EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels
Abstract The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets....
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| Format: | Article |
| Language: | English |
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BMC
2017-05-01
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| Series: | Genome Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s13059-017-1232-0 |
| _version_ | 1819132778369777664 |
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| author | Josquin Daron R. Keith Slotkin |
| author_facet | Josquin Daron R. Keith Slotkin |
| author_sort | Josquin Daron |
| collection | DOAJ |
| description | Abstract The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset. EpiTEome outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads. EpiTEome characterizes the previously discarded fraction of DNA methylation at sites of new insertions, enabling future investigation into the epigenetic regulation of non-reference and transposed elements. |
| first_indexed | 2024-12-22T09:36:48Z |
| format | Article |
| id | doaj.art-925f3797118d4b599d12f6c66991ad2e |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-22T09:36:48Z |
| publishDate | 2017-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-925f3797118d4b599d12f6c66991ad2e2022-12-21T18:30:48ZengBMCGenome Biology1474-760X2017-05-0118111010.1186/s13059-017-1232-0EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levelsJosquin Daron0R. Keith Slotkin1Department of Molecular Genetics, The Ohio State UniversityDepartment of Molecular Genetics, The Ohio State UniversityAbstract The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset. EpiTEome outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads. EpiTEome characterizes the previously discarded fraction of DNA methylation at sites of new insertions, enabling future investigation into the epigenetic regulation of non-reference and transposed elements.http://link.springer.com/article/10.1186/s13059-017-1232-0MethylomeTransposable elementsInsertion siteBisulfiteSplit readsBioinformatics |
| spellingShingle | Josquin Daron R. Keith Slotkin EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels Genome Biology Methylome Transposable elements Insertion site Bisulfite Split reads Bioinformatics |
| title | EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels |
| title_full | EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels |
| title_fullStr | EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels |
| title_full_unstemmed | EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels |
| title_short | EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels |
| title_sort | epiteome simultaneous detection of transposable element insertion sites and their dna methylation levels |
| topic | Methylome Transposable elements Insertion site Bisulfite Split reads Bioinformatics |
| url | http://link.springer.com/article/10.1186/s13059-017-1232-0 |
| work_keys_str_mv | AT josquindaron epiteomesimultaneousdetectionoftransposableelementinsertionsitesandtheirdnamethylationlevels AT rkeithslotkin epiteomesimultaneousdetectionoftransposableelementinsertionsitesandtheirdnamethylationlevels |