Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells
The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still u...
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MDPI AG
2022-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/9/1515 |
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| author | Xiaolong Li Xiaoqian Zhang Yandong Luo Ru Liu Yan Sun Shuhong Zhao Mei Yu Jianhua Cao |
| author_facet | Xiaolong Li Xiaoqian Zhang Yandong Luo Ru Liu Yan Sun Shuhong Zhao Mei Yu Jianhua Cao |
| author_sort | Xiaolong Li |
| collection | DOAJ |
| description | The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still unknown. Studying the variation in genome structure, especially the large fragments of insertions and deletions (InDels), is one of the proper ways to reveal these issues. In this study, an All-seq method was established by combining Mate-pair and Shotgun sequencing methods, and the detection and verification of large fragments of InDels were performed on 3D4/21 cells. The results showed that there were 844 InDels with a length of more than 1 kb, of which 12 regions were deletions of more than 100 kb in the 3D4/21 cell genome. In addition, compared with porcine primary alveolar macrophages, 82 genes including the <i>CD163</i> had lost transcription in 3D4/21 cells, and 72 genes gained transcription as well. Further referring to the Hi-C structure, it was found that the fusion of the topologically associated domains (TADs) caused by the deletion may lead to abnormal gene function. The results of this study provide a basis for elaborating the genome structure and functional variation in 3D4/21 cells, provide a method for rapid and convenient detection of large-scale InDels, and provide useful clues for the study of the porcine immune function genome and the molecular mechanism of virus infection. |
| first_indexed | 2024-03-09T23:57:51Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T23:57:51Z |
| publishDate | 2022-08-01 |
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| series | Genes |
| spelling | doaj.art-d3dbcf5a41964fb7a76e42a526f9763e2023-11-23T16:23:21ZengMDPI AGGenes2073-44252022-08-01139151510.3390/genes13091515Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 CellsXiaolong Li0Xiaoqian Zhang1Yandong Luo2Ru Liu3Yan Sun4Shuhong Zhao5Mei Yu6Jianhua Cao7Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaThe porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still unknown. Studying the variation in genome structure, especially the large fragments of insertions and deletions (InDels), is one of the proper ways to reveal these issues. In this study, an All-seq method was established by combining Mate-pair and Shotgun sequencing methods, and the detection and verification of large fragments of InDels were performed on 3D4/21 cells. The results showed that there were 844 InDels with a length of more than 1 kb, of which 12 regions were deletions of more than 100 kb in the 3D4/21 cell genome. In addition, compared with porcine primary alveolar macrophages, 82 genes including the <i>CD163</i> had lost transcription in 3D4/21 cells, and 72 genes gained transcription as well. Further referring to the Hi-C structure, it was found that the fusion of the topologically associated domains (TADs) caused by the deletion may lead to abnormal gene function. The results of this study provide a basis for elaborating the genome structure and functional variation in 3D4/21 cells, provide a method for rapid and convenient detection of large-scale InDels, and provide useful clues for the study of the porcine immune function genome and the molecular mechanism of virus infection.https://www.mdpi.com/2073-4425/13/9/15153D4/21 cellstructure variationInDelsalveolar macrophagespig |
| spellingShingle | Xiaolong Li Xiaoqian Zhang Yandong Luo Ru Liu Yan Sun Shuhong Zhao Mei Yu Jianhua Cao Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells Genes 3D4/21 cell structure variation InDels alveolar macrophages pig |
| title | Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells |
| title_full | Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells |
| title_fullStr | Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells |
| title_full_unstemmed | Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells |
| title_short | Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells |
| title_sort | large fragment indels reshape genome structure of porcine alveolar macrophage 3d4 21 cells |
| topic | 3D4/21 cell structure variation InDels alveolar macrophages pig |
| url | https://www.mdpi.com/2073-4425/13/9/1515 |
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