Abstract
Background: Pseudouridine (Ψ) is the most abundant RNA modification and has important functions in a series of biological and cellular processes. Although experimental techniques have made great contributions to identify Ψ sites, they are still labor-intensive and costineffective. In the past few years, a series of computational approaches have been developed, which provided rapid and efficient approaches to identify Ψ sites.
Results: To provide the readership with a clear landscape about the recent development in this important area, in this review, we summarized and compared the representative computational approaches developed for identifying Ψ sites. Moreover, future directions in computationally identifying Ψ sites were discussed as well.
Conclusion: We anticipate that this review will provide novel insights into the researches on pseudouridine modification.
Keywords: Epitranscriptome, RNA modification, pseudouridine, support vector machine, nucleotide physicochemical property, web server.
Graphical Abstract
[PMID: 13463012]
[http://dx.doi.org/10.1080/15476286.2016.1259781] [PMID: 27911188]
[http://dx.doi.org/10.1016/j.tibs.2013.01.002] [PMID: 23391857]
[http://dx.doi.org/10.1073/pnas.1617402113] [PMID: 27911836]
[http://dx.doi.org/10.1016/j.molcel.2010.01.032] [PMID: 20227365]
[http://dx.doi.org/10.1128/MCB.24.13.5797-5807.2004] [PMID: 15199136]
[http://dx.doi.org/10.1080/152165400410182] [PMID: 10902565]
[http://dx.doi.org/10.1016/j.cell.2014.08.028] [PMID: 25219674]
[http://dx.doi.org/10.1080/15476286.2016.1276150] [PMID: 28045575]
[http://dx.doi.org/10.1261/rna.060053.116] [PMID: 28138061]
[http://dx.doi.org/10.1080/15476286.2018.1462654] [PMID: 29683381]
[http://dx.doi.org/10.1080/07391102.1998.10509006] [PMID: 9669557]
[http://dx.doi.org/10.4161/15476286.2014.992278] [PMID: 25616362]
[http://dx.doi.org/10.1016/j.celrep.2014.07.004] [PMID: 25127136]
[http://dx.doi.org/10.1261/rna.049650.115] [PMID: 25780180]
[http://dx.doi.org/10.3390/genes8110301] [PMID: 29104216]
[PMID: 5362809]
[http://dx.doi.org/10.1093/jnci/51.1.271] [PMID: 4720877]
[http://dx.doi.org/10.1038/emboj.2010.316] [PMID: 21131909]
[http://dx.doi.org/10.15252/embr.201642682] [PMID: 27558685]
[http://dx.doi.org/10.1074/jbc.M116.739482] [PMID: 27519417]
[http://dx.doi.org/10.1371/journal.pone.0110799] [PMID: 25353621]
[http://dx.doi.org/10.1038/nchembio.1836] [PMID: 26075521]
[http://dx.doi.org/10.1038/nature13802] [PMID: 25192136]
[http://dx.doi.org/10.1186/1471-2105-15-326] [PMID: 25272949]
[http://dx.doi.org/10.1093/bioinformatics/btv366] [PMID: 26076723]
[http://dx.doi.org/10.1186/s12859-018-2321-0] [PMID: 30157750]
[http://dx.doi.org/10.1016/j.omtn.2019.03.010]
[http://dx.doi.org/10.1093/nar/gkx934] [PMID: 29040692]
[http://dx.doi.org/10.1261/rna.069112.118] [PMID: 30425123]
[http://dx.doi.org/10.1093/bioinformatics/btz015] [PMID: 30624619]
[http://dx.doi.org/10.1093/bioinformatics/btx479] [PMID: 28961687]
[PMID: 31157855]
[http://dx.doi.org/10.1016/j.ab.2018.09.002] [PMID: 30201554]
[http://dx.doi.org/10.1016/j.ygeno.2018.01.005] [PMID: 29360500]
[http://dx.doi.org/10.1016/j.ab.2014.06.022] [PMID: 25016190]
[http://dx.doi.org/10.1155/2014/623149] [PMID: 24967386]
[http://dx.doi.org/10.1093/bioinformatics/btu083] [PMID: 24504871]
[http://dx.doi.org/10.1016/j.chemolab.2014.12.011]
[http://dx.doi.org/10.1093/nar/gku1019] [PMID: 25361964]
[http://dx.doi.org/10.7150/ijbs.24616] [PMID: 29989083]
[http://dx.doi.org/10.1093/bioinformatics/bty668] [PMID: 30052767]
[http://dx.doi.org/10.1016/j.ab.2014.04.001] [PMID: 24732113]
[http://dx.doi.org/10.1093/bioinformatics/btu602] [PMID: 25231908]
[http://dx.doi.org/10.1039/C5MB00155B] [PMID: 26099739]
[http://dx.doi.org/10.1016/j.ab.2013.05.024] [PMID: 23756733]
[http://dx.doi.org/10.1155/2013/530696] [PMID: 23762187]
[PMID: 28186907]
[PMID: 30378494]
[http://dx.doi.org/10.3934/mbe.2019123] [PMID: 31137222]
[PMID: 30247625]
[PMID: 30428009]
[http://dx.doi.org/10.1016/j.jtbi.2012.08.016] [PMID: 22960368]
[http://dx.doi.org/10.1016/j.jtbi.2017.03.031] [PMID: 28411111]
[http://dx.doi.org/10.1186/1748-7188-6-26] [PMID: 22115189]
[http://dx.doi.org/10.1016/j.neucom.2018.04.082]
[http://dx.doi.org/10.1016/j.jpdc.2017.08.009]
[http://dx.doi.org/10.2174/1574893612666170707095707]
[http://dx.doi.org/10.1016/j.ymeth.2019.02.009] [PMID: 30772464]
[http://dx.doi.org/10.1186/s12859-016-1405-y] [PMID: 27919220]
[http://dx.doi.org/10.3390/molecules22101732] [PMID: 29039790]
[http://dx.doi.org/10.1021/acs.jproteome.9b00012] [PMID: 30698979]
[http://dx.doi.org/10.1371/journal.pone.0086879] [PMID: 24466278]
[http://dx.doi.org/10.3389/fimmu.2018.01695] [PMID: 30100904]
[http://dx.doi.org/10.3389/fimmu.2018.01783] [PMID: 30108593]
[http://dx.doi.org/10.1109/TPAMI.2005.159] [PMID: 16119262]
[http://dx.doi.org/10.1016/j.jtbi.2016.04.032] [PMID: 27155042]
[http://dx.doi.org/10.1016/j.neucom.2014.12.123]