Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq
Abstract Background ΦC31 integrase, a site-specific recombinase, can efficiently target attB-bearing transgenes to endogenous pseudo attP sites within mammalian genomes. The sequence features of endogenous binding sites will help us to fully understand the site-specific recognition function by ΦC31...
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | Hereditas |
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| Online Access: | http://link.springer.com/article/10.1186/s41065-018-0079-z |
| _version_ | 1818993540110221312 |
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| author | Lijuan Qu Lei Wang Xueyuan Zhu Yan Zhang Qiang Ou Aying Ma Fengying Sheng Xiaoqing Wei Yue Dai Guoting Li Shuwu Xie |
| author_facet | Lijuan Qu Lei Wang Xueyuan Zhu Yan Zhang Qiang Ou Aying Ma Fengying Sheng Xiaoqing Wei Yue Dai Guoting Li Shuwu Xie |
| author_sort | Lijuan Qu |
| collection | DOAJ |
| description | Abstract Background ΦC31 integrase, a site-specific recombinase, can efficiently target attB-bearing transgenes to endogenous pseudo attP sites within mammalian genomes. The sequence features of endogenous binding sites will help us to fully understand the site-specific recognition function by ΦC31 integrase. The present study was aimed to uncover the global map of ΦC31 integrase binding sites in bovine cells and analysis the features of these binding sites by comprehensive bioinformatics methods. Results In this study, we constructed a ChIP-seq method that can be used to uncover the global binding sites by phiC31 integrase. 6740 potential ΦC31 integrase binding sites were identified. A sequence motif was found that contains inverted repeats and has similarities to wild-type attP site. Using REPEATMASKER, we identified a total of 20,183 repeat-regions distributed in 50 repeat types for the 6740 binding sites. These sites enriched in “regulation of GTPase activity” of in the GO category of biological process and KEGG pathway of signal transmembrane transporter activity. Conclusion This study is the first time to uncover the global map of binding sites for ΦC31 integrase using ChIP-sequencing method and analysis the features of these binding sites. This method will help us to fully understand the mechanism of the site-specific integration function by phiC31 integrase and will potentially boost its genetic manipulations in both gene therapy and generation of transgenic animals. |
| first_indexed | 2024-12-20T20:43:40Z |
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| id | doaj.art-90f216b0df4f42cbb8ea0e002d093657 |
| institution | Directory Open Access Journal |
| issn | 1601-5223 |
| language | English |
| last_indexed | 2024-12-20T20:43:40Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Hereditas |
| spelling | doaj.art-90f216b0df4f42cbb8ea0e002d0936572022-12-21T19:27:05ZengBMCHereditas1601-52232019-01-01156111010.1186/s41065-018-0079-zGlobal mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seqLijuan Qu0Lei Wang1Xueyuan Zhu2Yan Zhang3Qiang Ou4Aying Ma5Fengying Sheng6Xiaoqing Wei7Yue Dai8Guoting Li9Shuwu Xie10Department of Laboratory Medicine, Shanghai Eighth People’s HospitalDepartment of Laboratory Medicine, Shanghai Eighth People’s HospitalDepartment of Laboratory Medicine, Shanghai Eighth People’s HospitalDepartment of Laboratory Medicine, Shanghai Eighth People’s HospitalDepartment of Laboratory Medicine, Shanghai Eighth People’s HospitalDepartment of Respiratory Medicine, Shanghai First People’s Hospital, Shanghai Jiaotong University School of MedicineDepartment of Laboratory Medicine, Shanghai Eighth People’s HospitalDepartment of Laboratory Medicine, Shanghai Eighth People’s HospitalDepartment of Laboratory Medicine, Shanghai Eighth People’s HospitalLab of Reproductive Pharmacology, NHC Key Lab of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan UniversityLab of Reproductive Pharmacology, NHC Key Lab of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan UniversityAbstract Background ΦC31 integrase, a site-specific recombinase, can efficiently target attB-bearing transgenes to endogenous pseudo attP sites within mammalian genomes. The sequence features of endogenous binding sites will help us to fully understand the site-specific recognition function by ΦC31 integrase. The present study was aimed to uncover the global map of ΦC31 integrase binding sites in bovine cells and analysis the features of these binding sites by comprehensive bioinformatics methods. Results In this study, we constructed a ChIP-seq method that can be used to uncover the global binding sites by phiC31 integrase. 6740 potential ΦC31 integrase binding sites were identified. A sequence motif was found that contains inverted repeats and has similarities to wild-type attP site. Using REPEATMASKER, we identified a total of 20,183 repeat-regions distributed in 50 repeat types for the 6740 binding sites. These sites enriched in “regulation of GTPase activity” of in the GO category of biological process and KEGG pathway of signal transmembrane transporter activity. Conclusion This study is the first time to uncover the global map of binding sites for ΦC31 integrase using ChIP-sequencing method and analysis the features of these binding sites. This method will help us to fully understand the mechanism of the site-specific integration function by phiC31 integrase and will potentially boost its genetic manipulations in both gene therapy and generation of transgenic animals.http://link.springer.com/article/10.1186/s41065-018-0079-zΦC31 integraseBinding sitesChIP-seqSequence motif |
| spellingShingle | Lijuan Qu Lei Wang Xueyuan Zhu Yan Zhang Qiang Ou Aying Ma Fengying Sheng Xiaoqing Wei Yue Dai Guoting Li Shuwu Xie Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq Hereditas ΦC31 integrase Binding sites ChIP-seq Sequence motif |
| title | Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq |
| title_full | Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq |
| title_fullStr | Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq |
| title_full_unstemmed | Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq |
| title_short | Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq |
| title_sort | global mapping of binding sites for phic31 integrase in transgenic maden darby bovine kidney cells using chip seq |
| topic | ΦC31 integrase Binding sites ChIP-seq Sequence motif |
| url | http://link.springer.com/article/10.1186/s41065-018-0079-z |
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