基于机器学习的RNA编辑位点预测方法综述
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摘要
RNA编辑是一个十分重要的生物细胞分子机制。作为转录后修饰的一步,它可以增加蛋白质组学多样性,改变转录产物的稳定性,调节基因表达等。RNA编辑失调会导致各种疾病,包括神经疾病和癌症。在动物中,腺苷到肌苷(A-to-I)的编辑是最普遍的。高通量测序技术的进步大大提高了在全局范围内检测和量化RNA编辑的能力,使得RNA编辑的大规模全基因组分析变得可行,产生了一系列基于高通量测序技术的RNA编辑位点预测方法。通过对这些方法进行介绍、总结和分析,为RNA编辑的进一步研究提供一些思路。
RNA editing is an important molecular mechanism of biological cells. As a step of post-transcriptional modification, it can increase proteomic diversity, alter the stability of transcription products, regulate gene expression, and so on. RNA editing disorders can lead to a variety of diseases, including neurological diseases and cancer. Among animals, the editing of adenosine to inosine(A-to-I) is the commonest. Advances in high-throughput sequencing technology have greatly improved the ability to detect and quantify RNA editing globally, which can make large-scale genome-wide analysis of RNA editing feasible, thereby resulting in a series of prediction methods of RNA editing sites based on high-throughput sequencing technology. This article will introduce and summarize these methods and provide new perspectives for further research of RNA editing.
RNA editing is an important molecular mechanism of biological cells. As a step of post-transcriptional modification, it can increase proteomic diversity, alter the stability of transcription products, regulate gene expression, and so on. RNA editing disorders can lead to a variety of diseases, including neurological diseases and cancer. Among animals, the editing of adenosine to inosine(A-to-I) is the commonest. Advances in high-throughput sequencing technology have greatly improved the ability to detect and quantify RNA editing globally, which can make large-scale genome-wide analysis of RNA editing feasible, thereby resulting in a series of prediction methods of RNA editing sites based on high-throughput sequencing technology. This article will introduce and summarize these methods and provide new perspectives for further research of RNA editing.
引文
[1]ROSENTHAL J J, SEEBURG P H. A-to-I RNA editing: effects on proteins key to neural excitability[J]. Neuron, 2012, 74(3): 432-439.DOI:10.1016/j.neuron.2012.04.010.
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[7]PICARDI E, D’ANTONIO M, CARRABINO D, et al. ExpEdit: a webserver to explore human RNA editing in RNA-seq experiments[J]. Bioinformatics, 2011, 27(9): 1311-1312.DOI:10.1093/bioinformatics/btr117.
[8]LIANG G, KITAMURA K, WANG Z, et al. RNA editing of hepatitis B virus transcripts by activation-induced cytidine deaminase[J]. Proceedings of the National Academy of Science, 2013, 110(6): 2246-2251.DOI:10.1073/pnas.1221921110.
[9]SUN J M, YANG D M, OSMARK P, et al. Discriminative prediction of A-to-I RNA editing events from DNA sequence[J]. PLoS One, 2016, 11(10): e0164962.DOI:DOI:10.1371/journal.pone.0164962.
[10]RAMASWAMI G, ZHANG R, PISKOL R, et al. Identifying RNA editing sites using RNA sequencing data alone[J]. Nature Methods, 2013, 10(2): 128-132.
[11]ZHANG Q, XIAO X. Genome sequence-independent identification of RNA editing sites[J]. Nature Methods, 2015, 12(4): 347-350. DOI: 10.1038/nmeth.3314.
[12]XIONG Heng, LIU Dongbing, LI Qiye, et al. RED-ML: a novel, effective RNA editing detection method based on machine learning[J]. Gigascience, 2017, 6(5): 1-8.DOI:10.1093/gigascience/gix012.
[13]PENG Zhiyu,CHENG Yanbing, TAN B C, et al. Comprehensive analysis of RNA-seq data reveals extensive RNA editing in a human transcriptome[J]. Nature Biotechnology, 2012, 30(3): 253-260. DOI:10.1038/nbt.2122.
[14]KIM M S, HUR B, KIM S. RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data[J]. BMC Genomics, 2016, 17 (Suppl 1): 5. DOI:10.1186/s12864-015-2301-y.
[15]BAHN J H, LEE J H, LI G, et al. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing[J]. Genome Research, 2012, 22(1): 142-150.DOI:10.1101/gr.124107.111.
[16]PARK E, WILLIAMS B, WOLD B J, et al. RNA editing in the human ENCODE RNA-seq data[J]. Genome Research, 2012, 22(9): 1626-1633.
[17]ZHU Shanshan, XIANG Jianfeng, CHEN Tian,et al. Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences[J]. BMC Genomics, 2013, 14(1): 206. DOI:10.1186/1471-2164-14-206.
[18]PICARDI E, PESOLE G. REDItools: high-throughput RNA editing detection made easy[J]. Bioinformatics, 2013, 29(14): 1813-1814.DOI: 10.1093/bioinformatics/btt287.
[19]EISENBERG E, ADAMSKY K, COHEN L, et al. Identification of RNA editing sites in the SNP database[J]. Nucleic Acids Research, 2005, 33(14): 4612-4617.DOI: 10.1093/nar/gki771.
[20]RAMASWAMI G, LI J B. RADAR: a rigorously annotated database of A-to-I RNA editing[J]. Nucleic Acids Research, 2014, 42(Database issue): D109-113.DOI: 10.1093/nar/gkt996.
