A-to-I nonsynonymous RNA editing was significantly enriched in the ubiquitination site and correlated with clinical features and immune response
Abstract RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the most well-studied type of RNA editing. About 0.5% of A-to-I editing sites were located in the coding regions. Despite of thousands of identifi...
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Published in | Scientific reports Vol. 12; no. 1; pp. 15079 - 12 |
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Main Authors | , , |
Format | Journal Article |
Language | English |
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05.09.2022
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Abstract | Abstract
RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the most well-studied type of RNA editing. About 0.5% of A-to-I editing sites were located in the coding regions. Despite of thousands of identified A-to-I nonsynonymous editing sites, the function of nonsynonymous editing was poorly studied. Here, we found that the nonsynonymous editing was significantly enriched in the ubiquitination site, compared to the synonymous editing. This enrichment was also in a modification type dependent manner, since it was not significantly enriched in other modification types. This observation was consistent with previous study that the codons for lysine (AAG and AAA) were enriched in the preferred deamination site for RNA editing. The peptides from proteomic data in CPTAC supported that mRNAs harboring edited ubiquitination sites can be translated into protein in cells. We identified the editing sites on ubiquitination site were significantly differential edited between tumor and para-tumor samples as well as among different subtypes in TCGA datasets and also correlated with clinical outcome, especially for the nonsynonymous editing sites on GSTM5, WDR1, SSR4 and PSMC4. Finally, the enrichment analysis revealed that the function of these above genes was specifically enriched in the immune response pathway. Our study shed a light on understanding the functions of nonsynonymous editing in tumorigenesis and provided nonsynonymous editing targets for potential cancer diagnosis and therapy. |
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AbstractList | RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the most well-studied type of RNA editing. About 0.5% of A-to-I editing sites were located in the coding regions. Despite of thousands of identified A-to-I nonsynonymous editing sites, the function of nonsynonymous editing was poorly studied. Here, we found that the nonsynonymous editing was significantly enriched in the ubiquitination site, compared to the synonymous editing. This enrichment was also in a modification type dependent manner, since it was not significantly enriched in other modification types. This observation was consistent with previous study that the codons for lysine (AAG and AAA) were enriched in the preferred deamination site for RNA editing. The peptides from proteomic data in CPTAC supported that mRNAs harboring edited ubiquitination sites can be translated into protein in cells. We identified the editing sites on ubiquitination site were significantly differential edited between tumor and para-tumor samples as well as among different subtypes in TCGA datasets and also correlated with clinical outcome, especially for the nonsynonymous editing sites on GSTM5, WDR1, SSR4 and PSMC4. Finally, the enrichment analysis revealed that the function of these above genes was specifically enriched in the immune response pathway. Our study shed a light on understanding the functions of nonsynonymous editing in tumorigenesis and provided nonsynonymous editing targets for potential cancer diagnosis and therapy.RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the most well-studied type of RNA editing. About 0.5% of A-to-I editing sites were located in the coding regions. Despite of thousands of identified A-to-I nonsynonymous editing sites, the function of nonsynonymous editing was poorly studied. Here, we found that the nonsynonymous editing was significantly enriched in the ubiquitination site, compared to the synonymous editing. This enrichment was also in a modification type dependent manner, since it was not significantly enriched in other modification types. This observation was consistent with previous study that the codons for lysine (AAG and AAA) were enriched in the preferred deamination site for RNA editing. The peptides from proteomic data in CPTAC supported that mRNAs harboring edited ubiquitination sites can be translated into protein in cells. We identified the editing sites on ubiquitination site were significantly differential edited between tumor and para-tumor samples as well as among different subtypes in TCGA datasets and also correlated with clinical outcome, especially for the nonsynonymous editing sites on GSTM5, WDR1, SSR4 and PSMC4. Finally, the enrichment analysis revealed that the function of these above genes was specifically enriched in the immune response pathway. Our study shed a light on understanding the functions of nonsynonymous editing in tumorigenesis and provided nonsynonymous editing targets for potential cancer diagnosis and therapy. Abstract RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the most well-studied type of RNA editing. About 0.5% of A-to-I editing sites were located in the coding regions. Despite of thousands of identified A-to-I nonsynonymous editing sites, the function of nonsynonymous editing was poorly studied. Here, we found that the nonsynonymous editing was significantly enriched in the ubiquitination site, compared to the synonymous editing. This enrichment was also in a modification type dependent manner, since it was not significantly enriched in other modification types. This observation was consistent with