Generalized nuclear localization of retroelement transcripts
Abstract Background LINE-1s, Alus and SVAs are the only retrotransposition competent elements in humans. Their mobilization followed by insertional mutagenesis is often linked to disease. Apart from these rare integration events, accumulation of retrotransposition intermediates in the cytoplasm is p...
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| Format: | Article |
| Language: | English |
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BMC
2022-12-01
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| Series: | Mobile DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13100-022-00287-x |
| _version_ | 1797985497031639040 |
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| author | Simanti Das Amanda E. Jones John M. Abrams |
| author_facet | Simanti Das Amanda E. Jones John M. Abrams |
| author_sort | Simanti Das |
| collection | DOAJ |
| description | Abstract Background LINE-1s, Alus and SVAs are the only retrotransposition competent elements in humans. Their mobilization followed by insertional mutagenesis is often linked to disease. Apart from these rare integration events, accumulation of retrotransposition intermediates in the cytoplasm is potentially pathogenic due to induction of inflammatory response pathways. Although the retrotransposition of LINE-1 and Alu retroelements has been studied in considerable detail, there are mixed observations about the localization of their RNAs. Results We undertook a comprehensive and unbiased approach to analyze retroelement RNA localization using common cell lines and publicly available datasets containing RNA-sequencing data from subcellular fractions. Using our customized analytic pipeline, we compared localization patterns of RNAs transcribed from retroelements and single-copy protein coding genes. Our results demonstrate a generalized characteristic pattern of retroelement RNA nuclear localization that is conserved across retroelement classes as well as evolutionarily young and ancient elements. Preferential nuclear enrichment of retroelement transcripts was consistently observed in cell lines, in vivo and across species. Moreover, retroelement RNA localization patterns were dynamic and subject to change during development, as seen in zebrafish embryos. Conclusion The pronounced nuclear localization of transcripts arising from ancient as well as de novo transcribed retroelements suggests that these transcripts are retained in the nucleus as opposed to being re-imported to the nucleus or degraded in the cytoplasm. This raises the possibility that there is adaptive value associated with this localization pattern to the host, the retroelements or possibly both. |
| first_indexed | 2024-04-11T07:19:09Z |
| format | Article |
| id | doaj.art-b98e6aa1167c48589053b3e8a3a954d2 |
| institution | Directory Open Access Journal |
| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-04-11T07:19:09Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Mobile DNA |
| spelling | doaj.art-b98e6aa1167c48589053b3e8a3a954d22022-12-22T04:37:49ZengBMCMobile DNA1759-87532022-12-0113111510.1186/s13100-022-00287-xGeneralized nuclear localization of retroelement transcriptsSimanti Das0Amanda E. Jones1John M. Abrams2Department of Cell Biology, University of Texas Southwestern Medical CenterDepartment of Cell Biology, University of Texas Southwestern Medical CenterDepartment of Cell Biology, University of Texas Southwestern Medical CenterAbstract Background LINE-1s, Alus and SVAs are the only retrotransposition competent elements in humans. Their mobilization followed by insertional mutagenesis is often linked to disease. Apart from these rare integration events, accumulation of retrotransposition intermediates in the cytoplasm is potentially pathogenic due to induction of inflammatory response pathways. Although the retrotransposition of LINE-1 and Alu retroelements has been studied in considerable detail, there are mixed observations about the localization of their RNAs. Results We undertook a comprehensive and unbiased approach to analyze retroelement RNA localization using common cell lines and publicly available datasets containing RNA-sequencing data from subcellular fractions. Using our customized analytic pipeline, we compared localization patterns of RNAs transcribed from retroelements and single-copy protein coding genes. Our results demonstrate a generalized characteristic pattern of retroelement RNA nuclear localization that is conserved across retroelement classes as well as evolutionarily young and ancient elements. Preferential nuclear enrichment of retroelement transcripts was consistently observed in cell lines, in vivo and across species. Moreover, retroelement RNA localization patterns were dynamic and subject to change during development, as seen in zebrafish embryos. Conclusion The pronounced nuclear localization of transcripts arising from ancient as well as de novo transcribed retroelements suggests that these transcripts are retained in the nucleus as opposed to being re-imported to the nucleus or degraded in the cytoplasm. This raises the possibility that there is adaptive value associated with this localization pattern to the host, the retroelements or possibly both.https://doi.org/10.1186/s13100-022-00287-xRetroelementsRNANuclear localizationRNA-sequencingLINE-1Development |
| spellingShingle | Simanti Das Amanda E. Jones John M. Abrams Generalized nuclear localization of retroelement transcripts Mobile DNA Retroelements RNA Nuclear localization RNA-sequencing LINE-1 Development |
| title | Generalized nuclear localization of retroelement transcripts |
| title_full | Generalized nuclear localization of retroelement transcripts |
| title_fullStr | Generalized nuclear localization of retroelement transcripts |
| title_full_unstemmed | Generalized nuclear localization of retroelement transcripts |
| title_short | Generalized nuclear localization of retroelement transcripts |
| title_sort | generalized nuclear localization of retroelement transcripts |
| topic | Retroelements RNA Nuclear localization RNA-sequencing LINE-1 Development |
| url | https://doi.org/10.1186/s13100-022-00287-x |
| work_keys_str_mv | AT simantidas generalizednuclearlocalizationofretroelementtranscripts AT amandaejones generalizednuclearlocalizationofretroelementtranscripts AT johnmabrams generalizednuclearlocalizationofretroelementtranscripts |