.nlm.nih.gov/33922141/

Frank, J. A. and C. Feschotte (2017). "Co-option of endogenous viral sequences for host cell function." Curr Opin Virol 25: 81-89. https://pubmed.ncbi.nlm.nih.gov/28818736/

Fu, B., H. Ma, et al. (2019). "Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development." Int J Mol Sci 20(3). https://pubmed.ncbi.nlm.nih.gov/30759824/

Fu, H., W. Zhang, et al. (2021). "Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells." Genome Biol 22(1): 201. https://pubmed.ncbi.nlm.nih.gov/34243810/

Grow, E. J., R. A. Flynn, et al. (2015). "Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells." Nature 522(7555): 221-225. https://pubmed.ncbi.nlm.nih.gov/25896322/

Hirakawa, M., H. Nishihara, et al. (2009). "Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes." Gene 441(1-2): 100-110. https://pubmed.ncbi.nlm.nih.gov/19166919/

Hou, J., D. Lu, et al. (2019). "Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses." Planta 250(1): 23-40. https://pubmed.ncbi.nlm.nih.gov/30993403/

Huda, A., N. J. Bowen, et al. (2011). "Epigenetic regulation of transposable element derived human gene promoters." Gene 475(1): 39-48. https://pubmed.ncbi.nlm.nih.gov/21215797/

Huda, A., E. Tyagi, et al. (2011). "Prediction of transposable element derived enhancers using chromatin modification profiles." PLoS One 6(11): e27513. https://pubmed.ncbi.nlm.nih.gov/22087331/

Izsvak, Z., J. Wang, et al. (2016). "Pluripotency and the endogenous retrovirus HERVH: Conflict or serendipity?" Bioessays 38(1): 109-117. https://pubmed.ncbi.nlm.nih.gov/26735931/

Jacques, P. E., J. Jeyakani, et al. (2013). "The majority of primate-specific regulatory sequences are derived from transposable elements." PLoS Genet 9(5): e1003504. https://pubmed.ncbi.nlm.nih.gov/23675311/

Jjingo, D., A. Huda, et al. (2011). "Effect of the transposable element environment of human genes on gene length and expression." Genome Biol Evol 3: 259-271. https://pubmed.ncbi.nlm.nih.gov/21362639/

Joly-Lopez, Z., E. Forczek, et al. (2017). "Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements." Front Plant Sci 8: 2027. https://pubmed.ncbi.nlm.nih.gov/29250089/

Joly-Lopez, Z., D. R. Hoen, et al. (2016). "Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements." Mol Biol Evol 33(8): 1937-1956. https://pubmed.ncbi.nlm.nih.gov/27189548/

Jouffroy, O., S. Saha, et al. (2016). "Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening." BMC Genomics 17(1): 624. https://pubmed.ncbi.nlm.nih.gov/27519651/

Kannan, S., D. Chernikova, et al. (2015). "Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes." Front Bioeng Biotechnol 3: 71. https://pubmed.ncbi.nlm.nih.gov/26106594/

Kunarso, G., N. Y. Chia, et al. (2010). "Transposable elements have rewired the core regulatory network of human embryonic stem cells." Nat Genet 42(7): 631-634. https://pubmed.ncbi.nlm.nih.gov/20526341/

Lapp, H. E. and R. G. Hunter (2016). "The dynamic genome: transposons and environmental adaptation in the nervous system." Epigenomics 8(2): 237-249. https://pubmed.ncbi.nlm.nih.gov/26791965/

Lennartsson, A., E. Arner, et al. (2015). "Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors." Epigenetics Chromatin 8: 55. https://pubmed.ncbi.nlm.nih.gov/26673794/

Lisch, D. and J. L. Bennetzen (2011). "Transposable element origins of epigenetic gene regulation." Curr Opin Plant Biol 14(2): 156-161. https://pubmed.ncbi.nlm.nih.gov/21444239/

Liu, M. and M. V. Eiden (2011). "Role of human endogenous retroviral long terminal repeats (LTRs) in maintaining the integrity of the human germ line." Viruses 3(6): 901-905. https://pubmed.ncbi.nlm.nih.gov/21994760/

