动物反转录转座子研究进展

doi:10.3969/j.issn.1674-7968.2021.01.012

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Abstract Retrotransposons are a type of functional element that can complete self-replication in the genome, use RNA as an intermediary, and integrate into other sites of the genome under the action of reverse transcriptase. The increasing copy number of retrotransposons in the biological genome is a major reason for the enlargement of the genome, and it is also the main source of genetic variation and the driving force for genome evolution. The transposition of retrotransposons breaks, rearranges, and forms chromosomes. Structural mutations such as insertion mutations also participate in the apparent regulation of the genome and the formation of heterochromatin structures, and are closely linked to changes in the structure and function of genes; the effects of retrotransposons on genomes, transcriptomes, and functional genes have become postgenomes research hotspots of the times. This article reviews the structural characteristics of animal transposon, its function in gene expression, the role of transposon in animal genome evolution in recent years, and its application as a molecular marker in animal production. This review provids reference for the functional role of retrotransposons in animal genomes and transcriptomes, as well as in animal production, and animal genetics and breeding.

Key words： Retrotransposon Structure Function Gene expression

Received: 18 June 2020

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S813.3

Corresponding Authors: *wxyan@yzu.edu.cn

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	AN Ya-Long
	CHEN Zi-Xuan
	CHI Cheng-Lin
	CHEN Cai
	SONG Cheng-Yi
	WANG Xiao-Yan

Cite this article:

AN Ya-Long,CHEN Zi-Xuan,CHI Cheng-Lin, et al. Research Progress of Animal Retrotransposons[J]. 农业生物技术学报, 2021, 29(1): 125-136.

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http://journal05.magtech.org.cn/Jwk_ny/EN/10.3969/j.issn.1674-7968.2021.01.012 OR http://journal05.magtech.org.cn/Jwk_ny/EN/Y2021/V29/I1/125

