RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs
Abstract Background Long INterspersed Element-1 (LINE-1) is an autonomous retroelement able to “copy-and-paste” itself into new loci of the host genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p, a nucleic acid chaperone, and ORF2p, a prote...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-02-01
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| Series: | Mobile DNA |
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| Online Access: | https://doi.org/10.1186/s13100-021-00233-3 |
| _version_ | 1818946125644693504 |
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| author | Erica M. Briggs Wilson McKerrow Paolo Mita Jef D. Boeke Susan K. Logan David Fenyö |
| author_facet | Erica M. Briggs Wilson McKerrow Paolo Mita Jef D. Boeke Susan K. Logan David Fenyö |
| author_sort | Erica M. Briggs |
| collection | DOAJ |
| description | Abstract Background Long INterspersed Element-1 (LINE-1) is an autonomous retroelement able to “copy-and-paste” itself into new loci of the host genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p, a nucleic acid chaperone, and ORF2p, a protein with endonuclease and reverse transcriptase activity. Both proteins bind LINE-1 mRNA in cis and are necessary for retrotransposition. While LINE-1 transcription is usually repressed in most healthy somatic cells through a plethora of mechanisms, ORF1p expression has been observed in nearly 50% of tumors, and new LINE-1 insertions have been documented in a similar fraction of tumors, including prostate cancer. Results Here, we utilized RNA ImmunoPrecipitation (RIP) and the L1EM analysis software to identify ORF1p bound RNA in prostate cancer cells. We identified LINE-1 loci that were expressed in parental androgen sensitive and androgen independent clonal derivatives. In all androgen independent cells, we found higher levels of LINE-1 RNA, as well as unique expression patterns of LINE-1 loci. Interestingly, we observed that ORF1p bound many non-LINE-1 mRNA in all prostate cancer cell lines evaluated, and polyA RNA, and RNA localized in p-bodies were especially enriched. Furthermore, the expression levels of RNAs identified in our ORF1p RIP correlated with RNAs expressed in LINE-1 positive tumors from The Cancer Genome Atlas (TCGA). Conclusion Our results show a significant remodeling of LINE-1 loci expression in androgen independent cell lines when compared to parental androgen dependent cells. Additionally, we found that ORF1p bound a significant amount of non-LINE-1 mRNA, and that the enriched ORF1p bound mRNAs are also amplified in LINE-1 expressing TCGA prostate tumors, indicating the biological relevance of our findings to prostate cancer. |
| first_indexed | 2024-12-20T08:10:02Z |
| format | Article |
| id | doaj.art-86bc85fe67f342998a10702c72579a23 |
| institution | Directory Open Access Journal |
| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-12-20T08:10:02Z |
| publishDate | 2021-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Mobile DNA |
| spelling | doaj.art-86bc85fe67f342998a10702c72579a232022-12-21T19:47:18ZengBMCMobile DNA1759-87532021-02-0112111310.1186/s13100-021-00233-3RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAsErica M. Briggs0Wilson McKerrow1Paolo Mita2Jef D. Boeke3Susan K. Logan4David Fenyö5Departments of Biochemistry and Molecular Pharmacology, New York UniversityDepartments of Biochemistry and Molecular Pharmacology, New York UniversityDepartments of Biochemistry and Molecular Pharmacology, New York UniversityDepartments of Biochemistry and Molecular Pharmacology, New York UniversityDepartments of Biochemistry and Molecular Pharmacology, New York UniversityDepartments of Biochemistry and Molecular Pharmacology, New York UniversityAbstract Background Long INterspersed Element-1 (LINE-1) is an autonomous retroelement able to “copy-and-paste” itself into new loci of the host genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p, a nucleic acid chaperone, and ORF2p, a protein with endonuclease and reverse transcriptase activity. Both proteins bind LINE-1 mRNA in cis and are necessary for retrotransposition. While LINE-1 transcription is usually repressed in most healthy somatic cells through a plethora of mechanisms, ORF1p expression has been observed in nearly 50% of tumors, and new LINE-1 insertions have been documented in a similar fraction of tumors, including prostate cancer. Results Here, we utilized RNA ImmunoPrecipitation (RIP) and the L1EM analysis software to identify ORF1p bound RNA in prostate cancer cells. We identified LINE-1 loci that were expressed in parental androgen sensitive and androgen independent clonal derivatives. In all androgen independent cells, we found higher levels of LINE-1 RNA, as well as unique expression patterns of LINE-1 loci. Interestingly, we observed that ORF1p bound many non-LINE-1 mRNA in all prostate cancer cell lines evaluated, and polyA RNA, and RNA localized in p-bodies were especially enriched. Furthermore, the expression levels of RNAs identified in our ORF1p RIP correlated with RNAs expressed in LINE-1 positive tumors from The Cancer Genome Atlas (TCGA). Conclusion Our results show a significant remodeling of LINE-1 loci expression in androgen independent cell lines when compared to parental androgen dependent cells. Additionally, we found that ORF1p bound a significant amount of non-LINE-1 mRNA, and that the enriched ORF1p bound mRNAs are also amplified in LINE-1 expressing TCGA prostate tumors, indicating the biological relevance of our findings to prostate cancer.https://doi.org/10.1186/s13100-021-00233-3LINE-1L1EMORF1pProstate cancerProcessing bodiesRNA |
| spellingShingle | Erica M. Briggs Wilson McKerrow Paolo Mita Jef D. Boeke Susan K. Logan David Fenyö RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs Mobile DNA LINE-1 L1EM ORF1p Prostate cancer Processing bodies RNA |
| title | RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs |
| title_full | RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs |
| title_fullStr | RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs |
| title_full_unstemmed | RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs |
| title_short | RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs |
| title_sort | rip seq reveals line 1 orf1p association with p body enriched mrnas |
| topic | LINE-1 L1EM ORF1p Prostate cancer Processing bodies RNA |
| url | https://doi.org/10.1186/s13100-021-00233-3 |
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