Lopes, F. R., D. Jjingo, et al. (2013). "Transcriptional activity, chromosomal distribution and expression effects of transposable elements in coffea genomes." PLoS One 8(11): e78931. https://pubmed.ncbi.nlm.nih.gov/24244387/

Lu, X., F. Sachs, et al. (2014). "The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity." Nat Struct Mol Biol. https://pubmed.ncbi.nlm.nih.gov/24681886/

Lv, Y., F. Hu, et al. (2019). "Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response." BMC Genomics 20(1): 864. https://pubmed.ncbi.nlm.nih.gov/31729949/

Lynch, V. J., R. D. Leclerc, et al. (2011). "Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals." Nat Genet 43(11): 1154-1159. https://pubmed.ncbi.nlm.nih.gov/21946353/

Lynch, V. J., M. C. Nnamani, et al. (2015). "Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy." Cell Rep 10(4): 551-561. https://pubmed.ncbi.nlm.nih.gov/25640180/

Lyon, M. F. (2000). "LINE-1 elements and X chromosome inactivation: a function for "junk" DNA?" Proc Natl Acad Sci U S A 97(12): 6248-6249. https://pubmed.ncbi.nlm.nih.gov/10841528/

Lyon, M. F. (2003). "The Lyon and the LINE hypothesis." Semin Cell Dev Biol 14(6): 313-318. https://pubmed.ncbi.nlm.nih.gov/15015738/

Maezawa, S., A. Sakashita, et al. (2020). "Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition." Nat Struct Mol Biol 27(10): 978-988. https://pubmed.ncbi.nlm.nih.gov/32895557/

Makarevitch, I., A. J. Waters, et al. (2015). "Transposable elements contribute to activation of maize genes in response to abiotic stress." PLoS Genet 11(1): e1004915. https://pubmed.ncbi.nlm.nih.gov/25569788/

Maumus, F., A. E. Allen, et al. (2009). "Potential impact of stress activated retrotransposons on genome evolution in a marine diatom." BMC Genomics 10: 624. https://pubmed.ncbi.nlm.nih.gov/20028555/

McEwen, G. K., D. K. Goode, et al. (2009). "Early evolution of conserved regulatory sequences associated with development in vertebrates." PLoS Genet 5(12): e1000762. https://pubmed.ncbi.nlm.nih.gov/20011110/

Micale, L., M. N. Loviglio, et al. (2012). "A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish." PLoS One 7(10): e46642. https://pubmed.ncbi.nlm.nih.gov/23118857/

Mikkelsen, T. S., M. J. Wakefield, et al. (2007). "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences." Nature 447(7141): 167-177. https://pubmed.ncbi.nlm.nih.gov/17495919/

Muino, J. M., S. de Bruijn, et al. (2016). "Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor." Mol Biol Evol 33(1): 185-200. https://pubmed.ncbi.nlm.nih.gov/26429922/

Mulholland, C. B., A. Nishiyama, et al. (2020). "Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals." Nat Commun 11(1): 5972. https://pubmed.ncbi.nlm.nih.gov/33235224/

Nakanishi, A., N. Kobayashi, et al. (2012). "A SINE-derived element constitutes a unique modular enhancer for mammalian diencephalic Fgf8." PLoS One 7(8): e43785. https://pubmed.ncbi.nlm.nih.gov/22937095/

Negi, P., A. N. Rai, et al. (2016). "Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response." Front Plant Sci 7: 1448. https://pubmed.ncbi.nlm.nih.gov/27777577/

Nishihara, H. (2019). "Retrotransposons spread potential cis-regulatory elements during mammary gland evolution." Nucleic Acids Res 47(22): 11551-11562. https://pubmed.ncbi.nlm.nih.gov/31642473/

Nishihara, H. (2020). "Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation." Genes Genet Syst 94(6): 269-281. https://pubmed.ncbi.nlm.nih.gov/31932541/