[1] 陈才. 2019. 猪转座组注释、活性分析及其对基因组、转录组和功能基因的影响[D]. 博士学位论文, 扬州大学, 导师: 宋成义, 李碧春, pp. 113-115.
(Chen C.2019.Porcine transposable group annotation, activity analysis and its influence on genome, transcriptome and functional genes[D]. Thesis for Ph.D., Yangzhou University, Supervisor: Song C Y, Li B C, pp. 113-115.)
[2] 陈伟, 陈才, 王宵燕, 等. 2019. 猪VRTN基因SINE转座子插入多态与生长和繁殖性状的关联分析[J]. 农业生物技术学报, 27(2): 464-470.
(Chen W, Chen C, Wang X Y, et al.2019. Association analysis of insertion polymorphisms of swine VRTN gene SINE transposon with growth and reproduction traits[J]. Journal of Agricultural Biotechnology, 27(2): 464-470.)
[3] 李兰会, 杜小龙, 王麒, 等. 2019. 601 bp SINE插入突变导致水貂Agouti基因沉默[J]. 农业生物技术学报, 27(2): 297-306.
(Li L H, Du X L, Wang Q, et al.2019. 601 bp SINE insertion mutation causes gene silencing in mink Agouti[J]. Journal of Agricultural Biotechnology, 27(2): 297-306.)
[4] 林悦龙, 肖开转, 连玲, 等. 2019. 植物反转录转座子功能研究进展[J]. 科学通报, 64(1): 35-48.
(Lin Y L, Xiao K Z, Lian L, et al.2019. Research progress on the function of plant retrotransposons[J]. Chinese Science Bulletin, 64(1): 35-48.)
[5] Abrusán G, Krambeck H J.2006. Competition may determine the diversity of transposable elements[J]. Theoretical Population Biology, 70(3): 364-375.
[6] Asaf L, Noa S, Gil A.2008. TranspoGene and microTranspoGene: Transposed elements influence on the transcriptome of seven vertebrates and invertebrates[J]. Nucleic Acids Research, 36: D47-52.
[7] Batzer M A, Deininger P L.2002. Alu repeats and human genomic diversity[J]. Nature Reviews, Genetics, 3(5): 370-379.
[8] Belancio V P, Hedges D J, Deininger P.2006. LINE-1 RNA splicing and influences on mammalian gene expression[J]. Nucleic Acids Research, 34(5): 1512-1521.
[9] Böhne A, Brunet F, Galiana-Arnoux D, et al.2008. Transposable elements as drivers of genomic and biological diversity in vertebrates[J]. Chromosome Research, 16(1): 203-215.
[10] Brandt J, Schrauth S, Veith A M, et al.2004. Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals[J]. Gene, 345(1): 101-111.
[11] Bulger M, Groudine M.2011. Functional and Mechanistic Diversity of Distal Transcription Enhancers[J]. 144(3): 327-339.
[12] Cai C, Wei W, Xiaoyan W, et al.2019. Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs[J]. Mobile DNA, 10: 19.
[13] Cai H N, Levine M.1997. The gypsy insulator can function as a promoter-specific silencer in the Drosophila embryo[J]. The EMBO Journal, 16(7): 1732-1741.
[14] Chessa B, Pereira F, Arnaud F, et al.2009. Revealing the history of sheep domestication using retrovirus integrations[J]. Science, 324(5926): 532-536.
[15] Cohen C J, Lock W M, Mager D L.2009. Endogenous retroviral LTRs as promoters for human genes: A critical assessment[J]. Gene, 448(2): 105-114.
[16] Denli A M, Narvaiza I, Kerman B E, et al.2015. Primate-specific ORF0 contributes to retrotransposon-mediated diversity[J]. Cell, 163(3): 583-593.
[17] Devor E J, Peek A S, Lanier W, et al.2009. Marsupial-specific microRNAs evolved from marsupial-specific transposable elements[J]. Gene, 448(2): 187-191.
[18] Ding M, Liu Y, Liao X, et al.2018. Enhancer RNAs (eRNAs): New Insights into Gene Transcription and Disease Treatment[J]. Journal of Cancer, 9(13): 2334-2340.
[19] Doolittle W F, Sapienza C.1980. Selfish genes, the phenotype paradigm and genome evolution[J]. Nature, 284(5757): 601-603.
[20] Eickbush T H, Jamburuthugoda V K.2008. The diversity of retrotransposons and the properties of their reverse transcriptases[J]. Virus Research, 134(1-2): 221-234.
[21] Franchini L F, Lopez-Leal R, et al.2011. Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons[J]. Proceedings of the National Academy of Sciences of the USA,108(37): 15270-15275.
[22] François C, Patrick M, Edgar B, et al.2012. Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy[J]. Proceedings of the National Academy of Sciences of the USA,109(13): 4980-4985.
[23] Gal-Mark N, Schwartz S, Ast G.2008. Alternative splicing of Alu exons--two arms are better than one[J]. Nucleic Acids Research, 36(6): 2012-2023.
[24] Galit L M, Oren R, Eddo K, et al.2008. Intronic Alus influence alternative splicing[J]. PLoS Genetics,4(9): e1000204.
[25] Garcia-Pérez J L. 2016. Transposons and Retrotransposons[M]. Humana Press, New York, pp. 3-11.
[26] Gianfrancesco O, Geary B, Savage A L, et al.2019. The role of SINE-VNTR-Alu (SVA) retrotransposons in shaping the human genome[J]. International Journal of Molecular Sciences, 20(23): 5977.
[27] Gifford R J, Blomberg J, Coffin J M.et al.2018. Nomenclature for endogenous retrovirus (ERV) loci[J]. Retrovirology, 15(1): 59.
[28] Gkikas M, Daniel B M, Robert B.2015. The decline of human endogenous retroviruses: Extinction and survival[J]. Retrovirology, 12: 8.
[29] Goodrich J A.2010. Genomic gems: SINE RNAs regulate mRNA production[J]. Current Opinion in Genetics & Development, 20(2): 149-155.
