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Journal of Integrative Agriculture  2023, Vol. 22 Issue (2): 526-536    DOI: 10.1016/j.jia.2022.08.128
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
A 314-bp SINE Insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs

GU Hao1*, DU Zhan-yu1*, Eduard MURANI2, Enrico D’ALESSANDRO3, CHEN Cai1, WANG Xiao-yan1, MAO Jiu-de4, Klaus WIMMERS2, SONG Cheng-yi1

1 College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, P.R.China

2 Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf 18196, Germany

3 Department of Veterinary Science, Unit of Animal Production, University of Messina, Messina 98168, Italy

4 Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA

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Retrotransposons, a type of DNA fragment that can mobilize itself on genome, can generate genetic variations and develop for molecular markers based on the insertion polymorphism.  Zinc finger proteins (ZNFs) are among the most abundant proteins in eukaryotic animals, and their functions are extraordinarily diverse and particularly important in gene regulation.  In the current study, bioinformatic prediction was performed to screen for retrotransposon insertion polymorphisms (RIPs) in six ZNF genes (ZNF2, ZNF3, ZNF7, ZNF8, ZNF10 and ZNF12).  Six RIPs in these ZNFs, including one short interspersed nuclear element (SINE) RIP in intron 1 and one long interspersed nuclear element 1 (L1) RIP in intron 3 of ZNF2, one SINE RIP in 5´ flanking region and one SINE RIP in intron 2 of ZNF3, one SINE RIP in 3´ UTR of ZNF7 and one L1 RIP in intron 2 of ZNF12, were discovered and their presence was confirmed by PCR.  The impact of the SINE RIP in the first intron of ZNF2, which is close to the core promoter of ZNF2, on the gene activity was investigated by dual-luciferase assay in three cell lines.  Our results showed that the SINE insertion in the intron 1 of ZNF2 repressed the core promoter activity extremely significantly (P<0.01) in cervical cancer cells and porcine primary embryonic fibroblasts (HeLa and PEF), thus SINE may act as a repressor.  This SINE RIP also significantly (P<0.05) affected the corrected back fat thickness in Yorkshire pigs.  The corrected back fat thickness of individuals with SINE insertion in the first intron of ZNF2 was significantly (P<0.05) higher than that of individuals without SINE insertion.  In summary, our data suggested that RIPs play important roles in the genetic variations of these ZNF genes and SINE RIP in the intron 1 of ZNF2 may provide a useful molecular marker for the screening of fat deposition in the pig breeding.

Keywords:  retrotransposon       ZNF2       polymorphism       repressor       fat deposition  
Received: 16 August 2021   Accepted: 22 January 2022
Fund: This research was supported by the National Natural Science Foundation of China (32002146 and 31872977), the China Postdoctoral Science Foundation (2020M671630), the Jiangsu Postdoctoral Science Foundation of China (2021K221B) to Chen Cai, the Jiangsu Agriculture Science and Technology Innovation Fund, China [CX (19) 2016], and the Priority Academic Program Development of Jiangsu Higher Education Institutions and the High-end Talent Support Program of Yangzhou University, China to Song Chengyi.
About author:  Received 16 August, 2021 Accepted 22 January, 2022 GU Hao, E-mail:; DU Zhan-yu, E-mail:; Correspondence SONG Cheng-yi, Tel: +86-514-87979034, E-mail: * These authors contributed equally to this study.

Cite this article: 

GU Hao, DU Zhan-yu, Eduard MURANI, Enrico D’ALESSANDRO, CHEN Cai, WANG Xiao-yan, MAO Jiu-de, Klaus WIMMERS, SONG Cheng-yi. 2023. A 314-bp SINE Insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs. Journal of Integrative Agriculture, 22(2): 526-536.