Nishihara, H., N. Kobayashi, et al. (2016). "Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate." PLoS Genet 12(10): e1006380. https://pubmed.ncbi.nlm.nih.gov/27741242/

Notwell, J. H., T. Chung, et al. (2015). "A family of transposable elements co-opted into developmental enhancers in the mouse neocortex." Nat Commun 6: 6644. https://pubmed.ncbi.nlm.nih.gov/25806706/

Okada, N., T. Sasaki, et al. (2010). "Emergence of mammals by emergency: exaptation." Genes Cells 15(8): 801-812. https://pubmed.ncbi.nlm.nih.gov/20633052/

Oliver, M. J., O. Schofield, et al. (2010). "Density dependent expression of a diatom retrotransposon." Mar Genomics 3(3-4): 145-150. https://pubmed.ncbi.nlm.nih.gov/21798208/

Piskurek, O. and D. J. Jackson (2012). "Transposable elements: from DNA parasites to architects of metazoan evolution." Genes (Basel) 3(3): 409-422. https://pubmed.ncbi.nlm.nih.gov/24704977/

Policarpi, C., L. Crepaldi, et al. (2017). "Enhancer SINEs Link Pol III to Pol II Transcription in Neurons." Cell Rep 21(10): 2879-2894. https://pubmed.ncbi.nlm.nih.gov/29212033/

Polychronopoulos, D., J. W. D. King, et al. (2017). "Conserved non-coding elements: developmental gene regulation meets genome organization." Nucleic Acids Res 45(22): 12611-12624. https://pubmed.ncbi.nlm.nih.gov/29121339/

Qiu, Y. and C. Köhler (2020). "Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs." Biochem Soc Trans 48(3): 1005-1017. https://pubmed.ncbi.nlm.nih.gov/32573687/

Ramachandran, D., M. R. McKain, et al. (2020). "Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae." G3 (Bethesda) 10(12): 4387-4398. https://pubmed.ncbi.nlm.nih.gov/32988994/

Rishishwar, L., L. Wang, et al. (2018). "Evidence for positive selection on recent human transposable element insertions." Gene 675: 69-79. https://pubmed.ncbi.nlm.nih.gov/29953920/

Roman, A. C., F. J. Gonzalez-Rico, et al. (2011). "B1-SINE retrotransposons: Establishing genomic insulatory networks." Mob Genet Elements 1(1): 66-70. https://pubmed.ncbi.nlm.nih.gov/22016846/

Roman, A. C., F. J. Gonzalez-Rico, et al. (2011). "Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch." Genome Res 21(3): 422-432. https://pubmed.ncbi.nlm.nih.gov/21324874/

Römer, C., M. Singh, et al. (2017). "How to tame an endogenous retrovirus: HERVH and the evolution of human pluripotency." Curr Opin Virol 25: 49-58. https://pubmed.ncbi.nlm.nih.gov/28750248/

Sakashita, A., S. Maezawa, et al. (2020). "Endogenous retroviruses drive species-specific germline transcriptomes in mammals." Nat Struct Mol Biol 27(10): 967-977. https://pubmed.ncbi.nlm.nih.gov/32895553/

Sakurai, T., S. Nakagawa, et al. (2017). "Novel endogenous retrovirus-derived transcript expressed in the bovine placenta is regulated by WNT signaling." Biochem J 474(20): 3499-3512. https://pubmed.ncbi.nlm.nih.gov/28899944/

Salces-Ortiz, J., C. Vargas-Chavez, et al. (2020). "Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster." Philos Trans R Soc Lond B Biol Sci 375(1795): 20190341. https://pubmed.ncbi.nlm.nih.gov/32075557/

Santangelo, A. M., F. S. de Souza, et al. (2007). "Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene." PLoS Genet 3(10): 1813-1826. https://pubmed.ncbi.nlm.nih.gov/17922573/

Santoni, F. A., J. Guerra, et al. (2012). "HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency." Retrovirology 9: 111. https://pubmed.ncbi.nlm.nih.gov/23253934/