[30] Gray M M, Sutter N B, Ostrander E A, et al.2010. The IGF1 small dog haplotype is derived from Middle Eastern grey wolves[J]. BMC Biology, 8: 118.
[31] Hancks D C, Goodier J L, Mandal P K, et al.2011. Retrotransposition of marked SVA elements by human L1s in cultured cells[J]. Human Molecular Genetics, 20(17): 3386-3400.
[32] Hata K, Sakaki Y, 1997. Identification of critical CpG sites for repression of L1 transcription by DNA methylation[J]. Gene, 189(2): 227-234.
[33] Igor V.2010. Transposable elements in disease-associated cryptic exons[J]. Human Genetics, 127(2): 135-154.
[34] Imamoto S, Watanbe M, Imamoto M, et al.2010. Study on the effect of SINE insertion in a SILV (Pmel 17) gene on the fundi of longhaired Miniature Dachshunds[J]. Journal of Veterinary Medicine Japan, 63(5): 385-389.
[35] Iskow RC, McCabe M T, Mills R E, et al.2010. Natural mutagenesis of human genomes by endogenous retrotransposons[J]. Cell, 141(7): 1253-1261.
[36] Jordan I K, Rogozin I B, Glazko G V, et al.2003. Origin of a substantial fraction of human regulatory sequences from transposable elements[J]. Trends in Genetics, 19(2): 68-72.
[37] Julija R, Annette D, Sergiu C, et al.2012. The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery[J]. Nucleic Acids Research,40(4): 1666-1683.
[38] Junna K, Kazuo N.2018. Tracking the continuous evolutionary processes of an endogenous retrovirus of the domestic cat: ERV-DC[J]. Viruses, 10(4): 179.
[39] Kamath P L, Elleder D, Bao L, et al.2014. The population history of endogenous retroviruses in mule deer (Odocoileus hemionus)[J]. The Journal of Heredity,105(2): 173-187.
[40] Kannan S, Chernikova D, Rogozin I B, et al.2015. Transposable element insertions in long intergenic non-coding RNA genes[J]. Frontiers in Bioengineering and Biotechnology, 3: 71.
[41] Kapusta A, Kronenberg Z, Lynch V J.et al.2013. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs[J]. PLoS Genetics, 9(4): e1003470.
[42] Kazazian Jr. H H.2004. Mobile elements: Drivers of genome evolution[J]. Science (New York, N.Y.), 303(5664): 1626-1632.
[43] Kelley D, Rinn J.2012. Transposable elements reveal a stem cell-specific class of long noncoding RNAs[J]. Genome Biology, 13(11): R107.
[44] Kim H, Bakshi A, Kim J, et al.2015. Retrotransposon-derived promoter of mammalian Aebp2[J]. PloS One, 10(4): e0126966.
[45] Konkel M K, Batzer M A.2010. A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome[J]. Seminars in Cancer Biology, 20(4): 211-221.
[46] Konkel M K, Walker J A, Batzer M A.2010. LINEs and SINEs of primate evolution[J]. Evolutionary Anthropology, 19(6): 236-249.
[47] Lander E S, Linton L M, Birren B, et al., 2001. Initial sequencing and analysis of the human genome[J]. Nature, 409(6822): 860-921.
[48] Landry J-R, Rouhi A, Medstrand P, et al.2002. The Opitz syndrome gene Mid1 is transcribed from a human endogenous retroviral promoter[J]. Molecular Biology and Evolution,19(11): 1934-1942.
[49] Lee J, Mun S, Kim D H, et al.2017. Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome[J]. Mobile DNA, 8(1): 2.
[50] Lev-Maor C, Sorek R, Shomron N, et al.2003. The birth of an alternatively spliced exon: 3' splice-site selection in alu exons[J]. Science, 300(5623): 1288-1291.
[51] Li J, Davis B W, Jern P.2019. Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken[J]. Mobile DNA, 10: 38.
[52] Li J, Kannan M, Trivett A L, et al.2014. An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition[J]. Nucleic Acids Research,42(7): 4546-4562.
[53] Liang X W, Cui X S, Sun S C, 2013. Superovulation induces defective methylation in line-1 retrotransposon elements in blastocyst[J]. Reproductive Biology and Endocrinology, 11(1): 69.
[54] Liu D, Li Y, Tang W, et al.2014. Population structure of Coilia nasus in the Yangtze River revealed by insertion of short interspersed elements[J]. Biochemical Systematics and Ecology, 54: 103-112.
[55] Martin S L, Branciforte D, Keller D, et al.2003. Trimeric structure for an essential protein in L1 retrotransposition[J]. Proceedings of the National Academy of Sciences of the USA, 100(24): 13815-13820.
[56] Mastrangelo M F, Weinstock K G, Shafer B K, et al.1992. Disruption of a silencer domain by a retrotransposon[J]. Genetics, 131(3): 519-529.
[57] McClintock B.1950. The origin and behavior of mutable loci in maize[J]. Proceedings of the National Academy of Sciences of the USA, 36(6): 344-355.
[58] Michael H, Nicholas D.2013. The intertwining of transposable elements and non-coding RNAs[J]. International Journal of Molecular Sciences, 14(7): 13307-13328.
[59] Mills R E, Bennett E A, Iskow R C, et al.2007. Which transposable elements are active in the human genome?[J]. Trends in Genetics, 23(4): 183-191.
[60] Moran V A, Perera R J, Khalil A M.2012. Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs[J]. Nucleic acids research, 40(14): 6391-6340.
[61] Oliver K R, Greene W K.2009. Transposable elements: Powerful facilitators of evolution[J]. Bioessays, 31: 703-714.
