RNA editing in plants: A comprehensive survey of bioinformatics tools and databases

Plant Physiology and Biochemistry - Tập 137 - Trang 53-61 - 2019
Claudio Lo Giudice1, Irene Hernández2, Luigi R. Ceci1, Graziano Pesole1,3, Ernesto Picardi1,3
1IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy
2Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, C/Pedro Cerbuna, 12, 50009, Zaragoza, Spain
3Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Bari, Italy

Tài liệu tham khảo

Benjamini, 2001, Controlling the false discovery rate in behavior genetics research, Behav. Brain Res., 125, 279, 10.1016/S0166-4328(01)00297-2 Blanchette, 2004, Aligning multiple genomic sequences with the threaded blockset aligner, Genome Res., 14, 708, 10.1101/gr.1933104 Breiman, 2001, Random forests, Mach. Learn., 45, 5, 10.1023/A:1010933404324 Castandet, 2016, ChloroSeq, an optimized chloroplast RNA-seq bioinformatic pipeline, reveals remodeling of the organellar transcriptome under heat stress, G3 (Bethesda), 6, 2817, 10.1534/g3.116.030783 Chateigner-Boutin, 2008, CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts, Plant J., 56, 590, 10.1111/j.1365-313X.2008.03634.x Cheng, 2016, Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants, Plant J., 85, 532, 10.1111/tpj.13121 Cui, 2006, ChloroplastDB: the chloroplast genome database, Nucleic Acids Res., 34, D692, 10.1093/nar/gkj055 Cummings, 2004, Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA, BMC Bioinf., 5, 132, 10.1186/1471-2105-5-132 Du, 2008, Prediction of C-to-U RNA editing sites in plant mitochondria using both biochemical and evolutionary information, J. Theor. Biol., 253, 579, 10.1016/j.jtbi.2008.04.006 Du, 2007, Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features, Biochem. Biophys. Res. Commun., 358, 336, 10.1016/j.bbrc.2007.04.130 Du, 2009, CURE-Chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants, BMC Bioinf., 10, 135, 10.1186/1471-2105-10-135 Edera, 2018, Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria, Plant Mol. Biol., 97, 215, 10.1007/s11103-018-0734-9 He, 2007, dbRES: a web-oriented database for annotated RNA editing sites, Nucleic Acids Res., 35, D141, 10.1093/nar/gkl815 Ichinose, 2016, RNA editing and its molecular mechanism in plant organelles, Genes, 8, 10.3390/genes8010005 Kim, 2013, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, R36, 10.1186/gb-2013-14-4-r36 Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317 Kingsford, 2008, What are decision trees?, Nat. Biotechnol., 26, 1011, 10.1038/nbt0908-1011 Kiran, 2010, DARNED: a DAtabase of RNa EDiting in humans, Bioinformatics, 26, 1772, 10.1093/bioinformatics/btq285 Knie, 2016, Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns - a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles, BMC Evol. Biol., 16, 134, 10.1186/s12862-016-0707-z Langmead, B. and S.L. Salzberg, Fast gapped-read alignment with Bowtie 2. Nat. Methods. 9(4): p. 357-359. Larkin, 2007, Clustal W and clustal X version 2.0, Bioinformatics, 23, 2947, 10.1093/bioinformatics/btm404 Lenz, 2018, Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0, BMC Bioinf., 19, 255, 10.1186/s12859-018-2244-9 Li, 2019, Plant editosome database: a curated database of RNA editosome in plants, Nucleic Acids Res., 47, D170, 10.1093/nar/gky1026 Licht, 2016, Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications, J. Cell Biol., 213, 15, 10.1083/jcb.201511041 Lo Giudice, 2018, REDIdb 3.0: a comprehensive collection of RNA editing events in plant organellar genomes, Front. Plant Sci., 9, 482, 10.3389/fpls.2018.00482 McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110 Mitchell, 1998, 209 Mower, 2009, The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments, Nucleic Acids