Abyzov A, Iskow R, Gokcumen O, Radke D W, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M, Consortium 1000 Genomes Project. 2013. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Research, 23, 2042–2052.
Beck C R, Garcia-Perez J L, Badge R M, Moran J V. 2011. LINE-1 elements in structural variation and disease. Annual Review of Genomics and Human Genetics, 12, 187–215.
Bin H U, Mo D, Wang X, Liu X, Chen Y. 2016. Effects of back fat, growth rate, and age at first mating on Yorkshire and Landrace sow longevity in China. Journal of Integrative Agriculture, 15, 2809–2818.
Chen C, Wang W, Wang X, Shen D, Wang S, Wang Y, Gao B, Wimmers K, Mao J, Li K, Song C. 2019. Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. Mobile DNA, 10, 1–24.
Cherni L, Frigi S, Ennafaa H, Mtiraoui N, Mahjoub T, Benammar-Elgaaied A. 2011. Human Alu insertion polymorphisms in North African populations. Human Biology, 83, 611–626.
Chessa B, Pereira F, Arnaud F, Amorim A, Goyache F, Mainland I, Kao R R, Pemberton J M, Beraldi D, Stear M J. 2009. Revealing the history of sheep domestication using retrovirus integrations. Science, 324, 532–536.
Doolittle W F, Sapienza C. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature, 284, 601–603.
Du P, Chen M, Lan Y, Yang Y, Deng C. 2020. The role of miRNA-181 targeting phosphatase and tensin homologue deleted on chromosome ten in the regulation of phosphatidylinositol-3-kinase/Akt signaling pathway in renal injury of hyperuricemia rats. Chinese Journal of Rheumatology, 12, 530–535.
Ecco G, Imbeault M, Trono D. 2017. KRAB zinc finger proteins. Development, 144, 2719–2729.
Elleder D, Kim O, Padhi A, Bankert J G, Simeonov I, Schuster S C, Wittekindt N E, Motameny S, Poss M. 2012. Polymorphic integrations of an endogenous gammaretrovirus in the mule deer genome. Journal of Virology, 86, 2787–2796.
Estécio M R H, Gallegos J, Dekmezian M, Lu Y, Liang S, Issa J P J. 2012. SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Molecular Cancer Research, 10, 1332–1342.
Ewing A D, Ballinger T J, Earl D, Harris C C, Ding L, Wilson R K, Haussler D. 2013. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biology, 14, 1–14.
Fedoroff N, Wessler S, Shure M. 1983. Isolation of the transposable maize controlling elements Ac and Ds. Cell, 35, 235–242.
Finnegan D J. 1989. Eukaryotic transposable elements and genome evolution. Trends in Genetics, 5, 103–107.
Flavell A J, Knox M R, Pearce S R, Ellis T H N. 1998. Retrotransposon‐based insertion polymorphisms (RBIP) for high throughput marker analysis. The Plant Journal, 16, 643–650.
Havecker E R, Gao X, Voytas D F. 2004. The diversity of LTR retrotransposons. Genome Biology, 5, 1–6.
Hron T, Fabryova H, Elleder D. 2020. Insight into the epigenetic landscape of a currently endogenizing gammaretrovirus in mule deer (Odocoileus hemionus). Genomics, 112, 886–896.
Hsu C C, Su C J, Jeng M F, Chen W H, Chen H H. 2019. A HORT1 retrotransposon insertion in the PeMYB11 promoter causes harlequin/black flowers in Phalaenopsis orchids. Plant Physiology, 180, 1535–1548.
Isernia C, Malgieri G, Russo L, D’Abrosca G, Baglivo I, Pedone P V, Fattorusso R. 2020. Zinc fingers. Metal Ions in Life Sciences, 20, 415–435.
Jacques P E, Jeyakani J, Bourque G. 2013. The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genetics, 9, e1003504.
Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A. 1999. IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics, 98, 704–711.
Kalla S E, Moghadam H K, Tomlinson M, Seebald A, Allen J J, Whitney J, Choi J D, Sutter N B. 2020. Polymorphic SINEC_Cf retrotransposons in the genome of the dog (Canis familiaris). bioRxiv, doi: 10.1101/2020.10.27.358119.
