A 314-bp SINE insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs
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 extraord...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-02-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311922002064 |
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| author | Hao GU Zhan-yu DU Eduard MURANI Enrico D'ALESSANDRO Cai CHEN Xiao-yan WANG Jiu-de MAO Klaus WIMMERS Cheng-yi SONG |
| author_facet | Hao GU Zhan-yu DU Eduard MURANI Enrico D'ALESSANDRO Cai CHEN Xiao-yan WANG Jiu-de MAO Klaus WIMMERS Cheng-yi SONG |
| author_sort | Hao GU |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-10T19:51:39Z |
| format | Article |
| id | doaj.art-5c69eede4a4b41199449db72c95486d1 |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-04-10T19:51:39Z |
| publishDate | 2023-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-5c69eede4a4b41199449db72c95486d12023-01-28T04:07:39ZengElsevierJournal of Integrative Agriculture2095-31192023-02-01222526536A 314-bp SINE insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigsHao GU0Zhan-yu DU1Eduard MURANI2Enrico D'ALESSANDRO3Cai CHEN4Xiao-yan WANG5Jiu-de MAO6Klaus WIMMERS7Cheng-yi SONG8College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, P.R.ChinaCollege of Animal Science & Technology, Yangzhou University, Yangzhou 225009, P.R.ChinaLeibniz Institute for Farm Animal Biology (FBN), Dummerstorf 18196, GermanyDepartment of Veterinary Science, Unit of Animal Production, University of Messina, Messina 98122, ItalyCollege of Animal Science & Technology, Yangzhou University, Yangzhou 225009, P.R.ChinaCollege of Animal Science & Technology, Yangzhou University, Yangzhou 225009, P.R.ChinaBond Life Science Center, University of Missouri, Columbia, MO, 65211, USALeibniz Institute for Farm Animal Biology (FBN), Dummerstorf 18196, GermanyCollege of Animal Science & Technology, Yangzhou University, Yangzhou 225009, P.R.China; Correspondence SONG Cheng-yi, Tel: +86-514-87979034Retrotransposons, 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.http://www.sciencedirect.com/science/article/pii/S2095311922002064retrotransposonZNF2polymorphismrepressorfat deposition |
| spellingShingle | Hao GU Zhan-yu DU Eduard MURANI Enrico D'ALESSANDRO Cai CHEN Xiao-yan WANG Jiu-de MAO Klaus WIMMERS Cheng-yi SONG 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 retrotransposon ZNF2 polymorphism repressor fat deposition |
| title | A 314-bp SINE insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs |
| title_full | A 314-bp SINE insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs |
| title_fullStr | A 314-bp SINE insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs |
| title_full_unstemmed | A 314-bp SINE insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs |
| title_short | A 314-bp SINE insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs |
| title_sort | 314 bp sine insertion in the znf2 promoter region may act as a repressor related to regulation of fat deposition in pigs |
| topic | retrotransposon ZNF2 polymorphism repressor fat deposition |
| url | http://www.sciencedirect.com/science/article/pii/S2095311922002064 |
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