Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration
Abstract Background The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2017-05-01
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| Series: | Mobile DNA |
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| Online Access: | http://link.springer.com/article/10.1186/s13100-017-0091-2 |
| _version_ | 1828446104961679360 |
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| author | Manoj Kannan Jingfeng Li Sarah E. Fritz Kathryn E. Husarek Jonathan C. Sanford Teresa L. Sullivan Pawan Kumar Tiwary Wenfeng An Jef D. Boeke David E. Symer |
| author_facet | Manoj Kannan Jingfeng Li Sarah E. Fritz Kathryn E. Husarek Jonathan C. Sanford Teresa L. Sullivan Pawan Kumar Tiwary Wenfeng An Jef D. Boeke David E. Symer |
| author_sort | Manoj Kannan |
| collection | DOAJ |
| description | Abstract Background The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. Results Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny. In cancer cell lines, the newly inserted sequences typically underwent rapid transcriptional gene silencing, but they lacked cytosine methylation even after many cell divisions. L1 reporter expression was reversible and oscillated frequently. Silenced or variegated reporter expression was strongly and uniformly reactivated by treatment with inhibitors of histone deacetylation, revealing the mechanism for their silencing. By contrast, de novo integrants retrotransposed by L1 in pluripotent mouse embryonic stem (ES) cells underwent rapid silencing by dense cytosine methylation. Similarly, de novo cytosine methylation also was identified at new integrants when studied in several distinct somatic tissues of adult founder mice. Pre-existing L1 elements in cultured human cancer cells were stably silenced by dense cytosine methylation, whereas their transcription modestly increased when cytosine methylation was experimentally reduced in cells lacking DNA methyltransferases DNMT1 and DNMT3b. As a control, reporter genes mobilized by piggyBac (PB), a DNA transposon, revealed relatively stable and robust expression without apparent silencing in both cultured cancer cells and ES cells. Conclusions We hypothesize that the de novo methylation marks at newly inserted sequences retrotransposed by L1 in early pre-implantation development are maintained or re-established in adult somatic tissues. By contrast, histone deacetylation reversibly silences L1 reporter insertions that had mobilized at later timepoints in somatic development and differentiation, e.g., in cancer cell lines. We conclude that the cellular contexts of L1 retrotransposition can determine expression or silencing of newly integrated sequences. We propose a model whereby reporter expression from somatic TE insertions reflects the timing, molecular mechanism, epigenetic controls and the genomic, cellular and developmental contexts of their integration. |
| first_indexed | 2024-12-10T22:07:12Z |
| format | Article |
| id | doaj.art-dd69d43bc0c047fbb3b89686c598e427 |
| institution | Directory Open Access Journal |
| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-12-10T22:07:12Z |
| publishDate | 2017-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Mobile DNA |
| spelling | doaj.art-dd69d43bc0c047fbb3b89686c598e4272022-12-22T01:31:43ZengBMCMobile DNA1759-87532017-05-018111910.1186/s13100-017-0091-2Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integrationManoj Kannan0Jingfeng Li1Sarah E. Fritz2Kathryn E. Husarek3Jonathan C. Sanford4Teresa L. Sullivan5Pawan Kumar Tiwary6Wenfeng An7Jef D. Boeke8David E. Symer9Department of Biological Sciences, Birla Institute of Technology and Science PilaniLaboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer InstituteBiomedical Sciences Graduate Program, The Ohio State UniversityBiomedical Sciences Graduate Program, The Ohio State UniversityBiomedical Sciences Graduate Program, The Ohio State UniversityLaboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer InstituteLaboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer InstituteDepartment of Molecular Biology and Genetics, The Johns Hopkins University School of MedicineDepartment of Molecular Biology and Genetics, The Johns Hopkins University School of MedicineLaboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer InstituteAbstract Background The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. Results Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny. In cancer cell lines, the newly inserted sequences typically underwent rapid transcriptional gene silencing, but they lacked cytosine methylation even after many cell divisions. L1 reporter expression was reversible and oscillated frequently. Silenced or variegated reporter expression was strongly and uniformly reactivated by treatment with inhibitors of histone deacetylation, revealing the mechanism for their silencing. By contrast, de novo integrants retrotransposed by L1 in pluripotent mouse embryonic stem (ES) cells underwent rapid silencing by dense cytosine methylation. Similarly, de novo cytosine methylation also was identified at new integrants when studied in several distinct somatic tissues of adult founder mice. Pre-existing L1 elements in cultured human cancer cells were stably silenced by dense cytosine methylation, whereas their transcription modestly increased when cytosine methylation was experimentally reduced in cells lacking DNA methyltransferases DNMT1 and DNMT3b. As a control, reporter genes mobilized by piggyBac (PB), a DNA transposon, revealed relatively stable and robust expression without apparent silencing in both cultured cancer cells and ES cells. Conclusions We hypothesize that the de novo methylation marks at newly inserted sequences retrotransposed by L1 in early pre-implantation development are maintained or re-established in adult somatic tissues. By contrast, histone deacetylation reversibly silences L1 reporter insertions that had mobilized at later timepoints in somatic development and differentiation, e.g., in cancer cell lines. We conclude that the cellular contexts of L1 retrotransposition can determine expression or silencing of newly integrated sequences. We propose a model whereby reporter expression from somatic TE insertions reflects the timing, molecular mechanism, epigenetic controls and the genomic, cellular and developmental contexts of their integration.http://link.springer.com/article/10.1186/s13100-017-0091-2Cytosine MethylationReporter ExpressionCulture Cancer CellEmbryonic Stem Cell CloneArtificial Intron |
| spellingShingle | Manoj Kannan Jingfeng Li Sarah E. Fritz Kathryn E. Husarek Jonathan C. Sanford Teresa L. Sullivan Pawan Kumar Tiwary Wenfeng An Jef D. Boeke David E. Symer Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration Mobile DNA Cytosine Methylation Reporter Expression Culture Cancer Cell Embryonic Stem Cell Clone Artificial Intron |
| title | Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration |
| title_full | Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration |
| title_fullStr | Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration |
| title_full_unstemmed | Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration |
| title_short | Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration |
| title_sort | dynamic silencing of somatic l1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration |
| topic | Cytosine Methylation Reporter Expression Culture Cancer Cell Embryonic Stem Cell Clone Artificial Intron |
| url | http://link.springer.com/article/10.1186/s13100-017-0091-2 |
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