[62] Orgel L E, Crick F H.1980. Selfish DNA: The ultimate parasite[J]. Nature, 284(5757): 604-607.
[63] Ostertag E M, Goodier J L Zhang Y, et al.2003. SVA elements are nonautonomous retrotransposons that cause disease in humans[J]. American Journal of Human Genetics, 73(6): 1444-1451.
[64] Parnell T J, Viering M M, Skjesol A, et al.2003.An endogenous suppressor of hairy-wing insulator separates regulatory domains in Drosophila[J]. Proceedings of the National Academy of Sciences of the USA, 100(23): 13436-13441.
[65] Pereira V, Enard D, Eyrewalker A.2009. The effect of transposable element insertions on gene expression evolution in rodents[J]. PloS One, 4(2): e4321.
[66] Pi W, Yang Z, Wang J, et al.2004. The LTR enhancer of ERV-9 human endogenous retrovirus is active in oocytes and progenitor cells in transgenic zebrafish and humans[J]. Proceedings of the National Academy of Sciences of the USA, 101(3): 805-810.
[67] Piriyapongsa J, Mariño-Ramírez L, Jordan I K.2007. Origin and evolution of human microRNAs from transposable elements[J]. Genetics, 176(2): 1323-1337.
[68] Platt R N, Vandewege M W, Ray DA.2018. Mammalian transposable elements and their impacts on genome evolution[J]. Chromosome Research: An International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology, 26(1-2): 25-43.
[69] Ponicsan S L, Kugel J F, Goodrich J A.2010. Genomic gems: SINE RNAs regulate mRNA production[J]. Current Opinion in Genetics & Development, 20(2): 149-155.
[70] Rodriguez-Terrones D, Torres-Padilla M E.2018. Nimble and ready to mingle: Transposon outbursts of early development[J]. Trends in Genetics, 34(10): 806-820.
[71] Román A C, González-Rico F J, Fernández-Salguero P M.2011a. B1-SINE retrotransposons: Establishing genomic insulatory networks[J]. 1(1): 66-70.
[72] Román A C, González-Rico F J, Moltó E, et al.2011b. Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch[J]. Genome Research, 21(3): 422-432.
[73] Romanish M T, Lock W M, van de Lagemaat L N, et al.2007. Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution[J]. PLoS genetics, 3(1): e10.
[74] Santangelo A M, de Souza F S J, Franchini L F, et al.2007. Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene[J]. PLoS Genetics, 3(10): 1813-1826.
[75] Savage A L, Bubb V J, Breen G, et al.2013. Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns[J]. BMC Evolutionary Biology, 13(1): 101.
[76] Sigurdsson M I, Smith A V, Bjornsson H T, et al.2012. The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system[J]. BMC Genetics, 13: 31.
[77] Smalheiser N R, Torvik V I.2005. Mammalian microRNAs derived from genomic repeats[J]. Trends in Genetics: TIG, 21(6): 322-326.
[78] Suntsova M, Gogvadze E V, Salozhin S, et al.2013. Human-specific endogenous retroviral insert serves as an enhancer for the schizophrenia-linked gene PRODH[J]. Proceedings of the National Academy of Sciences of the USA, 110(48): 19472-19477.
[79] Suzuki S, Ono R, Narita T, et al.2007. Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting[J]. PLoS Genetics, 3(4): e55.
[80] van de Lagemaat L N, Landry J-R, Mager D L, et al.2003. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions[J]. Trends in genetics: TIG, 19(10): 530-536.
[81] Wallace A D, Wendt G A, Barcellos L F,et al.2018. To ERV is human: A phenotype-wide scan linking polymorphic human endogenous Retrovirus-K insertions to complex phenotypes[J]. Frontiers in Genetics, 9: 298.
[82] Wang C, Ping Z D, Zhang H, et al.2014. Frequency and type of EAV-HP insertion in the 5'-flanking region of SLCO1B3 gene in five blue-egged chicken populations[J]. China Animal Husbandry & Veterinary Medicine, 41(10): 183-188.
[83] Wang W, Chen C, Wang X, et al.2020. Development of molecular markers based on the l1 retrotransposon insertion polymorphisms in pigs (Sus scrofa) and their association with economic traits[J]. Russian Journal of Genetics, 56(2): 183-191.
[84] Wang Z, Qu L, Yao J, et al.2013. An EAV-HP insertion in 5' flanking region of SLCO1B3 causes blue eggshell in the chicken[J]. PLoS Genetics, 9(1): e1003183.
[85] Youngson N A, Kocialkowski S, Peel N, et al.2005. A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting[J]. Journal of Molecular Evolution, 61(4): 481-490.
[86] Yu C, Jian X, Yang W, et al.2017. Polymorphic analysis of oocyan gene SLCO1B3 of Changshun blue-eggshell[J]. Genomics & Applied Biology. 36(7): 2816-2820.
[87] Yuan Z, Sun X, Liu H, et al.2017. MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes[J]. PloS One, 6(3): e17666.
[88] Zhang Y, Romanish M T, Mager D L.2011. Distributions of transposable elements reveal hazardous zones in mammalian introns[J]. PLoS Computational Biology, 7(5):e1002046.
[89] Ziarczyk P, Fourcade-Peronnet F, Simonart S, et al.1989. Functional analysis of Drosophila 1731 retrotransposon: Promoter function and steroid regulation[J]. Nucleic Acids Research, 17(21): 8631-8644.