The Potential Regulation of A-to-I RNA Editing on Genes in Parkinson's Disease
Parkinson's disease (PD) is characterized by dopaminergic neurodegeneration and an abnormal accumulation of α-synuclein aggregates. A number of genetic factors have been shown to increase the risk of PD. Exploring the underlying molecular mechanisms that mediate PD's transcriptomic diversi...
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| Veröffentlicht in: | Genes 2023-04, Vol.14 (4), p.919 |
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| creator | Wu, Sijia Xue, Qiuping Qin, Xinyu Wu, Xiaoming Kim, Pora Chyr, Jacqueline Zhou, Xiaobo Huang, Liyu |
| description | Parkinson's disease (PD) is characterized by dopaminergic neurodegeneration and an abnormal accumulation of α-synuclein aggregates. A number of genetic factors have been shown to increase the risk of PD. Exploring the underlying molecular mechanisms that mediate PD's transcriptomic diversity can help us understand neurodegenerative pathogenesis. In this study, we identified 9897 A-to-I RNA editing events associated with 6286 genes across 372 PD patients. Of them, 72 RNA editing events altered miRNA binding sites and this may directly affect miRNA regulations of their host genes. However, RNA editing effects on the miRNA regulation of genes are more complex. They can (1) abolish existing miRNA binding sites, which allows miRNAs to regulate other genes; (2) create new miRNA binding sites that may sequester miRNAs from regulating other genes; or (3) occur in the miRNA seed regions and change their targets. The first two processes are also referred to as miRNA competitive binding. In our study, we found 8 RNA editing events that may alter the expression of 1146 other genes via miRNA competition. We also found one RNA editing event that modified a miRNA seed region, which was predicted to disturb the regulation of four genes. Considering the PD-related functions of the affected genes, 25 A-to-I RNA editing biomarkers for PD are proposed, including the 3 editing events in the
,
, and
seed regions. These biomarkers may alter the miRNA regulation of 133 PD-related genes. All these analyses reveal the potential mechanisms and regulations of RNA editing in PD pathogenesis. |
| doi_str_mv | 10.3390/genes14040919 |
| format | Article |
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,
, and
seed regions. These biomarkers may alter the miRNA regulation of 133 PD-related genes. All these analyses reveal the potential mechanisms and regulations of RNA editing in PD pathogenesis.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes14040919</identifier><identifier>PMID: 37107677</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Alzheimer's disease ; Apoptosis ; Binding sites ; Biomarkers ; Biomarkers - metabolism ; Consortia ; Development and progression ; DNA testing ; Dopamine receptors ; Editing ; Gene expression ; Gene Expression Profiling ; Gene regulation ; Genetic aspects ; Genetic factors ; Humans ; Kinases ; Methods ; MicroRNAs ; MicroRNAs - genetics ; MicroRNAs - metabolism ; miRNA ; Molecular modelling ; Movement disorders ; Neurodegeneration ; Neurodegenerative diseases ; Parkinson Disease - genetics ; Parkinson Disease - metabolism ; Parkinson's disease ; Pathogenesis ; Proteins ; RNA editing ; RNA Editing - genetics ; RNA processing ; Synuclein ; Transcriptomics</subject><ispartof>Genes, 2023-04, Vol.14 (4), p.919</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 by the authors. 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c483t-98e89e3c9cd27b7947a7b0b6b2d3bc5219c8e6d7a7fbc222282983c08d6b6a603</citedby><cites>FETCH-LOGICAL-c483t-98e89e3c9cd27b7947a7b0b6b2d3bc5219c8e6d7a7fbc222282983c08d6b6a603</cites><orcidid>0000-0002-2863-6065 ; 0000-0003-0908-0986</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10137963/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10137963/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37107677$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wu, Sijia</creatorcontrib><creatorcontrib>Xue, Qiuping</creatorcontrib><creatorcontrib>Qin, Xinyu</creatorcontrib><creatorcontrib>Wu, Xiaoming</creatorcontrib><creatorcontrib>Kim, Pora</creatorcontrib><creatorcontrib>Chyr, Jacqueline</creatorcontrib><creatorcontrib>Zhou, Xiaobo</creatorcontrib><creatorcontrib>Huang, Liyu</creatorcontrib><title>The Potential Regulation of A-to-I