Res., 37, W253, 10.1093/nar/gkp337 O'Brien, 2003, GOBASE--a database of mitochondrial and chloroplast information, Nucleic Acids Res., 31, 176, 10.1093/nar/gkg090 Okuda, 2007, Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing, Proc. Natl. Acad. Sci. U. S. A., 104, 8178, 10.1073/pnas.0700865104 Phreaner, 1996, Incomplete editing of rps12 transcripts results in the synthesis of polymorphic polypeptides in plant mitochondria, Plant Cell, 8, 107 Picardi, 2013, REDItools: high-throughput RNA editing detection made easy, Bioinformatics, 29, 1813, 10.1093/bioinformatics/btt287 Picardi, 2010, Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing, Nucleic Acids Res., 38, 4755, 10.1093/nar/gkq202 Picardi, 2012, A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: de Novo Detection in Human Spinal Cord Tissue, PLoS One, 7, 10.1371/journal.pone.0044184 Picardi, 2014, Uncovering RNA editing sites in long non-coding RNAs, Front Bioeng Biotechnol, 2, 64, 10.3389/fbioe.2014.00064 Ramaswami, 2014, RADAR: a rigorously annotated database of A-to-I RNA editing, Nucleic Acids Res., 42, D109, 10.1093/nar/gkt996 Rudinger, 2009, RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal, Mol. Genet. Genom., 281, 473, 10.1007/s00438-009-0424-z Samuel, 1959, Some studies in machine learning using the game of checkers, IBM J. Res. Dev., 3, 210, 10.1147/rd.33.0210 Small, 2000, The PPR motif - a TPR-related motif prevalent in plant organellar proteins, Trends Biochem. Sci., 25, 46, 10.1016/S0968-0004(99)01520-0 Sosso, 2012, PPR2263, a DYW-Subgroup Pentatricopeptide repeat protein, is required for mitochondrial nad5 and cob transcript editing, mitochondrion biogenesis, and maize growth, Plant Cell, 24, 676, 10.1105/tpc.111.091074 Sun, 2016, The unexpected diversity of plant organelle RNA editosomes, Trends Plant Sci., 21, 962, 10.1016/j.tplants.2016.07.005 Sun, 2016, RED: a java-MySQL software for identifying and visualizing RNA editing sites using rule-based and statistical filters, PLoS One, 11, e0150465, 10.1371/journal.pone.0150465 Takenaka, 2013, RNA editing in plants and its evolution, Annu. Rev. Genet., 47, 335, 10.1146/annurev-genet-111212-133519 Takenaka, 2019, RNA editing mutants as surrogates for mitochondrial SNP mutants, Plant Physiol. Biochem., 135, 310, 10.1016/j.plaphy.2018.12.014 Tang, 2010, The mitochondrial PPR protein LOVASTATIN INSENSITIVE 1 plays regulatory roles in cytosolic and plastidial isoprenoid biosynthesis through RNA editing, Plant J., 61, 456, 10.1111/j.1365-313X.2009.04082.x Thompson, 2006, Genetic algorithm learning as a robust approach to RNA editing site prediction, BMC Bioinf., 7, 145, 10.1186/1471-2105-7-145 Tillich, 2006, The evolution of chloroplast RNA editing, Mol. Biol. Evol., 1912, 10.1093/molbev/msl054 Vapnik, 1995, 188 Wang, 2016, RES-Scanner: a software package for genome-wide identification of RNA-editing sites, GigaScience, 5, 37, 10.1186/s13742-016-0143-4 Wu, 2016, GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality, Methods Mol. Biol., 1418, 283, 10.1007/978-1-4939-3578-9_15 Wu, 2018, REDO: RNA editing detection in plant organelles based on variant calling results, J. Comput. Biol., 25, 509, 10.1089/cmb.2017.0214 Xiong, 2017, RNA editing responses to oxidative stress between a wild abortive type male-sterile line and its maintainer line, Front. Plant Sci., 8, 2023, 10.3389/fpls.2017.02023 Yuan, 2012, Functional disruption of the pentatricopeptide protein SLG1 affects mitochondrial RNA editing, plant development, and responses to abiotic stresses in Arabidopsis, Plant J., 70, 432, 10.1111/j.1365-313X.2011.04883.x Yura, 2009, RESOPS: a database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures, Plant Cell Physiol., 50, 1865, 10.1093/pcp/pcp132