RNA结合蛋白结合区内RNA编辑位点的研究

Q2 Biochemistry, Genetics and Molecular Biology High-Throughput Pub Date : 2019-11-29 DOI:10.3390/ht8040019
Tyler Weirick, G. Militello, M. R. Hosen, D. John, J. Moore, S. Uchida
{"title":"RNA结合蛋白结合区内RNA编辑位点的研究","authors":"Tyler Weirick, G. Militello, M. R. Hosen, D. John, J. Moore, S. Uchida","doi":"10.3390/ht8040019","DOIUrl":null,"url":null,"abstract":"Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNA Editor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affect the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncovered that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands were examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, human antigen R [HuR; encoded by ELAV-like protein 1 (ELAV1)], was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) compared to the control—suggesting that the presence of RNA editing islands influence HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP–RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2019-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht8040019","citationCount":"2","resultStr":"{\"title\":\"Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins\",\"authors\":\"Tyler Weirick, G. Militello, M. R. Hosen, D. John, J. Moore, S. Uchida\",\"doi\":\"10.3390/ht8040019\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNA Editor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affect the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncovered that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands were examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, human antigen R [HuR; encoded by ELAV-like protein 1 (ELAV1)], was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) compared to the control—suggesting that the presence of RNA editing islands influence HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP–RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.\",\"PeriodicalId\":53433,\"journal\":{\"name\":\"High-Throughput\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2019-11-29\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.3390/ht8040019\",\"citationCount\":\"2\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"High-Throughput\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3390/ht8040019\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"Biochemistry, Genetics and Molecular Biology\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"High-Throughput","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/ht8040019","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 2

摘要

表转录组学研究表明,RNA被多种酶修饰。在这些RNA修饰中,腺苷转肌苷(A-to-I)RNA编辑在哺乳动物转录组中频繁发生。这些RNA编辑位点可以通过检测从腺苷(A)到鸟嘌呤(G)的核苷酸变化,直接从RNA测序(RNA-seq)数据中检测到,鸟嘌呤取代了肌苷(I)。然而,必须对这种核苷酸变化进行仔细调查,以将测序错误和基因组突变与真正的编辑位点区分开来。在我们最近推出的一种易于使用的生物信息学工具RNA编辑器的基础上,我们研究了RNA编辑事件对RNA结合蛋白(RBP)结合的影响程度。通过使用生物信息学技术,我们发现RNA编辑位点经常出现在RBP结合区。此外,当检测RNA编辑岛时,RNA编辑位点的存在更加频繁,RNA编辑岛是RNA编辑位点以簇形式存在的区域。当一种RBP,即人类抗原R[HuR;由ELAV样蛋白1(ELAV1)编码]的结合通过实验定量时,与对照相比,在作用于RNA的RNA编辑酶腺苷脱氨酶(ADAR)沉默后,其结合减少,这表明RNA编辑岛的存在影响HuR与其靶区的结合。这些数据表明,RNA编辑是RBP-RNA相互作用的重要媒介,这一机制可能构成生物系统中转录后基因调控的另一种模式。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNA Editor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affect the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncovered that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands were examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, human antigen R [HuR; encoded by ELAV-like protein 1 (ELAV1)], was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) compared to the control—suggesting that the presence of RNA editing islands influence HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP–RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
High-Throughput
High-Throughput Biochemistry, Genetics and Molecular Biology-Biotechnology
CiteScore
3.60
自引率
0.00%
发文量
0
审稿时长
9 weeks
期刊介绍: High-Throughput (formerly Microarrays, ISSN 2076-3905) is a multidisciplinary peer-reviewed scientific journal that provides an advanced forum for the publication of studies reporting high-dimensional approaches and developments in Life Sciences, Chemistry and related fields. Our aim is to encourage scientists to publish their experimental and theoretical results based on high-throughput techniques as well as computational and statistical tools for data analysis and interpretation. The full experimental or methodological details must be provided so that the results can be reproduced. There is no restriction on the length of the papers. High-Throughput invites submissions covering several topics, including, but not limited to: -Microarrays -DNA Sequencing -RNA Sequencing -Protein Identification and Quantification -Cell-based Approaches -Omics Technologies -Imaging -Bioinformatics -Computational Biology/Chemistry -Statistics -Integrative Omics -Drug Discovery and Development -Microfluidics -Lab-on-a-chip -Data Mining -Databases -Multiplex Assays
期刊最新文献
Health Impact and Therapeutic Manipulation of the Gut Microbiome. Influence of the Ovine Genital Tract Microbiota on the Species Artificial Insemination Outcome. A Pilot Study in Commercial Sheep Farms. Dark Proteome Database: Studies on Disorder. Intra-Laboratory Evaluation of Luminescence Based High-Throughput Serum Bactericidal Assay (L-SBA) to Determine Bactericidal Activity of Human Sera against Shigella. Genetic Counseling and NGS Screening for Recessive LGMD2A Families.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1