previous study that the codons for lysine (AAG and AAA) were enriched in the preferred deamination site for RNA editing. The peptides from proteomic data in CPTAC supported that mRNAs harboring edited ubiquitination sites can be translated into protein in cells. We identified the editing sites on ubiquitination site were significantly differential edited between tumor and para-tumor samples as well as among different subtypes in TCGA datasets and also correlated with clinical outcome, especially for the nonsynonymous editing sites on GSTM5, WDR1, SSR4 and PSMC4. Finally, the enrichment analysis revealed that the function of these above genes was specifically enriched in the immune response pathway. Our study shed a light on understanding the functions of nonsynonymous editing in tumorigenesis and provided nonsynonymous editing targets for potential cancer diagnosis and therapy. RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the most well-studied type of RNA editing. About 0.5% of A-to-I editing sites were located in the coding regions. Despite of thousands of identified A-to-I nonsynonymous editing sites, the function of nonsynonymous editing was poorly studied. Here, we found that the nonsynonymous editing was significantly enriched in the ubiquitination site, compared to the synonymous editing. This enrichment was also in a modification type dependent manner, since it was not significantly enriched in other modification types. This observation was consistent with previous study that the codons for lysine (AAG and AAA) were enriched in the preferred deamination site for RNA editing. The peptides from proteomic data in CPTAC supported that mRNAs harboring edited ubiquitination sites can be translated into protein in cells. We identified the editing sites on ubiquitination site were significantly differential edited between tumor and para-tumor samples as well as among different subtypes in TCGA datasets and also correlated with clinical outcome, especially for the nonsynonymous editing sites on GSTM5, WDR1, SSR4 and PSMC4. Finally, the enrichment analysis revealed that the function of these above genes was specifically enriched in the immune response pathway. Our study shed a light on understanding the functions of nonsynonymous editing in tumorigenesis and provided nonsynonymous editing targets for potential cancer diagnosis and therapy. Abstract RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the most well-studied type of RNA editing. About 0.5% of A-to-I editing sites were located in the coding regions. Despite of thousands of identified A-to-I nonsynonymous editing sites, the function of nonsynonymous editing was poorly studied. Here, we found that the nonsynonymous editing was significantly enriched in the ubiquitination site, compared to the synonymous editing. This enrichment was also in a modification type dependent manner, since it was not significantly enriched in other modification types. This observation was consistent with previous study that the codons for lysine (AAG and AAA) were enriched in the preferred deamination site for RNA editing. The peptides from proteomic data in CPTAC supported that mRNAs harboring edited ubiquitination sites can be translated into protein in cells. We identified the editing sites on ubiquitination site were significantly differential edited between tumor and para-tumor samples as well as among different subtypes in TCGA datasets and also correlated with clinical outcome, especially for the nonsynonymous editing sites on GSTM5, WDR1, SSR4 and PSMC4. Finally, the enrichment analysis revealed that the function of these above genes was specifically enriched in the immune response pathway. Our study shed a light on understanding the functions of nonsynonymous editing in tumorigenesis and provided nonsynonymous editing targets for potential cancer diagnosis and therapy. |
ArticleNumber | 15079 |
Author | Wang, Jianjun Tu, Juchuanli Li, Haixia |
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Cites_doi | 10.1038/s41596-019-0279-7 10.3389/fonc.2020.593989 10.1111/j.1432-1033.1994.tb18710.x 10.1016/j.ccell.2018.03.026 10.1038/nm.3043 10.1158/0008-5472.CAN-17-0520 10.1038/379460a0 10.1016/j.celrep.2015.09.032 10.1038/s41576-018-0006-1 10.3389/fendo.2018.00762 10.1038/s41467-022-28841-4 10.1038/s41467-017-01890-w 10.1074/jbc.271.50.31795 10.1016/j.ccell.2015.08.013 10.7717/peerj.1499 10.7717/peerj.7107 10.1038/nprot.2009.97 10.1093/nar/gks961 10.1089/omi.2011.0118 10.1146/annurev.genet.30.1.405 10.1101/gr.164749.113 10.1146/annurev.genet.34.1.499 10.1186/s12943-020-01262-x 10.1038/ni0102-20 10.4155/fmc.15.148 10.18632/oncotarget.17034 10.1007/978-1-0716-0787-9_17 10.1038/nature11252 10.1016/j.ccell.2018.04.006 10.1038/nature11412 10.1016/j.biocel.2018.06.001 10.1016/j.ceb.2004.02.005 10.1093/bioinformatics/btr260 10.1038/s41467-018-06405-9 10.1038/ncomms10715 10.1093/nar/gku1267 10.3389/fimmu.2020.586613 10.1038/s41598-017-13580-0 10.1093/nar/gkt996 10.1093/bioinformatics/btu397 10.1038/ncomms1324 10.1093/bioinformatics/btq285 |
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RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the... RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the most... Abstract RNA editing is a post-transcriptional process that alters RNA sequence in a site-specific manner. A-to-I editing is the most abundant as well as the... |
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StartPage | 15079 |
SubjectTerms | Codons Deamination Editing Immune response Lysine Nucleotide sequence Peptides Post-transcription Proteomics RNA editing Tumorigenesis Ubiquitination |
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Title | A-to-I nonsynonymous RNA editing was significantly enriched in the ubiquitination site and correlated with clinical features and immune response |
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