RNA Editing on Genes in Parkinson's Disease</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Parkinson's disease (PD) is characterized by dopaminergic neurodegeneration and an abnormal accumulation of α-synuclein aggregates. A number of genetic factors have been shown to increase the risk of PD. Exploring the underlying molecular mechanisms that mediate PD's transcriptomic diversity can help us understand neurodegenerative pathogenesis. In this study, we identified 9897 A-to-I RNA editing events associated with 6286 genes across 372 PD patients. Of them, 72 RNA editing events altered miRNA binding sites and this may directly affect miRNA regulations of their host genes. However, RNA editing effects on the miRNA regulation of genes are more complex. They can (1) abolish existing miRNA binding sites, which allows miRNAs to regulate other genes; (2) create new miRNA binding sites that may sequester miRNAs from regulating other genes; or (3) occur in the miRNA seed regions and change their targets. The first two processes are also referred to as miRNA competitive binding. In our study, we found 8 RNA editing events that may alter the expression of 1146 other genes via miRNA competition. We also found one RNA editing event that modified a miRNA seed region, which was predicted to disturb the regulation of four genes. Considering the PD-related functions of the affected genes, 25 A-to-I RNA editing biomarkers for PD are proposed, including the 3 editing events in the
,
, and
seed regions. These biomarkers may alter the miRNA regulation of 133 PD-related genes. All these analyses reveal the potential mechanisms and regulations of RNA editing in PD pathogenesis.</description><subject>Alzheimer's disease</subject><subject>Apoptosis</subject><subject>Binding sites</subject><subject>Biomarkers</subject><subject>Biomarkers - metabolism</subject><subject>Consortia</subject><subject>Development and progression</subject><subject>DNA testing</subject><subject>Dopamine receptors</subject><subject>Editing</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene regulation</subject><subject>Genetic aspects</subject><subject>Genetic factors</subject><subject>Humans</subject><subject>Kinases</subject><subject>Methods</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>miRNA</subject><subject>Molecular modelling</subject><subject>Movement disorders</subject><subject>Neurodegeneration</subject><subject>Neurodegenerative diseases</subject><subject>Parkinson Disease - genetics</subject><subject>Parkinson Disease - metabolism</subject><subject>Parkinson's disease</subject><subject>Pathogenesis</subject><subject>Proteins</subject><subject>RNA editing</subject><subject>RNA Editing - genetics</subject><subject>RNA processing</subject><subject>Synuclein</subject><subject>Transcriptomics</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNptkstv1DAQhy0EolXpkSuyxAEuKeNH7PiEVn1RqSpVVc6W40xSl6xd4gSJ_x6v-tAuYnywNfPNbzz2EPKewZEQBr4MGDEzCRIMM6_IPgctKil5_XrrvEcOc76HYhI4QP2W7AnNQCut98nV7R3S6zRjnIMb6Q0Oy-jmkCJNPV1Vc6ou6M3Vip52YQ5xoCVwvilKQ6TXbvoZYk7xU6YnIaPL-I686d2Y8fBpPyA_zk5vj79Vl9_PL45Xl5WXjZgr02BjUHjjO65bbaR2uoVWtbwTra85M75B1RVv33perOGmER6aTrXKKRAH5Ouj7sPSrrHz5fqTG-3DFNZu-mOTC3Y3EsOdHdJvy4AJbZQoCp-fFKb0a8E823XIHsfRRUxLtrwBbZjWihX04z_ofVqmWPrbUKrmwogtanAj2hD7VAr7jahdaamlrEGoQh39hyqrw3XwKWIfin8noXpM8FPKecL-pUkGdjMEdmcICv9h-2Ve6OcvF38BuemqJg</recordid><startdate>20230415</startdate><enddate>20230415</enddate><creator>Wu, Sijia</creator><creator>Xue, Qiuping</creator><creator>Qin, Xinyu</creator><creator>Wu, Xiaoming</creator><creator>Kim, Pora</creator><creator>Chyr, Jacqueline</creator><creator>Zhou, Xiaobo</creator><creator>Huang, Liyu</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-2863-6065</orcidid><orcidid>https://orcid.org/0000-0003-0908-0986</orcidid></search><sort><creationdate>20230415</creationdate><title>The Potential Regulation of A-to-I RNA Editing on Genes in Parkinson's Disease</title><author>Wu, Sijia ; Xue, Qiuping ; Qin, Xinyu ; Wu, Xiaoming ; Kim, Pora ; Chyr, Jacqueline ; Zhou, Xiaobo ; Huang, Liyu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c483t-98e89e3c9cd27b7947a7b0b6b2d3bc5219c8e6d7a7fbc222282983c08d6b6a603</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Alzheimer's disease</topic><topic>Apoptosis</topic><topic>Binding sites</topic><topic>Biomarkers</topic><topic>Biomarkers - metabolism</topic><topic>Consortia</topic><topic>Development