Klug A. 2010. The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annual Review of Biochemistry, 79, 213–231.
Laity J H, Lee B M, Wright P E. 2001. Zinc finger proteins: New insights into structural and functional diversity. Current Opinion in Structural Biology, 11, 39–46.
Lee J, Mun S, Kim D H, Cho C S, Oh D Y, Han K 2017. Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome. Mobile DNA, 8, 1–8.
Lexa M, Steflova P, Martinek T, Vorlickova M, Vyskot B, Kejnovsky E. 2014. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics, 15, 1–12.
Li Y, Liang S, Liu H, Sun Y, Kang L, Jiang Y. 2015. Identification of a short interspersed repetitive element insertion polymorphism in the porcine MX1 promoter associated with resistance to porcine reproductive and respiratory syndrome virus infection. Animal Genetics, 46, 437–440.
Liu C, Ran X, Niu X, Li S, Wang J, Zhang Q. 2018. Insertion of 275-bp SINE into first intron of PDIA4 gene is associated with litter size in Xiang pigs. Animal Reproduction Science, 195, 16–23.
Magotra A, Naskar S, Das B, Ahmad T. 2015. A comparative study of SINE insertion together with a mutation in the first intron of follicle stimulating hormone beta gene in indigenous pigs of India. Molecular Biology Reports, 42, 465–470.
Matthews J M, Sunde M. 2002. Zinc fingers‐folds for many occasions. IUBMB Life, 54, 351–355.
McClintock B. 1950. The origin and behavior of mutable loci in maize. Proceedings of the National Academy of Sciences of the United States of America, 36, 344–355.
Orgel L E, Crick F H C. 1980. Selfish DNA: The ultimate parasite. Nature, 284, 604–607.
Peaston A E, Evsikov A V, Graber J H, De Vries W N, Holbrook A E, Solter D, Knowles B B. 2004. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Developmental Cell, 7, 597–606.
Richardson S R, Doucet A J, Kopera H C, Moldovan J B, Garcia-Perez J L, Moran J V. 2015. The influence of LINE‐1 and SINE retrotransposons on mammalian genomes. Microbiology Spectrum, 3, 3–2.
Rooney M F, Hill E W, Kelly V P, Porter R K. 2018. The “speed gene” effect of myostatin arises in Thoroughbred horses due to a promoter proximal SINE insertion. PLoS ONE, 13, e0205664.
Smit A F A. 1993. Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic Acids Research, 21, 1863–1872.
Smith C E L, Alexandraki A, Cordery S F, Parmar R, Bonthron D T, Valleley E M A. 2017. A tissue-specific promoter derived from a SINE retrotransposon drives biallelic expression of PLAGL1 in human lymphocytes. PLoS ONE, 12, e0185678.
Terreros M C, Alfonso-Sánchez M A, Novick G E, Luis J R, Lacau H, Lowery R K, Regueiro M, Herrera R J. 2009. Insights on human evolution: An analysis of Alu insertion polymorphisms. Journal of Human Genetics, 54, 603–611.
Theunissen O, Rudt F, Guddat U, Mentzel H, Pieler T. 1992. RNA and DNA binding zinc fingers in Xenopus TFIIIA. Cell, 71, 679–690.
Witzgall R, O’Leary E, Leaf A, Onaldi D, Bonventre J V. 1994. The Krüppel-associated box-A (KRAB-A) domain of zinc finger proteins mediates transcriptional repression. Proceedings of the National Academy of Sciences of the United States of America, 91, 4514–4518.
Zhao J, Li K, Yang Q, Du M, Liu X, Cao G. 2017. Enhanced adipogenesis in Mashen pigs compared with Large White pigs. Italian Journal of Animal Science, 16, 217–225.
Zhao Y, Hou Y, Xu Y, Luan Y, Zhou H, Qi X, Hu M, Wang D, Wang Z, Fu Y. 2021. A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nature Communications, 12, 1–17.
Zheng Y, Chen C, Chen W, Wang X Y, Wang W, Gao B, Wimmers K, Mao J D, Song C Y. 2020. Two new SINE insertion polymorphisms in pig Vertnin (VRTN) gene revealed by comparative genomic alignment. Journal of Integrative Agriculture, 19, 2514–2522.
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