Sasaki, T., H. Nishihara, et al. (2008). "Possible involvement of SINEs in mammalian-specific brain formation." Proc Natl Acad Sci U S A 105(11): 4220-4225. https://pubmed.ncbi.nlm.nih.gov/18334644/

Sexton, C. E., R. L. Tillett, et al. (2021). "The essential but enigmatic regulatory role of HERVH in pluripotency." Trends Genet. https://pubmed.ncbi.nlm.nih.gov/34340871/

Spirov, A. V., E. A. Zagriychuk, et al. (2014). "Evolutionary Design of Gene Networks: Forced Evolution by Genomic Parasites." Parallel Process Lett 24(2). https://pubmed.ncbi.nlm.nih.gov/25558118/

Srinivasachar Badarinarayan, S. and D. Sauter (2021). "Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections." J Virol 95(12). https://pubmed.ncbi.nlm.nih.gov/33883223/

Sun, M. A., G. Wolf, et al. (2021). "Endogenous retroviruses drive lineage-specific regulatory evolution across primate and rodent placentae." Mol Biol Evol. https://pubmed.ncbi.nlm.nih.gov/34320657/

Tashiro, K., A. Teissier, et al. (2011). "A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons." PLoS One 6(12): e28497. https://pubmed.ncbi.nlm.nih.gov/22174821/

Testori, A., L. Caizzi, et al. (2012). "The role of transposable elements in shaping the combinatorial interaction of transcription factors." BMC Genomics 13(1): 400. https://pubmed.ncbi.nlm.nih.gov/22897927/

Torres-Padilla, M. E. (2020). "On transposons and totipotency." Philos Trans R Soc Lond B Biol Sci 375(1795): 20190339. https://pubmed.ncbi.nlm.nih.gov/32075562/

Trizzino, M., Y. Park, et al. (2017). "Transposable elements are the primary source of novelty in primate gene regulation." Genome Res 27(10): 1623-1633. https://pubmed.ncbi.nlm.nih.gov/28855262/

Voronova, A., M. Rendón-Anaya, et al. (2020). "Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks." Genes (Basel) 11(10). https://pubmed.ncbi.nlm.nih.gov/33081418/

Wang, J., N. J. Bowen, et al. (2009). "A c-Myc regulatory subnetwork from human transposable element sequences." Mol Biosyst 5(12): 1831-1839. https://pubmed.ncbi.nlm.nih.gov/19763338/

Wang, J., C. Vicente-Garcia, et al. (2015). "MIR retrotransposon sequences provide insulators to the human genome." Proc Natl Acad Sci U S A 112(32): E4428-4437. https://pubmed.ncbi.nlm.nih.gov/26216945/

Wang, J., G. Xie, et al. (2014). "Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells." Nature 516(7531): 405-409. https://pubmed.ncbi.nlm.nih.gov/25317556/

Wang, X., G. Ai, et al. (2016). "Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato." New Phytol 209(4): 1442-1455. https://pubmed.ncbi.nlm.nih.gov/26494192/

Warren, I. A., M. Naville, et al. (2015). "Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates." Chromosome Res 23(3): 505-531. https://pubmed.ncbi.nlm.nih.gov/26395902/

Woolfe, A. and G. Elgar (2008). "Organization of conserved elements near key developmental regulators in vertebrate genomes." Adv Genet 61: 307-338. https://pubmed.ncbi.nlm.nih.gov/18282512/

Xiang, Y. and H. Liang (2021). "The Regulation and Functions of Endogenous Retrovirus in Embryo Development and Stem Cell Differentiation." Stem Cells Int 2021: 6660936. https://pubmed.ncbi.nlm.nih.gov/33727936/

Zhang, X. and L. J. Muglia (2021). "Baby's best Foe-riend: Endogenous retroviruses and the evolution of eutherian reproduction." Placenta 113: 1-7. https://pubmed.ncbi.nlm.nih.gov/33685754/

Zhao, H., W. Zhang, et al. (2018). "Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome." Plant Physiol 176(4): 2789-2803. https://pubmed.ncbi.nlm.nih.gov/29463772/