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dc.contributor.authorCao, Jichuan
dc.contributor.authorYu, Tianxiong
dc.contributor.authorXu, Bo
dc.contributor.authorHu, Zhongren
dc.contributor.authorZhang, Xiao-Ou
dc.contributor.authorTheurkauf, William E
dc.contributor.authorWeng, Zhiping
dc.date.accessioned2023-03-14T14:05:26Z
dc.date.available2023-03-14T14:05:26Z
dc.date.issued2023-02-10
dc.identifier.citationCao J, Yu T, Xu B, Hu Z, Zhang XO, Theurkauf WE, Weng Z. Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. Nucleic Acids Res. 2023 Feb 10:gkad054. doi: 10.1093/nar/gkad054. Epub ahead of print. PMID: 36762470.en_US
dc.identifier.eissn1362-4962
dc.identifier.doi10.1093/nar/gkad054en_US
dc.identifier.pmid36762470
dc.identifier.urihttp://hdl.handle.net/20.500.14038/51805
dc.description.abstractTransposons are mobile genetic elements prevalent in the genomes of most species. The distribution of transposons within a genome reflects the actions of two opposing processes: initial insertion site selection, and selective pressure from the host. By analyzing whole-genome sequencing data from transposon-activated Drosophila melanogaster, we identified 43 316 de novo and 237 germline insertions from four long-terminal-repeat (LTR) transposons, one LINE transposon (I-element), and one DNA transposon (P-element). We found that all transposon types favored insertion into promoters de novo, but otherwise displayed distinct insertion patterns. De novo and germline P-element insertions preferred replication origins, often landing in a narrow region around transcription start sites and in regions of high chromatin accessibility. De novo LTR transposon insertions preferred regions with high H3K36me3, promoters and exons of active genes; within genes, LTR insertion frequency correlated with gene expression. De novo I-element insertion density increased with distance from the centromere. Germline I-element and LTR transposon insertions were depleted in promoters and exons, suggesting strong selective pressure to remove transposons from functional elements. Transposon movement is associated with genome evolution and disease; therefore, our results can improve our understanding of genome and disease biology.en_US
dc.language.isoenen_US
dc.relation.ispartofNucleic Acids Researchen_US
dc.relation.urlhttps://doi.org/10.1093/nar/gkad054en_US
dc.rights© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen_US
dc.rightsAttribution-NonCommercial 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/*
dc.titleEpigenetic and chromosomal features drive transposon insertion in Drosophila melanogasteren_US
dc.typeJournal Articleen_US
dc.source.journaltitleNucleic acids research
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryEngland
dc.identifier.journalNucleic acids research
refterms.dateFOA2023-03-14T14:05:27Z
dc.contributor.departmentProgram in Bioinformatics and Integrative Biologyen_US
dc.contributor.departmentProgram in Molecular Medicineen_US


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© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License
(http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work
is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Except where otherwise noted, this item's license is described as © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com