and progression</topic><topic>DNA testing</topic><topic>Dopamine receptors</topic><topic>Editing</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene regulation</topic><topic>Genetic aspects</topic><topic>Genetic factors</topic><topic>Humans</topic><topic>Kinases</topic><topic>Methods</topic><topic>MicroRNAs</topic><topic>MicroRNAs - genetics</topic><topic>MicroRNAs - metabolism</topic><topic>miRNA</topic><topic>Molecular modelling</topic><topic>Movement disorders</topic><topic>Neurodegeneration</topic><topic>Neurodegenerative diseases</topic><topic>Parkinson Disease - genetics</topic><topic>Parkinson Disease - metabolism</topic><topic>Parkinson's disease</topic><topic>Pathogenesis</topic><topic>Proteins</topic><topic>RNA editing</topic><topic>RNA Editing - genetics</topic><topic>RNA processing</topic><topic>Synuclein</topic><topic>Transcriptomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wu, Sijia</creatorcontrib><creatorcontrib>Xue, Qiuping</creatorcontrib><creatorcontrib>Qin, Xinyu</creatorcontrib><creatorcontrib>Wu, Xiaoming</creatorcontrib><creatorcontrib>Kim, Pora</creatorcontrib><creatorcontrib>Chyr, Jacqueline</creatorcontrib><creatorcontrib>Zhou, Xiaobo</creatorcontrib><creatorcontrib>Huang, Liyu</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wu, Sijia</au><au>Xue, Qiuping</au><au>Qin, Xinyu</au><au>Wu, Xiaoming</au><au>Kim, Pora</au><au>Chyr, Jacqueline</au><au>Zhou, Xiaobo</au><au>Huang, Liyu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Potential Regulation of A-to-I RNA Editing on Genes in Parkinson's Disease</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2023-04-15</date><risdate>2023</risdate><volume>14</volume><issue>4</issue><spage>919</spage><pages>919-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>Parkinson's disease (PD) is characterized by dopaminergic neurodegeneration and an abnormal accumulation of α-synuclein aggregates. A number of genetic factors have been shown to increase the risk of PD. Exploring the underlying molecular mechanisms that mediate PD's transcriptomic diversity can help us understand neurodegenerative pathogenesis. In this study, we identified 9897 A-to-I RNA editing events associated with 6286 genes across 372 PD patients. Of them, 72 RNA editing events altered miRNA binding sites and this may directly affect miRNA regulations of their host genes. However, RNA editing effects on the miRNA regulation of genes are more complex. They can (1) abolish existing miRNA binding sites, which allows miRNAs to regulate other genes; (2) create new miRNA binding sites that may sequester miRNAs from regulating other genes; or (3) occur in the miRNA seed regions and change their targets. The first two processes are also referred to as miRNA competitive binding. In our study, we found 8 RNA editing events that may alter the expression of 1146 other genes via miRNA competition. We also found one RNA editing event that modified a miRNA seed region, which was predicted to disturb the regulation of four genes. Considering the PD-related functions of the affected genes, 25 A-to-I RNA editing biomarkers for PD are proposed, including the 3 editing events in the
,
, and
seed regions. These biomarkers may alter the miRNA regulation of 133 PD-related genes. All these analyses reveal the potential mechanisms and regulations of RNA editing in PD pathogenesis.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>37107677</pmid><doi>10.3390/genes14040919</doi><orcidid>https://orcid.org/0000-0002-2863-6065</orcidid><orcidid>https://orcid.org/0000-0003-0908-0986</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access |
| subjects | Alzheimer's disease Apoptosis Binding sites Biomarkers Biomarkers - metabolism Consortia Development and progression DNA testing Dopamine receptors Editing Gene expression Gene Expression Profiling Gene regulation Genetic aspects Genetic factors Humans Kinases Methods MicroRNAs MicroRNAs - genetics MicroRNAs - metabolism miRNA Molecular modelling Movement disorders Neurodegeneration Neurodegenerative diseases Parkinson Disease - genetics Parkinson Disease - metabolism Parkinson's disease Pathogenesis Proteins RNA editing RNA Editing - genetics RNA processing Synuclein Transcriptomics |
| title | The Potential Regulation of A-to-I RNA Editing on Genes in Parkinson's Disease |
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