[21]KIRAN A, BARANOV P V. DARNED: a Database of RNA Editing in humans[J]. Bioinformatics, 2010, 26(14): 1772-1776. DOI:10.1093/bioinformatics/btq285.
[22]CHANG C C, LIN C J. LIBSVM: a library for support vector machines[J]. DNA Research,2011, 2(3): 1-27.
[23]SCHOLKOPF B, PLATT J C, SHAWE-TAYLOR J, et al. Estimating the support of a high-dimensional distribution[J]. Neural Computation, 2001, 13(7): 1443-1471.DOI: 10.1162/089976601750264965.
[2]GARRETT S, ROSENTHAL J J. RNA editing underlies temperature adaptation in K+ channels from polar octopuses[J]. Science, 2012, 335(6070): 848-851.DOI: 10.1126/science.1212795.
[3]CHEN L, LI Y, LIN C H, et al. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma[J]. Nature Medicine, 2013, 19(2): 209-216.DOI: 10.1038/nm.3043.
[4]LI M, WANG I X, LI Y, et al. Widespread RNA and DNA sequence differences in the human transcriptome[J]. Science, 2011, 333(6038): 53-58.DOI:10.1126/science.1207018.
[5]SCHRIDER D R, GOUT J F, HAHN M W. Very few RNA and DNA sequence differences in the human transcriptome[J]. PLoS One, 2011, 6(10): e25842.DOI: 10.1371/journal.pone.0025842.
[6]RAMASWAMI G, LIN W, PISKOL R, et al. Accurate identification of human Alu and non-Alu RNA editing sites[J]. Nature Methods, 2012, 9(6): 579-581.DOI:10.1038/nmeth.1982.
[7]PICARDI E, D’ANTONIO M, CARRABINO D, et al. ExpEdit: a webserver to explore human RNA editing in RNA-seq experiments[J]. Bioinformatics, 2011, 27(9): 1311-1312.DOI:10.1093/bioinformatics/btr117.
[8]LIANG G, KITAMURA K, WANG Z, et al. RNA editing of hepatitis B virus transcripts by activation-induced cytidine deaminase[J]. Proceedings of the National Academy of Science, 2013, 110(6): 2246-2251.DOI:10.1073/pnas.1221921110.
[9]SUN J M, YANG D M, OSMARK P, et al. Discriminative prediction of A-to-I RNA editing events from DNA sequence[J]. PLoS One, 2016, 11(10): e0164962.DOI:DOI:10.1371/journal.pone.0164962.
[10]RAMASWAMI G, ZHANG R, PISKOL R, et al. Identifying RNA editing sites using RNA sequencing data alone[J]. Nature Methods, 2013, 10(2): 128-132.
[11]ZHANG Q, XIAO X. Genome sequence-independent identification of RNA editing sites[J]. Nature Methods, 2015, 12(4): 347-350. DOI: 10.1038/nmeth.3314.
[12]XIONG Heng, LIU Dongbing, LI Qiye, et al. RED-ML: a novel, effective RNA editing detection method based on machine learning[J]. Gigascience, 2017, 6(5): 1-8.DOI:10.1093/gigascience/gix012.
[13]PENG Zhiyu,CHENG Yanbing, TAN B C, et al. Comprehensive analysis of RNA-seq data reveals extensive RNA editing in a human transcriptome[J]. Nature Biotechnology, 2012, 30(3): 253-260. DOI:10.1038/nbt.2122.
[14]KIM M S, HUR B, KIM S. RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data[J]. BMC Genomics, 2016, 17 (Suppl 1): 5. DOI:10.1186/s12864-015-2301-y.
[15]BAHN J H, LEE J H, LI G, et al. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing[J]. Genome Research, 2012, 22(1): 142-150.DOI:10.1101/gr.124107.111.
[16]PARK E, WILLIAMS B, WOLD B J, et al. RNA editing in the human ENCODE RNA-seq data[J]. Genome Research, 2012, 22(9): 1626-1633.
[17]ZHU Shanshan, XIANG Jianfeng, CHEN Tian,et al. Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences[J]. BMC Genomics, 2013, 14(1): 206. DOI:10.1186/1471-2164-14-206.
[18]PICARDI E, PESOLE G. REDItools: high-throughput RNA editing detection made easy[J]. Bioinformatics, 2013, 29(14): 1813-1814.DOI: 10.1093/bioinformatics/btt287.
[19]EISENBERG E, ADAMSKY K, COHEN L, et al. Identification of RNA editing sites in the SNP database[J]. Nucleic Acids Research, 2005, 33(14): 4612-4617.DOI: 10.1093/nar/gki771.
[20]RAMASWAMI G, LI J B. RADAR: a rigorously annotated database of A-to-I RNA editing[J]. Nucleic Acids Research, 2014, 42(Database issue): D109-113.DOI: 10.1093/nar/gkt996.
[21]KIRAN A, BARANOV P V. DARNED: a Database of RNA Editing in humans[J]. Bioinformatics, 2010, 26(14): 1772-1776. DOI:10.1093/bioinformatics/btq285.
[22]CHANG C C, LIN C J. LIBSVM: a library for support vector machines[J]. DNA Research,2011, 2(3): 1-27.
[23]SCHOLKOPF B, PLATT J C, SHAWE-TAYLOR J, et al. Estimating the support of a high-dimensional distribution[J]. Neural Computation, 2001, 13(7): 1443-1471.DOI: 10.1162/089976601750264965.